Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 178 of 182
Found at i:54030001 original size:91 final size:88
Alignment explanation
Indices: 54029766--54030020 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 88
54029756 AAAAAAAATT
* * *
54029766 AAAAACATAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACATAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
54029831 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * * *
54029853 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACATAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
54029916 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
54029942 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACATAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
54030006 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
54030021 ACAAAAATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 31 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (88 bp):
AAAAACATAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:54030250 original size:72 final size:72
Alignment explanation
Indices: 54030101--54030366 Score: 367
Period size: 72 Copynumber: 3.7 Consensus size: 72
54030091 GGCGTGCCCC
* **** * * *
54030101 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTA-A-AATTTAAAAATACCTCAA
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAA
54030164 CGTGTCTT
65 CGTGTCTT
54030172 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
54030237 GTGTCTT
66 GTGTCTT
*
54030244 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
*
54030309 GTGTCCT
66 GTGTCTT
** * *
54030316 GAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
54030367 AAAAGGCTTA
Statistics
Matches: 178, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
70 5 0.03
71 40 0.22
72 133 0.75
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (72 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
GTGTCTT
Found at i:54030352 original size:143 final size:142
Alignment explanation
Indices: 54030033--54030370 Score: 385
Period size: 143 Copynumber: 2.4 Consensus size: 142
54030023 AAAAATTAAA
* * * * * **
54030033 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
* **** *
54030096 GCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAAAATTTAAAAATACCT
66 GCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAAAAAATTAAAAATACCT
*
54030161 CAACGTGTCTTG
131 CAACGTGTCCTG
** * * *
54030173 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAACAAAAATTAAAAATACCTCAACG
* ** * *
54030238 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTA
65 TGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAA-A-AAATTAAAAATA
*
54030302 CCTCAGCGTGTCCTG
128 CCTCAACGTGTCCTG
*
54030317 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
54030371 GGCTTAACTC
Statistics
Matches: 163, Mismatches: 29, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
140 25 0.15
141 1 0.01
142 9 0.06
143 64 0.39
144 64 0.39
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (142 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
GCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAAAAAATTAAAAATACCT
CAACGTGTCCTG
Found at i:54030396 original size:337 final size:339
Alignment explanation
Indices: 54029943--54030559 Score: 1071
Period size: 337 Copynumber: 1.8 Consensus size: 339
54029933 TAGATTGAAA
* *
54029943 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGT
*
54030008 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC
65 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTATCGCAATATGAGTCAATTTAAAAC
* *
54030073 ATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
130 ATAAACTAAAAATACCCCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
**
54030138 TTTTTTAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
195 TTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
*
54030203 GAATTTTG-AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
260 G-ATTTTGAAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
54030267 TATGAGTTGAATTTTG
324 TATGAGTTGAATTTTG
* *
54030283 AAAACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTAGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGT
*
54030346 TGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTATCGCAATATGAGTCAATTTAAAAT
65 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTATCGCAATATGAGTCAATTTAAAAC
*
54030410 ATAAACTAAAAATACCCCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATTTGAGTTGATTTT
130 ATAAACTAAAAATACCCCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
54030475 TTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
195 TTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
54030540 GATTTTGAAAAACAAAAATT
260 GATTTTGAAAAACAAAAATT
54030560 AAAAGGCTTA
Statistics
Matches: 263, Mismatches: 12, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
336 6 0.02
337 198 0.75
338 35 0.13
340 24 0.09
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (339 bp):
AAAACAGAAATTGAAAATACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTT
GATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTATCGCAATATGAGTCAATTTAAAACA
TAAACTAAAAATACCCCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
TTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
ATTTTGAAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
TGAGTTGAATTTTG
Found at i:54030537 original size:193 final size:192
Alignment explanation
Indices: 54030244--54030738 Score: 792
Period size: 193 Copynumber: 2.6 Consensus size: 192
54030234 AACGTGTCTT
* * *** * * *
54030244 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGC
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAA-A-AAATTTAAAATACCTCAAC
* ** *
54030309 GTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGC
64 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGC
*
54030374 TTAACTCACCTATCGCAATATGAGTCAATTTAAAATATAAACTAAAAATACCCCGGCGTGCCCC
129 TTAACTCACCTATCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCCCGGCGTGCCCC
*
54030438 GAGGCTCAACTCACTTCTCGCAATTTGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACG
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTT-AAAATACCTCAACG
54030503 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCT
65 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCT
* ** *
54030568 TAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTTGGGGTGCCCC
130 TAACTCACCTATCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCCCGGCGTGCCCC
54030631 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTGTAAAATACCTCAACG
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATT-TAAAATACCTCAACG
54030696 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
65 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
54030739 CCTTGGAAAG
Statistics
Matches: 280, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
192 5 0.02
193 237 0.85
194 38 0.14
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (192 bp):
GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAATACCTCAACGT
GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTT
AACTCACCTATCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCCCGGCGTGCCCC
Found at i:54042536 original size:18 final size:18
Alignment explanation
Indices: 54042515--54042955 Score: 110
Period size: 18 Copynumber: 24.6 Consensus size: 18
54042505 CGAAAATTTT
* *
54042515 TTTTTTAAAATACGAGAA
1 TTTTTGAAAACACGAGAA
54042533 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
54042551 --TTTGTAAACACGA-ATA
1 TTTTTGAAAACACGAGA-A
* *
54042567 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
54042584 TTTTTGGAAAAAAACGA-AA
1 TTTTT-G-AAAACACGAGAA
* * *
54042603 TTTTCTTAAAACACGACATTTT
1 TTTT-TGAAAACACGAGA---A
*
54042625 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAGAA
* * *
54042642 TTTTT-AAAACAAGACATT
1 TTTTTGAAAACACGAGA-A
54042660 TTTTTG-AAACA--A-AA
1 TTTTTGAAAACACGAGAA
* *
54042674 TTTTTTCTTAAAA-A--AAAA
1 --TTTT-TGAAAACACGAGAA
* *
54042692 ATTTT--AAATACGAGAA
1 TTTTTGAAAACACGAGAA
*
54042708 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
54042725 TTTTT-AAAACACGGAAAAA
1 TTTTTGAAAACAC-G-AGAA
*
54042744 TTTTTTTTTAAAACACGA-AA
1 ---TTTTTGAAAACACGAGAA
* *
54042764 TTTTTTTTTTGAAAACAAGAAAA
1 -----TTTTTGAAAACACGAGAA
*
54042787 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAGAA
54042804 -TTTTGAAAACACGA-AGA
1 TTTTTGAAAACACGAGA-A
*
54042821 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAGAA
*
54042838 TTTTT-AAAAGCACGAGGA
1 TTTTTGAAAA-CACGAGAA
* *
54042856 TTATTGAAAGCACGA-AGA
1 TTTTTGAAAACACGAGA-A
* * *
54042874 TTTAT-AAAAAACGACAA
1 TTTTTGAAAACACGAGAA
*
54042891 TTTTTG-AAATACGAGAAA
1 TTTTTGAAAACACGAG-AA
* * *
54042909 TTTTT-TAAACGCGAAAA
1 TTTTTGAAAACACGAGAA
** *
54042926 TTTTTTTCAAACACGAAAA
1 -TTTTTGAAAACACGAGAA
*
54042945 CTTTTGAAAAC
1 TTTTTGAAAAC
54042956 GCGAAAATTC
Statistics
Matches: 325, Mismatches: 51, Indels: 94
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.01
14 1 0.00
15 3 0.01
16 34 0.10
17 102 0.31
18 103 0.32
19 24 0.07
20 18 0.06
21 2 0.01
22 26 0.08
23 9 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:54042554 original size:16 final size:16
Alignment explanation
Indices: 54042521--54042586 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
54042511 TTTTTTTTTT
*
54042521 AAAATACGAGAATTTTTG
1 AAAACACGAGAA--TTTG
54042539 AAAACACGAGAATTTG
1 AAAACACGAGAATTTG
* *
54042555 TAAACACGA-ATATTTT
1 AAAACACGAGA-ATTTG
*
54042571 AGAAACACGAAAATTT
1 A-AAACACGAGAATTT
54042587 TTGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.39
17 12 0.29
18 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAACACGAGAATTTG
Found at i:54042745 original size:19 final size:17
Alignment explanation
Indices: 54042516--54042964 Score: 167
Period size: 17 Copynumber: 25.1 Consensus size: 17
54042506 GAAAATTTTT
* *
54042516 TTTTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
*
54042533 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
* *
54042551 TTTGT-AAACACGAATA
1 TTTTTAAAACACGAAAA
54042567 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
* *
54042584 TTTTTGGAAAAAAACGAAAT
1 TTTTT---AAAACACGAAAA
**
54042604 TTTCTTAAAACACGACATTTT
1 TTT-TTAAAACACGA-A--AA
* **
54042625 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAAAA
* **
54042642 TTTTTAAAACAAGACATT
1 TTTTTAAAACACGA-AAA
* *
54042660 TTTTTGAAACA--AAATTT
1 TTTTTAAAACACGAAA--A
54042677 TTTCTTAAAA-A--AAAA
1 TTT-TTAAAACACGAAAA
* * *
54042692 ATTTT-AAATACGAGAA
1 TTTTTAAAACACGAAAA
54042708 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
54042725 TTTTTAAAACACGGAAAAA
1 TTTTTAAAACAC-G-AAAA
*
54042744 TTTTTTTTTAAAACACGAAATTTTT
1 ----TTTTTAAAACACGAAA----A
*
54042769 TTTTTGAAAACAAGAAAA
1 TTTTT-AAAACACGAAAA
* * *
54042787 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
54042804 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
54042821 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
**
54042838 TTTTTAAAAGCACGAGGA
1 TTTTTAAAA-CACGAAAA
* * *
54042856 TTATTGAAAGCACGAAGA
1 TT-TTTAAAACACGAAAA
* * *
54042874 TTTATAAAAAACGACAA
1 TTTTTAAAACACGAAAA
* *
54042891 TTTTTGAAATACGAGAAA
1 TTTTTAAAACACGA-AAA
* *
54042909 TTTTTTAAACGCGAAAA
1 TTTTTAAAACACGAAAA
*
54042926 TTTTTTTCAAACACGAAAA
1 --TTTTTAAAACACGAAAA
* *
54042945 CTTTTGAAAACGCGAAAA
1 -TTTTTAAAACACGAAAA
54042963 TT
1 TT
54042965 CGAAAATTTC
Statistics
Matches: 325, Mismatches: 72, Indels: 70
0.70 0.15 0.15
Matches are distributed among these distances:
13 3 0.01
14 3 0.01
15 6 0.02
16 17 0.05
17 120 0.37
18 92 0.28
19 25 0.08
20 21 0.06
21 15 0.05
22 11 0.03
23 12 0.04
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:54042763 original size:22 final size:21
Alignment explanation
Indices: 54042708--54042791 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 21
54042698 AATACGAGAA
54042708 TTTTTAAAACACGAAAA----
1 TTTTTAAAACACGAAAATTTT
54042725 TTTTTAAAACACGGAAAAATTTT
1 TTTTTAAAACAC-G-AAAATTTT
*
54042748 TTTTTAAAACACGAAATTTTT
1 TTTTTAAAACACGAAAATTTT
*
54042769 TTTTTGAAAACAAGAAAATTTT
1 TTTTT-AAAACACGAAAATTTT
54042791 T
1 T
54042792 GAAACACTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
17 12 0.21
18 1 0.02
19 4 0.07
21 12 0.21
22 16 0.28
23 12 0.21
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTTAAAACACGAAAATTTT
Found at i:54042960 original size:18 final size:19
Alignment explanation
Indices: 54042915--54042963 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
54042905 GAAATTTTTT
* **
54042915 AAACGCGAAAATTTTTTTC
1 AAACGCGAAAATCTTTTGA
*
54042934 AAACACGAAAA-CTTTTGA
1 AAACGCGAAAATCTTTTGA
54042952 AAACGCGAAAAT
1 AAACGCGAAAAT
54042964 TCGAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (19 bp):
AAACGCGAAAATCTTTTGA
Found at i:54043008 original size:18 final size:17
Alignment explanation
Indices: 54042959--54043009 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
54042949 TGAAAACGCG
54042959 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
54042976 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
54042994 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
54043010 GAAACAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:54043522 original size:8 final size:8
Alignment explanation
Indices: 54043504--54043569 Score: 84
Period size: 7 Copynumber: 8.4 Consensus size: 8
54043494 ATTGAACCCC
54043504 CTTTTTCTT
1 CTTTTT-TT
54043513 CTTTTTTT
1 CTTTTTTT
54043521 CTTTTTTT
1 CTTTTTTT
54043529 C-TTTTTT
1 CTTTTTTT
*
54043536 CCTTTTTT
1 CTTTTTTT
54043544 C-TTTTTT
1 CTTTTTTT
54043551 C-TTTTTT
1 CTTTTTTT
54043558 CTTCTTTTT
1 CTT-TTTTT
54043567 CTT
1 CTT
54043570 CCTTTTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.39
8 19 0.35
9 14 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
CTTTTTTT
Found at i:54043530 original size:16 final size:15
Alignment explanation
Indices: 54043506--54043582 Score: 86
Period size: 14 Copynumber: 5.1 Consensus size: 15
54043496 TGAACCCCCT
54043506 TTTTCTTCTTTTTTTC
1 TTTT-TTCTTTTTTTC
*
54043522 TTTTTTTCTTTTTTCC
1 -TTTTTTCTTTTTTTC
54043538 TTTTTTC-TTTTTTC
1 TTTTTTCTTTTTTTC
54043552 TTTTTTCTTCTTTTTC
1 TTTTTTCTT-TTTTTC
**
54043568 TTCCTT-TTTTTTTC
1 TTTTTTCTTTTTTTC
54043582 T
1 T
