Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold501
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: 1397941
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 110142 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1351245 original size:179 final size:179
Alignment explanation
Indices: 1350915--1351294 Score: 496
Period size: 179 Copynumber: 2.1 Consensus size: 179
1350905 TATTTGGTGA
* * * *
1350915 GAATGGGGCCTCGGGGAATCCCAGTCGACCTTCAAAAGGACTCGGGTTTACACGGCCGTTAACAG
1 GAATGGGGCCTCGGGGAAGCCCAGTCGACCTTCAAAAGGAATCAGGTTTACACGGCCATTAACAG
* * *
1350980 GCTTAGTTAGCCTGGCAAAAATAGGAAATTTCGTATAATACAATTATAATGGGATATCTTTCAAG
66 GCTAAGCTAGCCTGGCAAAAATAGGAAATTTCGTATAATAAAATTATAATGGGATATCTTTCAAG
* * ** *
1351045 GGAACAGCTTACATTCTGTATCCCATGTTTGAGACTTCATATTTGCTAG
131 CGAACAGCTAACACCCTGTATCCCATATTTGAGACTTCATATTTGCTAG
* * * * *
1351094 GGATGGGGCCTCAGGGAAGCCCAGTCGATCC-TCAAAAGGAATTAGTTTTACACGGTCATTAACA
1 GAATGGGGCCTCGGGGAAGCCCAGTCGA-CCTTCAAAAGGAATCAGGTTTACACGGCCATTAACA
*
1351158 GGCTAAGCTAGCCTGGCGAAAATAGGAAATTTCGTATAATAAAATTATAATGGGATATCTTTC-A
65 GGCTAAGCTAGCCTGGCAAAAATAGGAAATTTCGTATAATAAAATTATAATGGGATATCTTTCAA
* * * * *
1351222 -CGAAGCTGGCTAATACCCTGTATCCCATATTTGGGCCTTCATATTTGCTTG
130 GCGAA-C-AGCTAACACCCTGTATCCCATATTTGAGACTTCATATTTGCTAG
*
1351273 GAATGGGGCCCCGGGGAAGCCC
1 GAATGGGGCCTCGGGGAAGCCC
1351295 TGTCTTTTGT
Statistics
Matches: 172, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
177 3 0.02
178 2 0.01
179 165 0.96
180 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (179 bp):
GAATGGGGCCTCGGGGAAGCCCAGTCGACCTTCAAAAGGAATCAGGTTTACACGGCCATTAACAG
GCTAAGCTAGCCTGGCAAAAATAGGAAATTTCGTATAATAAAATTATAATGGGATATCTTTCAAG
CGAACAGCTAACACCCTGTATCCCATATTTGAGACTTCATATTTGCTAG
Found at i:1351559 original size:21 final size:21
Alignment explanation
Indices: 1351535--1351649 Score: 99
Period size: 21 Copynumber: 5.5 Consensus size: 21
1351525 ACCCCAACAA
1351535 ACCCCAATGAAACCCAATGAT
1 ACCCCAATGAAACCCAATGAT
* *
1351556 ACCCCAATGAACCCCAGTGAT
1 ACCCCAATGAAACCCAATGAT
* * *
1351577 ACCCAAAT-ATACCTAATGAT
1 ACCCCAATGAAACCCAATGAT
** * *
1351597 ACCCCTTTGATACCAAATGAT
1 ACCCCAATGAAACCCAATGAT
**
1351618 ATTCCAATG-AACCCAAATGAT
1 ACCCCAATGAAACCC-AATGAT
*
1351639 ACCCCTATGAA
1 ACCCCAATGAA
1351650 CTTTGAAATA
Statistics
Matches: 71, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
20 16 0.23
21 54 0.76
22 1 0.01
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (21 bp):
ACCCCAATGAAACCCAATGAT
Found at i:1351562 original size:31 final size:31
Alignment explanation
Indices: 1351524--1351582 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1351514 TGCGTCATTT
1351524 TACCCCAACAAACCCCAATGAAACCCAATGA
1 TACCCCAACAAACCCCAATGAAACCCAATGA
** * *
1351555 TACCCCAATGAACCCCAGTGATACCCAA
1 TACCCCAACAAACCCCAATGAAACCCAA
1351583 ATATACCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.39, G:0.08, T:0.12
Consensus pattern (31 bp):
TACCCCAACAAACCCCAATGAAACCCAATGA
Found at i:1351580 original size:11 final size:11
Alignment explanation
Indices: 1351535--1351648 Score: 87
Period size: 10 Copynumber: 10.9 Consensus size: 11
1351525 ACCCCAACAA
1351535 ACCCCAATGA-
1 ACCCCAATGAT
*
1351545 AACCCAATGAT
1 ACCCCAATGAT
1351556 ACCCCAATGA-
1 ACCCCAATGAT
*
1351566 ACCCCAGTGAT
1 ACCCCAATGAT
*
1351577 ACCCAAAT-AT
1 ACCCCAATGAT
*
1351587 A-CCTAATGAT
1 ACCCCAATGAT
**
1351597 ACCCCTTTGAT
1 ACCCCAATGAT
*
1351608 A-CCAAATGAT
1 ACCCCAATGAT
**
1351618 ATTCCAATGA-
1 ACCCCAATGAT
*
1351628 ACCCAAATGAT
