Adding Lassa virus

data/community/JoiRichi/lassa/gpc/CHANGELOG.md

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+## Unreleased
+
+Initial release for Nextclade v3!
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/JoiRichi/lassa/gpc/README.md

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+# LASV dataset
+
+| Key  | Value  |
+| :-- | :-- |
+| name  | Lassa GPC Tree |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_004296 |
+| workflow  | https://github.com/nextstrain/lassa/tree/main/nextclade  |
+| path  | `nextstrain/lassa` |
+
+
+## Scope of this dataset
+
+This Nextclade dataset places query sequences on a GPC scaffold tree for Lassa lineage assignments.
+
+## Features
+
+This dataset supports:
+
+- Assignment of lineages
+- Phylogenetic placement
+- Sequence quality control (QC)
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/JoiRichi/lassa/gpc/genome_annotation.gff3

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+##sequence-region GPC 1 672
+NC_004296	feature	source	1	1476	.	+	.	gene=nuc
+NC_004296	feature	gene	1	1476	.	+	.	gene_name=GPC

data/community/JoiRichi/lassa/gpc/pathogen.json

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+{
+  "files": {
+    "reference": "reference.fasta",
+    "pathogenJson": "pathogen.json",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "treeJson": "tree.json",
+    "examples": "sequences.fasta",
+    "readme": "README.md",
+    "changelog": "CHANGELOG.md"
+  },
+  "schemaVersion": "3.0.0",
+  "defaultCds": "GPC",
+  "attributes": {
+    "name": "Lassa Global Tree",
+    "reference name": "Josiah",
+    "reference accession": "NC_004296"
+  },
+  "alignmentParams": {
+    "penaltyGapExtend": 1,
+    "penaltyGapOpen": 8,
+    "penaltyGapOpenInFrame": 9,
+    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyMismatch": 1,
+    "scoreMatch": 5,
+    "retryReverseComplement": true,
+    "allowedMismatches": 10,
+    "minSeedCover": 0.22,
+    "minLength": 663
+  },
+  "qc": {
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 20,
+      "scoreBias": 4
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true
+    },
+    "privateMutations": {
+      "enabled": true,
+      "cutoff": 12,
+      "typical": 4,
+      "weightLabeledSubstitutions": 1,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "enabled": true,
+      "clusterCutOff": 3,
+      "scoreWeight": 50,
+      "windowSize": 50
+    }
+  }
+}

data/community/JoiRichi/lassa/gpc/reference.fasta

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+>NC_004296
+atgggacaaatagtgacattcttccaggaagtgcctcatgtaatagaagaggtgatgaacattgttctcattgcactgtctgtactagcagtgctgaaaggtctgtacaattttgcaacgtgtggccttgttggtttggtcactttcctcctgttgtgtggtaggtcttgcacaaccagtctttataaaggggtttatgagcttcagactctggaactaaacatggagacactcaatatgaccatgcctctctcctgcacaaagaacaacagtcatcattatataatggtgggcaatgagacaggactagaactgaccttgaccaacacgagcattattaatcacaaattttgcaatctgtctgatgcccacaaaaagaacctctatgaccacgctcttatgagcataatctcaactttccacttgtccatccccaacttcaatcagtatgaggcaatgagctgcgattttaatgggggaaagattagtgtgcagtacaacctgagtcacagctatgctggggatgcagccaaccattgtggtactgttgcaaatggtgtgttacagacttttatgaggatggcttggggtgggagctacattgctcttgactcaggccgtggcaactgggactgtattatgactagttatcaatatctgataatccaaaatacaacctgggaagatcactgccaattctcgagaccatctcccatcggttatctcgggctcctctcacaaaggactagagatatttatattagtagaagattgctaggcacattcacatggacactgtcagattctgaaggtaaagacacaccagggggatattgtctgaccaggtggatgctaattgaggctgaactaaaatgcttcgggaacacagctgtggcaaaatgtaatgagaagcatgatgaggaattttgtgacatgctgaggctgtttgacttcaacaaacaagccattcaaaggttgaaagctgaagcacaaatgagcattcagttgatcaacaaagcagtaaatgctttgataaatgaccaacttataatgaagaaccatctacgggacatcatgggaattccatactgtaattacagcaagtattggtacctcaaccacacaactactgggagaacatcactgcccaaatgttggcttgtatcaaatggttcatacttgaacgagacccacttttctgatgatattgaacaacaagctgacaatatgatcactgagatgttacagaaggagtatatggagaggcaggggaagacaccattgggtctagttgacctctttgtgttcagtacaagtttctatcttattagcatcttccttcacctagtcaaaataccaactcataggcatattgtaggcaagtcgtgtcccaaacctcacagattgaatcatatgggcatttgttcctgtggactctacaaacagcctggtgtgcctgtgaaatggaagagatga

data/community/JoiRichi/lassa/l/CHANGELOG.md

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+## Unreleased
+
+Initial release for Nextclade v3!
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/JoiRichi/lassa/l/README.md

