Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 41 of 66
Found at i:14702509 original size:39 final size:40
Alignment explanation
Indices: 14702465--14702552 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
14702455 TTCAATGTTG
* * *
14702465 CTGCAGCGAAATTTCTACCCA-AAAACAGAATGTTTCTCA
1 CTGCAGCGAAATTGCAACCCAGAAAACAGAAAGTTTCTCA
*
14702504 CTGCAGCGAAATTGCAACCCAGAAAACAGAAAGTTTCTCG
1 CTGCAGCGAAATTGCAACCCAGAAAACAGAAAGTTTCTCA
*
14702544 CTGTAGCGA
1 CTGCAGCGA
14702553 GAATGCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 19 0.44
40 24 0.56
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (40 bp):
CTGCAGCGAAATTGCAACCCAGAAAACAGAAAGTTTCTCA
Found at i:14703862 original size:19 final size:20
Alignment explanation
Indices: 14703828--14703865 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
14703818 AAAGAAGACC
14703828 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
14703848 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
14703866 GTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:14708656 original size:2 final size:2
Alignment explanation
Indices: 14708651--14708686 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
14708641 TTCTGTTATC
14708651 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14708687 GGTTTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:14708668 original size:19 final size:19
Alignment explanation
Indices: 14708646--14708684 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
14708636 TATACTTCTG
*
14708646 TTATCTATATATATATATA
1 TTATATATATATATATATA
14708665 TTATATATATATATATATA
1 TTATATATATATATATATA
14708684 T
1 T
14708685 ATGGTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:14710363 original size:38 final size:40
Alignment explanation
Indices: 14710277--14710379 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 40
14710267 ACCCAGCTCA
* *
14710277 TGTACATCCCCCCACATCGTGCACATAGCCGACACCATCG
1 TGTACATCCCCCCACATTGTGCACATAGCAGACACCATCG
* * **
14710317 TGTGCATCCCCCCACATTGTGCACA-ATCAG-TGCCATCG
1 TGTACATCCCCCCACATTGTGCACATAGCAGACACCATCG
*
14710355 TGTACATCCACCCACATTGTGCACA
1 TGTACATCCCCCCACATTGTGCACA
14710380 CGAGCACTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 29 0.53
39 3 0.05
40 23 0.42
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (40 bp):
TGTACATCCCCCCACATTGTGCACATAGCAGACACCATCG
Found at i:14722426 original size:144 final size:144
Alignment explanation
Indices: 14722162--14722436 Score: 363
Period size: 144 Copynumber: 1.9 Consensus size: 144
14722152 TCTGTAAAGG
* * * ** * *
14722162 CCTTCTAATGTGTGAATGTGACATGACTTTTTTTTTTTTGGAACACGAGATAAAAATTTTTATTA
1 CCTTCTAATGTGTGAATGTGACATGAATATTTCTTTAGTGAAACACAAGATAAAAATTTTTATTA
** *
14722227 AAAAGATCAAATTAATATTATTACATTAAATAATTCAGACTCACGTAAACAAAATCAAATTAAAT
66 AAAAGATCAAACAAATATTATTACATTAAATAATTCAGACCCACGTAAACAAAATCAAATTAAAT
14722292 AATATTAATAAAAA
131 AATATTAATAAAAA
* * ** *
14722306 CCTTCTAATGTGTGAATGTGACATGAATATTTCTTTAGTGAAAGATAAGATTCATATTTTTATTA
1 CCTTCTAATGTGTGAATGTGACATGAATATTTCTTTAGTGAAACACAAGATAAAAATTTTTATTA
* * **
14722371 AAGAA-ATCAAACAAATATTATTACATTAAATAATTCTGACCCACGTCAATGAAATCAAATTAAA
66 AA-AAGATCAAACAAATATTATTACATTAAATAATTCAGACCCACGTAAACAAAATCAAATTAAA
14722435 TA
130 TA
14722437 CAACCATTCT
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
144 109 0.98
145 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (144 bp):
CCTTCTAATGTGTGAATGTGACATGAATATTTCTTTAGTGAAACACAAGATAAAAATTTTTATTA
AAAAGATCAAACAAATATTATTACATTAAATAATTCAGACCCACGTAAACAAAATCAAATTAAAT
AATATTAATAAAAA
Found at i:14731595 original size:20 final size:20
Alignment explanation
Indices: 14731557--14731595 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
14731547 TCAGAATTGA
*
14731557 ATTCATCATGATAACTCAAT
1 ATTCATCATGATAAATCAAT
14731577 ATTCATCCATGA-AAATCAA
1 ATTCAT-CATGATAAATCAA
14731596 GAACAAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTCATCATGATAAATCAAT
Found at i:14736891 original size:35 final size:35
Alignment explanation
Indices: 14736845--14736913 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
14736835 ATGGTAGACT
*
14736845 AATTTTATTCAAGTAATCAAAACTAGAAGCTTAAA
1 AATTTTATTCAAGTAATCAAAACTAGAAGATTAAA
14736880 AATTTTATTCAAGTAATCAAAACTAGAAGATTAA
1 AATTTTATTCAAGTAATCAAAACTAGAAGATTAA
14736914 TTAAAAGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (35 bp):
AATTTTATTCAAGTAATCAAAACTAGAAGATTAAA
Found at i:14741710 original size:60 final size:60
Alignment explanation
Indices: 14741617--14741748 Score: 219
Period size: 60 Copynumber: 2.2 Consensus size: 60
14741607 AAAAAGTTTT
* *
14741617 TCGCTGCAGCGAAATTGTAACCCAAAAACAGAAAGTTTCTTGCTGCAGCAAGATTCAATC
1 TCGCTGCAGCGAAATTGCAACCCAAAAACAGAAAGTTTCTTGCTGCAGCAAGAATCAATC
* * *
14741677 TCGCTGCAGCGAAATTGCAACCCAGAAACAGAAAGTTTCTTGCTGCAGCAAGAATGAATT
1 TCGCTGCAGCGAAATTGCAACCCAAAAACAGAAAGTTTCTTGCTGCAGCAAGAATCAATC
14741737 TCGCTGCAGCGA
1 TCGCTGCAGCGA
14741749 GAAGCTACAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (60 bp):
TCGCTGCAGCGAAATTGCAACCCAAAAACAGAAAGTTTCTTGCTGCAGCAAGAATCAATC
Found at i:14742168 original size:43 final size:43
Alignment explanation
Indices: 14742115--14742224 Score: 166
Period size: 43 Copynumber: 2.6 Consensus size: 43
14742105 TCACCAGCTC
* ** * *
14742115 ATGCGTACTCCCTACTCGCACATGGCTGGGTCATCATTGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCATCGGCTT
*
14742158 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCATCGGCTT
14742201 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
14742225 GCCGAGTCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTGGGTCATCATCGGCTT
Found at i:14744490 original size:17 final size:17
Alignment explanation
Indices: 14744468--14744504 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
14744458 AAATGGGGAT
14744468 TGCTCCCCCTAAATGTG
1 TGCTCCCCCTAAATGTG
* *
14744485 TGCTCCCCCTTAGTGTG
1 TGCTCCCCCTAAATGTG
14744502 TGC
1 TGC
14744505 ATATTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.35, G:0.22, T:0.32
Consensus pattern (17 bp):
TGCTCCCCCTAAATGTG
Found at i:14820313 original size:41 final size:42
Alignment explanation
Indices: 14820211--14820360 Score: 155
Period size: 42 Copynumber: 3.6 Consensus size: 42
14820201 TATTGACCTG
* *
14820211 GCTATGTGTGAGTAGGAGT-TCGCAAAAGTCGATGATGACCCA
1 GCTATGTGTGAGTAGGAGTGT-GCATAAGCCGATGATGACCCA
* * * * *
14820253 GCTAAGTGTGAATGGGAGTGTACATAAGCCGATGATGACCGA
1 GCTATGTGTGAGTAGGAGTGTGCATAAGCCGATGATGACCCA
* *
14820295 G-TATGTGTGAGTAGGAGTGCGCATAAGCCGTTGATGACCCA
1 GCTATGTGTGAGTAGGAGTGTGCATAAGCCGATGATGACCCA
* *
14820336 GCCATGTGCT-AGTAGG-GAGTGCATA
1 GCTATGTG-TGAGTAGGAGTGTGCATA
14820361 TGAGCTAATG
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 41 0.47
42 45 0.51
43 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.23
Consensus pattern (42 bp):
GCTATGTGTGAGTAGGAGTGTGCATAAGCCGATGATGACCCA
Found at i:14821769 original size:31 final size:31
Alignment explanation
Indices: 14821701--14821810 Score: 132
Period size: 31 Copynumber: 3.5 Consensus size: 31
14821691 GGAAAATGAA
* *
14821701 TAAATTGATAAGAAAGAAAATATATTAGAGGAT
1 TAAATTGAAAAGAAA-TAAA-ATATTAGAGGAT
* *
14821734 TAAATTGAAAAGAAATAAAATACTAGAGGAC
1 TAAATTGAAAAGAAATAAAATATTAGAGGAT
*
14821765 TAAATTGAAAA-AGAATAAAAAATTAGAGGAT
1 TAAATTGAAAAGA-AATAAAATATTAGAGGAT
*
14821796 TGAATTGAAAAGAAA
1 TAAATTGAAAAGAAA
14821811 AATAAGGAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.01
31 48 0.72
32 4 0.06
33 14 0.21
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (31 bp):
TAAATTGAAAAGAAATAAAATATTAGAGGAT
Found at i:14822578 original size:26 final size:26
Alignment explanation
Indices: 14822530--14822591 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
14822520 ATGAATTAAA
*
14822530 CATGATTTTAAAATTCTAAAATTGAG
1 CATGAGTTTAAAATTCTAAAATTGAG
* *
14822556 CATGAGTTTAAAATTTTAGAATTGAG
1 CATGAGTTTAAAATTCTAAAATTGAG
14822582 CATGAGTTTA
1 CATGAGTTTA
14822592 TTGAGCTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (26 bp):
CATGAGTTTAAAATTCTAAAATTGAG
