Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 160 of 172
Found at i:52448304 original size:31 final size:30
Alignment explanation
Indices: 52448242--52448305 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
52448232 AAATCTGGGA
* *
52448242 TTTTTTTTTAAATTTTGAATTTTCTTGATT
1 TTTTTTTTTAAATTTTGAATTATATTGATT
*
52448272 TTTTATTTTTATATTTTGAATTATA-TGTATT
1 TTTT-TTTTTAAATTTTGAATTATATTG-ATT
52448303 TTT
1 TTT
52448306 AGATTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (30 bp):
TTTTTTTTTAAATTTTGAATTATATTGATT
Found at i:52452139 original size:19 final size:20
Alignment explanation
Indices: 52452089--52452138 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 20
52452079 TTTTTGCACA
*
52452089 TTTAAAATTTTTATATACAT
1 TTTAGAATTTTTATATACAT
52452109 TTTAGAATTTTTA-ATA-AT
1 TTTAGAATTTTTATATACAT
*
52452127 TTTTGAATTTTT
1 TTTAGAATTTTT
52452139 TTAATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.46
19 3 0.11
20 12 0.43
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAGAATTTTTATATACAT
Found at i:52452234 original size:21 final size:21
Alignment explanation
Indices: 52452204--52452249 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52452194 TAAATGCACA
*
52452204 TTTTACTTTTTTTTAAAAAAAC
1 TTTTAC-TTTTTTGAAAAAAAC
*
52452226 TTTTA-TTTTTTGAAAAAATC
1 TTTTACTTTTTTGAAAAAAAC
52452246 TTTT
1 TTTT
52452250 TTTGTTGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTACTTTTTTGAAAAAAAC
Found at i:52452236 original size:20 final size:20
Alignment explanation
Indices: 52452211--52452249 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52452201 ACATTTTACT
*
52452211 TTTTTTTAAAAAAACTTTTA
1 TTTTTTGAAAAAAACTTTTA
*
52452231 TTTTTTGAAAAAATCTTTT
1 TTTTTTGAAAAAAACTTTT
52452250 TTTGTTGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTTGAAAAAAACTTTTA
Found at i:52452257 original size:19 final size:18
Alignment explanation
Indices: 52452210--52452257 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
52452200 CACATTTTAC
52452210 TTTTTTTT-AAAAAAACTT
1 TTTTTTTTGAAAAAAAC-T
*
52452228 TTATTTTTTGAAAAAATCT
1 TT-TTTTTTGAAAAAAACT
52452247 TTTTTTGTTGA
1 TTTTTT-TTGA
52452258 CGTGGCATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTTTTTTGAAAAAAACT
Found at i:52457551 original size:11 final size:11
Alignment explanation
Indices: 52457506--52457553 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
52457496 TTTTTCCACT
*
52457506 TTTTGTCACTA
1 TTTTGTTACTA
52457517 TTTTGTTACTA
1 TTTTGTTACTA
** *
52457528 TTTCATTATTA
1 TTTTGTTACTA
*
52457539 TTTTGCTACTA
1 TTTTGTTACTA
52457550 TTTT
1 TTTT
52457554 ATTGTTAATG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (11 bp):
TTTTGTTACTA
Found at i:52458307 original size:194 final size:192
Alignment explanation
Indices: 52457951--52458325 Score: 520
Period size: 194 Copynumber: 1.9 Consensus size: 192
52457941 AACATATGAA
* * **
52457951 ATATGTATGATTTTAAAATAAAAATTCGATTAAATTGTGAGTAAAATAAAATTTAAACATGTAAA
1 ATATGTACGATATTAAAATAAAAATTCGATTAAATTGTGAGTAAAATAAAATTTAAACACATAAA
* *
52458016 TACATCACATTAATAATACTAAATGCACTACAATTGTCCATCATGACGTTGGCATCAATCTTGAG
66 TACATCACATTAAGAATACTAAATGCACTACAATTGTCCATCATGACGTTGGCATCAATCTTAAG
*
52458081 TTAATGTTATGTTCACTTGTGACACCAACTCAATCAACAACAGTATCAATACAACACAATAG
131 TTAATGTTATGTTCACTTGTGACACCAACTCAATCAACAACAGTACCAATACAACACAATAG
* *
52458143 ATATGTACGATATTAAAATGATTAAAATT-GATTAAATTGTGAGTAAAATGAAATTTAACCACAT
1 ATATGTACGATATTAAAAT-A--AAAATTCGATTAAATTGTGAGTAAAATAAAATTTAAACACAT
* * * ** * *
52458207 AAATACATCATATTAAGAATACTTAATGTACTACAATTGTTTATCATGATGTTGTCATCAATCTT
63 AAATACATCACATTAAGAATACTAAATGCACTACAATTGTCCATCATGACGTTGGCATCAATCTT
* * * *
52458272 AAGTTAGTGTTGA-GTTGACTTGTGACACCAACTCAATCAATAACATTACCAATA
128 AAGTTAATGTT-ATGTTCACTTGTGACACCAACTCAATCAACAACAGTACCAATA
52458326 TCTACAATTG
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
192 17 0.11
193 1 0.01
194 134 0.84
195 7 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (192 bp):
ATATGTACGATATTAAAATAAAAATTCGATTAAATTGTGAGTAAAATAAAATTTAAACACATAAA
TACATCACATTAAGAATACTAAATGCACTACAATTGTCCATCATGACGTTGGCATCAATCTTAAG
TTAATGTTATGTTCACTTGTGACACCAACTCAATCAACAACAGTACCAATACAACACAATAG
Found at i:52458692 original size:18 final size:20
Alignment explanation
Indices: 52458671--52458721 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
52458661 AATTAAAACA
52458671 ATTTTTAAAATT-CAAAA-T
1 ATTTTTAAAATTCCAAAAGT
*
52458689 ATTTATAAAAATTCCAAAAGTT
1 ATTT-TTAAAATTCCAAAAG-T
52458711 ATATTTTAAAA
1 AT-TTTTAAAA
52458722 AAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 5 0.19
22 8 0.31
23 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTTTAAAATTCCAAAAGT
Found at i:52460521 original size:4 final size:4
Alignment explanation
Indices: 52460499--52460557 Score: 91
Period size: 4 Copynumber: 14.8 Consensus size: 4
52460489 AAAGATAAAA
* * *
52460499 AGTG AGCG AGCG AGCG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
52460547 AGTG AGTG AGT
1 AGTG AGTG AGT
52460558 TTTACATTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.25, C:0.05, G:0.49, T:0.20
Consensus pattern (4 bp):
AGTG
Found at i:52469114 original size:31 final size:31
Alignment explanation
Indices: 52469071--52469144 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
52469061 TTTAAAAAAA
* *
52469071 TTTAATACTTTTTTTTA-CATATTTT-TAATAT
1 TTTAATAATTTTTTTTACCAT-TTTTACAAT-T
52469102 TTTAATAATTTTTTTTACCATTTTTACAATT
1 TTTAATAATTTTTTTTACCATTTTTACAATT
*
52469133 TTTTATAATTTT
1 TTTAATAATTTT
52469145 ACAATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTAATAATTTTTTTTACCATTTTTACAATT
Found at i:52469116 original size:21 final size:21
Alignment explanation
Indices: 52469092--52469154 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
52469082 TTTTTACATA
*
52469092 TTTTTAATATTTTAATAATTT
1 TTTTTAATATTTTAACAATTT
** *
52469113 TTTTTACCATTTTTACAATTT
1 TTTTTAATATTTTAACAATTT
*
52469134 TTTAT-A-ATTTT-ACAATTT
1 TTTTTAATATTTTAACAATTT
52469152 TTT
1 TTT
52469155 AACTTTTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 10 0.28
19 5 0.14
21 21 0.58
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAATATTTTAACAATTT
Found at i:52469144 original size:18 final size:18
Alignment explanation
Indices: 52469083--52469155 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 18
52469073 TAATACTTTT
*
52469083 TTTTACATATTTTTAAT-A
1 TTTTACA-ATTTTTTATAA
* *
52469101 TTTTAATAATTTTTTTTACCA
1 TTTT-ACAATTTTTTATA--A
52469122 TTTTTACAATTTTTTATAA
1 -TTTTACAATTTTTTATAA
52469141 TTTTACAATTTTTTA
1 TTTTACAATTTTTTA
52469156 ACTTTTTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 26 0.58
19 3 0.07
21 12 0.27
22 4 0.09
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTACAATTTTTTATAA
Found at i:52469162 original size:18 final size:18
Alignment explanation
Indices: 52469112--52469162 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
52469102 TTTAATAATT
*
52469112 TTTTTTACCATTTTTACAA
1 TTTTTTAAC-TTTTTACAA
*
52469131 TTTTTTATA-ATTTTACAA
1 TTTTTTA-ACTTTTTACAA
52469149 TTTTTTAACTTTTT
1 TTTTTTAACTTTTT
52469163 TGAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 1 0.04
18 19 0.70
19 7 0.26
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTAACTTTTTACAA
Found at i:52475610 original size:18 final size:18
Alignment explanation
Indices: 52475587--52475628 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
52475577 AATAGGTTTC
52475587 TAATTAAATAAATTT-AAT
1 TAATTAAA-AAATTTAAAT
*
52475605 TAATTAAAAATTTTAAAT
1 TAATTAAAAAATTTAAAT
52475623 TAATTA
1 TAATTA
52475629 CACTTTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTAAAAAATTTAAAT
Found at i:52477732 original size:25 final size:26
Alignment explanation
Indices: 52477692--52477740 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
52477682 ACCATAAAGG
52477692 CTTTTCCACAAGATTAGCCACAAAAA
1 CTTTTCCACAAGATTAGCCACAAAAA
*
52477718 CTTTT-CACAATATTAGCCACAAA
1 CTTTTCCACAAGATTAGCCACAAA
52477741 GGCTTCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.27
Consensus pattern (26 bp):
CTTTTCCACAAGATTAGCCACAAAAA
Found at i:52483300 original size:5 final size:5
Alignment explanation
Indices: 52483290--52483314 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52483280 TTACAAGTGA
52483290 GGGGT GGGGT GGGGT GGGGT GGGGT
1 GGGGT GGGGT GGGGT GGGGT GGGGT
52483315 AGGGATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GGGGT
Found at i:52484683 original size:15 final size:17
Alignment explanation
Indices: 52484650--52484691 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
52484640 GCAATTAGGG
52484650 TTAGGGTTTTGAGAATT
1 TTAGGGTTTTGAGAATT
*
52484667 TT-GGGTTTTTA-AATT
1 TTAGGGTTTTGAGAATT
52484682 TTAGGGTTTT
1 TTAGGGTTTT