54043583 GCTGGGCTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 20 0.37
15 10 0.19
16 20 0.37
17 4 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:54043541 original size:14 final size:15
Alignment explanation
Indices: 54043515--54043565 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
54043505 TTTTTCTTCT
*
54043515 TTTTTTCTTTTTTTC
1 TTTTTTCCTTTTTTC
54043530 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
54043545 TTTTTT-CTTTTTTC
1 TTTTTTCCTTTTTTC
54043559 TTCTTTT
1 TT-TTTT
54043566 TCTTCCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 10 0.29
15 24 0.71
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:54043545 original size:23 final size:22
Alignment explanation
Indices: 54043511--54043582 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 22
54043501 CCCCTTTTTC
54043511 TTCTTTTTTTCTTTTTTTCTTTT
1 TTCTTTTTTTC-TTTTTTCTTTT
*
54043534 TTCCTTTTTTCTTTTTTCTTTT
1 TTCTTTTTTTCTTTTTTCTTTT
*
54043556 TTCTTCTTTTTCTTCCTTT-TTTT
1 TTCTT-TTTTTCTT-TTTTCTTTT
54043579 TTCT
1 TTCT
54043583 GCTGGGCTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 15 0.34
23 26 0.59
24 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTCTTTTTTTCTTTTTTCTTTT
Found at i:54043729 original size:12 final size:12
Alignment explanation
Indices: 54043712--54043737 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54043702 CTTTCCCTTC
54043712 TTTTTTTTTGCT
1 TTTTTTTTTGCT
54043724 TTTTTTTTTGCT
1 TTTTTTTTTGCT
54043736 TT
1 TT
54043738 GATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGCT
Found at i:54043747 original size:19 final size:17
Alignment explanation
Indices: 54043723--54043779 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 17
54043713 TTTTTTTTGC
54043723 TTTTTTTTTTGCTTTGATT
1 TTTTTTTTTTGC-TTG-TT
*
54043742 TTTTTTTTTGGGCTTGTT
1 TTTTTTTTT-TGCTTGTT
*
54043760 TTTTTTTTTT-TTTGTT
1 TTTTTTTTTTGCTTGTT
54043776 TTTT
1 TTTT
54043780 CTTGGGCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 9 0.26
18 11 0.32
19 12 0.35
20 2 0.06
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTGCTTGTT
Found at i:54043748 original size:20 final size:18
Alignment explanation
Indices: 54043723--54043779 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
54043713 TTTTTTTTGC
54043723 TTTTTTTTTTGCTTTGATTT
1 TTTTTTTTTTGC-TTG-TTT
**
54043743 TTTTTTTTGGGCTTGTTT
1 TTTTTTTTTTGCTTGTTT
54043761 TTTTTTTTTT--TTGTTT
1 TTTTTTTTTTGCTTGTTT
54043777 TTT
1 TTT
54043780 CTTGGGCTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.27
18 11 0.33
19 3 0.09
20 10 0.30
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTTGCTTGTTT
Found at i:54043888 original size:24 final size:24
Alignment explanation
Indices: 54043868--54043927 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
54043858 CTTTTCTTTT
*
54043868 TCTTTT-TTCTTTCTTTCTTCTTCC
1 TCTTTTCTTC-TTCCTTCTTCTTCC
54043892 TCTTTTCTTCTTCCTTCTTCTTCC
1 TCTTTTCTTCTTCCTTCTTCTTCC
*
54043916 T-TCTTCTTCTTC
1 TCTTTTCTTCTTC
54043928 AAAGTCTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 10 0.30
24 20 0.61
25 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTTTCTTCTTCCTTCTTCTTCC
Found at i:54043890 original size:3 final size:3
Alignment explanation
Indices: 54043856--54043927 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
54043846 TTTTTATTAT
* *
54043856 TTC TT- TTC TTT TTC TT- TT- TTC TTTC TTTC TTC TTC CTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC
54043899 TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
54043928 AAAGTCTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:54043895 original size:13 final size:13
Alignment explanation
Indices: 54043879--54043927 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
54043869 CTTTTTTCTT
54043879 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
54043892 TCTTTTCTTCTT-C
1 TC-TTTCTTCTTCC
54043905 -C-TTCTTCTTCC
1 TCTTTCTTCTTCC
54043916 T-TCTTCTTCTTC
1 TCT-TTCTTCTTC
54043928 AAAGTCTAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 1 0.03
13 12 0.39
14 9 0.29
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTTCTTCTTCC
Found at i:54043911 original size:10 final size:10
Alignment explanation
Indices: 54043896--54043924 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54043886 TCTTCCTCTT
54043896 TTCTTCTTCC
1 TTCTTCTTCC
54043906 TTCTTCTTCC
1 TTCTTCTTCC
54043916 TTCTTCTTC
1 TTCTTCTTC
54043925 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:54044018 original size:10 final size:10
Alignment explanation
Indices: 54043983--54044032 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
54043973 ACGCCGGTAC
54043983 TCTT-TCTTT
1 TCTTCTCTTT
* *
54043992 TCTTCTCCTC
1 TCTTCTCTTT
54044002 T-TTCTCTTT
1 TCTTCTCTTT
54044011 TCTTCTCTTT
1 TCTTCTCTTT
*
54044021 TCTTCTTTTT
1 TCTTCTCTTT
54044031 TC
1 TC
54044033 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:54044030 original size:19 final size:19
Alignment explanation
Indices: 54043987--54044029 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
54043977 CGGTACTCTT
54043987 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
54044006 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
54044023 TTCTTTT
1 -TCTTTT
54044030 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:54044314 original size:29 final size:29
Alignment explanation
Indices: 54044281--54044397 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
54044271 TGTAATTTTT
*
54044281 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
54044310 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
54044340 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
54044369 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
54044398 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:54044336 original size:30 final size:30
Alignment explanation
Indices: 54044296--54044397 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
54044286 ATTTAGGATT
*
54044296 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54044326 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
54044356 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54044386 AAAATGCAATTT
1 AAAATGAAATTT
54044398 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54047947 original size:10 final size:10
Alignment explanation
Indices: 54047882--54047950 Score: 60
Period size: 10 Copynumber: 7.4 Consensus size: 10
54047872 AGTTAAAATA
54047882 TATATTATA-
1 TATATTATAT
*
54047891 -ATATAATAT
1 TATATTATAT
*
54047900 TATATCT-TAA
1 TATAT-TATAT
*
54047910 T-TATTA-AG
1 TATATTATAT
54047918 TATA-TATAT
1 TATATTATAT
54047927 TATATTATAT
1 TATATTATAT
54047937 TATATTATAT
1 TATATTATAT
54047947 TATA
1 TATA
54047951 ATAAATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
8 12 0.25
9 10 0.21
10 26 0.54
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (10 bp):
TATATTATAT
Found at i:54048023 original size:6 final size:6
Alignment explanation
Indices: 54048010--54048044 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
54048000 AACGAAATAG
*
54048010 AAAGAA AAA-AA AAAGAA AAAGAA AAAGAG AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