Found at i:14822705 original size:59 final size:59
Alignment explanation
Indices: 14822594--14822725 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
14822584 TGAGTTTATT
* * *
14822594 GAGCTTGGTCTAAGATGTTGTTGAACATGATTTGATTTACTAATAAGAATCAGTGTATA
1 GAGCTTGGTTTAAGATGCTATTGAACATGATTTGATTTACTAATAAGAATCAGTGTATA
** * * *
14822653 GAGCTTGGTTTAAGATGCTATTGAGTATGATTTGATTTACT-A-AGGCACATCAGTTTATT
1 GAGCTTGGTTTAAGATGCTATTGAACATGATTTGATTTACTAATAAG-A-ATCAGTGTATA
14822712 GAGCTTGGTTTAAG
1 GAGCTTGGTTTAAG
14822726 TTGTTAGGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 2 0.03
58 2 0.03
59 59 0.94
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (59 bp):
GAGCTTGGTTTAAGATGCTATTGAACATGATTTGATTTACTAATAAGAATCAGTGTATA
Found at i:14849604 original size:2 final size:2
Alignment explanation
Indices: 14849591--14849635 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
14849581 NNNNNNNNCG
*
14849591 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14849633 TA T
1 TA T
14849636 CAATCATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14849744 original size:42 final size:42
Alignment explanation
Indices: 14849680--14849830 Score: 176
Period size: 42 Copynumber: 3.6 Consensus size: 42
14849670 TCATATGCAT
* * ** * *
14849680 TCCTACTAGCACATGGTTGGGTCAACATTGGCTCATGCACAC
1 TCCTACTCGCACATAGCCGGGTCAACATCGGCTTATGCACAC
* * * * *
14849722 TCTTACTCGTACATAGCCGGGTCAGCATCAGCTTATGCGCAC
1 TCCTACTCGCACATAGCCGGGTCAACATCGGCTTATGCACAC
* * *
14849764 TCCTACTCACACATAGCCAGGTCAGCATCGGCTTATGCACAC
1 TCCTACTCGCACATAGCCGGGTCAACATCGGCTTATGCACAC
14849806 TCCTACTCGCACATAGCCGGGTCAA
1 TCCTACTCGCACATAGCCGGGTCAA
14849831 TATCATTACA
Statistics
Matches: 89, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (42 bp):
TCCTACTCGCACATAGCCGGGTCAACATCGGCTTATGCACAC
Found at i:14856773 original size:12 final size:11
Alignment explanation
Indices: 14856754--14856783 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
14856744 TGAATTTGAG
14856754 AAAAAGAAAAA
1 AAAAAGAAAAA
14856765 AAGAAAGAAAAA
1 AA-AAAGAAAAA
14856777 AAAAAGA
1 AAAAAGA
14856784 GAAAGGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:14856780 original size:17 final size:18
Alignment explanation
Indices: 14856752--14856788 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
14856742 TGTGAATTTG
14856752 AGAAAAAGAAAAAAAGAA
1 AGAAAAAGAAAAAAAGAA
*
14856770 AGAAAAA-AAAAAGAGAA
1 AGAAAAAGAAAAAAAGAA
14856787 AG
1 AG
14856789 GATGAAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAAAAAGAA
Found at i:14857215 original size:21 final size:21
Alignment explanation
Indices: 14857187--14857234 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
14857177 TGTTGAATAG
*
14857187 TTAA-TTTAAGTTGTTTTAGT
1 TTAATTTTAAGTTGTTTTAGC
** *
14857207 TTAATTTTACTTTGTTTTGGC
1 TTAATTTTAAGTTGTTTTAGC
14857228 TTAATTT
1 TTAATTT
14857235 ACTTTAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (21 bp):
TTAATTTTAAGTTGTTTTAGC
Found at i:14860450 original size:21 final size:21
Alignment explanation
Indices: 14860424--14860464 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14860414 GCTATAAATA
* *
14860424 TCATTTTCTAGCAGCTTCTTC
1 TCATTTTCCAACAGCTTCTTC
14860445 TCATTTTCCAACAGCTTCTT
1 TCATTTTCCAACAGCTTCTT
14860465 ATTCTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.07, T:0.46
Consensus pattern (21 bp):
TCATTTTCCAACAGCTTCTTC
Found at i:14861077 original size:43 final size:43
Alignment explanation
Indices: 14861029--14861114 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
14861019 TGTGTGATAG
* *
14861029 TGATGACCCAGCTATGTGC-GGTGTGGGAGTGCACATGAGCTGA
1 TGATGACCCAGCTATGTGCAAGT-AGGGAGTGCACATGAGCTGA
**
14861072 TGATGACCTGGCTATGTGCAAGTAGGGAGTGCACATGAGCTGA
1 TGATGACCCAGCTATGTGCAAGTAGGGAGTGCACATGAGCTGA
14861115 GTGTGGCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.23
Consensus pattern (43 bp):
TGATGACCCAGCTATGTGCAAGTAGGGAGTGCACATGAGCTGA
Found at i:14870198 original size:18 final size:20
Alignment explanation
Indices: 14870175--14870225 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
14870165 TAGGCCGAAC
14870175 CTTCCTTTCTTT-TTT-TTA
1 CTTCCTTTCTTTCTTTATTA
*
14870193 CTTCC-TTCTTTCTTTATTT
1 CTTCCTTTCTTTCTTTATTA
14870212 C-TCCTTTC-TTCTTT
1 CTTCCTTTCTTTCTTT
14870226 CTCTTTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTCCTTTCTTTCTTTATTA
Found at i:14870225 original size:22 final size:21
Alignment explanation
Indices: 14870179--14870248 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
14870169 CCGAACCTTC
* * *
14870179 CTTTCTTTTTTTTACTTCCTT
1 CTTTCTTTTTTCTCCTTTCTT
14870200 CTTTCTTTATTTCTCCTTTCTT
1 CTTTCTTT-TTTCTCCTTTCTT
*
14870222 CTTTCTCTTTTCTTCCTTTCTCT
1 CTTTCTTTTTTC-TCCTTTCT-T
14870245 CTTT
1 CTTT
14870249 GCTTCCAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.29
22 25 0.60
23 5 0.12
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTTCTTTTTTCTCCTTTCTT
Found at i:14870228 original size:14 final size:14
Alignment explanation
Indices: 14870209--14870253 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
14870199 TCTTTCTTTA
14870209 TTTCTCCTTTCTTC
1 TTTCTCCTTTCTTC
*
14870223 TTTCTCTTTTCTTCC
1 TTTCTCCTTTCTT-C
14870238 TTTCTCTCTTTGCTTC
1 TTTCTC-CTTT-CTTC
14870254 CAAGTTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.46
15 7 0.27
16 4 0.15
17 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTCTCCTTTCTTC
Found at i:14883594 original size:17 final size:17
Alignment explanation
Indices: 14883574--14883613 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
14883564 CCCTAAGTGA
14883574 GTGCTATCCC-TTAATGT
1 GTGCT-TCCCTTTAATGT
*
14883591 GTGCTTCCCTTTAGTGT
1 GTGCTTCCCTTTAATGT
14883608 GTGCTT
1 GTGCTT
14883614 ATTTTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (17 bp):
GTGCTTCCCTTTAATGT
Found at i:14892628 original size:38 final size:39
Alignment explanation
Indices: 14892586--14892688 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 39
14892576 ATAGTGCCCG
*
14892586 TGTGCACGATGTGGGGGGATGTACACGAT-AGCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGAGC-CGGATA
* * * * *
14892624 TGTGCACGATGTTGGGGGATGCACATGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGAT-GAGCCGGATA
14892664 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
14892689 TGAGCCGGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 26 0.48
39 3 0.06
40 25 0.46
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGAGCCGGATA
Found at i:14893147 original size:21 final size:21
Alignment explanation
Indices: 14893104--14893147 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
14893094 TAGCCGAAAA
* **
14893104 CTCGCTGTAGCGAAATTCATT
1 CTCGCTGCAGCGAAAAACATT
*
14893125 CTCGCTGCAGCGAAAAACTTT
1 CTCGCTGCAGCGAAAAACATT
14893146 CT
1 CT
14893148 GTTTTGTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (21 bp):
CTCGCTGCAGCGAAAAACATT
Found at i:14897750 original size:38 final size:40
Alignment explanation
Indices: 14897699--14897800 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
14897689 ATAGTGCCCG
* *
14897699 TGTGCACAATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* *
14897737 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
14897777 TGTGCACGATGT-GGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
14897801 TGACCCGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
38 27 0.48
39 15 0.27
40 14 0.25
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:14901849 original size:2 final size:2
Alignment explanation
Indices: 14901842--14901874 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14901832 AATTTAAATA
14901842 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
14901875 NAAAGTAGTA
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:14901887 original size:65 final size:64
Alignment explanation
Indices: 14901811--14901940 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 64
14901801 GAAGCCTTTT
*
14901811 AAAGTAGTAGGCTAGACATTTAATTTAAATAATATATATATATATATATATATATATATATATA
1 AAAGTAGTAGGCTAGACATTTAAGTTAAATAATATATATATATATATATATATATATATATATA