52484692 AAGGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 15 0.65
17 2 0.09
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (17 bp):
TTAGGGTTTTGAGAATT
Found at i:52484692 original size:15 final size:15
Alignment explanation
Indices: 52484650--52484693 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
52484640 GCAATTAGGG
52484650 TTAGGGTTTTGAGAATT
1 TTAGGGTTTT-A-AATT
52484667 TT-GGGTTTTTAAATT
1 TTAGGG-TTTTAAATT
52484682 TTAGGGTTTTAA
1 TTAGGGTTTTAA
52484694 GGAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.48
16 7 0.28
17 6 0.24
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (15 bp):
TTAGGGTTTTAAATT
Found at i:52484805 original size:96 final size:98
Alignment explanation
Indices: 52484681--52484885 Score: 251
Period size: 96 Copynumber: 2.1 Consensus size: 98
52484671 GTTTTTAAAT
* ** *
52484681 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAGTG-TTTGTTAATTAAATTAATT
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAG-GATTACTTAAGTAAATTAATT
* *
52484744 ACT-AATTTTAA-AAAATTAGATTATGG-TTTAGTG
65 A-TAAATTTAAATAAAATTAGATTA-GGATTTAGGG
* * *
52484777 TTTATGGTTTTTAAGG-AAAAAATCAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAGGATTACTTAAGTAAATTAATTA
52484841 TAAATTTAAATAAAATTAGATTAGGATTTTAGGG
66 TAAATTTAAATAAAATTAGATTAGGA-TTTAGGG
52484875 TTTAGGGTTTT
1 TTTAGGGTTTT
52484886 AGGGTATTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
95 2 0.02
96 55 0.59
97 20 0.22
98 16 0.17
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.42
Consensus pattern (98 bp):
TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAGGATTACTTAAGTAAATTAATTA
TAAATTTAAATAAAATTAGATTAGGATTTAGGG
Found at i:52484885 original size:15 final size:15
Alignment explanation
Indices: 52484861--52484890 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52484851 TAAAATTAGA
52484861 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
52484876 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
52484891 ATTTAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:52485207 original size:126 final size:126
Alignment explanation
Indices: 52484973--52485511 Score: 882
Period size: 126 Copynumber: 4.3 Consensus size: 126
52484963 AACAGCTTCT
52484973 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
* * * * *
52485038 ATAGTGTCAAAAACACTTCAAGCAGGATGCATTGTCAGTAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
* * * * *
52485099 ACGTAGACGCTCTTTTGCTACAGTAGTATCTTAAAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
*
52485164 ATAGTGTAAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
52485225 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
* *
52485290 ATAGTGGT-AGAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
* **
52485351 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
*
52485416 ATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAACAAAAGTACTAAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
* * *
52485477 ACGTGGACGCTCTTTTGCTATAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
52485512 TAACTTGGGC
Statistics
Matches: 384, Mismatches: 27, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
125 2 0.01
126 380 0.99
127 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
ATAGTGTCAAAAACGCTTCAAACAGGATGCATTTTCAGCAAAAGTACTAAAAGAAGCTCCC
Found at i:52488600 original size:55 final size:55
Alignment explanation
Indices: 52488538--52488717 Score: 197
Period size: 55 Copynumber: 3.2 Consensus size: 55
52488528 TACATGAAAT
52488538 AATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
1 AATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
* * * * *
52488593 AATATAAAAGTAAATT-ACAA--TTACTTTATTTAAAACAACCTTTT-ATCTAATTACATGAAA
1 AATATAAAA--ATATTCAAAATGTTGCTTTATTTAAAATAA--TTTTCAT-T--TT--ATTAAA
52488653 TAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
1 -AATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
52488709 AATATAAAA
1 AATATAAAA
52488718 GTAAATTACA
Statistics
Matches: 101, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
54 16 0.16
55 20 0.20
56 13 0.13
57 4 0.04
58 4 0.04
59 4 0.04
60 13 0.13
61 11 0.11
62 16 0.16
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (55 bp):
AATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
Found at i:52488730 original size:116 final size:116
Alignment explanation
Indices: 52488526--52488792 Score: 525
Period size: 116 Copynumber: 2.3 Consensus size: 116
52488516 TTTATATTTT
52488526 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
52488591 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
52488642 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
52488707 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
52488758 ATTACATGAAATAATATAAAAAGATTCAAAATGTT
1 ATTACATGAAATAATATAAAAATATTCAAAATGTT
52488793 TGTACAATAT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 150 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:52489201 original size:18 final size:18
Alignment explanation
Indices: 52489175--52489217 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
52489165 GACTAGAAAA
* *
52489175 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGCT
52489193 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
52489211 AGGATAC
1 AGGATAC
52489218 GTACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:52489312 original size:30 final size:30
Alignment explanation
Indices: 52489278--52489336 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
52489268 TGTTGGGCTC
* *
52489278 GGTGACTGTGTAGGTC-CTGTTGCTGGGCCG
1 GGTGACTGTGT-GGGCGCTGTTGATGGGCCG
*
52489308 GGTGATTGTGTGGGCGCTGTTGATGGGCC
1 GGTGACTGTGTGGGCGCTGTTGATGGGCC
52489337 TGCGTCGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.07, C:0.17, G:0.46, T:0.31
Consensus pattern (30 bp):
GGTGACTGTGTGGGCGCTGTTGATGGGCCG
Found at i:52489672 original size:7 final size:7
Alignment explanation
Indices: 52489662--52489688 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52489652 GTTAAATAAA
52489662 AAATACT
1 AAATACT
52489669 AAATACT
1 AAATACT
52489676 AAATACT
1 AAATACT
52489683 AAATAC
1 AAATAC
52489689 GAATCCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATACT
Found at i:52489673 original size:14 final size:14
Alignment explanation
Indices: 52489654--52489687 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52489644 AAATATTAGT
52489654 TAAATAAAAAATAC
1 TAAATAAAAAATAC
**
52489668 TAAATACTAAATAC
1 TAAATAAAAAATAC
52489682 TAAATA
1 TAAATA
52489688 CGAATCCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATAAAAAATAC
Found at i:52491175 original size:384 final size:384
Alignment explanation
Indices: 52490466--52491233 Score: 1500
Period size: 384 Copynumber: 2.0 Consensus size: 384
52490456 TCTATCAACG
*
52490466 CACTAATAAGTTTCGGGTCCAACTTGCACCCCCGGCCTATCATCGCCACGTGCCAAAAACCCGCT
1 CACTAATAAGTTTCGGGTCCAACTTGCACCCCCGGCCTATCATCGCCACGTGCCAAAAACCAGCT
*
52490531 TCCCGTAGGTAATCCTCTATCAACGGTGATGGAGGACCAGTCATGTTACGGATATAGCATTGCAA
66 TCCCGTAGGTAATCCTCTATCAACGGTGATGGAGGACCAATCATGTTACGGATATAGCATTGCAA
52490596 TATCCGATCTACAGACTTTTATAAGAAATAATAAAATAAAAATTATTTAAATTTGCATAAATGAC
131 TATCCGATCTACAGACTTTTATAAGAAATAATAAAATAAAAATTATTTAAATTTGCATAAATGAC
52490661 AGAAATCTTAAATAATATTTAAATATTAAATTTTACACTTACCATTTGCATTTGTTCAACGGATA
196 AGAAATCTTAAATAATATTTAAATATTAAATTTTACACTTACCATTTGCATTTGTTCAACGGATA
52490726 TGTGTTTATCATCGAAGCGAATTAATTCTCCGGCCACTGCTAACACGATCAATTTTTTTTATTTT
261 TGTGTTTATCATCGAAGCGAATTAATTCTCCGGCCACTGCTAACACGATCAATTTTTTTTATTTT
52490791 AAAAAATAAATCTAGAAAAAATATAATTAGAGCTTTTTTGAAAAAAATTAATGAGAGTT
326 AAAAAATAAATCTAGAAAAAATATAATTAGAGCTTTTTTGAAAAAAATTAATGAGAGTT
*
52490850 CACTAATAAGTTTCGGGTCCAACTTGCACCCCCGGCCTATCATCGTCACGTGCCAAAAACCAGCT
1 CACTAATAAGTTTCGGGTCCAACTTGCACCCCCGGCCTATCATCGCCACGTGCCAAAAACCAGCT
52490915 TCCCGTAGGTAATCCTCTATCAACGGTGATGGAGGACCAATCATGTTACGGATATAGCATTGCAA
66 TCCCGTAGGTAATCCTCTATCAACGGTGATGGAGGACCAATCATGTTACGGATATAGCATTGCAA
*
52490980 TATCCGATCTACAGACTTTTATAATAAATAATAAAATAAAAATTATTTAAATTTGCATAAATGAC
131 TATCCGATCTACAGACTTTTATAAGAAATAATAAAATAAAAATTATTTAAATTTGCATAAATGAC
52491045 AGAAATCTTAAATAATATTTAAATATTAAATTTTACACTTACCATTTGCATTTGTTCAACGGATA
196 AGAAATCTTAAATAATATTTAAATATTAAATTTTACACTTACCATTTGCATTTGTTCAACGGATA
52491110 TGTGTTTATCATCGAAGCGAATTAATTCTCCGGCCACTGCTAACACGATCAATTTTTTTTATTTT
261 TGTGTTTATCATCGAAGCGAATTAATTCTCCGGCCACTGCTAACACGATCAATTTTTTTTATTTT
52491175 AAAAAATAAATCTAGAAAAAATATAATTAGAGCTTTTTTGAAAAAAATTAATGAGAGTT
326 AAAAAATAAATCTAGAAAAAATATAATTAGAGCTTTTTTGAAAAAAATTAATGAGAGTT
52491234 TTTGAGAGGA
Statistics
Matches: 380, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
384 380 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (384 bp):