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+# LASV dataset
+
+| Key  | Value  |
+| :-- | :-- |
+| name  | Lassa L Segment Tree |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_004297 |
+| workflow  | https://github.com/nextstrain/lassa/tree/main/nextclade  |
+| path  | `nextstrain/lassa` |
+
+
+## Scope of this dataset
+
+This Nextclade dataset places query sequences on a L scaffold tree for Lassa lineage assignments.
+
+## Features
+
+This dataset supports:
+
+- Assignment of lineages
+- Phylogenetic placement
+- Sequence quality control (QC)
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/JoiRichi/lassa/l/genome_annotation.gff3

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+##sequence-region NC_004297 1 7279
+NC_004297	source	region	1	7279	.	+	.	gene=nuc
+NC_004297	source	gene	66	365	.	+	.	gene_name=Z
+NC_004297	source	gene	466	7122	.	-	.	gene_name=L

data/community/JoiRichi/lassa/l/pathogen.json

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+{
+  "files": {
+    "reference": "reference.fasta",
+    "pathogenJson": "pathogen.json",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "treeJson": "tree.json",
+    "examples": "sequences.fasta",
+    "readme": "README.md",
+    "changelog": "CHANGELOG.md"
+  },
+  "schemaVersion": "3.0.0",
+  "defaultCds": "L",
+  "attributes": {
+    "name": "Lassa Global Tree",
+    "reference name": "Josiah",
+    "reference accession": "NC_004297"
+  },
+  "alignmentParams": {
+    "penaltyGapExtend": 1,
+    "penaltyGapOpen": 8,
+    "penaltyGapOpenInFrame": 9,
+    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyMismatch": 1,
+    "scoreMatch": 5,
+    "retryReverseComplement": true,
+    "allowedMismatches": 10,
+    "minSeedCover": 0.12,
+    "minLength": 800
+  },
+  "qc": {
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 20,
+      "scoreBias": 4
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true
+    },
+    "privateMutations": {
+      "enabled": true,
+      "cutoff": 12,
+      "typical": 4,
+      "weightLabeledSubstitutions": 1,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "enabled": true,
+      "clusterCutOff": 3,
+      "scoreWeight": 50,
+      "windowSize": 50
+    }
+  }
+}