*
14901875 NAAAGTAGTAGGCTAGACATTTAAGTTAATTAATATATATATATATATATATATATATATATATA
1 -AAAGTAGTAGGCTAGACATTTAAGTTAAATAATATATATATATATATATATATATATATATATA
14901940 A
1 A
14901941 CGCAGAGAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 1 0.02
65 62 0.98
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (64 bp):
AAAGTAGTAGGCTAGACATTTAAGTTAAATAATATATATATATATATATATATATATATATATA
Found at i:14901914 original size:2 final size:2
Alignment explanation
Indices: 14901907--14901939 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14901897 AAGTTAATTA
14901907 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
14901940 ACGCAGAGAA
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:14902678 original size:59 final size:59
Alignment explanation
Indices: 14902579--14902755 Score: 257
Period size: 59 Copynumber: 3.0 Consensus size: 59
14902569 GCATGTCCTC
*
14902579 TACACAAGGGTTGTTCATGTTCATGTTTTTGTTTTGCCCTGATATTTCTGATTAAATTTA
1 TACA-AAGGGTTGTTCATGTTCATGTTTTTGTTTTCCCCTGATATTTCTGATTAAATTTA
* *
14902639 TTCAAAGGGTTGTTCATGTTCATGTTTTTGTTGTCCCCTGATATTTCTGATTAAATTTA
1 TACAAAGGGTTGTTCATGTTCATGTTTTTGTTTTCCCCTGATATTTCTGATTAAATTTA
* ** * *
14902698 TACGAAGGGTTGTTCATGACCATGTTTTCGTTTTCTCCT-ATTATTTCTGATTAAATTT
1 TACAAAGGGTTGTTCATGTTCATGTTTTTGTTTTCCCCTGA-TATTTCTGATTAAATTT
14902756 TGTTGAATAC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 1 0.01
59 102 0.96
60 3 0.03
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (59 bp):
TACAAAGGGTTGTTCATGTTCATGTTTTTGTTTTCCCCTGATATTTCTGATTAAATTTA
Found at i:14903794 original size:26 final size:27
Alignment explanation
Indices: 14903764--14903828 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
14903754 ATGCTAATGC
*
14903764 AATTATCTATATTTT-TTGT-TATTATT
1 AATTATCTATATTTTATTATATATT-TT
* *
14903790 AATTATTTTTATTTTATTATATATTTT
1 AATTATCTATATTTTATTATATATTTT
14903817 -ATTATC-ATATTT
1 AATTATCTATATTT
14903829 CCTATTCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 5 0.16
26 18 0.56
27 5 0.16
28 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
AATTATCTATATTTTATTATATATTTT
Found at i:14903814 original size:18 final size:19
Alignment explanation
Indices: 14903765--14903821 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
14903755 TGCTAATGCA
*
14903765 ATTATCTATAT-TTTTTGTT
1 ATTAT-TATATATTTTTATT
14903784 ATTATTA-ATTATTTTTATT
1 ATTATTATA-TATTTTTATT
14903803 -TTATTATATA-TTTTATT
1 ATTATTATATATTTTTATT
14903820 AT
1 AT
14903822 CATATTTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 8 0.24
18 12 0.36
19 13 0.39
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTATTATATATTTTTATT
Found at i:14903816 original size:12 final size:13
Alignment explanation
Indices: 14903799--14903828 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14903789 TAATTATTTT
14903799 TATTTTATTAT-A
1 TATTTTATTATCA
14903811 TATTTTATTATCA
1 TATTTTATTATCA
14903824 TATTT
1 TATTT
14903829 CCTATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATTATCA
Found at i:14903977 original size:16 final size:16
Alignment explanation
Indices: 14903956--14904019 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
14903946 GTGAACAAAA
*
14903956 ATTATATATTTTTTTT
1 ATTATATATTTTTATT
14903972 ATTATACTATTTTTATT
1 ATTATA-TATTTTTATT
*
14903989 -TTATGTATTTTTA-T
1 ATTATATATTTTTATT
* *
14904003 ATT-TTTATTATTATT
1 ATTATATATTTTTATT
14904018 AT
1 AT
14904020 ATTTTTCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.22
15 13 0.32
16 10 0.24
17 9 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTATATATTTTTATT
Found at i:14903984 original size:14 final size:15
Alignment explanation
Indices: 14903967--14904021 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
14903957 TTATATATTT
14903967 TTTTTATTATA-CTA
1 TTTTTATTATATCTA
* *
14903981 TTTTTATTTTATGTA
1 TTTTTATTATATCTA
* *
14903996 TTTTTA-TATTTTTA
1 TTTTTATTATATCTA
*
14904010 TTATTATTATAT
1 TTTTTATTATAT
14904022 TTTTCATAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTATTATATCTA
Found at i:14903992 original size:19 final size:16
Alignment explanation
Indices: 14903956--14904000 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
14903946 GTGAACAAAA
14903956 ATTATATATTTTTTTT
1 ATTATATATTTTTTTT
*
14903972 ATTATACTATTTTTATT
1 ATTATA-TATTTTTTTT
*
14903989 -TTATGTATTTTT
1 ATTATATATTTTT
14904001 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 10 0.38
17 9 0.35
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
ATTATATATTTTTTTT
Found at i:14904007 original size:17 final size:16
Alignment explanation
Indices: 14903981--14904024 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
14903971 TATTATACTA
14903981 TTTT-TATTTTATGTAT
1 TTTTATATTTTAT-TAT
14903997 TTTTATATTTTTATTAT
1 TTTTATA-TTTTATTAT
*
14904014 TATTATATTTT
1 TTTTATATTTT
14904025 TCATAAGCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 8 0.32
17 11 0.44
18 6 0.24
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTATATTTTATTAT
Found at i:14904025 original size:17 final size:18
Alignment explanation
Indices: 14903987--14904025 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
14903977 ACTATTTTTA
*
14903987 TTTTATGTATTTTTATAT
1 TTTTATGTATTATTATAT
14904005 TTTTAT-TATTATTATAT
1 TTTTATGTATTATTATAT
14904022 TTTT
1 TTTT
14904026 CATAAGCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATGTATTATTATAT
Found at i:14922076 original size:26 final size:27
Alignment explanation
Indices: 14922046--14922110 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
14922036 ATGCTAATGC
*
14922046 AATTATCTATATTTT-TTGT-TATTATT
1 AATTATCTATATTTTATTATATATT-TT
* *
14922072 AATTATTTTTATTTTATTATATATTTT
1 AATTATCTATATTTTATTATATATTTT
14922099 -ATTATC-ATATTT
1 AATTATCTATATTT
14922111 CCTATTCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 5 0.16
26 18 0.56
27 5 0.16
28 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
AATTATCTATATTTTATTATATATTTT
Found at i:14922096 original size:18 final size:19
Alignment explanation
Indices: 14922047--14922103 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
14922037 TGCTAATGCA
*
14922047 ATTATCTATAT-TTTTTGTT
1 ATTAT-TATATATTTTTATT
14922066 ATTATTA-ATTATTTTTATT
1 ATTATTATA-TATTTTTATT
14922085 -TTATTATATA-TTTTATT
1 ATTATTATATATTTTTATT
14922102 AT
1 AT
14922104 CATATTTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 8 0.24
18 12 0.36
19 13 0.39
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTATTATATATTTTTATT
Found at i:14922098 original size:12 final size:13
Alignment explanation
Indices: 14922081--14922110 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14922071 TAATTATTTT
14922081 TATTTTATTAT-A
1 TATTTTATTATCA
14922093 TATTTTATTATCA
1 TATTTTATTATCA
14922106 TATTT
1 TATTT
14922111 CCTATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATTATCA
Found at i:14922243 original size:32 final size:31
Alignment explanation
Indices: 14922207--14922321 Score: 87
Period size: 32 Copynumber: 3.6 Consensus size: 31
14922197 GACAAATTGT
14922207 TTATAATTCTATGTTATTTTAGTGAACAAAAA
1 TTATAATTCTAT-TTATTTTAGTGAACAAAAA
* * * **
14922239 TTATANTTTCCATTTATACTTA--G-ACAAATTGC
1 TTATA-ATTCTATTTAT-TTTAGTGAACAAA--AA
14922271 TTATAATTCTATATTATTTTAGTGAACAAAAA
1 TTATAATTCTAT-TTATTTTAGTGAACAAAAA
14922303 TTATATATT-T-TTTATTTTA
1 TTATA-ATTCTATTTATTTTA
14922322 TGTATTTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
30 13 0.20
31 10 0.16
32 24 0.38
33 12 0.19
34 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATAATTCTATTTATTTTAGTGAACAAAAA
Found at i:14922255 original size:64 final size:63
Alignment explanation
Indices: 14922181--14922308 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 63
14922171 GTTCTTATGT
* *
14922181 TTTCCATTTATAATTAGACAAATTGTTTATAATTCTATGTTATTTTAGTGAACAAAAATTATA
1 TTTCCATTTATAATTAGACAAATTGCTTATAATTCTATATTATTTTAGTGAACAAAAATTATA
*
14922244 NTTTCCATTTATACTTAGACAAATTGCTTATAATTCTATATTATTTTAGTGAACAAAAATTATA
1 -TTTCCATTTATAATTAGACAAATTGCTTATAATTCTATATTATTTTAGTGAACAAAAATTATA
14922308 T
1 T