1 ACCCCAATGAT
*
1351639 ACCCCTATGA
1 ACCCCAATGA
1351649 ACTTTGAAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
9 5 0.06
10 38 0.48
11 36 0.46
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.21
Consensus pattern (11 bp):
ACCCCAATGAT
Found at i:1351589 original size:31 final size:31
Alignment explanation
Indices: 1351534--1351642 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
1351524 TACCCCAACA
* *
1351534 AACCCCAATGAAACCC-AATGATACCCCAATG
1 AACCCCAATGATACCCAAATGAT-ACCCAATG
* *
1351565 AACCCCAGTGATACCCAAAT-ATACCTAATG
1 AACCCCAATGATACCCAAATGATACCCAATG
** *
1351595 ATACCCCTTTGATA-CCAAATGATATTCCAATG
1 A-ACCCCAATGATACCCAAATGATA-CCCAATG
*
1351627 AACCCAAATGATACCC
1 AACCCCAATGATACCC
1351643 CTATGAACTT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
30 13 0.21
31 38 0.61
32 11 0.18
ACGTcount: A:0.39, C:0.31, G:0.09, T:0.20
Consensus pattern (31 bp):
AACCCCAATGATACCCAAATGATACCCAATG
Found at i:1352371 original size:17 final size:17
Alignment explanation
Indices: 1352349--1352389 Score: 68
Period size: 15 Copynumber: 2.5 Consensus size: 17
1352339 AGATATTAAC
1352349 CAGACACACATTTTGCA
1 CAGACACACATTTTGCA
1352366 CAG--ACACATTTTGCA
1 CAGACACACATTTTGCA
1352381 CAGACACAC
1 CAGACACAC
1352390 GGAGGGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.68
17 7 0.32
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.20
Consensus pattern (17 bp):
CAGACACACATTTTGCA
Found at i:1352374 original size:15 final size:15
Alignment explanation
Indices: 1352354--1352388 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1352344 TTAACCAGAC
1352354 ACACATTTTGCACAG
1 ACACATTTTGCACAG
1352369 ACACATTTTGCACAG
1 ACACATTTTGCACAG
1352384 ACACA
1 ACACA
1352389 CGGAGGGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (15 bp):
ACACATTTTGCACAG
Found at i:1352430 original size:1 final size:1
Alignment explanation
Indices: 1352424--1352448 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1352414 CCCTACCCTA
1352424 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1352449 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1352458 original size:6 final size:6
Alignment explanation
Indices: 1352448--1352476 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1352438 CCCCCCCCCC
1352448 CAAAAA -AAAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
1352477 ACTTTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:1355052 original size:2 final size:2
Alignment explanation
Indices: 1355045--1355090 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1355035 CCCACTGTAC
1355045 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1355087 CT CT
1 CT CT
1355091 TAATCCGCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1356389 original size:189 final size:182
Alignment explanation
Indices: 1356056--1356427 Score: 426
Period size: 189 Copynumber: 2.0 Consensus size: 182
1356046 CAGTCACAGA
* *
1356056 GAATAAAAATCACTTCGCTGTAAGTGTCAATTCATTATTAGCGTGTTCTCTATATCTGTGTGTTT
1 GAATAAAAATCACTTCGCTGTAAGCGTCAATTCATTATTAGCGTGTTCTCTATATCCGTGTGTTT
* * *** * *
1356121 ACTGTATATCTATATGCTTAATTCATGGTTATATATTTATATGTACATGTATTAACGCCCATATA
66 ACTGTAAATCTATATGCTTAATACATGAACATATATTTATATGTACATGTATTAACACACATATA
* * * *
1356186 TAGATGTTTAAAGAATAAGGACTCATTCTTTGAGTATTATGAGGTGATAATTTCGGTCG
131 T--A-----AAGGAATAAAGAATCATTCTTTGAGTATAATGAGGTGATAATTTCGGTCG
* *
1356245 GAATGAAAATCACTTCGCTGTAAGCGTCAATTCATTA-TATGCGTGTTTTCTATATCCGTGTGTT
1 GAATAAAAATCACTTCGCTGTAAGCGTCAATTCATTATTA-GCGTGTTCTCTATATCCGTGTGTT