CACTAATAAGTTTCGGGTCCAACTTGCACCCCCGGCCTATCATCGCCACGTGCCAAAAACCAGCT
TCCCGTAGGTAATCCTCTATCAACGGTGATGGAGGACCAATCATGTTACGGATATAGCATTGCAA
TATCCGATCTACAGACTTTTATAAGAAATAATAAAATAAAAATTATTTAAATTTGCATAAATGAC
AGAAATCTTAAATAATATTTAAATATTAAATTTTACACTTACCATTTGCATTTGTTCAACGGATA
TGTGTTTATCATCGAAGCGAATTAATTCTCCGGCCACTGCTAACACGATCAATTTTTTTTATTTT
AAAAAATAAATCTAGAAAAAATATAATTAGAGCTTTTTTGAAAAAAATTAATGAGAGTT
Found at i:52491272 original size:20 final size:20
Alignment explanation
Indices: 52491234--52491284 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
52491224 AATGAGAGTT
52491234 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGA-G-ATTTAAGAGAAA
* *
52491256 TTTGAGAGATTTGAGAGGAA
1 TTTGAGAGATTTAAGAGAAA
52491276 TTTGAGAGA
1 TTTGAGAGA
52491285 ATATTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 19 0.70
21 1 0.04
22 7 0.26
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (20 bp):
TTTGAGAGATTTAAGAGAAA
Found at i:52491291 original size:11 final size:10
Alignment explanation
Indices: 52491234--52491291 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
52491224 AATGAGAGTT
52491234 TTTGAGAGGAA
1 TTTGAGA-GAA
*
52491245 TTTAAGAGAAA
1 TTTGAGAG-AA
52491256 TTTGAGAG-A
1 TTTGAGAGAA
52491265 TTTGAGAGGAA
1 TTTGAGA-GAA
52491276 TTTGAGAGAA
1 TTTGAGAGAA
52491286 TATTGA
1 T-TTGA
52491292 AAGATTGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.20
10 6 0.15
11 27 0.66
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:52491297 original size:31 final size:31
Alignment explanation
Indices: 52491234--52491297 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
52491224 AATGAGAGTT
*
52491234 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
*
52491265 TTTGAGAGGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGGAATTTAAGAGAAAT-TTGAAAGA
52491296 TT
1 TT
52491298 GAAGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (31 bp):
TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
Found at i:52514141 original size:28 final size:27
Alignment explanation
Indices: 52514082--52514135 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
52514072 CCAAGATGGG
*
52514082 ATGTTTGAAATTTATCTCGGGATTCCC
1 ATGTTTGAAATTTATCACGGGATTCCC
*
52514109 ATGTTTCGAAATTTTTTCACGGGATTC
1 ATGTTT-GAAA-TTTATCACGGGATTC
52514136 TCTGTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 4 0.17
29 13 0.57
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
ATGTTTGAAATTTATCACGGGATTCCC
Found at i:52514962 original size:18 final size:16
Alignment explanation
Indices: 52514940--52514982 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
52514930 AGCAATTTAA
52514940 TTTTTTTTCTTTTATGT
1 TTTTTTTTCTTTTAT-T
* *
52514957 TCTTTTTTCCTTTTCTT
1 T-TTTTTTTCTTTTATT
52514974 TTTTTTTTC
1 TTTTTTTTC
52514983 ATTCTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 12 0.55
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTTTTATT
Found at i:52514979 original size:17 final size:18
Alignment explanation
Indices: 52514940--52514982 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
52514930 AGCAATTTAA
52514940 TTTTTTTT-CTTTTATGT
1 TTTTTTTTCCTTTTATGT
* *
52514957 TCTTTTTTCCTTTTCT-T
1 TTTTTTTTCCTTTTATGT
52514974 TTTTTTTTC
1 TTTTTTTTC
52514983 ATTCTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTTCCTTTTATGT
Found at i:52516148 original size:15 final size:15
Alignment explanation
Indices: 52516100--52516150 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
52516090 ATATTATAAT
52516100 AATATAAATAATTAA
1 AATATAAATAATTAA
* * *
52516115 AATCTAACAT--CTCA
1 AATATAA-ATAATTAA
52516129 AATATAAATAATTAA
1 AATATAAATAATTAA
52516144 AATATAA
1 AATATAA
52516151 CCTACACAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:52522368 original size:21 final size:21
Alignment explanation
Indices: 52522330--52522369 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52522320 CAGTTTGATC
*
52522330 AATTAGGTATTCTTTTGTCAT
1 AATTAGGTATTCTATTGTCAT
52522351 AATTAGGGTATT-TATTGTC
1 AATTA-GGTATTCTATTGTC
52522370 GAATGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.50
Consensus pattern (21 bp):
AATTAGGTATTCTATTGTCAT
Found at i:52525463 original size:26 final size:28
Alignment explanation
Indices: 52525409--52525464 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
52525399 ACCTCTACCA
52525409 TGTGAGCCGTCATCTTCCTCCTCCTTCCC
1 TGTGAGCCGTCATCTT-CTCCTCCTTCCC
52525438 TGTGAGCCGTCATC-T-TCCTCCTTCCC
1 TGTGAGCCGTCATCTTCTCCTCCTTCCC
52525464 T
1 T
52525465 ATTCTATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 12 0.44
28 1 0.04
29 14 0.52
ACGTcount: A:0.07, C:0.43, G:0.14, T:0.36
Consensus pattern (28 bp):
TGTGAGCCGTCATCTTCTCCTCCTTCCC
Found at i:52527579 original size:45 final size:43
Alignment explanation
Indices: 52527517--52527624 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 43
52527507 AAAAATGTGG
* * *
52527517 CATAAAACAATTCAAAATAATAAGGCAGTTTTAAA-TAAATAAT
1 CATAAAACAATTTAAAATAATAAGGCA-ATTTAAAGTAAAGAAT
*
52527560 ACATAAAACAATTTTAAAATAAAAAGGCAATTTAAAGTAAAGAAT
1 -CATAAAACAA-TTTAAAATAATAAGGCAATTTAAAGTAAAGAAT
*
52527605 -ATAAAACAATTTATAATAAT
1 CATAAAACAATTTAAAATAAT
52527625 TAATATATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 9 0.16
43 9 0.16
44 16 0.29
45 22 0.39
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.28
Consensus pattern (43 bp):
CATAAAACAATTTAAAATAATAAGGCAATTTAAAGTAAAGAAT
Found at i:52527922 original size:22 final size:23
Alignment explanation
Indices: 52527870--52527923 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
52527860 CTATATAGTC
*
52527870 TTAAAATTAATAATAATAAAGGT
1 TTAAAATAAATAATAATAAAGGT
*
52527893 TTACAATAAATAAT-A-AAAGAGT
1 TTAAAATAAATAATAATAAAG-GT
52527915 TTAAAATAA
1 TTAAAATAA
52527924 TTTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 12 0.44
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAATAAATAATAATAAAGGT
Found at i:52534666 original size:3 final size:3
Alignment explanation
Indices: 52534658--52534691 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52534648 AACTCTATCT
52534658 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
52534692 CTTCATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52544813 original size:17 final size:18
Alignment explanation
Indices: 52544791--52544830 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
52544781 TAAAAATTTC
*
52544791 AAAATTAT-ATTTTTTTA
1 AAAATTATAAATTTTTTA
52544808 AAAATTATAAAATTTTTTA
1 AAAATTAT-AAATTTTTTA
52544827 AAAA
1 AAAA
52544831 AATTCTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
19 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTATAAATTTTTTA
Found at i:52546110 original size:9 final size:9
Alignment explanation
Indices: 52546082--52546133 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
52546072 TAAAAATATA
52546082 TATATATTT
1 TATATATTT
*
52546091 AATTGATATTT
1 TA-T-ATATTT
52546102 TATATATTT
1 TATATATTT
52546111 TATGATATTT
1 TAT-ATATTT
*
52546121 TGTATATTT
1 TATATATTT
52546130 TATA
1 TATA
52546134 ATTAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 19 0.53
10 10 0.28
11 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (9 bp):
TATATATTT
Found at i:52546116 original size:19 final size:19
Alignment explanation
Indices: 52546082--52546132 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
52546072 TAAAAATATA
*
52546082 TATATATTTAATTGATATTT
1 TATATATTTTA-TGATATTT
52546102 TATATATTTTATGATATTT
1 TATATATTTTATGATATTT
*
52546121 TGTATATTTTAT
1 TATATATTTTAT
52546133 AATTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (19 bp):
TATATATTTTATGATATTT
Found at i:52546939 original size:5 final size:5
Alignment explanation
Indices: 52546929--52546957 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
52546919 ATTCAATTTT
52546929 TAATA TAATA TAATA TAATA TAATA -AATA
1 TAATA TAATA TAATA TAATA TAATA TAATA
52546958 ATAAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:52549060 original size:20 final size:20
Alignment explanation
Indices: 52549022--52549063 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52549012 TTCTATATTT
*
52549022 TTTTAAAAATATCAGTTTAA
1 TTTTAAAAAAATCAGTTTAA
* *
52549042 TTTTAAAAAAATTATTTTAA
1 TTTTAAAAAAATCAGTTTAA
52549062 TT
1 TT
52549064 ACTATTTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAAAAAAATCAGTTTAA
Found at i:52555205 original size:3 final size:3
Alignment explanation
Indices: 52554968--52555189 Score: 94
Period size: 3 Copynumber: 74.7 Consensus size: 3
52554958 TATTTGTTGA
* * * * * * *
52554968 TAT TAT TAC TAT TAC TAT TAT CAT TAT TGT TAC TGT TAT GTTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
52555014 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAGT GGA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T -TAT TAT