14922309 ATTTTTTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (63 bp):
TTTCCATTTATAATTAGACAAATTGCTTATAATTCTATATTATTTTAGTGAACAAAAATTATA
Found at i:14922320 original size:7 final size:7
Alignment explanation
Indices: 14922308--14922341 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
14922298 AAAAATTATA
14922308 TATTTTT
1 TATTTTT
14922315 TATTTTAT
1 TATTTT-T
14922323 GTATTTTT
1 -TATTTTT
14922331 TATTTTT
1 TATTTTT
14922338 TATT
1 TATT
14922342 ATTAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (7 bp):
TATTTTT
Found at i:14922327 original size:16 final size:16
Alignment explanation
Indices: 14922303--14922336 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
14922293 TGAACAAAAA
14922303 TTATATATTTTTTATT
1 TTATATATTTTTTATT
*
14922319 TTATGTATTTTTTATT
1 TTATATATTTTTTATT
14922335 TT
1 TT
14922337 TTATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTATATATTTTTTATT
Found at i:14922353 original size:26 final size:23
Alignment explanation
Indices: 14922308--14922356 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
14922298 AAAAATTATA
*
14922308 TATTTTTTATTTTATGTATTTTT
1 TATTTTTTATTTTATATATTTTT
14922331 TATTTTTTATTATTAATTATATTTTT
1 TATTTTTTATT-TT-A-TATATTTTT
14922357 CATAAGCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 2 0.09
25 1 0.05
26 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (23 bp):
TATTTTTTATTTTATATATTTTT
Found at i:14935104 original size:13 final size:13
Alignment explanation
Indices: 14935086--14935110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14935076 GGAGAAATTG
14935086 TGATTTTATAAAA
1 TGATTTTATAAAA
14935099 TGATTTTATAAA
1 TGATTTTATAAA
14935111 TTTTCTAAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:14941209 original size:4 final size:4
Alignment explanation
Indices: 14941195--14941264 Score: 58
Period size: 4 Copynumber: 17.8 Consensus size: 4
14941185 CAAACCGTGC
* *
14941195 CTTT CCTTT CTTT CTCT C-TT -TTT CTTT CTTT TTTT CTTT CCTTT CCTTT
1 CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT -CTTT
*
14941244 C-TC CTTT C-TT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTT
14941265 CCCTTCCTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
3 8 0.15
4 33 0.61
5 13 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:14941230 original size:22 final size:22
Alignment explanation
Indices: 14941194--14941264 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
14941184 GCAAACCGTG
*
14941194 CCTTTCCTTTCTTTCTCTCTTTT
1 CCTTT-CTTTCTTTCTCTCCTTT
* * *
14941217 TCTTTCTTTTTTTCTTTCCTTT
1 CCTTTCTTTCTTTCTCTCCTTT
*
14941239 CCTTTC-TCCTTTCT-T-CTTT
1 CCTTTCTTTCTTTCTCTCCTTT
14941258 -CTTTCTT
1 CCTTTCTT
14941265 CCCTTCCTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 5 0.12
19 5 0.12
20 1 0.03
21 6 0.15
22 19 0.47
23 4 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (22 bp):
CCTTTCTTTCTTTCTCTCCTTT
Found at i:14941272 original size:36 final size:35
Alignment explanation
Indices: 14941197--14941283 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 35
14941187 AACCGTGCCT
* * *
14941197 TTCCTTTCTTTCTCTCTTTTTCTTTCTTTTTTTCT
1 TTCCTTTCTTTCTCTCTTTTTCTTTCTTTCTTCCC
14941232 TTCCTTTCCTTTCTC-CTTTCTTCTTTCTTTCTTCCC
1 TTCCTTT-CTTTCTCTCTTT-TTCTTTCTTTCTTCCC
14941268 TTCC--TCTTTC-CTCTTT
1 TTCCTTTCTTTCTCTCTTT
14941284 GGCTATGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.02
33 9 0.20
34 1 0.02
35 11 0.24
36 24 0.52
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (35 bp):
TTCCTTTCTTTCTCTCTTTTTCTTTCTTTCTTCCC
Found at i:14941562 original size:11 final size:12
Alignment explanation
Indices: 14941541--14941565 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14941531 TATACTTTAC
14941541 TTTTCATTTTTT
1 TTTTCATTTTTT
14941553 TTTTCATTTTTT
1 TTTTCATTTTTT
14941565 T
1 T
14941566 ATTCCTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCATTTTTT
Found at i:14944434 original size:28 final size:30
Alignment explanation
Indices: 14944393--14944452 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
14944383 GTCTATGGGC
* *
14944393 AATTTTTCAGTTTT-TG-GGGCAAAAATGT
1 AATTTTTCACTTTTACGAGGGCAAAAATGT
* *
14944421 AATTTTTGACTTTTACGAGGGCAAAAGTGT
1 AATTTTTCACTTTTACGAGGGCAAAAATGT
14944451 AA
1 AA
14944453 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 1 0.04
30 13 0.50
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (30 bp):
AATTTTTCACTTTTACGAGGGCAAAAATGT
Found at i:14953795 original size:2 final size:2
Alignment explanation
Indices: 14953788--14953843 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
14953778 AAGCACTTTC
* *
14953788 TA TA TA TA TA TA CA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
14953830 TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA
14953844 CGTATGTGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:14953871 original size:8 final size:8
Alignment explanation
Indices: 14953858--14953894 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
14953848 TGTGTATGTG
14953858 TATGTGTA
1 TATGTGTA
14953866 TATGTGTA
1 TATGTGTA
14953874 TATGTGTA
1 TATGTGTA
* *
14953882 TATATATA
1 TATGTGTA
14953890 TATGT
1 TATGT
14953895 ACACATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (8 bp):
TATGTGTA
Found at i:14953905 original size:8 final size:8
Alignment explanation
Indices: 14953894--14953961 Score: 68
Period size: 8 Copynumber: 8.5 Consensus size: 8
14953884 TATATATATG
14953894 TACACATA
1 TACACATA
14953902 TACACATA
1 TACACATA
14953910 TACACATA
1 TACACATA
14953918 TACAC--A
1 TACACATA
14953924 TACACATA
1 TACACATA
*
14953932 CACATACATA
1 TAC--ACATA
*
14953942 TATACATA
1 TACACATA
* *
14953950 TATATATA
1 TACACATA
14953958 TACA
1 TACA
14953962 TAAAAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 6 0.12
8 39 0.76
10 6 0.12
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (8 bp):
TACACATA
Found at i:14953928 original size:14 final size:14
Alignment explanation
Indices: 14953894--14953961 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
14953884 TATATATATG
14953894 TACACATATACACATA
1 TACACATATACAC--A
14953910 TACACATATACACA
1 TACACATATACACA
14953924 TACAC--ATACACA
1 TACACATATACACA
* *
14953936 TACATATATACATA
1 TACACATATACACA
* *
14953950 TATATATATACA
1 TACACATATACA
14953962 TAAAAACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.23
14 23 0.49
16 13 0.28
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (14 bp):
TACACATATACACA
Found at i:14953954 original size:12 final size:12
Alignment explanation
Indices: 14953901--14953957 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
14953891 ATGTACACAT
*
14953901 ATACACATATAC
1 ATACATATATAC
*
14953913 --ACATATACAC
1 ATACATATATAC
* *
14953923 ATACACATACAC
1 ATACATATATAC
14953935 ATACATATATAC
1 ATACATATATAC
*
14953947 ATATATATATA
1 ATACATATATA
14953958 TACATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 8 0.22
12 29 0.78
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (12 bp):
ATACATATATAC
Found at i:14960973 original size:17 final size:17
Alignment explanation
Indices: 14960951--14960983 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14960941 TGAGGATTGC
14960951 TCCCCC-TAAGTGTGTGG
1 TCCCCCTTAA-TGTGTGG
14960968 TCCCCCTTAATGTGTG
1 TCCCCCTTAATGTGTG
14960984 CATATTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.30, G:0.24, T:0.33
Consensus pattern (17 bp):
TCCCCCTTAATGTGTGG
Found at i:14968745 original size:22 final size:22
Alignment explanation
Indices: 14968705--14968748 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14968695 TTAGAGTGGT
* * *
14968705 ATTAGAGCTTTTTGTTTTAAAG
1 ATTAGAGCTGTTGGGTTTAAAG
14968727 ATTAGAGCTGTTGGGTTTAAAG
1 ATTAGAGCTGTTGGGTTTAAAG
14968749 TTGTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (22 bp):
ATTAGAGCTGTTGGGTTTAAAG
Found at i:14968802 original size:5 final size:5
Alignment explanation
Indices: 14968792--14968817 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14968782 AGTGTGGGTC
14968792 AAGTT AAGTT AAGTT AAGTT AAGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT A