* * * * * * *
1356309 TACTGTAAATCTGTATGCTTAGTACATGAACGTATATTTATA-GATACGTGTATTAA-ATATAGA
65 TACTGTAAATCTATATGCTTAATACATGAACATATATTTATATG-TACATGTATTAACACACATA
*
1356372 TATTAAAGGAATAAAGAATCATTGTTTGAGTATAATGAGGTGATAATTTCGGTCG
129 TA-TAAAGGAATAAAGAATCATTCTTTGAGTATAATGAGGTGATAATTTCGGTCG
1356427 G
1 G
1356428 GCGTGGTCAA
Statistics
Matches: 157, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
182 46 0.29
187 1 0.01
188 7 0.04
189 103 0.66
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (182 bp):
GAATAAAAATCACTTCGCTGTAAGCGTCAATTCATTATTAGCGTGTTCTCTATATCCGTGTGTTT
ACTGTAAATCTATATGCTTAATACATGAACATATATTTATATGTACATGTATTAACACACATATA
TAAAGGAATAAAGAATCATTCTTTGAGTATAATGAGGTGATAATTTCGGTCG
Found at i:1358776 original size:179 final size:179
Alignment explanation
Indices: 1358476--1358920 Score: 583
Period size: 179 Copynumber: 2.5 Consensus size: 179
1358466 ATTAACATAA
* *
1358476 TTTACATGACCACTGAGAGGCTTAGCTAGCCTGGC-AGAAATGGGACATTTCGTATAATACAGTT
1 TTTACATGACCAGTAAGAGGCTTAGCTAGCCTGGCGA-AAATGGGACATTTCGTATAATACAGTT
* * * *
1358540 ATAATGTGATATCTTTCAAGGGGCTCGCTAACACCCTGTATCCCATATTTGGGCCTTCATAT-TT
65 ATAATGTGATATCTTTAAAGGGGCTAGCTAACACCCTGCATCCCATATTTGGGCCTTCATATCTA
* * * *
1358604 GGTGAGGATGGGGCCCCGGGAACGCCAAGTTGACCCTCAAAAGGAGTTGTG
130 GGT-AGCATGGGGCCCCGGGAACGCCAAGTTGACCCTCAAAAGAAATTGGG
** *
1358655 TTTACATGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATAAGACATTTTGTATAATACAGTTA
1 TTTACATGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGGGACATTTCGTATAATACAGTTA
* *
1358720 TAATG-GAATATTTTTAAAGGGGCTAGCTAACCCCCTGCATCCCATATTTGGGCCTTCATATCTA
66 TAATGTG-ATATCTTTAAAGGGGCTAGCTAACACCCTGCATCCCATATTTGGGCCTTCATATCTA
* ** *
1358784 GGTAGCATTGGGCCCCGGGAACGCTTAGTTGACCCTTAAAAGAAATTGGG
130 GGTAGCATGGGGCCCCGGGAACGCCAAGTTGACCCTCAAAAGAAATTGGG
* * * * *
1358834 TTTACACGACCAGTAACAGGC-TAGGCTAGCCTGGCGAAAATGGGACATTTCATTTAATACTGTT
1 TTTACATGACCAGTAAGAGGCTTA-GCTAGCCTGGCGAAAATGGGACATTTCGTATAATACAGTT
* * *
1358898 ATAATATGATATATTTCAAGGGG
65 ATAATGTGATATCTTTAAAGGGG
1358921 TCAAATTAAT
Statistics
Matches: 231, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
178 3 0.01
179 222 0.96
180 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (179 bp):
TTTACATGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGGGACATTTCGTATAATACAGTTA
TAATGTGATATCTTTAAAGGGGCTAGCTAACACCCTGCATCCCATATTTGGGCCTTCATATCTAG
GTAGCATGGGGCCCCGGGAACGCCAAGTTGACCCTCAAAAGAAATTGGG
Found at i:1359368 original size:2 final size:2
Alignment explanation
Indices: 1359363--1359395 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1359353 ACACGCACAG
1359363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1359396 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1364593 original size:164 final size:164
Alignment explanation
Indices: 1364157--1364693 Score: 652
Period size: 164 Copynumber: 3.2 Consensus size: 164
1364147 AAAGAATCAT
* * * *
1364157 CTGGCTGATTAGTCTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTGAAAAATTTACTCTATTTATTCCTATGTAAAAC-
* * * *
1364222 TTAACACACCCCTCCCGA-TGTGGCCCCACCTTACCCCCAGGGATCATGATTTTC-CATACTTTG
65 TT--C-GA--CC-CCC-ATTGTGGCCCCACCCTACCCTC-GGGGTCATGATTTTCACA-ACTTTG
*
1364285 AATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
121 AATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC
* * *
1364329 CTGGCTGATTAGTTTCTGAGAAGAGGATTTTTAAAAATTTACTCT-TTATATTCCTATGTGAAAC
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTGAAAAATTTACTCTATT-TATTCCTATGTAAAAC