52555061 T-T T-T TAT TAT ATAT GTA- TAT GTA- TAT ATAT T-T ATAT ATAT TAT
1 TAT TAT TAT TAT -TAT -TAT TAT -TAT TAT -TAT TAT -TAT -TAT TAT
* * * *
52555104 TAT TTT TAAT TAC T-T TAT T-T TAA TAT TTT TAT TA- TAT TA- TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
52555146 T-T GCT T-T T-T GTAT T-T CAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52555188 TA
1 TA
52555190 GTATATGTTT
Statistics
Matches: 166, Mismatches: 31, Indels: 44
0.69 0.13 0.18
Matches are distributed among these distances:
2 22 0.13
3 119 0.72
4 24 0.14
5 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:52555228 original size:19 final size:20
Alignment explanation
Indices: 52555190--52555238 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
52555180 ATTATTATTA
* *
52555190 GTATATGTTTTATTATATAT
1 GTATATATTTTATAATATAT
52555210 GTATATATTTT-TAATATAT
1 GTATATATTTTATAATATAT
*
52555229 ATATATATTT
1 GTATATATTT
52555239 ATGTAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
GTATATATTTTATAATATAT
Found at i:52555231 original size:17 final size:17
Alignment explanation
Indices: 52555206--52555239 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52555196 GTTTTATTAT
* *
52555206 ATATGTATATATTTTTA
1 ATATATATATATATTTA
52555223 ATATATATATATATTTA
1 ATATATATATATATTTA
52555240 TGTAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATATATATATTTA
Found at i:52555395 original size:23 final size:23
Alignment explanation
Indices: 52555358--52555401 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52555348 ACTTTCAATA
* *
52555358 CTATATTATGCATATATTTTTGT
1 CTATATTATACATATACTTTTGT
*
52555381 CTATATTATATATATACTTTT
1 CTATATTATACATATACTTTT
52555402 AATACTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (23 bp):
CTATATTATACATATACTTTTGT
Found at i:52562590 original size:20 final size:20
Alignment explanation
Indices: 52562554--52562592 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52562544 TCGTCATCTC
52562554 ATCTGATATTGTCAGGAGAA
1 ATCTGATATTGTCAGGAGAA
*
52562574 ATCTG-TATTAGTTAGGAGA
1 ATCTGATATT-GTCAGGAGA
52562593 TCAATAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCTGATATTGTCAGGAGAA
Found at i:52562761 original size:43 final size:43
Alignment explanation
Indices: 52562700--52562786 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
52562690 TAAAATACTA
* *
52562700 AAGTAGTCACTTTTGTTTACCTCAGTTTACATTTTAGTCACCT
1 AAGTAGTCACTTTTGTTTACCTCAATTTACATTTTAGCCACCT
*
52562743 AAGTAG-CTACTTTTGTTTACCTCAATTTACATTTTGGCCACCT
1 AAGTAGTC-ACTTTTGTTTACCTCAATTTACATTTTAGCCACCT
52562786 A
1 A
52562787 TGTTCGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (43 bp):
AAGTAGTCACTTTTGTTTACCTCAATTTACATTTTAGCCACCT
Found at i:52562778 original size:21 final size:21
Alignment explanation
Indices: 52562710--52562778 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
52562700 AAGTAGTCAC
*
52562710 TTTTGTTTACCTCAGTTTACA
1 TTTTGTTTACCTCAATTTACA
* *
52562731 TTTTAG-TCACCT-AA-GTAGCTA
1 TTTT-GTTTACCTCAATTTA-C-A
52562752 CTTTTGTTTACCTCAATTTACA
1 -TTTTGTTTACCTCAATTTACA
52562774 TTTTG
1 TTTTG
52562779 GCCACCTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 16 0.44
22 11 0.31
23 3 0.08
24 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTGTTTACCTCAATTTACA
Found at i:52564803 original size:7 final size:7
Alignment explanation
Indices: 52564791--52564815 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52564781 TAAACTAATA
52564791 ATATATT
1 ATATATT
52564798 ATATATT
1 ATATATT
52564805 ATATATT
1 ATATATT
52564812 ATAT
1 ATAT
52564816 GCTATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATATT
Found at i:52568620 original size:22 final size:22
Alignment explanation
Indices: 52568592--52568633 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52568582 TATATATATA
* *
52568592 TTTAAAATATTTGTTTAATTTT
1 TTTAAAAAAATTGTTTAATTTT
52568614 TTTAAAAAAATTGTTTAATT
1 TTTAAAAAAATTGTTTAATT
52568634 ACTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTAAAAAAATTGTTTAATTTT
Found at i:52569604 original size:20 final size:20
Alignment explanation
Indices: 52569581--52569619 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
52569571 AAATAAAATT
52569581 TATTTATTTATTTTTAAACG
1 TATTTATTTATTTTTAAACG
52569601 TATTTATTTATTTTTAAAC
1 TATTTATTTATTTTTAAAC
52569620 AAATTTTTTA
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:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTATTTATTTTTAAACG
Found at i:52569625 original size:20 final size:20
Alignment explanation
Indices: 52569582--52569630 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
52569572 AATAAAATTT
**
52569582 ATTTATTTATTTTTAAACGT
1 ATTTATTTATTTTTAAACAA
52569602 ATTTATTTATTTTTAAACAA
1 ATTTATTTATTTTTAAACAA
52569622 ATTT-TTTAT
1 ATTTATTTAT
52569631 CTAAAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTATTTATTTTTAAACAA
Found at i:52575349 original size:27 final size:27
Alignment explanation
Indices: 52575255--52575358 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
52575245 GGAAGCGTCA
* *
52575255 TGGTGGCTATGCCACAAATATCTG-ATC
1 TGGTGGCTCTGTCAC-AATATCTGTATC
*
52575282 TGGTGGCTCTGCCACATATATCTGT-TC
1 TGGTGGCTCTGTCACA-ATATCTGTATC
52575309 TGGTGGCTCTGTCACAATATCTGTATC
1 TGGTGGCTCTGTCACAATATCTGTATC
*
52575336 TGGTGACT-TCGTCACAATATCTG
1 TGGTGGCTCT-GTCACAATATCTG
52575359 GCAGCCTCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
26 10 0.14
27 60 0.86
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (27 bp):
TGGTGGCTCTGTCACAATATCTGTATC
Found at i:52575901 original size:19 final size:19
Alignment explanation
Indices: 52575877--52575924 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
52575867 TTTAGGACGC
52575877 GTTTTCAAAAACAGTAATT
1 GTTTTCAAAAACAGTAATT
*
52575896 GTTTTCAAAAGCAGTAATT
1 GTTTTCAAAAACAGTAATT
*
52575915 GATTTCAAAA
1 GTTTTCAAAA
52575925 TAACACAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (19 bp):
GTTTTCAAAAACAGTAATT
Found at i:52576457 original size:51 final size:51
Alignment explanation
Indices: 52576310--52576446 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
52576300 CTACCATCAA
* * *
52576310 ATCTCTAAGAATATAATATCATATCTTCTAAGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
52576361 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
52576412 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
52576447 AGTTACCATA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:52580413 original size:25 final size:25
Alignment explanation
Indices: 52580379--52580428 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
52580369 AGAAAAAAGA
52580379 AAGGTTTTCTTCCTTTTTCACTCTG
1 AAGGTTTTCTTCCTTTTTCACTCTG
52580404 AAGGTTTTCTTCCTTTTTCACTCTG
1 AAGGTTTTCTTCCTTTTTCACTCTG
52580429 TTAGGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (25 bp):
AAGGTTTTCTTCCTTTTTCACTCTG
Found at i:52599483 original size:14 final size:15
Alignment explanation
Indices: 52599464--52599496 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
52599454 GATTCATATA
52599464 TTTTTGTTTT-TTTT
1 TTTTTGTTTTGTTTT
52599478 TTTTTGTTTTGTTTT
1 TTTTTGTTTTGTTTT
52599493 TTTT
1 TTTT
52599497 AAGCTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTTGTTTTGTTTT
Found at i:52600203 original size:13 final size:14
Alignment explanation
Indices: 52600185--52600214 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52600175 ATTAACTTGA
52600185 AAATTAATTTAT-T
1 AAATTAATTTATAT
52600198 AAATTAATTTATAT
1 AAATTAATTTATAT
52600212 AAA
1 AAA
52600215 ATTGATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTAATTTATAT
Found at i:52603935 original size:26 final size:26
Alignment explanation
Indices: 52603904--52604011 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
52603894 TGAAATGCCC
*
52603904 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
52603930 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
52603956 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
52603982 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52604008 ATCA
1 ATCA
52604012 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52609500 original size:25 final size:27
Alignment explanation
Indices: 52609463--52609515 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
52609453 TCAAACATGC
52609463 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
52609489 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
52609515 A
1 A
52609516 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:52611034 original size:26 final size:26
Alignment explanation
Indices: 52610999--52611134 Score: 211
Period size: 26 Copynumber: 5.2 Consensus size: 26
52610989 CATGAAATTC
*
52610999 TTATCATGAAACATTTACCTAACCCC