14968818 GGTTTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (5 bp):
AAGTT
Found at i:14985513 original size:21 final size:22
Alignment explanation
Indices: 14985488--14985528 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
14985478 CCTAGTTGGA
*
14985488 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
14985509 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
14985529 AAAAAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:14985529 original size:20 final size:21
Alignment explanation
Indices: 14985488--14985532 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
14985478 CCTAGTTGGA
*
14985488 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
14985509 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
14985529 AAAA
1 AAAA
14985533 AGGTAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:14985533 original size:21 final size:20
Alignment explanation
Indices: 14985486--14985533 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
14985476 ACCCTAGTTG
*
14985486 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
14985506 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
14985528 GAAAAA
1 GAAAAA
14985534 GGTAAGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:14989641 original size:42 final size:42
Alignment explanation
Indices: 14989584--14989717 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
14989574 AGCCGGCTCA
14989584 TCATCATCAA-CTTATGCGCACTCCTACTCGCACATAGCTGGG
1 TCATCAT-AAGCTTATGCGCACTCCTACTCGCACATAGCTGGG
*
14989626 TCATCATAAGCTTATGCGCACTCCTACTCGCACATAGCCGGG
1 TCATCATAAGCTTATGCGCACTCCTACTCGCACATAGCTGGG
* * * * *
14989668 TCATCATCAGCTCATGTGCACTCCCACATCACACATAGCTGGG
1 TCATCATAAGCTTATGCGCACTCCTAC-TCGCACATAGCTGGG
14989711 TCATCAT
1 TCATCAT
14989718 TATCACACAA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 2 0.02
42 61 0.73
43 20 0.24
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (42 bp):
TCATCATAAGCTTATGCGCACTCCTACTCGCACATAGCTGGG
Found at i:15000666 original size:19 final size:19
Alignment explanation
Indices: 15000642--15000678 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15000632 AGGTTTGGTG
15000642 AGAAACCCTCAGCTAGTTA
1 AGAAACCCTCAGCTAGTTA
*
15000661 AGAAACCCTCGGCTAGTT
1 AGAAACCCTCAGCTAGTT
15000679 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (19 bp):
AGAAACCCTCAGCTAGTTA
Found at i:15006480 original size:22 final size:22
Alignment explanation
Indices: 15006455--15006548 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
15006445 CACAAGATTG
*
15006455 GTTTTTAGGCAATGCCTGACTA
1 GTTTTTAGGCATTGCCTGACTA
* * *
15006477 GTTTTTAGGCATTACGTGA-TT
1 GTTTTTAGGCATTGCCTGACTA
* *
15006498 GGTTTTAGGCATTGCATGACTA
1 GTTTTTAGGCATTGCCTGACTA
* * *
15006520 GTTTCTACGCATTGCGTGACT-
1 GTTTTTAGGCATTGCCTGACTA
15006541 GATTTTTA
1 G-TTTTTA
15006549 AGTAATGCCT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 18 0.32
22 39 0.68
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (22 bp):
GTTTTTAGGCATTGCCTGACTA
Found at i:15006518 original size:43 final size:44
Alignment explanation
Indices: 15006450--15006548 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 44
15006440 AGTATCACAA
* * *
15006450 GATTGGTTTTTAGGCAATGCCTGACTAGTTTTTAGGCATTACGT
1 GATTGGTTTTTAGGCAATGCATGACTAGTTTCTACGCATTACGT
* *
15006494 GATTGG-TTTTAGGCATTGCATGACTAGTTTCTACGCATTGCGT
1 GATTGGTTTTTAGGCAATGCATGACTAGTTTCTACGCATTACGT
* *
15006537 GACTGATTTTTA
1 GATTGGTTTTTA
15006549 AGTAATGCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 36 0.77
44 11 0.23
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (44 bp):
GATTGGTTTTTAGGCAATGCATGACTAGTTTCTACGCATTACGT
Found at i:15006523 original size:21 final size:21
Alignment explanation
Indices: 15006457--15006540 Score: 87
Period size: 22 Copynumber: 3.9 Consensus size: 21
15006447 CAAGATTGGT
* *
15006457 TTTTAGGCAATGCCTGACTAG
1 TTTTAGGCATTGCGTGACTAG
* * *
15006478 TTTTTAGGCATTACGTGATTGG
1 -TTTTAGGCATTGCGTGACTAG
*
15006500 TTTTAGGCATTGCATGACTAG
1 TTTTAGGCATTGCGTGACTAG
*
15006521 TTTCTACGCATTGCGTGACT
1 TTT-TAGGCATTGCGTGACT
15006541 GATTTTTAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
21 20 0.40
22 30 0.60
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (21 bp):
TTTTAGGCATTGCGTGACTAG
Found at i:15006582 original size:23 final size:23
Alignment explanation
Indices: 15006552--15006626 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
15006542 ATTTTTAAGT
15006552 AATGCCTTACTAACAAGTCACTC
1 AATGCCTTACTAACAAGTCACTC
*
15006575 AATGCCTTACTAGCAAGTCA-TGC
1 AATGCCTTACTAACAAGTCACT-C
* * *
15006598 AATGCCATA-TCAACCAGTCACGC
1 AATGCCTTACT-AACAAGTCACTC
15006621 AATGCC
1 AATGCC
15006627 CAAGGTCAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.05
23 42 0.95
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (23 bp):
AATGCCTTACTAACAAGTCACTC
Found at i:15006638 original size:21 final size:21
Alignment explanation
Indices: 15006612--15006758 Score: 98
Period size: 21 Copynumber: 6.9 Consensus size: 21
15006602 CCATATCAAC
*
15006612 CAGTCACGCAATGCCCAAGGT
1 CAGTCACGCAATGCCCAAAGT
* * * *
15006633 CAGTCATGTAATACCCAAAAAT
1 CAGTCACGCAATGCCC-AAAGT
* * ** **
15006655 TAGTCATGCAATGCTTAAAAA
1 CAGTCACGCAATGCCCAAAGT
* *
15006676 CTAGTCATGTAATGCCCAAAGT
1 C-AGTCACGCAATGCCCAAAGT
* *
15006698 CAGTCACACAATGTCCAAAGT
1 CAGTCACGCAATGCCCAAAGT
* *
15006719 CAGTCACGCAATGCCTAAA-A
1 CAGTCACGCAATGCCCAAAGT
*
15006739 CTAGTCACACAATGCCCAAA
1 C-AGTCACGCAATGCCCAAA
15006759 ACCACCAAAA
Statistics
Matches: 96, Mismatches: 27, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.68
22 30 0.31
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (21 bp):
CAGTCACGCAATGCCCAAAGT
Found at i:15006660 original size:22 final size:22
Alignment explanation
Indices: 15006634--15006695 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
15006624 GCCCAAGGTC
* *
15006634 AGTCATGTAATACCCAAAAATT
1 AGTCATGTAATGCCCAAAAACT
* **
15006656 AGTCATGCAATGCTTAAAAACT
1 AGTCATGTAATGCCCAAAAACT
15006678 AGTCATGTAATGCCCAAA
1 AGTCATGTAATGCCCAAA
15006696 GTCAGTCACA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (22 bp):
AGTCATGTAATGCCCAAAAACT
Found at i:15019194 original size:21 final size:24
Alignment explanation
Indices: 15019159--15019204 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
15019149 AAAACCCTAG
*
15019159 GTGGAAAACTTCAAGGGAA-AAGT
1 GTGGAAAACTTCAAGGAAACAAGT
15019182 GTGG-AAA-TTCAAGGAAACAAGT
1 GTGGAAAACTTCAAGGAAACAAGT
15019204 G
1 G
15019205 AAAAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.17
Consensus pattern (24 bp):
GTGGAAAACTTCAAGGAAACAAGT
Found at i:15028550 original size:42 final size:42
Alignment explanation
Indices: 15028487--15028599 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
15028477 ATCAGCTCAT
* * *
15028487 TGCACTCCCCACTAGCACATAGCTGGGTCAGCATCGGCTTATG
1 TGCACT-CCTACTAGCACATAGCTGGGTCAGCATCGACGTATG
* * * *
15028530 TGCACTCCTACTTGCACATAGCTAGATCATCATCGACGTATG
1 TGCACTCCTACTAGCACATAGCTGGGTCAGCATCGACGTATG
* *
15028572 TGCACTCCTACTCGCACATAGCCGGGTC
1 TGCACTCCTACTAGCACATAGCTGGGTC
15028600 CACATCAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
42 53 0.90
43 6 0.10
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (42 bp):
TGCACTCCTACTAGCACATAGCTGGGTCAGCATCGACGTATG
Found at i:15032553 original size:25 final size:24
Alignment explanation
Indices: 15032525--15032580 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
15032515 GGCTTTTCTA
* *
15032525 ATTTTTTTCTATTTGGGCTAAGCCC
1 ATTTTTTCCTA-TTGGGCCAAGCCC
* *
15032550 ATTTATCTCCTATTGGGCCATGCCC
1 ATTT-TTTCCTATTGGGCCAAGCCC
15032575 ATTTTT
1 ATTTTT
15032581 ATTTTCTACT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.46
Consensus pattern (24 bp):
ATTTTTTCCTATTGGGCCAAGCCC
Found at i:15032598 original size:28 final size:28
Alignment explanation
Indices: 15032562--15032615 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
15032552 TTATCTCCTA
*
15032562 TTGGGCCATGCCCATTTTTATTTTCTAC
1 TTGGACCATGCCCATTTTTATTTTCTAC
* *