54048045 TGAAGGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:54048775 original size:17 final size:15
Alignment explanation
Indices: 54048739--54048791 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
54048729 GTGATGAATT
54048739 TATTGAATTTATAT-
1 TATTGAATTTATATA
54048753 TAATTGAATTGGTATATA
1 T-ATTGAATT--TATATA
*
54048771 TATTGAATATATATA
1 TATTGAATTTATATA
54048786 TATTGA
1 TATTGA
54048792 TTATTTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 20 0.59
17 12 0.35
18 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (15 bp):
TATTGAATTTATATA
Found at i:54048978 original size:41 final size:40
Alignment explanation
Indices: 54048921--54049026 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 40
54048911 GACTTCGAGT
** ** **
54048921 CGATGAGACACAGGGTGTCAAATTATTACTTTGGATATATT
1 CGATGAGACATTGGGTGTCAAATTATTACTTCAG-TATAGC
* * *
54048962 CGATGAGGCATTGGGTG-CCAA-T-TTACTTCAGTTTAGC
1 CGATGAGACATTGGGTGTCAAATTATTACTTCAGTATAGC
54048999 CGATGAGACATTGGGTGTCAAATTATTA
1 CGATGAGACATTGGGTGTCAAATTATTA
54049027 TATCAAATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
37 19 0.37
38 10 0.20
39 2 0.04
40 6 0.12
41 14 0.27
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (40 bp):
CGATGAGACATTGGGTGTCAAATTATTACTTCAGTATAGC
Found at i:54053881 original size:18 final size:17
Alignment explanation
Indices: 54053854--54053887 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54053844 TCTTTTCGAT
54053854 TTATTATTTTTATTCTC
1 TTATTATTTTTATTCTC
*
54053871 TTATGTATTTTTTTTCT
1 TTAT-TATTTTTATTCT
54053888 TTTTTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTATTTTTATTCTC
Found at i:54054682 original size:3 final size:3
Alignment explanation
Indices: 54054674--54054719 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
54054664 ATTAATGTGT
54054674 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54054720 CACATTGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54054851 original size:25 final size:26
Alignment explanation
Indices: 54054793--54054851 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
54054783 AATACATTTG
*
54054793 TCTTATTTATATATTAGTTCTTTAAA
1 TCTTTTTTATATATTAGTTCTTTAAA
* **
54054819 TGCATTTTTATATATTAGTT-TTTGTA
1 T-CTTTTTTATATATTAGTTCTTTAAA
54054845 TCTTTTT
1 TCTTTTT
54054852 ACATAATTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 5 0.19
26 6 0.22
27 16 0.59
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (26 bp):
TCTTTTTTATATATTAGTTCTTTAAA
Found at i:54060500 original size:21 final size:23
Alignment explanation
Indices: 54060467--54060509 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
54060457 TCCTTTTAAC
54060467 TTTTACATATAATTAAAAATATT
1 TTTTACATATAATTAAAAATATT
*
54060490 TTTTA-AT-TAATTGAAAATAT
1 TTTTACATATAATTAAAAATAT
54060510 AATCTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTACATATAATTAAAAATATT
Found at i:54061871 original size:22 final size:22
Alignment explanation
Indices: 54061845--54061898 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
54061835 TTTAATTTTG
*
54061845 ATATAATTTAATTTATTTATTT
1 ATATAATTTAATTAATTTATTT
* * *
54061867 TTATAATTTCATTAATTTGTTT
1 ATATAATTTAATTAATTTATTT
*
54061889 ATATATTTTA
1 ATATAATTTA
54061899 CACCATTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
ATATAATTTAATTAATTTATTT
Found at i:54066215 original size:28 final size:31
Alignment explanation
Indices: 54066166--54066226 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
54066156 AATTTTTAAA
54066166 AAAAAAAATTTATATTCAAATTA-TAATTTAC
1 AAAAAAAATTTATATT-AAATTATTAATTTAC
*
54066197 AAAAAAAA-TTATATT-AATTATTTATTTAC
1 AAAAAAAATTTATATTAAATTATTAATTTAC
54066226 A
1 A
54066227 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.18
29 8 0.29
30 7 0.25
31 8 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAAAATTTATATTAAATTATTAATTTAC
Found at i:54067870 original size:19 final size:20
Alignment explanation
Indices: 54067841--54067891 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
54067831 TTTCTATATG
*
54067841 TTTTAGAATTTTTATAAA-TA
1 TTTT-GAATTTTTAAAAATTA
54067861 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
54067880 TTTTGAATTTTT
1 TTTTGAATTTTT
54067892 TGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 8 0.29
19 12 0.43
20 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:54076841 original size:13 final size:13
Alignment explanation
Indices: 54076820--54076850 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54076810 AGGATGATAT
*
54076820 AATTGCATATCAA
1 AATTACATATCAA
54076833 AATTACATATCAA
1 AATTACATATCAA
54076846 AATTA
1 AATTA
54076851 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (13 bp):
AATTACATATCAA
Found at i:54082159 original size:19 final size:19
Alignment explanation
Indices: 54082137--54082176 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54082127 CCAAGGGAAT
54082137 TTTTAATAAATTATT-ATTA
1 TTTTAA-AAATTATTAATTA
*
54082156 TTTTGAAAATTATTAATTA
1 TTTTAAAAATTATTAATTA
54082175 TT
1 TT
54082177 GGTAATAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTAATTA
Found at i:54088446 original size:21 final size:20
Alignment explanation
Indices: 54088403--54088447 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
54088393 GTAATTCGAT
* **
54088403 TTTATTATTTATTAATTTTA
1 TTTATTATTTAATAATTAAA
54088423 TTTATATATTTAATAATTAAA
1 TTTAT-TATTTAATAATTAAA
54088444 TTTA
1 TTTA
54088448 AATAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTATTTAATAATTAAA
Found at i:54089581 original size:2 final size:2
Alignment explanation
Indices: 54089574--54089599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54089564 TACCTGTCAC
54089574 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
54089600 TTTTCTCTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54091019 original size:9 final size:9
Alignment explanation
Indices: 54091007--54091083 Score: 75
Period size: 9 Copynumber: 8.6 Consensus size: 9
54090997 TTTTGGTTAA
*
54091007 AAATTAATC
1 AAATTAACC
54091016 AAATTAACC
1 AAATTAACC
54091025 AAATTAACC
1 AAATTAACC
*
54091034 GAATTAACC
1 AAATTAACC
*
54091043 GAATT-ACC
1 AAATTAACC
*
54091051 TGAATTAACC
1 -AAATTAACC
* *
54091061 GAATTACCC
1 AAATTAACC
*
54091070 GAATTAACC
1 AAATTAACC
54091079 AAATT
1 AAATT
54091084 GAATCACTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 3 0.05
9 55 0.90
10 3 0.05
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (9 bp):
AAATTAACC
Found at i:54091030 original size:18 final size:18
Alignment explanation
Indices: 54091007--54091083 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
54090997 TTTTGGTTAA
* *
54091007 AAATTAATCAAATTAACC
1 AAATTAACCGAATTAACC
54091025 AAATTAACCGAATTAACC
1 AAATTAACCGAATTAACC
*
54091043 GAATT-ACCTGAATTAACC
1 AAATTAACC-GAATTAACC
* *
54091061 GAATTACCCGAATTAACC
1 AAATTAACCGAATTAACC
54091079 AAATT
1 AAATT
54091084 GAATCACTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 3 0.06
18 47 0.90
19 2 0.04
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:54091039 original size:27 final size:27
