Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1532
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 192937 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1681084 original size:12 final size:12
Alignment explanation
Indices: 1681067--1681104 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1681057 CCTTGTGTCT
1681067 GTCTGTCCGTCC
1 GTCTGTCCGTCC
* *
1681079 GTCTGTCTGTCT
1 GTCTGTCCGTCC
1681091 GTCTGTCCGTCC
1 GTCTGTCCGTCC
1681103 GT
1 GT
1681105 AACAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.39
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:1681087 original size:20 final size:20
Alignment explanation
Indices: 1681062--1681101 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1681052 TCTAGCCTTG
1681062 TGTCTGTCTGTCCGTCCGTC
1 TGTCTGTCTGTCCGTCCGTC
*
1681082 TGTCTGTCTGTCTGTCCGTC
1 TGTCTGTCTGTCCGTCCGTC
1681102 CGTAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (20 bp):
TGTCTGTCTGTCCGTCCGTC
Found at i:1681527 original size:166 final size:164
Alignment explanation
Indices: 1681143--1681956 Score: 1104
Period size: 166 Copynumber: 4.9 Consensus size: 164
1681133 GCAACTATTT
* * *
1681143 ATTGCAGATGCTTGAAAGTTTTACACAGTGTTTGT-TAAGGCATGTCACATCGTGGGATATATTT
1 ATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTAT-AGGCATGCCATATCGTGGGATATATTT
* * *
1681207 TTGTACCAATCGGACGTCAACTCCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAATTTT
65 TTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTT-AGCAAAATTTT
*
1681272 CAAAGAAATTTTCGTCAAAGATTTCTCAACAAC-TATC
128 CAAACAAATTTTCGTCAAAGATTTCTCAACAACAT-TC
* * *
1681309 TATTGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGTCATATCGTGGGATATATTT
1 -ATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGGATATATTT
* *
1681374 GTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAACATTTTC
65 TTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAA-ATTTTC
* *
1681439 AAACAAATTTTTGTCAAAGAATTCTCAACAACAGTTC
129 AAACAAATTTTCGTCAAAGATTTCTCAACAACA-TTC
* * *
1681476 ATTGCATATGCTTGAAATTTTTACACAGTGTCTGTATAGACATGCCATATCGTGGGATATATTTT
1 ATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGGATATATTTT
1681541 TGTACCAATCGGACGT---C-TCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAACATTTTCA
66 TGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAA-ATTTTCA
* * * *
1681602 AACAAATTTTTGTCAAAGAATTCTCAACAACTGTTT
130 AACAAATTTTCGTCAAAGATTTCTCAACAAC-ATTC
* * * * * *
1681638 ATCGCAGATGCTTGAAA-TTTTACCAAACTATTTGTGTAGGCATGCCATATTGTGGGATATATTT
1 ATTGCAGATGCTTGAAATTTTTA-CACAGTGTTTGTATAGGCATGCCATATCGTGGGATATATTT
* *
1681702 TTGTATCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTC
65 TTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG-CAAAATTTTC
* * *
1681767 AAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTT
129 AAACAAATTTTCGTCAAAGATTTCTCAACAAC-ATTC
* * *
1681804 ATCGCAAATGCTTGAAATTTTTACACAGTGTTTGTATGGGCATGCCATATCGTGGGATATATTTT
1 ATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGGATATATTTT
* * *
1681869 TGTACCAATTGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTGAGCTAAAATTTTCA
66 TGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGC-AAAATTTTCA
*
1681933 AACAAATTTTGGTCAAAGATTTCT
130 AACAAATTTTCGTCAAAGATTTCT
1681957 TAGCAGCTAT
Statistics
Matches: 583, Mismatches: 51, Indels: 28
0.88 0.08 0.04
Matches are distributed among these distances:
161 5 0.01
162 141 0.24
163 1 0.00
164 1 0.00
165 44 0.08
166 277 0.48
167 112 0.19
168 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (164 bp):
ATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGGATATATTTT
TGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAATTTTCAA
ACAAATTTTCGTCAAAGATTTCTCAACAACATTC
Found at i:1681752 original size:328 final size:328
Alignment explanation
Indices: 1681134--1681956 Score: 1174
Period size: 328 Copynumber: 2.5 Consensus size: 328
1681124 TTTATCTCCG
* * * * *
1681134 CAACTATTTATTGCAGATGCTTGAAAGTTTTACACAGTGTTTGT-TAAGGCATGTCACATCGTGG
1 CAACTATTCATTGCAAATGCTTGAAATTTTTACACAGTGTTTGTAT-AGGCATGCCATATCGTGG
* *
1681198 GATATATTTTTGTACCAATCGGACGTCAACTCCCTGTTAAATGACGACTTTGCTTATTTTTTAAC
65 GATATATTTTTGTACCAATCGGACGT--ACT-CCTGTTAAATGACGACTTTGTTTA-TTTTT-AG
* *
1681263 CAAAATTTTCAAAGAAATTTTCGTCAAAGATTTCTCAACAACTATCTATTGCAGATGCTTGAAAT
125 CAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAACAACTATCTATCGCAGATGCTTGAAAT
*
1681328 TTTTACACAATATTTGTATAGGCATGTCATATCGTGGGATATATTTGTGTACCAATCAGACGTCA
190 TTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTGTGTACCAATCAGACGTCA
*