* * * *
1364393 TTCGACCTCCATTTTGGCCCCATCCTACCCTCGGGGTCATGATTTTCACAACTTGGAATCTACAC
65 TTCGACCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTTGAATCTACAC
* * * *
1364458 TGCCTAAGGATGCCTCC-CTTAAGTTTCAGCTTTC
130 TACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC
*
1364492 CTGGCTGATTAGTTTTTGAGAAGAAGATTTTGAAAAATTTACTCTATTTATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTGAAAAATTTACTCTATTTATTCCTATGTAAAACT
* *
1364557 TCGAGCCCCCATTGTGGCCCCACCCTACCTTCGGGGTCATGATTTTCACAACTTTAAATCTACAC
66 TCGA-CCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTTGAATCTACAC
**
1364622 TACCTGAGGATGCTTCCACATACCTTTCAGCTTTC
130 TACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC
** * *
1364657 CTGGCCAAAT-GGTTCTTGAGAAGAAGATTTATGAAAA
1 CTGGCTGATTAGTTTC-TGAGAAGAAGATTT-TGAAAA
1364694 TTTCTCAATT
Statistics
Matches: 318, Mismatches: 39, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
163 77 0.24
164 116 0.36
165 55 0.17
166 8 0.03
168 1 0.00
169 1 0.00
171 3 0.01
172 57 0.18
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (164 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTGAAAAATTTACTCTATTTATTCCTATGTAAAACT
TCGACCCCCATTGTGGCCCCACCCTACCCTCGGGGTCATGATTTTCACAACTTTGAATCTACACT
ACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC
Found at i:1365842 original size:166 final size:165
Alignment explanation
Indices: 1365240--1366016 Score: 936
Period size: 166 Copynumber: 4.6 Consensus size: 165
1365230 AAACTGTAAC
* * * * * * *
1365240 ACCCCCGATGGTAGCCCCATCCTACCCCCGCGGGTCATGATTTTCACAACTTGGAATTTACACTG
1 ACCCCCTATGGTGGCCCCACCCTA-CCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTA
* * * * *
1365305 TCTAAAGATGCTTCCACACAAGTTTCAGCTTTCCTGGATGATTAGTTTCTGAGGAGAAGA-TTTT
65 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGACTTTT
* *
1365369 AAAAGATTTACTCTATGTATTCCTATGTAAAACTTTATC-
130 -AAAGATTTACTCTATATATTCCTATGTAAAAC---GTCG
* * * * *
1365408 ACCGCCTATGGTGGCCCCATCCTACCCCCGGGGTCATGATTTTCACAGCTTTGTATCTACACTAC
1 ACCCCCTATGGTGGCCCCACCCTACCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTAC
* *
1365473 CTGAGGATGCTTCCACACACCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTTTGAGAAGAGG
66 CTGAGGATGCTT-------CCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAG
* *
1365538 ATTTTTAAAAATTTACTCTATATATTCCTATGTAAAACTGTAAC-
124 ACTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-GT--CG
* * * *
1365582 ACCCCCTATGGTGGCCCCACCCAACCTCGGGGGTCATGCA-TTTCACAACTTGGAATTTACACTA
1 ACCCCCTATGGTGGCCCCACCCTACCCCGGGGGTCATG-ATTTTCACAACTTTGAATCTACACTA
* * *
1365646 CCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGCATACTTTT
65 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGACTTTT
* *
1365711 ATAGATTTCCTCTATATATTCCTATGTAAAACGTCG
130 AAAGATTTACTCTATATATTCCTATGTAAAACGTCG
** *
1365747 AGTTCCC-ATTGTGGCCCCACCCTACCCCAGGGGGTCATGATTTTCACAACTTTGAATCTACACT
1 A-CCCCCTATGGTGGCCCCACCCTACCCC-GGGGGTCATGATTTTCACAACTTTGAATCTACACT
* * *
1365811 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATAAGTTTTTGAGAAGAATACTTT
64 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGACTTT
* *
1365876 TAAAGATTTACTCTATATATTCCTACGTAAAACTTCG
129 TAAAGATTTACTCTATATATTCCTATGTAAAACGTCG
* * * *
1365913 TACCCCC-ATTGTGGCCCCACCCTACCTCTGGGAGTCATGAATTTCACAACTTTGAATCTACACT
1 -ACCCCCTATGGTGGCCCCACCCTACC-CCGGGGGTCATGATTTTCACAACTTTGAATCTACACT
1365977 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
64 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