15032590 TTGGACCATGCCCTTTTTTTTTTTCT
1 TTGGACCATGCCCATTTTTATTTTCT
15032616 CTCATCCACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.24, G:0.13, T:0.52
Consensus pattern (28 bp):
TTGGACCATGCCCATTTTTATTTTCTAC
Found at i:15037519 original size:3 final size:3
Alignment explanation
Indices: 15037511--15037535 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
15037501 CCAGCAACTT
15037511 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
15037536 CTTTCACGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:15038371 original size:42 final size:42
Alignment explanation
Indices: 15038316--15038441 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 42
15038306 TGTTGATGTG
* *
15038316 GACCCGGCTATGTGCGAGTAGGAGTGTACATAAGTC-GATGAT
1 GACCCGGCTATGTGCAAGTAGGAGTGCACATAAG-CAGATGAT
* * *
15038358 GACCCGGTTATGTGTAAGTGGGAGTGCACATAAGCAGATGAT
1 GACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCAGATGAT
** * * * * *
15038400 GACCCAACCATGTGCTAGTGGGGAGTGCACATGAGCTGATGA
1 GACCCGGCTATGTGCAAGT-AGGAGTGCACATAAGCAGATGA
15038442 CGATGCGAGA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 48 0.70
43 20 0.29
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCAGATGAT
Found at i:15039495 original size:2 final size:2
Alignment explanation
Indices: 15039488--15039517 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15039478 TATAACAATG
15039488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15039518 CTTGATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15049448 original size:35 final size:35
Alignment explanation
Indices: 15049407--15049658 Score: 269
Period size: 35 Copynumber: 7.2 Consensus size: 35
15049397 ATAGTTGTTT
* *
15049407 AATTTAATCAATTAAGCCTAATAACTTAATTAAAC
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
* * *
15049442 AATTTAATTAATTAAGCCCAACAATTTACTTAAAC
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
* * *
15049477 AATTCTAATCAATTAGGCCCAATGACTTAATTAAAC
1 AATT-TAATTAATTAAGCCCAATAACTTAATTAAAC
* ****
15049513 AAATTTAATTAATTAGGCCCAATAACTTAATTGTTT
1 -AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
* * *
15049549 AATTTAATTAATTAGGCCTAAGAACTTAATTAAAC
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
*
15049584 AATTTAATTAATTAAGCCCAAT-GCTTTAATTAAAC
1 AATTTAATTAATTAAGCCCAATAAC-TTAATTAAAC
* *
15049619 AATTTAATTAATT-AG-GC-ACAACTTAATTAAAC
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
*
15049651 ATTTTAAT
1 AATTTAAT
15049659 CAAGTGCTTG
Statistics
Matches: 182, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
32 18 0.10
33 2 0.01
34 3 0.02
35 105 0.58
36 50 0.27
37 4 0.02
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (35 bp):
AATTTAATTAATTAAGCCCAATAACTTAATTAAAC
Found at i:15049518 original size:107 final size:104
Alignment explanation
Indices: 15049407--15049658 Score: 294
Period size: 107 Copynumber: 2.4 Consensus size: 104
15049397 ATAGTTGTTT
* * *
15049407 AATTTAATCAATTAAGCCTAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTACT
1 AATTTAATTAATTAAGCC-AATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
*
15049472 TAAACAATTCTAATCAATTAGGCCCAATGAC-TTAATTAAAC
65 TAAACAATT-TAATCAATTAAGCCCAATG-CTTTAATTAAAC
* **** * * *
15049513 AAATTTAATTAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCTAAGAACTTAA
1 -AATTTAATTAATTAAG-CCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAA
*
15049578 TTAAACAATTTAATTAATTAAGCCCAATGCTTTAATTAAAC
64 TTAAACAATTTAATCAATTAAGCCCAATGCTTTAATTAAAC
* * *
15049619 AATTTAATTAATT-AGGC-ACAACTTAATTAAACATTTTAAT
1 AATTTAATTAATTAAGCCAATAACTTAATTAAACAATTTAAT
15049659 CAAGTGCTTG
Statistics
Matches: 122, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
102 17 0.14
103 1 0.01
104 1 0.01
105 14 0.11
106 27 0.22
107 60 0.49
108 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (104 bp):
AATTTAATTAATTAAGCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAATT
AAACAATTTAATCAATTAAGCCCAATGCTTTAATTAAAC
Found at i:15049562 original size:142 final size:139
Alignment explanation
Indices: 15049386--15049651 Score: 390
Period size: 142 Copynumber: 1.9 Consensus size: 139
15049376 TCCTTAAGAA
* *
15049386 GCCCAATTAACATAGTTGTTTAATTTAATCAATTAAGCCTAATAACTTAATTAAACAATTTAATT
1 GCCCAATTAACATAATTGTTTAATTTAATCAATTAAGCCTAAGAACTTAATTAAACAATTTAATT
* *
15049451 AATTAAGCCCAACAATTTACTTAAACAATTCTAATCAATTAGGCCCAATGACTTAATTAAACAAA
66 AATTAAGCCCAACAATTTAATTAAACAATT-TAATCAATTAGGCAC-A--ACTTAATTAAACAAA
15049516 TTTAATTAATTAG
127 TTTAATTAATTAG
* * *
15049529 GCCCAA-TAACTTAATTGTTTAATTTAATTAATTAGGCCTAAGAACTTAATTAAACAATTTAATT
1 GCCCAATTAACATAATTGTTTAATTTAATCAATTAAGCCTAAGAACTTAATTAAACAATTTAATT
*** *
15049593 AATTAAGCCCAATGCTTTAATTAAACAATTTAATTAATTAGGCACAACTTAATTAAACA
66 AATTAAGCCCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAACA
15049652 TTTTAATCAA
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
138 13 0.12
140 1 0.01
141 13 0.12
142 79 0.71
143 6 0.05
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (139 bp):
GCCCAATTAACATAATTGTTTAATTTAATCAATTAAGCCTAAGAACTTAATTAAACAATTTAATT
AATTAAGCCCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAACAAATTTA
ATTAATTAG
Found at i:15054237 original size:15 final size:16
Alignment explanation
Indices: 15054217--15054246 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15054207 AGTGCATGAG
15054217 TTATGAACA-TCGGCA
1 TTATGAACAGTCGGCA
15054232 TTATGAACAGTCGGC
1 TTATGAACAGTCGGC
15054247 TCCCTTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (16 bp):
TTATGAACAGTCGGCA
Found at i:15055648 original size:2 final size:2
Alignment explanation
Indices: 15055641--15055679 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
15055631 TTGCATAAAC
15055641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT A
15055680 NATAAACACC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15058294 original size:21 final size:22
Alignment explanation
Indices: 15058269--15058309 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
15058259 CCTAGGTGGA
*
15058269 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
15058290 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
15058310 AAAAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:15058310 original size:20 final size:21
Alignment explanation
Indices: 15058269--15058313 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
15058259 CCTAGGTGGA
*
15058269 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
15058290 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
15058310 AAAA
1 AAAA
15058314 AAATGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:15058314 original size:21 final size:20
Alignment explanation
Indices: 15058267--15058314 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
15058257 ACCCTAGGTG
*
15058267 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
15058287 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
15058309 GAAAAA
1 GAAAAA
15058315 AATGTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:15065686 original size:2 final size:2
Alignment explanation
Indices: 15065679--15065704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15065669 CTATACATAC
15065679 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15065705 CAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15066369 original size:23 final size:23
Alignment explanation
Indices: 15066343--15066396 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
15066333 AGAGTAAAAT
15066343 AGCACAAAGGGCTTGTGAAAAGG
1 AGCACAAAGGGCTTGTGAAAAGG
15066366 AGCACAAAGGGCTTGTGAAAAGG
1 AGCACAAAGGGCTTGTGAAAAGG
*
15066389 TGCACAAA
1 AGCACAAA
15066397 AGCATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.15, G:0.31, T:0.13
Consensus pattern (23 bp):
AGCACAAAGGGCTTGTGAAAAGG
Found at i:15067154 original size:49 final size:48
Alignment explanation
Indices: 15067096--15067194 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 48
15067086 TCATTAGCTC
15067096 AAATTAAACCTTTAAACATAAGTTCTACCTCTAGTTACGCGTCTATGA
1 AAATTAAACCTTTAAACATAAGTTCTACCTCTAGTTACGCGTCTATGA
