Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2017
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14719
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:5444 original size:587 final size:588
Alignment explanation
Indices: 3013--7712 Score: 9059
Period size: 588 Copynumber: 8.0 Consensus size: 588
3003 ACCTAATTGA
3013 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
* *
3078 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGACAAGAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
* *
3143 CGAAAAGTAGGACATGCAAGTATGAGCGTACTCTCTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
*
3208 ATTACCTAAGGTCAAATTTGATTGCGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
3273 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
*
3338 CTTTTTGGTCCAACTAGAACACAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
*
3403 TTATTCAAGATACACTTGGGTTTTATTTTTAAACACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
3468 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
3533 AGAGAATTTGAAAACC-TGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
3597 TGC
586 TGC
3600 TGTTTGTAGTAATAAAACAA-TTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTA-ATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
3663 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
3728 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
3793 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
3858 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
3923 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
*
3988 TTATTGAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
4053 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
4118 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
4183 TGC
586 TGC
4186 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
*
4251 ATGTTTTAAGTTCCCAAACCGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
4316 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
4381 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
4446 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
4511 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
*
4576 TTTTTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
4641 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
4706 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
4771 TGC
586 TGC
4774 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
4839 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
4904 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
4969 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCAT-AAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
5033 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
*
5098 CTTTTTGGTCCAACTAGAATGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
* *
5163 TTATTGAAGATACACTTGGGTTTTATTTTTAAGTACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
5228 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
*
5293 AAAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
5358 TGC
586 TGC
5361 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
*
5426 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCATCAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
5491 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
* *
5556 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAACGGTAAGCTTAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
5621 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
*
5686 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTCTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
*
5751 TTATTGAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
5816 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
5881 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
5946 TGC
586 TGC
*
5949 TGTTTGTAGTAGTAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
6014 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
* * *
6079 CGAAAAGTAGGACATGCAGGTATGAGCGTACTTTTTAAGTTATCAAAGAAAAATCTAGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
6144 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
*
6209 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGTT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
6274 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
* *
6339 TTATTCAAGAGACCCTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
6404 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
6469 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
6534 TGC
586 TGC
*
6537 TGTTTGTAGTAATAAAACAATTTTCTTAGGCAATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
*
6602 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGATATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
6667 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
6732 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
6797 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
*
6862 CTTTTTGGTCCAACTAGAACGCAAGGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
*
6927 TTATTGAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
6992 CGTTTTGTAAAATAGTTCAAAATG-AAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
7056 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
7121 TGC
586 TGC
7124 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
1 TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
7189 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
66 ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
7254 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
131 CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
7319 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
196 ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
7384 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
261 GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
*
7449 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGTAAAAGATATGGATTTGTCATTGTGGATGA
326 CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
* *
7514 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCAATAAAGATGAAGCTTTAGAAAAATTTATCA
391 TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
7579 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
456 CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
*
7644 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTC
521 AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
7709 TGC
586 TGC
7712 T
1 T
7713 TCTAGAACTC
Statistics
Matches: 4053, Mismatches: 55, Indels: 9
0.98 0.01 0.00
Matches are distributed among these distances:
585 469 0.12
586 108 0.03
587 1216 0.30
588 2260 0.56
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (588 bp):
TGTTTGTAGTAATAAAACAATTTTCTTAGGCCATAGGGAAGGGAACATTTATGTTGTACATTTAG
ATGTTTTAAGTTCCCAAAACGTATGTTTTGTTGCCGGCAACAATGACATACCTTGGCTATGGCAC
CGAAAAGTAGGACATGCAAGTATGAGCGTACTTTTTAAGTTATCTAAGAAAAATCTCGTAATTGG
ATTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAAAGGTAAGCATAAAA
GAAATTCTTTTAAACCTATAAACATTGTCACGACTTCTAGAGTTCTACAACTAGTTCACATGGAT
CTTTTTGGTCCAACTAGAACGCAAAGTCTAGGAGGAAAAAGATATGGATTTGTCATTGTGGATGA
TTATTCAAGATACACTTGGGTTTTATTTTTAAGCACTAAAGATGAAGCTTTAGAAAAATTCATCA
CGTTTTGTAAAATAGTTCAAAATGAAAAAGGTTACTCCTTATCTAGTATAAGAAGTGATCACGGA
AGAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGATAACGGTATTAGCCATAATTTCTT
TGC
Found at i:9628 original size:13 final size:13
Alignment explanation
Indices: 9610--9634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9600 CAGCATTCTC
9610 TGTATCGATACAG
1 TGTATCGATACAG
9623 TGTATCGATACA
1 TGTATCGATACA
9635 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:12098 original size:13 final size:13
Alignment explanation
Indices: 12080--12104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12070 AGATTGCATA
12080 GTATCGATACATT
1 GTATCGATACATT
12093 GTATCGATACAT
1 GTATCGATACAT
12105 GACAAATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:12116 original size:19 final size:20
Alignment explanation
Indices: 12092--12142 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12082 ATCGATACAT
*
12092 TGTATCGATACATGACA-AA
1 TGTATCGATACATGAAAGAA
*
12111 TGTATCGATACTTGAAAGAA
1 TGTATCGATACATGAAAGAA
12131 TGTATCGATACA
1 TGTATCGATACA
12143 GGTCTTGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGAAAGAA
Found at i:12220 original size:13 final size:13
Alignment explanation
Indices: 12202--12227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12192 ACACACAATA
12202 TGTATCGATACAT
1 TGTATCGATACAT
12215 TGTATCGATACAT
1 TGTATCGATACAT
12228 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12243 original size:33 final size:32
Alignment explanation
Indices: 12182--12249 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
12172 CCTTAACTGT
*
12182 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
12214 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
12247 TTG
1 TTG
12250 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:12799 original size:13 final size:13
Alignment explanation
Indices: 12781--12805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12771 TAGCCAAACT
12781 TGTATCGATACAA
1 TGTATCGATACAA
12794 TGTATCGATACA
1 TGTATCGATACA
12806 CAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12886 original size:19 final size:19
Alignment explanation
Indices: 12859--12896 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12849 CTATATTTTC
*
12859 AAATAGTATCGATGCATCA
1 AAATAGTATCGATACATCA
*
12878 AAATTGTATCGATACATCA
1 AAATAGTATCGATACATCA
12897 CACGGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAATAGTATCGATACATCA
Done.