Alignment explanation
Indices: 54091008--54091083 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
54090998 TTTGGTTAAA
* *
54091008 AATTAATCAAATTAACCAAATTAACCG
1 AATTAACCGAATTAACCAAATTAACCG
*
54091035 AATTAACCGAATT-ACCTGAATTAACCG
1 AATTAACCGAATTAACC-AAATTAACCG
*
54091062 AATTACCCGAATTAACCAAATT
1 AATTAACCGAATTAACCAAATT
54091084 GAATCACTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.07
27 36 0.86
28 3 0.07
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTAACCG
Found at i:54106684 original size:13 final size:13
Alignment explanation
Indices: 54106661--54106704 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
54106651 CTATTTAAAT
54106661 ATAATTAAATATTA
1 ATAA-TAAATATTA
54106675 ATAATAAATATT-
1 ATAATAAATATTA
*
54106687 ATAAATAAATATCA
1 AT-AATAAATATTA
54106701 ATAA
1 ATAA
54106705 CTCTCGGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 19 0.70
14 6 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:54112929 original size:25 final size:22
Alignment explanation
Indices: 54112885--54112931 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
54112875 ATAATAATTG
*
54112885 ATATTTTAAAATTTTAATTAAA
1 ATATTTTAAAATTTGAATTAAA
54112907 ATATTATTAAAATTTAGAGATTAAA
1 ATATT-TTAAAATTT-GA-ATTAAA
54112932 TTTAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 1 0.05
25 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATTTTAAAATTTGAATTAAA
Found at i:54113677 original size:44 final size:43
Alignment explanation
Indices: 54113629--54113748 Score: 111
Period size: 42 Copynumber: 2.8 Consensus size: 43
54113619 AATTTTCTTT
**
54113629 ATATATTTTTTAGATTTTTTTTGAAAGTTTTTTATTTTTTAAAA
1 ATATA-TTTTTAGATTTTTTTTGAAAGTTTTTTAAATTTTAAAA
* * * *
54113673 ATATAAATTTTAGATTTTTTAT-ACA-TATTTTAAATTTTAAAA
1 ATAT-ATTTTTAGATTTTTTTTGAAAGTTTTTTAAATTTTAAAA
* * *
54113715 A-ATATTTTTGGTTTTTTTTTGTAAGTTTTGTTAA
1 ATATATTTTTAGATTTTTTTTGAAAGTTTT-TTAA
54113749 GAAAGAGACC
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
40 13 0.22
41 3 0.05
42 18 0.31
43 6 0.10
44 18 0.31
45 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (43 bp):
ATATATTTTTAGATTTTTTTTGAAAGTTTTTTAAATTTTAAAA
Found at i:54113944 original size:13 final size:13
Alignment explanation
Indices: 54113926--54114016 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
54113916 AACTAAGAAA
54113926 TTTTAAATAAATG
1 TTTTAAATAAATG
**
54113939 TTTTAAATATTTG
1 TTTTAAATAAATG
54113952 TTTTAAAT--A--
1 TTTTAAATAAATG
*
54113961 TTTAAATATTTAAAT-
1 TTTTAA-A--TAAATG
*
54113976 ATTTAAATAAATG
1 TTTTAAATAAATG
* **
54113989 TTTTAGATATTTG
1 TTTTAAATAAATG
54114002 TTTTAAATAAATG
1 TTTTAAATAAATG
54114015 TT
1 TT
54114017 GAAATTTCTC
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
9 5 0.09
10 1 0.02
12 6 0.10
13 40 0.69
14 2 0.03
15 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTTAAATAAATG
Found at i:54113966 original size:8 final size:8
Alignment explanation
Indices: 54113953--54113984 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
54113943 AAATATTTGT
54113953 TTTAAATA
1 TTTAAATA
54113961 TTTAAATA
1 TTTAAATA
54113969 TTTAAATA
1 TTTAAATA
54113977 TTTAAATA
1 TTTAAATA
54113985 AATGTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAATA
Found at i:54122571 original size:16 final size:17
Alignment explanation
Indices: 54122550--54122590 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
54122540 ATGTATACAC
54122550 ATATATAAT-AAGATAT
1 ATATATAATAAAGATAT
54122566 ATATAT-ATAAAGATAT
1 ATATATAATAAAGATAT
*
54122582 ATAAATAAT
1 ATATATAAT
54122591 TATAATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
ATATATAATAAAGATAT
Found at i:54138672 original size:24 final size:24
Alignment explanation
Indices: 54138645--54138690 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
54138635 AACCTAATTC
54138645 TAATCAA-ACTCAAATATATTATGT
1 TAATCAATACT-AAATATATTATGT
*
54138669 TAATCAATGCTAAATATATTAT
1 TAATCAATACTAAATATATTAT
54138691 ACTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (24 bp):
TAATCAATACTAAATATATTATGT
Found at i:54141676 original size:9 final size:9
Alignment explanation
Indices: 54141649--54141694 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
54141639 TGTAATTTTT
54141649 AAATTATAA
1 AAATTATAA
* *
54141658 AACTTTTAA
1 AAATTATAA
*
54141667 AAATTGTAA
1 AAATTATAA
54141676 AACATTATAA
1 AA-ATTATAA
54141686 AAATTATAA
1 AAATTATAA
54141695 GAAAATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATTATAA
Found at i:54141676 original size:18 final size:19
Alignment explanation
Indices: 54141649--54141694 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
54141639 TGTAATTTTT
*
54141649 AAATTATAAAAC-TTTTAA
1 AAATTATAAAACATTATAA
*
54141667 AAATTGTAAAACATTATAA
1 AAATTATAAAACATTATAA
54141686 AAATTATAA
1 AAATTATAA
54141695 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTATAAAACATTATAA
Found at i:54141705 original size:28 final size:28
Alignment explanation
Indices: 54141651--54141706 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
54141641 TAATTTTTAA
* * *
54141651 ATTATAAAACTTTTAAAAATTGTAAAAC
1 ATTATAAAAATTATAAAAAATGTAAAAC
*
54141679 ATTATAAAAATTATAAGAAAATGAAAAA
1 ATTATAAAAATTATAA-AAAATGTAAAA
54141707 GGGTAGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (28 bp):
ATTATAAAAATTATAAAAAATGTAAAAC
Found at i:54163921 original size:263 final size:263
Alignment explanation
Indices: 54163454--54163977 Score: 1039
Period size: 263 Copynumber: 2.0 Consensus size: 263
54163444 CTACGAAGAT
*
54163454 GAGGTTGATCAGACAGGCACTTGAAGCTTTGAAACATCAAATAATCTCTAAATGTCAGTAAGCTT
1 GAGGTTGATCAGACAGGCACTTGAAGCTTTGAAACATCAAATAATCTCTAAATGTCAGTAAGCTC
54163519 TGAAGCTTATGGATAGACTTTGGAAGTCTACTAAAATTCCGCCACCTAATCATACAACATTCATA
66 TGAAGCTTATGGATAGACTTTGGAAGTCTACTAAAATTCCGCCACCTAATCATACAACATTCATA
54163584 CTCTCACTTGCATTCTTACCATTTGTTCCTATAATGCACAAACTAAACTGAACCAAGGATCAATT
131 CTCTCACTTGCATTCTTACCATTTGTTCCTATAATGCACAAACTAAACTGAACCAAGGATCAATT
54163649 GAACCATAACACTTCACCTTTTAGATTTGTTAGACAATTGTGTTGTGTAATATAATGAATTCCCA
196 GAACCATAACACTTCACCTTTTAGATTTGTTAGACAATTGTGTTGTGTAATATAATGAATTCCCA
54163714 TAC
261 TAC
54163717 GAGGTTGATCAGACAGGCACTTGAAGCTTTGAAACATCAAATAATCTCTAAATGTCAGTAAGCTC
1 GAGGTTGATCAGACAGGCACTTGAAGCTTTGAAACATCAAATAATCTCTAAATGTCAGTAAGCTC
54163782 TGAAGCTTATGGATAGACTTTGGAAGTCTACTAAAATTCCGCCACCTAATCATACAACATTCATA
66 TGAAGCTTATGGATAGACTTTGGAAGTCTACTAAAATTCCGCCACCTAATCATACAACATTCATA
54163847 CTCTCACTTGCATTCTTACCATTTGTTCCTATAATGCACAAACTAAACTGAACCAAGGATCAATT
131 CTCTCACTTGCATTCTTACCATTTGTTCCTATAATGCACAAACTAAACTGAACCAAGGATCAATT
54163912 GAACCATAACACTTCACCTTTTAGATTTGTTAGACAATTGTGTTGTGTAATATAATGAATTCCCA
196 GAACCATAACACTTCACCTTTTAGATTTGTTAGACAATTGTGTTGTGTAATATAATGAATTCCCA
54163977 T
261 T
54163978 TATCAAGGTA
Statistics
Matches: 260, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 260 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (263 bp):
GAGGTTGATCAGACAGGCACTTGAAGCTTTGAAACATCAAATAATCTCTAAATGTCAGTAAGCTC
TGAAGCTTATGGATAGACTTTGGAAGTCTACTAAAATTCCGCCACCTAATCATACAACATTCATA
CTCTCACTTGCATTCTTACCATTTGTTCCTATAATGCACAAACTAAACTGAACCAAGGATCAATT