1 TTATCATGAAACATTTACCTAACCCA
52611025 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
52611051 TTATCATGAAACATTTACCTAGCCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
52611077 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
52611103 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
52611129 TTATCA
1 TTATCA
52611135 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
26 102 0.98
27 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:52614861 original size:9 final size:9
Alignment explanation
Indices: 52614819--52614863 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
52614809 ATTTTTAAAA
52614819 TTTTTAATT
1 TTTTTAATT
52614828 TTTTTAATT
1 TTTTTAATT
**
52614837 TTTAAAAGTAT
1 TTTTTAA-T-T
52614848 TTTTTAATT
1 TTTTTAATT
52614857 TTTTTAA
1 TTTTTAA
52614864 ACCATTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 22 0.73
10 2 0.07
11 6 0.20
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTTAATT
Found at i:52614870 original size:21 final size:20
Alignment explanation
Indices: 52614827--52614872 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
52614817 AATTTTTAAT
**
52614827 TTTTTTAATTTTTAAAAGTA
1 TTTTTTAATTTTTAAAACCA
*
52614847 TTTTTTAATTTTTTTAAACCA
1 TTTTTTAA-TTTTTAAAACCA
52614868 TTTTT
1 TTTTT
52614873 GGAGTTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTAATTTTTAAAACCA
Found at i:52619303 original size:20 final size:20
Alignment explanation
Indices: 52619274--52619315 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52619264 TGTCAGTCTT
* * *
52619274 ATGAATAGTGGAGTCAAGTC
1 ATGAACAGTGGAATCAAATC
52619294 ATGAACAGTGGAATCAAATC
1 ATGAACAGTGGAATCAAATC
52619314 AT
1 AT
52619316 AAATAGTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGAACAGTGGAATCAAATC
Found at i:52635605 original size:24 final size:24
Alignment explanation
Indices: 52635560--52635604 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
52635550 ATTATTTATA
52635560 ATTATGGTCAAATATTTTAAAATG
1 ATTATGGTCAAATATTTTAAAATG
52635584 ATTATGG-C-AATACTTTTAAAA
1 ATTATGGTCAAATA-TTTTAAAA
52635605 AATACTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (24 bp):
ATTATGGTCAAATATTTTAAAATG
Found at i:52635646 original size:13 final size:13
Alignment explanation
Indices: 52635594--52635646 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
52635584 ATTATGGCAA
*
52635594 TACTTTTAAAAAA
1 TACTTTTAAAAAG
*
52635607 TACTTTTGAAAAG
1 TACTTTTAAAAAG
*
52635620 T-GTTATTAAAAAG
1 TACTT-TTAAAAAG
*
52635633 TACTTTTAAGAAG
1 TACTTTTAAAAAG
52635646 T
1 T
52635647 GTTTTTGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (13 bp):
TACTTTTAAAAAG
Found at i:52635657 original size:26 final size:26
Alignment explanation
Indices: 52635597--52635659 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
52635587 ATGGCAATAC
*
52635597 TTTTAAAAAATACTTTTGAAAAGTGT
1 TTTTAAAAAGTACTTTTGAAAAGTGT
*
52635623 TATTAAAAAGTACTTTT-AAGAAGTGT
1 TTTTAAAAAGTACTTTTGAA-AAGTGT
*
52635649 TTTTGAAAAGT
1 TTTTAAAAAGT
52635660 TTGATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (26 bp):
TTTTAAAAAGTACTTTTGAAAAGTGT
Found at i:52638799 original size:29 final size:29
Alignment explanation
Indices: 52638735--52638804 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
52638725 ACTTTTTCTT
**
52638735 AATTTGGTACCTAAACTTTTTTGGGGCCC
1 AATTTGGTACCTAAACTTTTTTGAAGCCC
* * * **
52638764 AACTTGGTACCTAAGCTTTTTTTAAGTTC
1 AATTTGGTACCTAAACTTTTTTGAAGCCC
52638793 AATTTGGTACCT
1 AATTTGGTACCT
52638805 TAATTTATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (29 bp):
AATTTGGTACCTAAACTTTTTTGAAGCCC
Found at i:52645824 original size:12 final size:13
Alignment explanation
Indices: 52645796--52645825 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52645786 TCGTTTGTAC
52645796 TATATATCATGTT
1 TATATATCATGTT
52645809 TATATATCAT-TT
1 TATATATCATGTT
52645821 TATAT
1 TATAT
52645826 TAATGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (13 bp):
TATATATCATGTT
Found at i:52660451 original size:47 final size:47
Alignment explanation
Indices: 52660351--52660464 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
52660341 GAAAGACTTT
* *
52660351 AATAGTAATGTGATAGTAATGATAATAATAATACAGTAATAAAAAATG
1 AATAATAATGTGATAGTAATGATAATAATAATA-AGTAATAAAAAAGG
* *
52660399 -CTAATAATGTGATAGTAATGATAATAATAAT-AGTAGTAAAAATAGG
1 AATAATAATGTGATAGTAATGATAATAATAATAAGTAATAAAAA-AGG
*
52660445 AATAATACA-GTAATAGTAAT
1 AATAATA-ATGTGATAGTAAT
52660465 AAAAAGGAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
45 10 0.18
46 2 0.04
47 44 0.77
48 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (47 bp):
AATAATAATGTGATAGTAATGATAATAATAATAAGTAATAAAAAAGG
Found at i:52660564 original size:9 final size:9
Alignment explanation
Indices: 52660547--52660605 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
52660537 AAAAAGAAGG
*
52660547 AATAATAAT
1 AATAGTAAT
52660556 AATAGTAAT
1 AATAGTAAT
*
52660565 AA-A-AAAT
1 AATAGTAAT
*
52660572 AATAGTAAC
1 AATAGTAAT
* *
52660581 ATTAGTAGT
1 AATAGTAAT
52660590 AATAGTAAT
1 AATAGTAAT
52660599 AA-AGTAA
1 AATAGTAA
52660606 CGGTAATAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.13
8 7 0.18
9 27 0.69
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (9 bp):
AATAGTAAT
Found at i:52660758 original size:3 final size:3
Alignment explanation
Indices: 52660750--52660776 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52660740 TAATGATAAG
52660750 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
52660777 GGATGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52661239 original size:25 final size:26
Alignment explanation
Indices: 52661209--52661277 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
52661199 ATTTTGAAAA
52661209 AATGATAATAGTAAAAAA-TAATAGT
1 AATGATAATAGTAAAAAATTAATAGT
* **
52661234 AATGATAATACTAAAATAATTAATTTT
1 AATGATAATAGTAAAA-AATTAATAGT
*
52661261 AATAATAA-AGTAAAAAA
1 AATGATAATAGTAAAAAA
52661278 AGGATCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 17 0.46
26 8 0.22
27 12 0.32
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (26 bp):
AATGATAATAGTAAAAAATTAATAGT
Found at i:52662825 original size:86 final size:87
Alignment explanation
Indices: 52662651--52663283 Score: 737
Period size: 86 Copynumber: 7.3 Consensus size: 87
52662641 ATCTATAATT
* ** * * * * *
52662651 TTCAGCCTGTTACCCTACTGCTTAGGGG-TCAAGGTTCATCGTCTTTGATCTG-CTCTACTGCTG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTC-CCTACTG
* *
52662714 CCTAGGGAGATAAGATCT-GTAAA
65 CTTAGGGGGATAAGATCTAG-AAA
* * * *
52662737 TTCAGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATTTG-CTCCACTACTA
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCC-CTACTG
** *
52662801 CTTAGGAAGATAAGATCT-GCAA
65 CTTAGGGGGATAAGATCTAGAAA
* * * * * * *
52662823 TTCGGTCTGTTACCCTTCTGCTTAGGGGTTTAAGACCCCTAGTCTTCGATCTGTTTCCCTATTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGC
*
52662888 TTAAGGGGGTTAAGATCTAGAAA
66 TT-AGGGGGATAAGATCTAGAAA
* *
52662911 TTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTG-CTCCACTACTG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCC-CTACTG
* *
52662975 CTTAGGGAGATAAGATCT-GCAA
65 CTTAGGGGGATAAGATCTAGAAA
* ** * * *
52662997 TTCGGTATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGC
*
52663062 TTA-GGGGATTAAGATCTGGAAA
66 TTAGGGGGA-TAAGATCTAGAAA
* *
52663084 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG-CCTTCATCTTCGATCTGTTTCCCTATTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGC
* *
52663148 TTAGGGGGGTTAAGATCTGGAAA
66 TTA-GGGGGATAAGATCTAGAAA
*
52663171 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCTTTCGTCTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGC
*
52663236 TT-GGGGGGTAAGATCTAGAAA
66 TTAGGGGGATAAGATCTAGAAA
* *
52663257 TTCAACCTGTTACCCTACTGCTCAGGG
1 TTCAGCCTGTTACCCTACTGCTTAGGG
52663284 AGATAAGGCT
Statistics
Matches: 469, Mismatches: 66, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
85 4 0.01
86 220 0.47
87 156 0.33
88 89 0.19
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (87 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGC
TTAGGGGGATAAGATCTAGAAA
Found at i:52662889 original size:44 final size:43
Alignment explanation
Indices: 52662823--52663283 Score: 234
Period size: 44 Copynumber: 10.6 Consensus size: 43
52662813 AGATCTGCAA
* * *
52662823 TTCGGTCTGTTACCCTTCTGCTTAGGGGTTTAAGACCCCTAGTC
1 TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGA-CTCTAGTC
* * *
52662867 TTCGATCTGTTTCCCTATTGCTTAAGGGGGTTAAGA-TCTAGAAAT-
1 TTCGATCTGTTACCCTACTGCTT-AGGGGTTTAAGACTCTAG---TC
* * * * *
52662912 TTAG-CCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTC
1 TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACTC-TAGTC
* *