*
15067144 AANATTAAACCTTTAAACATAAGTTCTTCCTCTAGTTACGCGTCTATGA
1 AA-ATTAAACCTTTAAACATAAGTTCTACCTCTAGTTACGCGTCTATGA
15067193 AA
1 AA
15067195 GTTGAGGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 2 0.04
49 47 0.96
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.33
Consensus pattern (48 bp):
AAATTAAACCTTTAAACATAAGTTCTACCTCTAGTTACGCGTCTATGA
Found at i:15069092 original size:43 final size:43
Alignment explanation
Indices: 15069043--15069167 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
15069033 CCATATTCCG
* * *
15069043 CTCATGTGCACTCCTTAC-TCACACATAGTTGGGTCATCATCAA
1 CTCATGTGCACTCC-CACACCACACATAGCTGGGTCATCATCAA
* * *
15069086 TTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAG
1 CTCATGTGCACTCCCACACCACACATAGCTGGGTCATCATCAA
** *
15069129 CTCATGTGCACTCCCACA-CGTATATAGCTGGGTCATCAT
1 CTCATGTGCACTCCCACACCACACATAGCTGGGTCATCAT
15069168 TATCACACAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 21 0.29
43 51 0.71
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (43 bp):
CTCATGTGCACTCCCACACCACACATAGCTGGGTCATCATCAA
Found at i:15076977 original size:42 final size:41
Alignment explanation
Indices: 15076891--15077012 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 41
15076881 TCTCCCATCG
* ** * *
15076891 TCATCAGCTCATGTGCACTCCCCACTAACACATGGCTTGGTCA
1 TCATCAGCTTATGTGCACT-CCCACTCGCACATAGC-CGGTCA
*
15076934 TCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGATCA
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCCGG-TCA
* *
15076976 TCATCAGCTTATGTACACTCCTACTCGCACATAGCCG
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCCG
15077013 AGTCCACATC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.03
42 50 0.72
43 17 0.25
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.25
Consensus pattern (41 bp):
TCATCAGCTTATGTGCACTCCCACTCGCACATAGCCGGTCA
Found at i:15078336 original size:47 final size:47
Alignment explanation
Indices: 15078267--15078359 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
15078257 TTGCTATCAG
*
15078267 CATGTAAAGGGCATAAATGGTATCGTTGCTCGGGTTTGAGATGCCAT
1 CATGTAAAGGCCATAAATGGTATCGTTGCTCGGGTTTGAGATGCCAT
*
15078314 CATGTCAAGGCCATAAATGGTATCGTTGCTCGGGTTTGAGATGCCA
1 CATGTAAAGGCCATAAATGGTATCGTTGCTCGGGTTTGAGATGCCA
15078360 CCCGAGACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (47 bp):
CATGTAAAGGCCATAAATGGTATCGTTGCTCGGGTTTGAGATGCCAT
Found at i:15091355 original size:20 final size:20
Alignment explanation
Indices: 15091298--15091360 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
15091288 TATATACCCA
*
15091298 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
15091317 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
15091337 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
15091357 TCAT
1 TCAT
15091361 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:15091407 original size:43 final size:43
Alignment explanation
Indices: 15091359--15091477 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
15091349 TCACCAGCTC
** * *
15091359 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
15091402 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
15091445 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
15091478 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:15095514 original size:14 final size:15
Alignment explanation
Indices: 15095473--15095514 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
15095463 ATTTCTCTAG
15095473 CTTTTCTTCTTTT-T
1 CTTTTCTTCTTTTCT
* *
15095487 CCTTTCTTCCTTTCT
1 CTTTTCTTCTTTTCT
15095502 CTTTTCTT-TTTTC
1 CTTTTCTTCTTTTC
15095515 AGAACCGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
CTTTTCTTCTTTTCT
Found at i:15098637 original size:61 final size:61
Alignment explanation
Indices: 15098537--15098703 Score: 208
Period size: 61 Copynumber: 2.7 Consensus size: 61
15098527 AACTCATGTA
* * * * *
15098537 CATCATCACCGACATGTGCACTGCCCACTCAGGAAATGCACGGTTCTAATTATCACGATAT
1 CATCATTACCGGCATGTGCACTGCCCACTCAGCACATGCACGGTTCTAATTATCACGATAG
* * * * * * *
15098598 CATCATTATCGGCATGTGCATTGCCTACTCCGCACATGCATGGTTGTAATTATCATGATAG
1 CATCATTACCGGCATGTGCACTGCCCACTCAGCACATGCACGGTTCTAATTATCACGATAG
**
15098659 CATCATTACCGGCATGTGCACTGCCCACTTTGCACATGCACGGTT
1 CATCATTACCGGCATGTGCACTGCCCACTCAGCACATGCACGGTT
15098704 GCATTTATCA
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 88 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (61 bp):
CATCATTACCGGCATGTGCACTGCCCACTCAGCACATGCACGGTTCTAATTATCACGATAG
Found at i:15105753 original size:61 final size:61
Alignment explanation
Indices: 15105590--15105753 Score: 231
Period size: 61 Copynumber: 2.7 Consensus size: 61
15105580 CATCACCGGT
* *
15105590 ATGTGCACTACCCACTCTGCACATGCACGATTGTAATTATCACGACAACATCATTACTAGC
1 ATGTGCACTGCCCACTCTGCACATGCACGGTTGTAATTATCACGACAACATCATTACTAGC
* * *
15105651 ATGTGCACTGCCCACTCTGCACATGCACGGTTGTAACTATCACGACAGCATCATTA-TCGGC
1 ATGTGCACTGCCCACTCTGCACATGCACGGTTGTAATTATCACGACAACATCATTACT-AGC
* * * *
15105712 ATGTGCACTGCCCACTCCGTACATGCACGGTTGCATTTATCA
1 ATGTGCACTGCCCACTCTGCACATGCACGGTTGTAATTATCA
15105754 TACAATGATA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 1 0.01
61 91 0.99
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (61 bp):
ATGTGCACTGCCCACTCTGCACATGCACGGTTGTAATTATCACGACAACATCATTACTAGC
Found at i:15108552 original size:31 final size:31
Alignment explanation
Indices: 15108517--15108575 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15108507 ATTGAGCAAG
*
15108517 TTTGCTTTTTGAAAAAGGAATATTTGATTGA
1 TTTGCATTTTGAAAAAGGAATATTTGATTGA
*
15108548 TTTGCATTTTGAAAATGGAATATTTGAT
1 TTTGCATTTTGAAAAAGGAATATTTGAT
15108576 CTTCAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGCATTTTGAAAAAGGAATATTTGATTGA
Found at i:15111134 original size:29 final size:31
Alignment explanation
Indices: 15111085--15111145 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
15111075 GCAATGTTAT
15111085 AAAGAGGTTATGCTTGATCCT-TGAAAAGGC
1 AAAGAGGTTATGCTTGATCCTGTGAAAAGGC
*
15111115 AAAG-GGTTATGCTT-ACTCCTGTGAGAAGGC
1 AAAGAGGTTATGCTTGA-TCCTGTGAAAAGGC
15111145 A
1 A
15111146 TTGTGTGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 14 0.50
30 13 0.46
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (31 bp):
AAAGAGGTTATGCTTGATCCTGTGAAAAGGC
Found at i:15111157 original size:34 final size:34
Alignment explanation
Indices: 15111118--15111182 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
15111108 AAAAGGCAAA
15111118 GGGTTATGCTTACTCCTGT-GAGAAGGCATTGTGT
1 GGGTTATGCTTACTCCTGTGGA-AAGGCATTGTGT
* *
15111152 GGGTTATGCTTGCTCTTGTGGAAAGGCATTG
1 GGGTTATGCTTACTCCTGTGGAAAGGCATTG
15111183 CAAGGGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.35
Consensus pattern (34 bp):
GGGTTATGCTTACTCCTGTGGAAAGGCATTGTGT
Found at i:15111190 original size:34 final size:34
Alignment explanation
Indices: 15111116--15111197 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
15111106 TGAAAAGGCA
* *
15111116 AAGGGTTATGCTTACTCCTGTGAGAAGGCATTGT
1 AAGGGTTATGCTTGCTCCTGTGAGAAGGCATTGC
** *
15111150 GTGGGTTATGCTTGCTCTTGTG-GAAAGGCATTGC
1 AAGGGTTATGCTTGCTCCTGTGAG-AAGGCATTGC
*
15111184 AAGGGTTGTGCTTG
1 AAGGGTTATGCTTG
15111198 AGTTCGTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (34 bp):
AAGGGTTATGCTTGCTCCTGTGAGAAGGCATTGC
Found at i:15112610 original size:50 final size:50
Alignment explanation
Indices: 15112510--15112620 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
15112500 AGGCCAAAAC
* * * * * *
15112510 TCAACTCTAGGTAGAAAAATGAACCCATAGTTGACTGTGGGGATTGAGTAG
1 TCAACTATA-GTAGAAAAATAAACCCATAGTTGACTATAGAGATTAAGTAG
* *
15112561 TCAACTATAGTAGAAAAATAAAGCCATAGTTGACTATAGAGTTTAAGTAG
1 TCAACTATAGTAGAAAAATAAACCCATAGTTGACTATAGAGATTAAGTAG
**
15112611 TTGACTATAG
1 TCAACTATAG
15112621 CACCTTTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 42 0.84
51 8 0.16
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (50 bp):
TCAACTATAGTAGAAAAATAAACCCATAGTTGACTATAGAGATTAAGTAG
Found at i:15114899 original size:36 final size:36
Alignment explanation