GAACCATAACACTTCACCTTTTAGATTTGTTAGACAATTGTGTTGTGTAATATAATGAATTCCCA
TAC
Found at i:54164236 original size:35 final size:35
Alignment explanation
Indices: 54164197--54164265 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
54164187 GGATATCCAT
*
54164197 CCTCAGGTGGGGGCTTTAAGGATGGAGGCAGATTG
1 CCTCAGGCGGGGGCTTTAAGGATGGAGGCAGATTG
54164232 CCTCAGGCGGGGGCTTTAAGGATGGAGGCAGATT
1 CCTCAGGCGGGGGCTTTAAGGATGGAGGCAGATT
54164266 ACCCCACGAT
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:0.20, C:0.16, G:0.42, T:0.22
Consensus pattern (35 bp):
CCTCAGGCGGGGGCTTTAAGGATGGAGGCAGATTG
Found at i:54164866 original size:2 final size:2
Alignment explanation
Indices: 54164859--54164901 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54164849 GCAGCATTCG
54164859 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54164901 T
1 T
54164902 GATACTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54166638 original size:16 final size:16
Alignment explanation
Indices: 54166605--54166638 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54166595 ATATAGTGTT
* *
54166605 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
54166621 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
54166637 AA
1 AA
54166639 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:54169465 original size:21 final size:21
Alignment explanation
Indices: 54169439--54169479 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54169429 AGACGAGCAA
* *
54169439 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54169460 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54169480 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54171418 original size:16 final size:16
Alignment explanation
Indices: 54171385--54171418 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54171375 GGAGATTGTT
* *
54171385 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
54171401 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
54171417 AA
1 AA
54171419 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:54184747 original size:30 final size:29
Alignment explanation
Indices: 54184688--54184754 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
54184678 AACTTCTAAA
*
54184688 AAATC-ATTAACCGACCTCTAACTGAATT
1 AAATCGATTAACCGACCTCTAACCGAATT
54184716 AAATCGATTAACCGACCAAT-TAACCGAATT
1 AAATCGATTAACCGACC--TCTAACCGAATT
54184746 AAATCGATT
1 AAATCGATT
54184755 TGGTTGGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 5 0.14
29 11 0.31
30 18 0.51
31 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (29 bp):
AAATCGATTAACCGACCTCTAACCGAATT
Found at i:54185724 original size:18 final size:17
Alignment explanation
Indices: 54185692--54185725 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54185682 ATAAAAATAA
*
54185692 TATAAAAATTAATTAAT
1 TATAAAAATGAATTAAT
54185709 TATAAAAATGATATTAA
1 TATAAAAATGA-ATTAA
54185726 AGAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TATAAAAATGAATTAAT
Found at i:54188210 original size:139 final size:137
Alignment explanation
Indices: 54187960--54188381 Score: 487
Period size: 139 Copynumber: 3.1 Consensus size: 137
54187950 GAAACCTCAT
* * ** *
54187960 ACTCAAGGATGTAA-TAGCAATTATCTAACCATCTAACGAAAAGAGGTAATATGTTAGAAATATT
1 ACTCAAGAATGTAATTA-CAACTATCTAACCATCTAACG-AAAGAACTAATATGTTAAAAATATT
* *
54188024 AATTAAAA---AAAA--TTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATC
64 AATTAAAATTTAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
*
54188084 GAACTCGAG
129 AAACTCGAG
* * * * *
54188093 ACTCAAGAATGTACTTACGACTATCTAACCATCTAACGAAAGAATTAAAAAGTTAAAAATATTAA
1 ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
* * * * * * *
54188158 TTAAAATTTGAAAATGCTTGAAGTAACATGAAATAGAAAATACAAATATGAGTCGGAGATGAATT
66 TTAAAATTT-AAAA-GCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
*
54188223 AAACTTGAG
129 AAACTCGAG
* ** * * *
54188232 ACTCAAGGATGTAATTGTAACTATTTAACCATCTAACCAAAGAACTAATATGTTAAAAAAATTAA
1 ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
*
54188297 TTAAAGATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTCAGTAGAAGAAGAATC
66 TTAAA-ATTT-AAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
*
54188362 AAACTCGGG
129 AAACTCGAG
54188371 ACTCAAGAATG
1 ACTCAAGAATG
54188382 AAAACACTAG
Statistics
Matches: 239, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
132 28 0.12
133 31 0.13
134 2 0.01
136 4 0.02
139 166 0.69
140 8 0.03
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (137 bp):
ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
TTAAAATTTAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATCAA
ACTCGAG
Found at i:54193225 original size:22 final size:22
Alignment explanation
Indices: 54193200--54193242 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54193190 TAAAATAAAA
**
54193200 TTTTAAATATTTGTAGTTATTAT
1 TTTTAAA-ATTTAAAGTTATTAT
54193223 TTTTAAAATTTAAAGTTATT
1 TTTTAAAATTTAAAGTTATT
54193243 TCATATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTTAAAGTTATTAT
Found at i:54193975 original size:33 final size:34
Alignment explanation
Indices: 54193938--54194025 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 34
54193928 GAGTAAAACT
54193938 ATAATATATTATATAAAAATTTACA-TTTAAAAA
1 ATAATATATTATATAAAAATTTACATTTTAAAAA
* * *
54193971 ATAATAT-TTCATACATAAAATTTTTCATTTTAAGAA
1 ATAATATATT-AT--ATAAAAATTTACATTTTAAAAA
54194007 ATAATGATATT-TA-AAAAAT
1 ATAAT-ATATTATATAAAAAT
54194026 GTGAATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
32 2 0.04
33 14 0.31
34 1 0.02
35 11 0.24
36 13 0.29
37 2 0.04
38 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (34 bp):
ATAATATATTATATAAAAATTTACATTTTAAAAA
Found at i:54195892 original size:27 final size:27
Alignment explanation
Indices: 54195862--54195925 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
54195852 AATCAATTGC
**
54195862 AATTTTATTGGAAAGCATATTTATATT
1 AATTTTATTAAAAAGCATATTTATATT
*
54195889 AATTATT-TAAAAAAGCATATTTATATT
1 AATT-TTATTAAAAAGCATATTTATATT
*
54195916 AATTATATTA
1 AATTTTATTA
54195926 TGAAAAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (27 bp):
AATTTTATTAAAAAGCATATTTATATT
Found at i:54197116 original size:20 final size:20
Alignment explanation
Indices: 54197068--54197118 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
54197058 CATGCGGATG
* **
54197068 TTTATAATTTTTTTTATAAT
1 TTTATAAATTTTTGGATAAT
*
54197088 TTTAT-AATTTTTGGATATT
1 TTTATAAATTTTTGGATAAT
54197107 TTTATAAATTTT
1 TTTATAAATTTT
54197119 AAATTATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATAAATTTTTGGATAAT
Found at i:54210951 original size:18 final size:18
Alignment explanation
Indices: 54210928--54210990 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
54210918 CAAGAAATCA
54210928 ACTCCCTGTTTCCATGCT
1 ACTCCCTGTTTCCATGCT
* * *
54210946 ACTCCCCGTTTCCCTGAT
1 ACTCCCTGTTTCCATGCT
*
54210964 A-ACCC----TCCATGCT
1 ACTCCCTGTTTCCATGCT
54210977 ACTCCCTGTTTCCA
1 ACTCCCTGTTTCCA
54210991 CCATTCTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
17 3 0.09
18 20 0.61
ACGTcount: A:0.14, C:0.43, G:0.10, T:0.33
Consensus pattern (18 bp):
ACTCCCTGTTTCCATGCT