data/community/JoiRichi/lassa/l/reference.fasta

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+>NC_004297_LREF
+CGCACCGGGGATCCTAGGCAATTTGGTTGTCTTTTTTTGAGGCCTTGTGCGCTGTACTTCTCCAAATGGG
+AAACAAGCAAGCCAAAGCCCCAGAATCAAAAGACAGTCCGAGAGCCAGCCTGATCCCAGATGCCACACAT
+CTAGGGCCACAGTTCTGTAAGAGCTGCTGGTTCGAAAACAAGGGCCTGGTTGAGTGCAACAACCACTATC
+TGTGTCTCAACTGCCTCACCTTACTTCTAAGTGTCAGCAACAGGTGTCCCATTTGCAAGATGCCTCTCCC
+CACAAAACTGAGACCATCAGCCGCTCCAACAGCACCTCCAACCGGAGCAGCGGACAGCATCAGACCCCCA
+CCCTACAGTCCCTGAATCTCCCACCGACCCCCACCACTCCCATCCTCCCCCCGACACCCCCCGGGGGGAC
+CCCCCGCCGGGGGCCCCCCCGGGGGAGCCAACCATCACCAAAAAACTACTCAATGTCTTCGATGCATTCA
+TCCTTCCTAGTCAGCTCCTCACATGTTCTGCCCTTCAATCTCAATTTACCACCACTTGATTGTACCATCA
+CCTTTCCCCTTGACTTACTATAACAGAGAGCATAACCCTTGAACTCCACCCAGTTGTCCACTGCCTCAAG
+AACCGCACTCAAGATCCCCTCACAACTCGGCGCTGCAGCCCTAAGTGTGGAGACAATGTCCACCCCTGAC
+CACTGCATCCTTAACCCCAGCCTGTCTATCATCATATCACTCAATGCCCCAATCAGCAGGTCAGACGAAG
+TGTCCCCAACCTCTCTCACAAATATCTCAAGATCCTGGTCTTGTATAACAGGTGTAAAGGATGCCAATTT
+CTTTCCACATTCCCACAAGCCTCCCCTATGCACAACCAGGGGGGTTGGTTCAGTGCAAGGACCCACCAAT
+ACAAAGTCATACTCCGTAAACTGCAACCTTTCCATATCAACAACAATCTCAACAGGGGTCACATGCCCTA
+GTTGATTTGTGTCAATTAAAAACTCATTAATGATCTCGGTGTCAACATACCATGCTGATTTGCCCTTGAA
+AGTAGGTCCTGACAAAACCAGTCTCCAACAGTCTGACAAGACACACGGACTCACTGCACCTGAGTACATA
+ACGGTTACATCATGTACTAGATACTTGGCCTGTTGATTCATTGAGCCAGTATACTCAAGGTGGATGGCAA
+AGCTTTCCTTAAAACTAGCATCTTGACTTTTAACACGGAACCTCACTGTCTGACTCAGTTTTGCAGACCC
+TGGAGGTAGTGAAGCTACGGCATCAAAGAAATCCTCCAATGAGTCAAACTTAGGATCAACTAAACCTGAT
+GCGATCAATTGATTTTGATTGAATCTAGCTGGCTCAATATCAAAGTCTATCCAAGCATAACCCATCATCA
+GATCATGCTTAAACATTGGCCTTTCAACACCTTTGTGAATAACTTTCTCTACAAATGAAGAAAATGGACC
+CATTCTATGCAACCCTTCACCCTCTGGAACTGATGTCTTGTGTGGAAACCACGTGAAGGACCCCAATGTT
+CTTGTAGTCGCAACAAATGGTCTCACGTAAGACTCAAAATAAATTTGCCTCATGAAATTGTCAACAGCAT
+CACTAGTGCTCACTACTCTTTCTTCCACCATGGGTTCATGTGTCCTACTGTGAGACAACCTCAATTCAGA
+TGATAACACAATGTAATGTTCCTCTCTTTTCCATTTTACTATGTGTGAGACAAGAGACAAGGCTTCACAG
+TTAACATCCAACGCTACACAGAGATCTAGAAATTTTATTCTGGGTGACCACTTCATTTTGGTTGACGCTA
+GATCGCTCATGAATGGTAATATGTGTTTCTCAAACACTGATGGGTACAGCCTTCTTAAAGAATGAATGAT
+GTGATTCAAACCAACCCTATCCTCCAATAGTTTTGATGCAGTTGGCTTTAAGGGAAAATAGTCACAAGGG
+TTATGTTTGAAAAAATCAAACACCTTAACTGTCTTAGGTTCCCCTAAGACCCATGCACCCAGTTCTATTG
+CAGTTGATAAGGAGATGCACATATAATCCCATAACAAGGGTCTGAAATAACTGACCACACTTTCACCTCC
+ACTTCCATTTCTAAGTTCTAGCGGAACTTGCCAATATTGAATGCCATTAGAATTTGTCAACAATTTGATT
+CCCTTGACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTCTCTTTATTTGGTCCCCGAACAC
+ATTTGCTACCCAATGTTCTGCACAATCCTACAAAGCCAGATGCAATGGAACTTTGGAATGCAGATTTGTT
+GATAGCTTCAGACAGCAATTTTTGCGCACCTCGAGTGAAAGTGGAAGACAACTTATTTTGGATTGTTTTG