52662955 TTCGATCTGCT-CCACTACTGCTTAGGGAG-ATAAGA-TCT-G-C
1 TTCGATCTGTTACC-CTACTGCTTAGGG-GTTTAAGACTCTAGTC
* * * * * *
52662995 AATTCGGTATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGTC
1 --TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACTC-TAGTC
* * * **
52663041 TTCGATCTGTTTCCCTACTGCTTAGGGGATTAAGA-TCTGGAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACTCTAG-TC
* *
52663084 TTC-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC-CTTCA-TC
1 TTCGA-TCTGTTACCCTACTGCTTAGGGGTTTAAGACTC-T-AGTC
* * * * **
52663127 TTCGATCTGTTTCCCTATTGCTTAGGGGGGTTAAGA-TCTGGAAA
1 TTCGATCTGTTACCCTACTGCTTA-GGGGTTTAAGACTCTAG-TC
* * * *
52663171 TTC-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCTTTCGTC
1 TTCGA-TCTGTTACCCTACTGCTTAGGGGTTTAA-GACTCTAGTC
* ** **
52663215 TTCGATCTGTTTCCCTACTGCTT-GGGGGGTAAGA-TCTAGAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACTCTAG-TC
* * *
52663257 TTCAACCTGTTACCCTACTGCTCAGGG
1 TTCGATCTGTTACCCTACTGCTTAGGG
52663284 AGATAAGGCT
Statistics
Matches: 309, Mismatches: 74, Indels: 69
0.68 0.16 0.15
Matches are distributed among these distances:
40 1 0.00
41 5 0.02
42 49 0.16
43 93 0.30
44 137 0.44
45 22 0.07
46 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
TTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACTCTAGTC
Found at i:52662922 original size:174 final size:173
Alignment explanation
Indices: 52662657--52663283 Score: 807
Period size: 174 Copynumber: 3.6 Consensus size: 173
52662647 AATTTTCAGC
* *** * * * * * *
52662657 CTGTTACCCTACTGCTTAGGGG-TCAAGGTTCATCGTCTTTGATCTG-CTCTACTGCTGCCTAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTC-CCTACTGCTTAGG
* * *
52662720 GAGATAAGATCT-GTAAATTCAGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCTTCGTCTTC
65 GGGTTAAGATCTAG-AAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTC
* * *
52662784 GATTTGCTCCACTACTACTTAGGAAGATAAGATCTGCAATTCGGT
129 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCGGT
* * * *
52662829 CTGTTACCCTTCTGCTTAGGGGTTTAAGACCCCTAGTCTTCGATCTGTTTCCCTATTGCTTAAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTT-AGG
*
52662894 GGGTTAAGATCTAGAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCG
65 GGGTTAAGATCTAGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCG
52662959 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCGGT
130 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCGGT
* * *
52663003 ATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
* * *
52663068 GATTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG-CCTTCATCTTCGA
66 GGTTAAGATCTAGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGA
* * * * * * *
52663132 TCTGTTTCC-CTATTGCTTAGGGGGGTTAAGATCTGGAAATTCAGC
131 TCTG-CTCCACTACTGCTTA-GGGAGATAAGATCT-GCAATTCGGT
* *
52663177 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCTTTCGTCTTCGATCTGTTTCCCTACTGCTT-GGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
* * *
52663241 GGGTAAGATCTAGAAATTCAACCTGTTACCCTACTGCTCAGGG
66 GGTTAAGATCTAGAAATTCAGCCTGTTACCCTACTGCTTAGGG
52663284 AGATAAGGCT
Statistics
Matches: 400, Mismatches: 48, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
172 46 0.12
173 131 0.33
174 222 0.56
175 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (173 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
GGTTAAGATCTAGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGA
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCGGT
Found at i:52663010 original size:260 final size:261
Alignment explanation
Indices: 52662651--52663275 Score: 809
Period size: 260 Copynumber: 2.4 Consensus size: 261
52662641 ATCTATAATT
* ** * * * *
52662651 TTCAGCCTGTTACCCTACTGCTTAGGGG-TCAAGGTTCATCGTCTTTGATCTGCTCTACTGCTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGCTCCACTACTGC
* * * * * *
52662715 CTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCTTCGT
66 TTAGGGAGATAAGATCTGTAAATTCAGCATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGT
* * * * *
52662780 CTTCGATTTG-CTCCACTACTACTTAGGAAGA-TAAGATCT-GCAATTCGGTCTGTTACCCTTCT
131 CTTCGATCTGTCTCC-CTACTACTTAGG-AGATTAAGATCTGGAAATTCAGCCTGTTACCCTACT
52662842 GCTTAGGGGTTTAAGACCCCT-AGTCTTCGATCTGTTTCCCTATTGCTTAAGGGGGTTAAGATCT
194 GCTTAGGGGTTTAAG-CCCCTCA-TCTTCGATCTGTTTCCCTATTGCTTAAGGGGGTTAAGATCT
52662906 AGAAA
257 AGAAA
*
52662911 TTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGCTCCACTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGCTCCACTACTGC
* * *
52662976 TTAGGGAGATAAGATCTG-CAATTCGGTATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGT
66 TTAGGGAGATAAGATCTGTAAATTCAGCATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGT
* * *
52663040 CTTCGATCTGTTTCCCTACTGCTTAGGGGATTAAGATCTGGAAATTCAGCCTGTTACCCTACTGC
131 CTTCGATCTGTCTCCCTACTACTTAGGAGATTAAGATCTGGAAATTCAGCCTGTTACCCTACTGC
* * * *
52663105 TTAGGGGTTTAAGGCCTTCATCTTCGATCTGTTTCCCTATTGCTTAGGGGGGTTAAGATCTGGAA
196 TTAGGGGTTTAAGCCCCTCATCTTCGATCTGTTTCCCTATTGCTTAAGGGGGTTAAGATCTAGAA
52663170 A
261 A
* *
52663171 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCTTTCGTCTTCGATCTGTTTCC-CTACTG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTG-CTCCACTACTG
* * * * *
52663235 CTT-GGGGGGTAAGATCTAG-AAATTCAACCTGTTACCCTACT
65 CTTAGGGAGATAAGATCT-GTAAATTCAGCATGTTACCATACT
52663276 GCTCAGGGAG
Statistics
Matches: 318, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
259 14 0.04
260 217 0.68
261 87 0.27
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (261 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGCTCCACTACTGC
TTAGGGAGATAAGATCTGTAAATTCAGCATGTTACCATACTACTTAGGGGTTTAAGACCCTTCGT
CTTCGATCTGTCTCCCTACTACTTAGGAGATTAAGATCTGGAAATTCAGCCTGTTACCCTACTGC
TTAGGGGTTTAAGCCCCTCATCTTCGATCTGTTTCCCTATTGCTTAAGGGGGTTAAGATCTAGAA
A
Found at i:52675509 original size:9 final size:9
Alignment explanation
Indices: 52675492--52675550 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
52675482 AAAAAGAAGG
*
52675492 AATAATAAT
1 AATAGTAAT
52675501 AATAGTAAT
1 AATAGTAAT
*
52675510 AA-A-AAAT
1 AATAGTAAT
*
52675517 AATAGTAAC
1 AATAGTAAT
* *
52675526 ATTAGTAGT
1 AATAGTAAT
52675535 AATAGTAAT
1 AATAGTAAT
52675544 AA-AGTAA
1 AATAGTAA
52675551 CGGTAATAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.13
8 7 0.18
9 27 0.69
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (9 bp):
AATAGTAAT
Found at i:52675703 original size:3 final size:3
Alignment explanation
Indices: 52675695--52675721 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52675685 TAATGATAAG
52675695 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
52675722 GGATGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52676184 original size:25 final size:26
Alignment explanation
Indices: 52676154--52676222 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
52676144 ATTTTGAAAA
52676154 AATGATAATAGTAAAAAA-TAATAGT
1 AATGATAATAGTAAAAAATTAATAGT
* **
52676179 AATGATAATACTAAAATAATTAATTTT
1 AATGATAATAGTAAAA-AATTAATAGT
*
52676206 AATAATAA-AGTAAAAAA
1 AATGATAATAGTAAAAAA
52676223 AGGATCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 17 0.46
26 8 0.22
27 12 0.32
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (26 bp):
AATGATAATAGTAAAAAATTAATAGT
Found at i:52680215 original size:39 final size:39
Alignment explanation
Indices: 52680170--52680246 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
52680160 TAAATATCTG
52680170 TGTGTGTATATACATACATACATATATATATTATCCTCA
1 TGTGTGTATATACATACATACATATATATATTATCCTCA
*
52680209 TGTGTGTGTATACATACATACATATATATATTATCCTC
1 TGTGTGTATATACATACATACATATATATATTATCCTC
52680247 CCTTTGTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.42
Consensus pattern (39 bp):
TGTGTGTATATACATACATACATATATATATTATCCTCA
Found at i:52683747 original size:33 final size:31
Alignment explanation
Indices: 52683668--52683730 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
52683658 CTCCTCAAAG
52683668 TACAACTTTTCTCTCTTTTTTTGTTAATAAT
1 TACAACTTTTCTCTCTTTTTTTGTTAATAAT
52683699 TACAACTTTTCTCTCTTTTTTTGTTAATAAT
1 TACAACTTTTCTCTCTTTTTTTGTTAATAAT
52683730 T
1 T
52683731 TTATCTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (31 bp):
TACAACTTTTCTCTCTTTTTTTGTTAATAAT
Found at i:52685203 original size:108 final size:108
Alignment explanation
Indices: 52685014--52685224 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 108
52685004 GGTATCTAGG
52685014 CCAACTTGATAATCTCAATAACCTGAGGCATCTGTGAGTAACTTTTCTTAGTACTTCAGAAAATG
1 CCAACTTGATAATCTCAATAACCTGAGGCATCTGTGAGTAACTTTTCTTAGTACTTCAGAAAATG
52685079 TAAGGGAGCTCTACTCTGCATTAAACTCTTTGAGTTGGCTTTC
66 TAAGGGAGCTCTACTCTGCATTAAACTCTTTGAGTTGGCTTTC
*
52685122 CCAACTTGATAATCTCAATAACCTGAGGCATCTGTGAGTAACTTTTCTTTGTACTTCAGAAAATG
1 CCAACTTGATAATCTCAATAACCTGAGGCATCTGTGAGTAACTTTTCTTAGTACTTCAGAAAATG