Found at i:54218824 original size:27 final size:28
Alignment explanation
Indices: 54218769--54218821 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
54218759 TAAAAAAGCT
54218769 TATTATAAAAATATATATGTTATAAAAG
1 TATTATAAAAATATATATGTTATAAAAG
* *
54218797 TATTAT-AATATATTTAT-TTATAAAA
1 TATTATAAAAATATATATGTTATAAAA
54218822 AGTTACGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 9 0.39
28 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (28 bp):
TATTATAAAAATATATATGTTATAAAAG
Found at i:54219620 original size:19 final size:18
Alignment explanation
Indices: 54219577--54219620 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
54219567 CTATTTAGAA
* *
54219577 ATTTTTTATCGTGATAAT
1 ATTTTTTATAGTAATAAT
*
54219595 AATTTTTATAGTAATTAAT
1 ATTTTTTATAGTAA-TAAT
54219614 ATTTTTT
1 ATTTTTT
54219621 TAAATATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (18 bp):
ATTTTTTATAGTAATAAT
Found at i:54221214 original size:13 final size:13
Alignment explanation
Indices: 54221196--54221220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54221186 ATAATTCACC
54221196 AAATAAAATAAAT
1 AAATAAAATAAAT
54221209 AAATAAAATAAA
1 AAATAAAATAAA
54221221 CATGTCGATT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:54223564 original size:25 final size:25
Alignment explanation
Indices: 54223511--54223564 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
54223501 CGACCCGTTT
* * *
54223511 TTAATTAAAATTAAAATTAGTTTTT
1 TTAATTAAAATTAAAACTAATTTTA
54223536 TTAA-TAAAATTAAAACTAATTGTTA
1 TTAATTAAAATTAAAACTAATT-TTA
54223561 TTAA
1 TTAA
54223565 AATTAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATTAAAATTAAAACTAATTTTA
Found at i:54223583 original size:16 final size:16
Alignment explanation
Indices: 54223546--54223585 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54223536 TTAATAAAAT
* *
54223546 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
54223562 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
54223578 TAAAATTA
1 TAAAATTA
54223586 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:54223655 original size:66 final size:67
Alignment explanation
Indices: 54223574--54223717 Score: 245
Period size: 68 Copynumber: 2.1 Consensus size: 67
54223564 AAATTAATTG
* *
54223574 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAACTGTATTAATTGTTGTAACAAAATCTAACATTT
54223638 GA
66 GA
*
54223640 TTAGTAAATTTATCAAATTATTAATTGTATTAACTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAACTGTATTAATTGTTGTAACAAAATCTAACATT
54223705 TGA
65 TGA
54223708 TTAGTAAAAT
1 TTAGTAAAAT
54223718 AAACTTGATG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAACTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:54223827 original size:27 final size:29
Alignment explanation
Indices: 54223782--54223836 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
54223772 AAATAAACTT
54223782 AAAATAAAAAAAAACTA-TT-ATATTTTA
1 AAAATAAAAAAAAACTATTTAATATTTTA
*
54223809 AAAATAAAAAAGATA-TATTTAATATTTT
1 AAAATAAAAAA-AAACTATTTAATATTTT
54223837 CGGGCCGGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 13 0.54
28 4 0.17
29 7 0.29
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATAAAAAAAAACTATTTAATATTTTA
Found at i:54224235 original size:18 final size:18
Alignment explanation
Indices: 54224183--54224235 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
54224173 AATGGGTGAA
*
54224183 ATAACATTTCTAATATTTT
1 ATAA-ATTTCTAATTTTTT
*
54224202 ATAAATTTCTATTTTTTT
1 ATAAATTTCTAATTTTTT
* *
54224220 ATATATTTTTAATTTT
1 ATAAATTTCTAATTTT
54224236 AAAATAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
ATAAATTTCTAATTTTTT
Found at i:54226934 original size:16 final size:16
Alignment explanation
Indices: 54226915--54226948 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54226905 TTATAAAAAA
*
54226915 TAAAAAGAAAAGAATT
1 TAAAAAAAAAAGAATT
54226931 TAAAAAAAAAAGAATT
1 TAAAAAAAAAAGAATT
54226947 TA
1 TA
54226949 GCATGAAGTA
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:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
TAAAAAAAAAAGAATT
Found at i:54231573 original size:17 final size:18
Alignment explanation
Indices: 54231541--54231576 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54231531 TTGTTTCATT
*
54231541 AAAAATTATTTATTTTTG
1 AAAAATAATTTATTTTTG
*
54231559 AAAAATAATTTTTTTTTG
1 AAAAATAATTTATTTTTG
54231577 TGTTGGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
AAAAATAATTTATTTTTG
Found at i:54231633 original size:18 final size:18
Alignment explanation
Indices: 54231610--54231644 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54231600 ATTTTGTGTT
54231610 ATTTAATAAAAAA-ATTTC
1 ATTTAA-AAAAAATATTTC
54231628 ATTTAAAAAAAATATTT
1 ATTTAAAAAAAATATTT
54231645 TTAGTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTAAAAAAAATATTTC
Found at i:54235499 original size:38 final size:38
Alignment explanation
Indices: 54235419--54235499 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
54235409 TTAACAAAAG
* * * * *
54235419 GCATGATTATCATGTATTTAGTTCAATAGTAACAGTAG
1 GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
* * *
54235457 GCATGTTTAACATGTATTCAGTTTAACAATAACGGTAA
1 GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
54235495 GCATG
1 GCATG
54235500 CAACCAGTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (38 bp):
GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
Found at i:54240704 original size:13 final size:14
Alignment explanation
Indices: 54240668--54240706 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54240658 TGTAACAAAT
*
54240668 TTATAAAAAAATTC
1 TTATAAAAATATTC
54240682 TTATAAAAATATT-
1 TTATAAAAATATTC
*
54240695 TTTTAAAAATAT
1 TTATAAAAATAT
54240707 AAAAAGATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATAAAAATATTC
Found at i:54241910 original size:16 final size:16
Alignment explanation
Indices: 54241889--54241957 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
54241879 TTTGGTTCGC
54241889 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54241905 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54241921 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
*
54241938 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
54241954 TGTA
1 TGTA
54241958 ATAGCTAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:54241935 original size:33 final size:32
Alignment explanation
Indices: 54241889--54241957 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
54241879 TTTGGTTCGC
*
54241889 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTAGATTAGAGG
54241921 TGTATTGGGATTAGAGGTGTATTAGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTAGATTAGAGG
54241954 TGTA
1 TGTA
54241958 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTAGATTAGAGG
Found at i:54242214 original size:18 final size:17
Alignment explanation
Indices: 54242193--54242227 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54242183 TTATTATTAA
*
54242193 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54242211 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54242228 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54242313 original size:120 final size:120