1366017 TTATGGTTGT
Statistics
Matches: 534, Mismatches: 58, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
164 1 0.00
165 20 0.04
166 225 0.42
167 120 0.22
168 21 0.04
172 2 0.00
174 140 0.26
175 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (165 bp):
ACCCCCTATGGTGGCCCCACCCTACCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTAC
CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGACTTTTA
AAGATTTACTCTATATATTCCTATGTAAAACGTCG
Found at i:1366351 original size:13 final size:12
Alignment explanation
Indices: 1366330--1366362 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
1366320 ATAAAAACCC
1366330 ACAAAAAAACAA
1 ACAAAAAAACAA
1366342 ACAAACAAAACAA
1 ACAAA-AAAACAA
1366355 ACAAAAAA
1 ACAAAAAA
1366363 TAAAACCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAAAAAAACAA
Found at i:1366533 original size:1 final size:1
Alignment explanation
Indices: 1366527--1366570 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
1366517 CACAATGTAC
* * *
1366527 AAAAAAAAAACAAAAAAAAAAACAAAAAAACAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1366571 CATTTTGACC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1366544 original size:12 final size:12
Alignment explanation
Indices: 1366527--1366570 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
1366517 CACAATGTAC
1366527 AAAAAAAAAACA
1 AAAAAAAAAACA
1366539 AAAAAAAAAACA
1 AAAAAAAAAACA
1366551 AAAAAACAAAA-A
1 AAAAAA-AAAACA
1366563 AAAAAAAA
1 AAAAAAAA
1366571 CATTTTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.06
12 25 0.81
13 4 0.13
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:1366553 original size:22 final size:22
Alignment explanation
Indices: 1366525--1366572 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
1366515 TACACAATGT
*
1366525 ACAAAAAAAAAACAAAAAAAAAA
1 ACAAAAAAACAA-AAAAAAAAAA
1366548 ACAAAAAAACAAAAAAAAAAAA
1 ACAAAAAAACAAAAAAAAAAAA
1366570 ACA
1 ACA
1366573 TTTTGACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (22 bp):
ACAAAAAAACAAAAAAAAAAAA
Found at i:1366555 original size:20 final size:20
Alignment explanation
Indices: 1366530--1366568 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1366520 AATGTACAAA
1366530 AAAAAAACAAAAAAAAAAAC
1 AAAAAAACAAAAAAAAAAAC
1366550 AAAAAAACAAAAAAAAAAA
1 AAAAAAACAAAAAAAAAAA
1366569 AACATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAAAAC
Found at i:1366675 original size:15 final size:16
Alignment explanation
Indices: 1366655--1366694 Score: 66
Period size: 14 Copynumber: 2.6 Consensus size: 16
1366645 TAATATGAGG
1366655 CAAAAAAAAAC-ACAA
1 CAAAAAAAAACAACAA
1366670 C-AAAAAAAACAACAA
1 CAAAAAAAAACAACAA
1366685 CAAAAAAAAA
1 CAAAAAAAAA
1366695 ACGCGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAACAACAA
Found at i:1366676 original size:12 final size:12
Alignment explanation
Indices: 1366658--1366691 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1366648 TATGAGGCAA
1366658 AAAAAAACACAAC
1 AAAAAAA-ACAAC
1366671 AAAAAAAACAAC
1 AAAAAAAACAAC
1366683 AACAAAAAA
1 AA-AAAAAA
1366692 AAAACGCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAC
Found at i:1366676 original size:17 final size:15
Alignment explanation
Indices: 1366655--1366695 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1366645 TAATATGAGG
*
1366655 CAAAAAAAAACACAA
1 CAAAAAAAAAAACAA
*
1366670 CAAAAAAAACAACAA
1 CAAAAAAAAAAACAA
1366685 CAAAAAAAAAA
1 CAAAAAAAAAA
1366696 CGCGACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAACAA
Found at i:1370547 original size:16 final size:13
Alignment explanation
Indices: 1370514--1370538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1370504 CAGGGATGGG
1370514 GTAATGGTAATTT
1 GTAATGGTAATTT
1370527 GTAATGGTAATT
1 GTAATGGTAATT
1370539 GAGTGTAATT
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:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAATGGTAATTT
Found at i:1370566 original size:13 final size:13
Alignment explanation
Indices: 1370548--1370576 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1370538 TGAGTGTAAT
1370548 TAATTTATATATA
1 TAATTTATATATA
1370561 TAATTTATATATA
1 TAATTTATATATA
1370574 TAA
1 TAA
1370577 ATTAACTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTTATATATA
Found at i:1378442 original size:14 final size:15
Alignment explanation
Indices: 1378407--1378446 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1378397 AAAAAAATAA
*
1378407 CATACTTATAGATTT
1 CATACTTATTGATTT
*
1378422 CATACTTATTGCTTT
1 CATACTTATTGATTT
1378437 -ATACTTATTG
1 CATACTTATTG
1378447 TTGGGCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (15 bp):
CATACTTATTGATTT
Found at i:1379774 original size:27 final size:27
Alignment explanation
Indices: 1379744--1379800 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1379734 TAGTACGGAA
1379744 AACTGATGGTGCGCATGTCTGTGGTCG
1 AACTGATGGTGCGCATGTCTGTGGTCG
* *
1379771 AACTTATGGTGCGCATGTCTGTGTTCG
1 AACTGATGGTGCGCATGTCTGTGGTCG
1379798 AAC
1 AAC
1379801 GCACATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (27 bp):
AACTGATGGTGCGCATGTCTGTGGTCG
Found at i:1382141 original size:8 final size:8
Alignment explanation
Indices: 1382128--1382168 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
1382118 GATGACCTTG
1382128 GTTTTTTT
1 GTTTTTTT
1382136 G-TTTTTT
1 GTTTTTTT
1382143 GTTTTTTT
1 GTTTTTTT
1382151 GTTTGTTTT
1 GTTT-TTTT
*
1382160 TTTTTTTT
1 GTTTTTTT
1382168 G
1 G
1382169 CGAAAGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (8 bp):
GTTTTTTT
Found at i:1382148 original size:15 final size:16
Alignment explanation
Indices: 1382128--1382165 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1382118 GATGACCTTG
1382128 GTTTTTTTGTTT-TTT
1 GTTTTTTTGTTTGTTT
1382143 GTTTTTTTGTTTGTTT
1 GTTTTTTTGTTTGTTT
1382159 -TTTTTTT
1 GTTTTTTT
1382166 TTGCGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
GTTTTTTTGTTTGTTT
Found at i:1382157 original size:19 final size:17
Alignment explanation
Indices: 1382129--1382167 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1382119 ATGACCTTGG
1382129 TTTTTTTGTTTTTTGTTT
1 TTTTTTTGTTTTTT-TTT
1382147 TTTTGTTTGTTTTTTTTT
1 TTTT-TTTGTTTTTTTTT
1382165 TTT
1 TTT
1382168 GCGAAAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTT
Found at i:1389948 original size:2 final size:2
Alignment explanation
Indices: 1389941--1389997 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1389931 CAGTCATATG
1389941 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1389983 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
1389998 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1395759 original size:2 final size:2
Alignment explanation
Indices: 1395754--1395802 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1395744 TAATATATAT
* * *
1395754 AG AG AG AA AA AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1395796 AG AG AG A
1 AG AG AG A
1395803 TAAGTTATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Done.