52685187 TAAGGGAGCTCTACTCTGCATTAAACTCTTTGAGTTGG
66 TAAGGGAGCTCTACTCTGCATTAAACTCTTTGAGTTGG
52685225 TTTTACTCTG
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (108 bp):
CCAACTTGATAATCTCAATAACCTGAGGCATCTGTGAGTAACTTTTCTTAGTACTTCAGAAAATG
TAAGGGAGCTCTACTCTGCATTAAACTCTTTGAGTTGGCTTTC
Found at i:52706235 original size:23 final size:23
Alignment explanation
Indices: 52706209--52706252 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52706199 AGAATTCTAC
*
52706209 CCATC-AGCCTCTGCACACCATTT
1 CCATCTAGCC-CTACACACCATTT
52706232 CCATCTAGCCCTACACACCAT
1 CCATCTAGCCCTACACACCAT
52706253 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (23 bp):
CCATCTAGCCCTACACACCATTT
Found at i:52707211 original size:15 final size:16
Alignment explanation
Indices: 52707184--52707213 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52707174 TCAATTTGTT
52707184 TTTGGGAAAAAGAAAA
1 TTTGGGAAAAAGAAAA
52707200 TTTGGG-AAAAGAAA
1 TTTGGGAAAAAGAAA
52707214 TCAATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (16 bp):
TTTGGGAAAAAGAAAA
Found at i:52707331 original size:58 final size:56
Alignment explanation
Indices: 52707263--52707379 Score: 146
Period size: 58 Copynumber: 2.0 Consensus size: 56
52707253 TTAATTATAG
* * *
52707263 TTAAACTTAATCACTTTAA-TATTAAATTAATATAATACTTATTAAGATAAATATTAAA
1 TTAAACTTAAT-A-TTAAACTATTAAATTAATAAAATAC-TATCAAGATAAATATTAAA
* *
52707321 TTAAATTTAATATTAAATCTATTAAATTAATAAAATACTATCAAGATAAGTATTAAA
1 TTAAACTTAATATTAAA-CTATTAAATTAATAAAATACTATCAAGATAAATATTAAA
52707378 TT
1 TT
52707380 TAAAATGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 4 0.08
57 20 0.38
58 28 0.54
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (56 bp):
TTAAACTTAATATTAAACTATTAAATTAATAAAATACTATCAAGATAAATATTAAA
Found at i:52713807 original size:16 final size:16
Alignment explanation
Indices: 52713786--52713826 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
52713776 AGAAATCCTT
52713786 GTTCATTTCTAAATGA
1 GTTCATTTCTAAATGA
52713802 GTTCATTTCTAAATGA
1 GTTCATTTCTAAATGA
*
52713818 ATTCATTTC
1 GTTCATTTC
52713827 ATATTTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (16 bp):
GTTCATTTCTAAATGA
Found at i:52713884 original size:6 final size:6
Alignment explanation
Indices: 52713862--52713896 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
52713852 TTCCAAATGA
52713862 TTTCAT TTCTCCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TT-T-CAT TTTCAT TTTCAT TTTCAT TTT
52713897 GGAGAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCAT
Found at i:52719907 original size:24 final size:25
Alignment explanation
Indices: 52719855--52719909 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
52719845 TTGATGAATC
*
52719855 TTATTTTATTAATTCATTTAAGTAA
1 TTATTTTATTAATTCATTGAAGTAA
52719880 --ATTTTATATAATT-ATTGAA-TAA
1 TTATTTTAT-TAATTCATTGAAGTAA
52719902 TTATTTTA
1 TTATTTTA
52719910 AAAACCACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 3 0.12
23 12 0.46
24 11 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATTTTATTAATTCATTGAAGTAA
Found at i:52720677 original size:26 final size:26
Alignment explanation
Indices: 52720621--52720677 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
52720611 AAATTTATTT
*
52720621 ATAAGCATGCTTCGCAAAATTAAACA
1 ATAATCATGCTTCGCAAAATTAAACA
* *
52720647 ATAATCATGCTTCGCCAAATTGAACA
1 ATAATCATGCTTCGCAAAATTAAACA
52720673 ATAAT
1 ATAAT
52720678 GCTTTCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (26 bp):
ATAATCATGCTTCGCAAAATTAAACA
Found at i:52723129 original size:16 final size:16
Alignment explanation
Indices: 52723108--52723139 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52723098 ACGAAGAGAT
52723108 AAGGTACAATATGCAC
1 AAGGTACAATATGCAC
52723124 AAGGTACAATATGCAC
1 AAGGTACAATATGCAC
52723140 GCCTGATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
AAGGTACAATATGCAC
Found at i:52729749 original size:18 final size:19
Alignment explanation
Indices: 52729720--52729759 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
52729710 ATTTCACCAA
52729720 AACAGATAGTAAAATGGTC
1 AACAGATAGTAAAATGGTC
52729739 AACAG-TAGTAAAATGGTC
1 AACAGATAGTAAAATGGTC
52729757 AAC
1 AAC
52729760 CGCAAAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (19 bp):
AACAGATAGTAAAATGGTC
Found at i:52730799 original size:19 final size:19
Alignment explanation
Indices: 52730766--52730822 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
52730756 TTATAAATAA
52730766 TAAATTTTAGA-AAAATTAT
1 TAAATTTTA-ATAAAATTAT
*
52730785 TAAATTTTAATAAAAAT-T
1 TAAATTTTAATAAAATTAT
* *
52730803 TAAAATTTATTAAAAATTAT
1 TAAATTTTAAT-AAAATTAT
52730823 ATTTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 11 0.35
19 19 0.61
20 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAAATTTTAATAAAATTAT
Found at i:52730811 original size:18 final size:18
Alignment explanation
Indices: 52730784--52730820 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52730774 AGAAAAATTA
*
52730784 TTAAATTTTAATAAAAAT
1 TTAAAATTTAATAAAAAT
*
52730802 TTAAAATTTATTAAAAAT
1 TTAAAATTTAATAAAAAT
52730820 T
1 T
52730821 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATTTAATAAAAAT
Found at i:52731118 original size:10 final size:10
Alignment explanation
Indices: 52731105--52731195 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
52731095 TATTTTTATA
52731105 TTTATAATTT
1 TTTATAATTT
*
52731115 TTTACAATTT
1 TTTATAATTT
* *
52731125 CTGTA-AA-AT
1 -TTTATAATTT
*
52731134 TTTACAATTT
1 TTTATAATTT
52731144 TTTAT-ATTCT
1 TTTATAATT-T
*
52731154 TTTATGA-TT
1 TTTATAATTT
52731163 TTTAT-ATTT
1 TTTATAATTT
*
52731172 TTTCTAATTT
1 TTTATAATTT
* *
52731182 TTAATAAATT
1 TTTATAATTT
52731192 TTTA
1 TTTA
52731196 ATATTTGAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 4 0.06
9 18 0.29
10 37 0.59
11 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTATAATTT
Found at i:52731166 original size:19 final size:18
Alignment explanation
Indices: 52731142--52731184 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
52731132 ATTTTACAAT
*
52731142 TTTTTATATTCTTTTATGA
1 TTTTTATATT-TTTTATAA
*
52731161 TTTTTATATTTTTTCTAA
1 TTTTTATATTTTTTATAA
52731179 TTTTTA
1 TTTTTA
52731185 ATAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTATATTTTTTATAA
Found at i:52731935 original size:21 final size:21
Alignment explanation
Indices: 52731906--52731947 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52731896 CACTTAAATT
52731906 TGTTATTGAGGTCTCGAGACA
1 TGTTATTGAGGTCTCGAGACA
* *
52731927 TGTTCTTGATGTCTCGAGACA
1 TGTTATTGAGGTCTCGAGACA
52731948 AATGATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
TGTTATTGAGGTCTCGAGACA
Found at i:52732513 original size:136 final size:136
Alignment explanation
Indices: 52732264--52732535 Score: 535
Period size: 136 Copynumber: 2.0 Consensus size: 136
52732254 TCAAATTCAG
52732264 AAAAAGCTAATTTTGAGGGCTCTTAGGCATTCTAAAGCCTATAAATACACCCTAGAGGAGGAAGA
1 AAAAAGCTAATTTTGAGGGCTCTTAGGCATTCTAAAGCCTATAAATACACCCTAGAGGAGGAAGA
52732329 AAAGGGAGACACAAAATAGGGAGTAAGAAATTACTCCAAGGAAGCCAATTGATCCATCTCAGAAG
66 AAAGGGAGACACAAAATAGGGAGTAAGAAATTACTCCAAGGAAGCCAATTGATCCATCTCAGAAG
52732394 CTAGAT
131 CTAGAT
*
52732400 AAAAGGCTAATTTTGAGGGCTCTTAGGCATTCTAAAGCCTATAAATACACCCTAGAGGAGGAAGA
1 AAAAAGCTAATTTTGAGGGCTCTTAGGCATTCTAAAGCCTATAAATACACCCTAGAGGAGGAAGA
52732465 AAAGGGAGACACAAAATAGGGAGTAAGAAATTACTCCAAGGAAGCCAATTGATCCATCTCAGAAG
66 AAAGGGAGACACAAAATAGGGAGTAAGAAATTACTCCAAGGAAGCCAATTGATCCATCTCAGAAG
52732530 CTAGAT
131 CTAGAT
52732536 TCACCATCAA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (136 bp):
AAAAAGCTAATTTTGAGGGCTCTTAGGCATTCTAAAGCCTATAAATACACCCTAGAGGAGGAAGA
AAAGGGAGACACAAAATAGGGAGTAAGAAATTACTCCAAGGAAGCCAATTGATCCATCTCAGAAG
CTAGAT
Found at i:52734260 original size:18 final size:18
Alignment explanation
Indices: 52734246--52734286 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52734236 CTCTATCACT
*
52734246 TCATATACATATATCTTA
1 TCATATACATATATCCTA
*
52734264 TCATATACATATAT-ATA
1 TCATATACATATATCCTA
52734281 TCATAT
1 TCATAT
52734287 CACCCCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TCATATACATATATCCTA
Found at i:52735710 original size:56 final size:56
Alignment explanation
Indices: 52735650--52735785 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
52735640 TCCTAGACAG
* * *
52735650 GGTCTTACTCTCACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAACGTATAAAACGC
* *
52735706 GGTCTTACTCGCACATATATATCGGAGTCACATATCAATGTCAACGTATAAAACGC
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAACGTATAAAACGC
52735762 GGTCTTACTCGCACACATATATCG
1 GGTCTTACTCGCACACATATATCG
52735786 ATGCCATGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAACGTATAAAACGC
Found at i:52737129 original size:19 final size:19
Alignment explanation
Indices: 52737105--52737170 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
52737095 TATTAAAAAA
*
52737105 TATATCTATATATACCAAT
1 TATATCTATATATAACAAT
* * *
52737124 TATATCAAAATATTAAAAAAAT
1 TATATC--TATA-TATAACAAT
*
52737146 TATATCTATATATATCAAT
1 TATATCTATATATAACAAT
52737165 TATATC
1 TATATC
52737171 AAAACCACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 18 0.50
20 3 0.08
21 3 0.08
22 12 0.33
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATCTATATATAACAAT
Found at i:52737154 original size:41 final size:39
Alignment explanation
Indices: 52737091--52737174 Score: 141
Period size: 41 Copynumber: 2.1 Consensus size: 39
52737081 CAAAACTACT
52737091 AAAATATTAAAAAATATATCTATATATACCAATTATATC
1 AAAATATTAAAAAATATATCTATATATACCAATTATATC
*
52737130 AAAATATTAAAAAAATTATATCTATATATATCAATTATATC
1 AAAATATT-AAAAAA-TATATCTATATATACCAATTATATC
52737171 AAAA
1 AAAA
52737175 CCACATAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 8 0.19
40 6 0.14
41 28 0.67
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (39 bp):
AAAATATTAAAAAATATATCTATATATACCAATTATATC
Found at i:52739485 original size:17 final size:19
Alignment explanation
Indices: 52739465--52739503 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52739455 ATTTATTAAT
52739465 ATTTAATTAT-AATTA-TA
1 ATTTAATTATAAATTATTA
*
52739482 ATTTAATTTTAAATTATTA
1 ATTTAATTATAAATTATTA
52739501 ATT
1 ATT
52739504 CACATTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 5 0.26
19 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAATTATAAATTATTA
Found at i:52741213 original size:14 final size:15
Alignment explanation
Indices: 52741172--52741214 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
52741162 ATTTAGGGTT
*
52741172 AAATCTATAAGAAATTA
1 AAATCT-TAA-AAATGA
52741189 AAATCTTAAAAATGA
1 AAATCTTAAAAATGA
52741204 AAAT-TTAAAAA
1 AAATCTTAAAAA
52741215 GTAAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 9 0.36
16 3 0.12
17 6 0.24
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AAATCTTAAAAATGA
Found at i:52743926 original size:13 final size:14
Alignment explanation
Indices: 52743901--52743930 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52743891 CACAAATTTT
52743901 ATTTTATATTAATA
1 ATTTTATATTAATA
52743915 ATTTTA-ATTAATA
1 ATTTTATATTAATA
52743928 ATT
1 ATT
52743931 ATAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTATATTAATA
Found at i:52743937 original size:14 final size:14
Alignment explanation
Indices: 52743908--52743948 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
52743898 TTTATTTTAT
*
52743908 ATTAATAATT-TTA
1 ATTAATAATTATAA
52743921 ATTAATAATTATAA
1 ATTAATAATTATAA
52743935 ATTAA-ATATTATAA
1 ATTAATA-ATTATAA
52743949 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAATAATTATAA
Found at i:52746696 original size:21 final size:21
Alignment explanation
Indices: 52746672--52746713 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52746662 TATGCGAATC
*
52746672 TTTTCTT-TTTTGGTGTTTGTT
1 TTTTCTTGTTTTGAT-TTTGTT
52746693 TTTTCTTGTTTTGATTTTGTT
1 TTTTCTTGTTTTGATTTTGTT
52746714 GGTAAGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.02, C:0.05, G:0.17, T:0.76
Consensus pattern (21 bp):
TTTTCTTGTTTTGATTTTGTT
Found at i:52753740 original size:19 final size:19
Alignment explanation
Indices: 52753716--52753755 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52753706 AAAACTAAAG
52753716 TAGTTTACATCCTTTTGTA
1 TAGTTTACATCCTTTTGTA
52753735 TAGTTTACATCCTTTTGTA
1 TAGTTTACATCCTTTTGTA
52753754 TA
1 TA
52753756 TCTTTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (19 bp):
TAGTTTACATCCTTTTGTA
Found at i:52756641 original size:17 final size:17
Alignment explanation
Indices: 52756619--52756671 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
52756609 TTATGATAAA
52756619 TATAATATTAGTTATCG
1 TATAATATTAGTTATCG
* *
52756636 TATAAT-TT-GTGATAAG
1 TATAATATTAGTTAT-CG
*
52756652 TATAATATTAATTATCG
1 TATAATATTAGTTATCG
52756669 TAT
1 TAT
52756672 TATTAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 12 0.43
18 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (17 bp):
TATAATATTAGTTATCG
Found at i:52756649 original size:33 final size:33
Alignment explanation
Indices: 52756604--52756671 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
52756594 AAATAATGTA
*
52756604 ATAATTTATGATAAATATAATATTAGTTATCGT
1 ATAATTTATGATAAATATAATATTAATTATCGT
* *
52756637 ATAATTTGTGATAAGTATAATATTAATTATCGT
1 ATAATTTATGATAAATATAATATTAATTATCGT
52756670 AT
1 AT
52756672 TATTAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (33 bp):
ATAATTTATGATAAATATAATATTAATTATCGT
Found at i:52760122 original size:22 final size:24
Alignment explanation
Indices: 52760068--52760122 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
52760058 TATATAACTG
52760068 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
52760090 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
52760112 ATAATATATAT
1 ATAATATATAT
52760123 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:52760218 original size:116 final size:117
Alignment explanation
Indices: 52760097--52760315 Score: 404
Period size: 116 Copynumber: 1.9 Consensus size: 117
52760087 ATAATATTAT
*
52760097 ATATAAATTATTCATATAATATATATTAAAAAAATTGACTATTAATATGTACTAAAAATATATAC
1 ATATAAATTATTCATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATAC
52760162 -GGGGGTAAGCGGCATACACTAATAAATATAATAATAATAACATATACGGGG
66 GGGGGGTAAGCGGCATACACTAATAAATATAATAATAATAACATATACGGGG
*
52760213 ATATAAATTATTCATATAATATATATTAAAAAAATTGACTATTAATACGTATTAAAAATATATAC
1 ATATAAATTATTCATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATAC
*
52760278 GGGGGGTAAGCGGCATTCACTAATAAATATAATAATAA
66 GGGGGGTAAGCGGCATACACTAATAAATATAATAATAA
52760316 CCATGTAATA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 63 0.64
117 36 0.36
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.32
Consensus pattern (117 bp):
ATATAAATTATTCATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATAC
GGGGGGTAAGCGGCATACACTAATAAATATAATAATAATAACATATACGGGG
Found at i:52760346 original size:116 final size:114
Alignment explanation
Indices: 52760110--52760349 Score: 302
Period size: 116 Copynumber: 2.1 Consensus size: 114
52760100 TAAATTATTC
*
52760110 ATATAATATATATTAAAAAAATTGACTATTAATATGTACTAAAAATATATACGGGGGTAAGCGGC
1 ATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATACGGGGGTAAGCGGC
* * * ** **
52760175 ATACACTAATAAATATAATAATAATAACATATACGGGGATATAAATTATTC
66 ATACACTAATAAATATAATAATAACAACATATAC--GAATACAAAAGATAA
*
52760226 ATATAATATATATTAAAAAAATTGACTATTAATACGTATTAAAAATATATACGGGGGGTAAGCGG
1 ATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATAC-GGGGGTAAGCGG
* * ** *
52760291 CATTCACTAATAAATATAATAATAACCATGTAATAC-AATACCAAAAGGTAA
65 CATACACTAATAAATATAATAATAACAACAT-ATACGAATA-CAAAAGATAA
52760342 ATATAATA
1 ATATAATA
52760350 AAATGATATT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
115 3 0.03
116 62 0.58
117 38 0.36
118 4 0.04
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (114 bp):
ATATAATATATATTAAAAAAATTGACTATTAATACGTACTAAAAATATATACGGGGGTAAGCGGC
ATACACTAATAAATATAATAATAACAACATATACGAATACAAAAGATAA
Found at i:52760436 original size:3 final size:3
Alignment explanation
Indices: 52760423--52760461 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
52760413 ACAGTAACAT
*
52760423 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52760462 AACACAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52760572 original size:3 final size:3
Alignment explanation
Indices: 52760556--52760611 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
52760546 ACTAATGTAC
*
52760556 AAT AAT AACT -AT AAT AAT AAT AAT AAT AAT AAAT AAT AAT ATT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
52760602 ATT AAT AAT A
1 AAT AAT AAT A
52760612 TGAAAATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 41 0.89
4 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:52760647 original size:31 final size:31
Alignment explanation
Indices: 52760611--52760711 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
52760601 TATTAATAAT
*
52760611 ATGAAAATAACAAGGATATTTAGCTAAAAAA
1 ATGAAAATAACAAGGATATTTAGATAAAAAA
* * * * * * * *
52760642 ATGAAAA-ACAAAACGAAAATAATATTAATAAT
1 ATGAAAATA-ACAAGGATATTTAGA-TAAAAAA
52760674 ATGAAAATAACAAGGATATTTAGATAAAAAA
1 ATGAAAATAACAAGGATATTTAGATAAAAAA
*
52760705 ACGAAAA
1 ATGAAAA
52760712 ACAAAACGAA
Statistics
Matches: 49, Mismatches: 18, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
30 1 0.02
31 26 0.53
32 21 0.43
33 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (31 bp):
ATGAAAATAACAAGGATATTTAGATAAAAAA
Done.