+ACAATGGTAGGAATCTTCTCATCATCTAGGTTCACAGCACCTGAATATATTATCTTTTGTCTCAACACCA
+TTCTTAAAGGATGATGCGCAGCCAAGTTTAGCCAAGAATACTCAAGGTCAGACTCAGATGGGGGCTCAAC
+ATCCAACAGCTCACAAAGATTTCTTAGTGATGAGAGGTGCTCACTAGACAAATAGTTTGTTGTGAACTCT
+TCATGGAGTTGCCCAGTCTTCAACCTATTGTACAGTTTTCTTAACATAGATCTAATCTTGCTGCAAGCAT
+TAGGAATCAATCCCTCTATTTGCCTCATAATCCTATAACTACGGTTGCCATCTACCCAGTCTCTAACATC
+TGTCTCGCAATTCAATAAGAATGGGTCAATAGGGTATCTTGCATATTGCAAAGGATTTAAGGTTCTTTTC
+TGTATTAGATTACATAAGTGAACAGGGACACCATTCGCAACCGACTGATCAATGATTGTGTCAATTGTTT
+CTGCCAGTTGGTGTGGCTCTTTACACTTTATATTGTGAAGAGCTGCTGCAACGAACTTTGTCAATAATGG
+CACTTCATCTCCCCAAACAAAAAATCTAGATTTAAACTCTGCAACAAACCTGCCAATGACACTTTTAGGG
+CTCACAAACTTATTGAGTTGATCACTCATATAATAGTGGAACTCTATTAGAGTCCTAAATTCTTCTGGGT
+CTCTTTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGAGAAATCTGATCATCACTAGAGGTATAAGCATC
+TATCGTACCACCGCATATACAACTGATAGCATAATTAATGAACCTCTCTGAAATGAGGGCATAAAAATCT
+GATGTGTTGTGTAATATTCCTTGACCCATGTCAAGTATTGAACTGATGTGAGAAGGCACTACACCAGCTT
+GGAAATTAGAGTAAAAGAAATCTTCTGTTATTGACTGTTTAGTTTTCTTCCTTAACCCTAGTTGGGCTTT
+AATGAAAGACTTCATCATGGCTGTCACCACATTAAAAGGTATTTCCACCATTTTGTGCATATGCCACATA
+AGTAGGGTTGAGAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCCTTTGAGAGGAAAATTAAATTCT
+GTAAGACAGTCAAGAACAAAAATGGACACATCATTGGGCCCCACTTACTATGATCCATGCTATAAGACAC
+ATGTGCCAATGAAACATTCAATTTCATGGAAAGGATAGCATTTTCAAATTCCTTCTCGTTGTTCAGGCAA
+CTCCCTGATAACTGTAGGCTTATAGCTTCAAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAA
+GATCACCAATATATAATTCTCTGTTACCACCCACTTGTTCTTTATATGACAAAGAAAACTTAAGCCTTCC
+TGTATCAGGTCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAATTCTTTAACATT
+GCTGTGGTACAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAATTGCTCTCCCTTTCACTAATTC
+TTACATCATCAGAGAGTTTACCCATATCAAACTTGAAATTAAGGTTCCTTGACTTATAATGAGTGTACCT
+CCCCATAAGTGTATTCGCATTCATGATCAAGAGTATGGACTTAAAACACTGAAAGTATTCATGGTTAAAG
+TATGTCCTTGTTGACACTGCCTTTGTCAACTCTCCAATAGGACACTGTGACATATGTCCACAGTAAAAAT
+ACTTCTGCTTCAATCTACTATTCTCATAGACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAGAT
+ATCATGATCAAACTCCTCAACCATGTGATTGGATAATTCACCCTTGATCAACCTAATGTAAAACTTATTT
+GAGACAATCTCATCTAGATCATTTATTGATGGTTGGCCATCACCATTAGGGCCTGAGCCTAGCTTGACAG
+GTTCCCTATACTGATCAACAATTTTTTCAACAGTCTCCTTTAGCTGATCAAAATAATCGCTTGCACCTCC
+ATCGAGCAAAATTTCGTCTAGGTCAGCCCCATCAGCATCACTTTTGAGCTGCCCAGATCCTAGAACCAAA
+TTGCTCATTGCCTGCTGAACTTTGTACTCATAGTCCTGCTTGTTGAGAAGGTACTTTCCTTTCCTTGAGA
+AGACTTCAGTGAGCTGCGACACGGCCAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTAGAACC
+ATCTGTGTATTTATTAACAACAACACTTTTCTTGCTGGCTAAATCCAAGGCTGCACTGCCACTGGTGATG
+AGAGGATCTTTGATTTCCCTTTTTACTTCCCTCTCCTTAAATAGTGAACCATTGTTAAAAGAGGATGTAA