1681393 ACTTCCTGTTAAATGACGACTTTGTTTATTTTTAG-CAAACATTTTCAAACAAATTTTTGTCAAA
255 ACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAA-ATTTTCAAACAAATTTTCGTCAAA
1681457 GAATTCTCAA
319 GAATTCTCAA
* * *
1681467 CAAC-AGTTCATTGCATATGCTTGAAATTTTTACACAGTGTCTGTATAGACATGCCATATCGTGG
1 CAACTA-TTCATTGCAAATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGG
1681531 GATATATTTTTGTACCAATCGGACGT-CTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAC
65 GATATATTTTTGTACCAATCGGACGTACTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAA-
* * * *
1681595 ATTTTCAAACAAATTTTTGTCAAAGAATTCTCAACAACTGTTTATCGCAGATGCTTGAAA-TTTT
129 ATTTTCAAACAAATTTTCGTCAAAGATTTCTCAACAACTATCTATCGCAGATGCTTGAAATTTTT
* * * *
1681659 AC-CAAACTATTTGTGTAGGCATGCCATATTGTGGGATATATTTTTGTATCAATCAGACGTCAAC
194 ACAC-AA-TATTTGTATAGGCATGCCATATCGTGGGATATATTTGTGTACCAATCAGACGTCAAC
*
1681723 TTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAT
257 TTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAA
*
1681788 TTCTCAG
322 TTCTCAA
* * * *
1681795 CAGCTATTTATCGCAAATGCTTGAAATTTTTACACAGTGTTTGTATGGGCATGCCATATCGTGGG
1 CAACTATTCATTGCAAATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGG
* * *
1681860 ATATATTTTTGTACCAATTGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTGAGCTA
66 ATATATTTTTGTACCAATCGGACGT--AC-TCCTGTTAAATGACGACTTTGTTTATTTTTAGC-A
*
1681924 AAATTTTCAAACAAATTTTGGTCAAAGATTTCT
127 AAATTTTCAAACAAATTTTCGTCAAAGATTTCT
1681957 TAGCAGCTAT
Statistics
Matches: 443, Mismatches: 35, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
326 1 0.00
327 13 0.03
328 254 0.57
329 28 0.06
330 2 0.00
331 36 0.08
332 29 0.07
333 79 0.18
334 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (328 bp):
CAACTATTCATTGCAAATGCTTGAAATTTTTACACAGTGTTTGTATAGGCATGCCATATCGTGGG
ATATATTTTTGTACCAATCGGACGTACTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAT
TTTCAAACAAATTTTCGTCAAAGATTTCTCAACAACTATCTATCGCAGATGCTTGAAATTTTTAC
ACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTGTGTACCAATCAGACGTCAACTTCC
TGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAATTCT
CAA
Found at i:1683494 original size:4 final size:4
Alignment explanation
Indices: 1683485--1683528 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
1683475 TACCCTTGTG
* * * *
1683485 TGTC TGTC TGTC TGTC TTTC CGTC CGTC TGCC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
1683529 CGTCCATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.23, T:0.45
Consensus pattern (4 bp):
TGTC
Found at i:1683513 original size:24 final size:24
Alignment explanation
Indices: 1683486--1683533 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1683476 ACCCTTGTGT
* *
1683486 GTCTGTCTGTCTGTCTTTCCGTCC
1 GTCTGCCTGTCTGTCTGTCCGTCC
1683510 GTCTGCCTGTCTGTCTGTCCGTCC
1 GTCTGCCTGTCTGTCTGTCCGTCC
1683534 ATAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (24 bp):
GTCTGCCTGTCTGTCTGTCCGTCC
Found at i:1683519 original size:20 final size:20
Alignment explanation
Indices: 1683490--1683532 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1683480 TTGTGTGTCT
* *
1683490 GTCTGTCTGTCTTTCCGTCC
1 GTCTGCCTGTCTGTCCGTCC
*
1683510 GTCTGCCTGTCTGTCTGTCC
1 GTCTGCCTGTCTGTCCGTCC
1683530 GTC
1 GTC
1683533 CATAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (20 bp):
GTCTGCCTGTCTGTCCGTCC
Found at i:1684470 original size:165 final size:166
Alignment explanation
Indices: 1683559--1684684 Score: 1501
Period size: 166 Copynumber: 6.8 Consensus size: 166
1683549 GTCGCATTTA
* * * * *
1683559 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAAGACAGTATTTGTATAGGCATGCCATAC
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1683624 CGTGGGAAATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATT
66 CGTGGG--ATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATT
* * *
1683689 TTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * * *
1683727 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* *
1683792 CGTGGGATGA-ATTTTCGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
66 CGTGGGAT-ATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTT
* * *
1683856 TTTGCCAAAATTTGT-AAACAAATTTCCGTCAAAGAAT
130 TTAGCCAAAATTT-TCAAACAAATTTTCGTCAAAGATT
** * * *
1683893 TCTCA-CTAATTATTTATCGCATATGCCTGAAATTTTAACATACTATTTGTTTAGGCATGCCATA
1 TCTCAGC-AGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATA
* * * *
1683957 TTGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCTTGTTAAATGACGACTTTGTTTATTT
65 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTT
1684022 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
1684059 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * ** * * *
1684124 CGTTGGATATATTTTTGTACCAATCGGGTGTCCACTTCCTGTTAAATTAGGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
* *
1684189 TAGCCAACATTTTCAAATAAATTTTCGTCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
1684225 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTGAACACACTATTTCTTTAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * * * ** *
1684290 TGTGAGATGTATTTTTGTACCGATTGGATGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
* *
1684355 TTGCCAAAATTTTCAAACAAA-TTTCGTCAAGGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * * *
1684390 TCTCAGCAGCTATTTATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCAAAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * * *
1684455 CGTGGGATATATTTTTGTACCAATCTGACGTCATCTTCCTGTTAAATGA-GTCCTTTATTTA-TT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATG-ACTTTGTTTATTT
* *
1684518 TTAGCCAAAATTTTCAAACAAATTTTCCTTAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
1684555 TCTCAGCAGCTATTTATTGCAGATGCTTGAAATTTCAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * * * * * * *
1684620 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATG-TCGACTTTGCTTATTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGAT-GACTTTGTTTATTT
1684684 T
130 T
1684685 GCATATTCAC
Statistics
Matches: 847, Mismatches: 100, Indels: 24
0.87 0.10 0.02
Matches are distributed among these distances:
164 24 0.03
165 238 0.28
166 516 0.61
167 3 0.00
168 66 0.08
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:1691222 original size:2 final size:2
Alignment explanation
Indices: 1691215--1691285 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
1691205 TGTCTGTTTA
*
1691215 TC TC TC TC TC -C TC TC TT TC -C TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1691255 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1691286 GTTTGACTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1693873 original size:16 final size:16
Alignment explanation
Indices: 1693852--1693892 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1693842 AAAAATATTG
1693852 AAAGTGCGTAATTTTT
1 AAAGTGCGTAATTTTT
1693868 AAAGTGCGTAATTTTT
1 AAAGTGCGTAATTTTT
*
1693884 TAAGTGCGT
1 AAAGTGCGT
1693893 TGTTACACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (16 bp):
AAAGTGCGTAATTTTT
Found at i:1706217 original size:12 final size:11
Alignment explanation
Indices: 1706198--1706249 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
1706188 CATTTATTTC
1706198 TTTTTTTGTGT
1 TTTTTTTGTGT
1706209 TTATTTTTGTGT
1 TT-TTTTTGTGT
*
1706221 TTTTTTTTTGT
1 TTTTTTTGTGT
1706232 TTTGTTTT-T-T
1 TTT-TTTTGTGT
1706242 TTTTTTTG
1 TTTTTTTG
1706250 GGGGGGGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 14 0.38
12 15 0.41
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:1706242 original size:13 final size:12
Alignment explanation
Indices: 1706198--1706248 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
1706188 CATTTATTTC
*
1706198 TTTTTTTGTGTT
1 TTTTTTTGTTTT
*
1706210 TATTTTTGTGTTT
1 TTTTTTTGT-TTT
1706223 TTTTTTTGTTTT
1 TTTTTTTGTTTT
1706235 GTTTTTTT-TTTT
1 -TTTTTTTGTTTT
1706247 TT
1 TT
1706249 GGGGGGGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 2 0.06
12 15 0.44
13 17 0.50
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:1706247 original size:18 final size:18
Alignment explanation
Indices: 1706213--1706246 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1706203 TTGTGTTTAT
1706213 TTTTGTGTTTTTTTTTTG
1 TTTTGTGTTTTTTTTTTG
1706231 TTTTGT-TTTTTTTTTT
1 TTTTGTGTTTTTTTTTT
1706247 TTGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTGTGTTTTTTTTTTG
Found at i:1707460 original size:22 final size:21
Alignment explanation
Indices: 1707435--1707475 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1707425 TCTTTAAGTC
1707435 ACCTTTAAGACATATTTAAGCT
1 ACCTTTAAG-CATATTTAAGCT
*
1707457 ACCTTTAAGCATCTTTAAG
1 ACCTTTAAGCATATTTAAG
1707476 TAGCATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (21 bp):
ACCTTTAAGCATATTTAAGCT
Found at i:1707475 original size:21 final size:22
Alignment explanation
Indices: 1707425--1707476 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1707415 TGTCCAAACT
1707425 TCTTTAAGTCACCTTTAAGACA
1 TCTTTAAGTCACCTTTAAGACA
*
1707447 TATTTAAG-CTACCTTTAAG-CA
1 TCTTTAAGTC-ACCTTTAAGACA
1707468 TCTTTAAGT
1 TCTTTAAGT
1707477 AGCATTTACG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (22 bp):
TCTTTAAGTCACCTTTAAGACA
Done.