Indices: 15114843--15114948 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
15114833 GATATTTTTT
* * *
15114843 ACAAATATGGCCAAGCTGTGGGGCTAAGAATACCAT
1 ACAAATATGGCCAAGATGTGGGGGTAAGAATACCAC
**
15114879 ATGAATATGGCCTAA-ATGTGGGGGTAAGAATACCAC
1 ACAAATATGGCC-AAGATGTGGGGGTAAGAATACCAC
*
15114915 ACAAATATGGTCAAGATGTGGGGGTAAGAATACC
1 ACAAATATGGCCAAGATGTGGGGGTAAGAATACC
15114949 GTACATGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.03
36 56 0.93
37 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (36 bp):
ACAAATATGGCCAAGATGTGGGGGTAAGAATACCAC
Found at i:15119145 original size:3 final size:3
Alignment explanation
Indices: 15119132--15119172 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
15119122 ACTACAAATA
15119132 AAT AA- AAT AAT AAT AAT AAT AAT AAAT AA- AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AA
15119173 ATACAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:15119152 original size:12 final size:11
Alignment explanation
Indices: 15119132--15119173 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
15119122 ACTACAAATA
15119132 AATAAAATAAT
1 AATAAAATAAT
15119143 AATAATAATAAT
1 AATAA-AATAAT
15119155 AAATAAAATAAAT
1 -AATAAAAT-AAT
15119168 AATAAA
1 AATAAA
15119174 TACAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.18
12 15 0.54
13 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:15119704 original size:17 final size:15
Alignment explanation
Indices: 15119673--15119763 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 15
15119663 TTTTTTACGA
15119673 AAAAATATAATAATAAT
1 AAAAATATAA-AAT-AT
15119690 AAAAATATAGAAATAT
1 AAAAATATA-AAATAT
* * *
15119706 GAAAAAAATATATATAC
1 -AAAAATATA-AAATAT
15119723 AAAAATATAAAA-AT
1 AAAAATATAAAATAT
* *
15119737 ATAAA-ATAAAATAA
1 AAAAATATAAAATAT
15119751 AAAAATATAAAAT
1 AAAAATATAAAAT
15119764 TTTTGTCACT
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.10
14 10 0.17
15 9 0.15
16 10 0.17
17 24 0.40
18 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAAATATAAAATAT
Found at i:15119736 original size:8 final size:8
Alignment explanation
Indices: 15119673--15119762 Score: 71
Period size: 8 Copynumber: 11.5 Consensus size: 8
15119663 TTTTTTACGA
15119673 AAAAATAT
1 AAAAATAT
*
15119681 AATAATAAT
1 AAAAAT-AT
15119690 AAAAATAT
1 AAAAATAT
*
15119698 AGAAATAT
1 AAAAATAT
*
15119706 GAAAAAAAT
1 -AAAAATAT
* * *
15119715 ATATATAC
1 AAAAATAT
15119723 AAAAATAT
1 AAAAATAT
15119731 AAAAATAT
1 AAAAATAT
15119739 --AAA-AT
1 AAAAATAT
*
15119744 -AAAATAA
1 AAAAATAT
15119751 AAAAATAT
1 AAAAATAT
15119759 AAAA
1 AAAA
15119763 TTTTTGTCAC
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
5 2 0.03
6 6 0.10
7 1 0.02
8 41 0.65
9 13 0.21
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:15119747 original size:20 final size:20
Alignment explanation
Indices: 15119679--15119763 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
15119669 ACGAAAAAAT
15119679 ATAATAATAATAAAAATATAGAA
1 ATAA-AATAA-AAAAATATA-AA
* * *
15119702 ATATGAA-AAAAATATATATAC
1 ATA-AAATAAAAAAATATA-AA
*
15119723 A-AAAATATAAAAATATAAA
1 ATAAAATAAAAAAATATAAA
15119742 ATAAAATAAAAAAATATAAA
1 ATAAAATAAAAAAATATAAA
15119762 AT
1 AT
15119764 TTTTGTCACT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.08
20 29 0.58
21 10 0.20
22 2 0.04
23 5 0.10
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAAAATAAAAAAATATAAA
Found at i:15143382 original size:54 final size:54
Alignment explanation
Indices: 15143300--15143404 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
15143290 TCATTATGTG
15143300 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
*
15143354 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
15143405 GTGTCACCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.18
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:15144280 original size:19 final size:19
Alignment explanation
Indices: 15144256--15144292 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15144246 TAAGAAGAGA
15144256 AAGGAAATGAAAA-GAAAAC
1 AAGGAAA-GAAAATGAAAAC
15144275 AAGGAAAGAAAATGAAAA
1 AAGGAAAGAAAATGAAAA
15144293 AAAATTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.22, T:0.05
Consensus pattern (19 bp):
AAGGAAAGAAAATGAAAAC
Found at i:15145151 original size:10 final size:10
Alignment explanation
Indices: 15145136--15145166 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
15145126 TAGGTGTTTG
15145136 GAGAGAGAAA
1 GAGAGAGAAA
15145146 GAGAGAGAAA
1 GAGAGAGAAA
15145156 GAGAGAGAAA
1 GAGAGAGAAA
15145166 G
1 G
15145167 CTCCCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:15145847 original size:42 final size:42
Alignment explanation
Indices: 15145792--15145910 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
15145782 TGTTGATGTG
* * * *
15145792 GACCCGGCTATGTGTGAGTAAGAGTGCACATACG-TCGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCT-GATGAT
* *
15145834 GACCTGGCTATGTGCGAGTAGGAATGCGCATAAGCTGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCTGATGAT
**
15145876 GACCCAACTATGTGCGAGTAGGAGTGCGCATAAGC
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGC
15145911 CAATGCTAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 65 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCTGATGAT
Found at i:15145931 original size:42 final size:42
Alignment explanation
Indices: 15145843--15145932 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
15145833 TGACCTGGCT
** * *
15145843 ATGTGCGAGTAGGAATGCGCATAAGCTGATGATGACCCAACT
1 ATGTGCGAGTAGGAATGCGCATAAGCCAATGATAACCCAACC
* * * *
15145885 ATGTGCGAGTAGGAGTGCGCATAAGCCAATGCTAACCTAGCC
1 ATGTGCGAGTAGGAATGCGCATAAGCCAATGATAACCCAACC
15145927 ATGTGC
1 ATGTGC
15145933 TAGTGGGGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (42 bp):
ATGTGCGAGTAGGAATGCGCATAAGCCAATGATAACCCAACC
Found at i:15146302 original size:39 final size:39
Alignment explanation
Indices: 15146248--15146349 Score: 168
Period size: 39 Copynumber: 2.6 Consensus size: 39
15146238 CATGGTTCTC
15146248 GCTGCAGCGAGAAAGTTTGTGTTTTATGGCTTGAATCTT
1 GCTGCAGCGAGAAAGTTTGTGTTTTATGGCTTGAATCTT
15146287 GCTGCAGCGAGAAAGTTTGTGTTTTATGGCTTGAATCTT
1 GCTGCAGCGAGAAAGTTTGTGTTTTATGGCTTGAATCTT
* * * *
15146326 GCTACAGCGAAAAACTTTCTGTTT
1 GCTGCAGCGAGAAAGTTTGTGTTT
15146350 CGCTTAGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (39 bp):
GCTGCAGCGAGAAAGTTTGTGTTTTATGGCTTGAATCTT
Found at i:15147471 original size:16 final size:18
Alignment explanation
Indices: 15147452--15147490 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
15147442 TAAATATTAA
15147452 TATT-TAAAA-ATTATTT
1 TATTATAAAATATTATTT
15147468 TATTAATAAAATATTATTT
1 TATT-ATAAAATATTATTT
15147487 TATT
1 TATT
15147491 CCAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
18 5 0.25
19 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATAAAATATTATTT
Found at i:15151425 original size:13 final size:13
Alignment explanation
Indices: 15151407--15151437 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
15151397 TGCCTCTTTC
15151407 ACCTTTTCCTTAA
1 ACCTTTTCCTTAA
15151420 ACC-TTTCCTTAA
1 ACCTTTTCCTTAA
15151432 ACCTTT
1 ACCTTT
15151438 GCAAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (13 bp):
ACCTTTTCCTTAA
Found at i:15152779 original size:54 final size:54
Alignment explanation
Indices: 15152635--15152783 Score: 237
Period size: 54 Copynumber: 2.8 Consensus size: 54
15152625 TTTTCAAGAA
**
15152635 AGCTCATGTGCATCCCACCACATCGTGCACATAGCTAGACATCTCATCTCACCC
1 AGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCTCATCTCACCC
*
15152689 AGCTCATGTGCATCCCACCACATCGTGCAGATAGCCGGACATC-CTATCTCACCC
1 AGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCTC-ATCTCACCC
* *
15152743 AGCTCATGTGCATCCCACCACATCGTGCATAAAGCCGGACA
1 AGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
15152784 GTATCTGTCA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 1 0.01
54 88 0.99
ACGTcount: A:0.26, C:0.38, G:0.16, T:0.20
Consensus pattern (54 bp):
AGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCTCATCTCACCC
Done.