+GAAGAGATAAATACTTCTTTGAAACACCAGGCCTTTTATAATCTGGTCCCTCGATAGTTGTGCATCCATC
+TTTACTTAAAAACTTTTTTGCATTGTAGACCATGTCATCCAATTCTTCCTCAGTGGCTGTGTCTGCAGGA
+TTAGTGCTCACATGACCAAATCTCACCTTTGGTTCCAGAAACTTCTCAAAACATTTTATCTGATCTGTCA
+ATCTATCTGGTGTTTCTTTCGTAATGAAGTGGCACATGTAGGAAACATTCAAAATGAACTTGAACCTATT
+AGTCATCATGCTCTTCACATCCTCAGATAAAACCAGATTCATTAATGTCCTTATTAACCTATAGAGCAGG
+AACTCAACATCAGTGATTAATTCTTCCCTTATTTTGTCAATGAGGTCCTTATGATGATAATCTGATAGAT
+AAGCCATTACAAAGTACCTAAGATTTTGGAGGAGCTTTTGAGAACGTTTACTGGGGTGAGCTAAAATTAA
+AACCAGGATCATCTTTGTCAGAGACCTGATATTGTTCAACTGCCCTTCCAGCTCATTGCAATCTTCTATC
+CAAGAAATCATAGTGCTTATTGTTGTTTGTAAAACCTCAGCTGAAAATATTGCTGGAAAATATCTTTTAG
+GATCAGCATAAAATGAGCACACCTCACCAACTTTGTTATCATTAATAGCATAGCACTTCGAGCACTCCCC
+TGTCTTTTGATAAATCAGTTGTAATTCAGTGTTACCCAATGAAAACTCTTGACAATATGCTTCTTTGCAT
+CTGACCACTTGATACCTTGCGGGTCCAAATTCATTCTGTCTCAGCTTTACGGTAGAAGAAGTTTTCATAG
+AGTTCACCAAAGCGAGGCTCAATGAGGAAAGTCTCTCTAAGTCAGTGGTTCCCAGTAGTTCCACATCCCC
+CATCACATAAGGGAATGTTTCTTCCTCTGTTCTCTGATAACTGATTGTTGGGACAACTCCGGAGACATCA
+AAGTCCATAATCAAATCATAGCTGTTAAGGCAGATCACCTCCATATCAATTTTATAGTGGTCCACACTGA
+TCCCAACATCCTTTAAAGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGGATTTGATT
+CTTACTCAAACACTGGGAGGACTGTGTGATTCTAGATCTTAGCCTGTTGCCTCGCTCTCCCCATTTCTCG
+AGATCCCTCTTTGTTGCCTCCAAAGAAACTAGTCTATCTTTAACTCTTAAGAAGCAAGACCCCAACCACC
+CTTTTAAACACTTTTGTTTCATCAGGTCATGCTTACTTGCAAGGAGAATTAGTGCATCAAAAATTAATAG
+AAGTTTCCTCCTTGTGTTCAATATCCTCAAAGATTTTACTTTATTTAGGAATGATCTCCAGCATTGAACC
+TGACATTCTCCAATAGTTTGGTTTCCCCTTTTTTCATTCCCCTCATCAACATTTGCATACAAAAATCTCA
+ATATTGGTGATGCTCTCTTGAACTGGTAAATTAAGTGTTCGATATTGTCTTCTGCAACTACCTTATCAGC
+GTACAAATTGTTAAGCTCATTAAGTAACTGGCTCTTATCAACCTTTAAAAACTGACCTTCTATCTCTCCT
+TTCCTCAATCTGTTCCTAAACACTTGATACTCCTCTTCGATCTGCAGCTTTACCTCATGAGCTGTTAATT
+TATTATTGATGCCCTGGTGGCATGAGGCAATCACTTCCTCATAATGATTAGAGCGATTGTCCATCAGAAC
+ATTTAAACTCTCCACCCCTGATAATCTACCCGAAGTCATGAATAAAGATTCACAGAGTCTGCTATACTCT
+GACTCTTCAAAAAGTGAATTACTCTCCTGTGCATACTTTAAAAGTGAGAAGAGCGTATCCCTCAACTTAT
+CATTGACCCAGTCAGGTATTTGTTCATTGTAGAATGATGTTCTCCCGTCTATAAGTGGTATTAAATTGAT
+GTCGACACTCTTCAGGTCTTCTTTCAGCTGCTCTAATTTTTTGAAGTCCTCAATGTACTTCTGCTCAAAG
+TTAGCAGGAGATGATCTAACAAAACACTCCAGCAGTATTAGAACATTGCCCGTCAGTTTGTAACCGTCCG
+GGTACCACAAACATAGTGAAGGTGTCAAGATTCCATGGTCATGGAGAATTCTTTCCACAGATTTGTCCTC
+ACTGTTATGCTCGCAACCATTTGCGTTGCAAGAATCAACCTCAATACAGAGGGACAAGAGTTTCAACCCT
+TCCATTAATAGCATCCTAGGCTCTGTCTGCACAAGAAATGCTAACTTCTGTCTTGACAATCTCTCGTTGT
+CCACTAGGTATTTTGATACTAAGTCTTTGACACAGGCTATGTCTTCCTCCATGTTTAGCTGCAGGTATGA
+TGTTCAGAACCCTCAGAACATGTGGTCTGCTAGAGCAACAGTTCGCTATGGGATAGGGTCCCGTAGGGGC
+ACAGAAGACACAAGAGGCAATTAAAGACAATTAAATAAGATAGCCTTAATGCCTAGGATCCTCGGTGCG