Alignment explanation
Indices: 54242176--54242599 Score: 794
Period size: 120 Copynumber: 3.5 Consensus size: 120
54242166 ATCATATTTA
54242176 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
54242241 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
54242296 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
54242361 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
54242416 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
**
54242481 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATATTTT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
54242536 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
54242600 GCAGAAATTT
Statistics
Matches: 294, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 294 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:54242454 original size:18 final size:17
Alignment explanation
Indices: 54242433--54242467 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54242423 TTATTATTAA
*
54242433 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54242451 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54242468 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54242574 original size:18 final size:17
Alignment explanation
Indices: 54242553--54242587 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54242543 TTATTATTAA
*
54242553 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54242571 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54242588 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54242738 original size:14 final size:15
Alignment explanation
Indices: 54242699--54242740 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54242689 TTTTAACATA
*
54242699 ATTATTATTAAATAT
1 ATTATAATTAAATAT
54242714 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
54242728 A-TATAATTTAATA
1 ATTATAATTAAATA
54242741 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:54242790 original size:517 final size:517
Alignment explanation
Indices: 54242080--54243105 Score: 1786
Period size: 517 Copynumber: 2.0 Consensus size: 517
54242070 TAGAATACCC
*
54242080 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
* *
54242145 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
* * *
54242210 TATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATTAATTTACTGAAATCATAATATA
131 TATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATA
* *
54242275 TGATACTGTAAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT
196 TGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT
* *
54242340 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATA
261 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATA
* *
54242405 AAATATAAATT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
326 AAATATAAATTGAA-ATAATTATTATTAAATAAAATTTAATTAAAATATATAATTTAATAAAATT
* * * *
54242469 CTTAATAATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATAT-AT
390 CTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
*
54242533 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
455 TTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* * *
54242597 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
*
54242662 ATATCAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
54242727 TATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATA
131 TATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATA
*
54242792 TGATACTATAAAATATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT
196 TGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT
54242857 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATA
261 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATA
* * *
54242922 AAATATAATTTGAAATAATTATTATTAAATAAAATTTAATTAAAATATATGATTTAATAAAATTT
326 AAATATAAATTGAAATAATTATTATTAAATAAAATTTAATTAAAATATATAATTTAATAAAATTC
54242987 TTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATT
391 TTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATT
*
54243052 TGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
456 TGAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
54243106 TAAAATAATT
Statistics
Matches: 481, Mismatches: 26, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
517 473 0.98
518 8 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (517 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTATAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATA
TGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT
AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATA
AAATATAAATTGAAATAATTATTATTAAATAAAATTTAATTAAAATATATAATTTAATAAAATTC
TTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATT
TGAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
Found at i:54242851 original size:18 final size:17
Alignment explanation
Indices: 54242830--54242864 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54242820 TTATTATTAA
*
54242830 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54242848 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54242865 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54242961 original size:277 final size:276
Alignment explanation
Indices: 54242414--54242953 Score: 749
Period size: 277 Copynumber: 1.9 Consensus size: 276
54242404 AAAATATAAA
* *
54242414 TTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATC
* * * *
54242479 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATATTTTAACATAAT
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAAT
* * * *
54242544 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATT
131 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACACAAATA
* ** * * * * * ** *
54242609 TGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATA
196 TGATTTACTAAATTAATATTGATACTATAAAATAAATTTAAATAAGATTATTAATAT-AATAATA
54242674 AATAATTTAATCATATT
260 AATAATTTAATCATATT
54242691 TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATC
1 TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATC
54242756 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAAT
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAAT
* **
54242821 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTA
131 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACA--CAAA
*
54242886 TATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATAATTATTATTAA-
194 TATG-ATTTACT-AAAT--TAATAT-TGATACTATAAAATA-AATTT-AAATAA-GATTATTAAT
54242950 ATAA
251 ATAA
54242954 AATTTAATTA
Statistics
Matches: 228, Mismatches: 25, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
277 180 0.79
279 4 0.02
280 4 0.02
281 4 0.02
283 5 0.02
284 9 0.04
285 7 0.03
286 7 0.03
287 8 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (276 bp):
TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAAT
TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACACAAATA
TGATTTACTAAATTAATATTGATACTATAAAATAAATTTAAATAAGATTATTAATATAATAATAA
ATAATTTAATCATATT
Found at i:54243091 original size:18 final size:17
Alignment explanation
Indices: 54243068--54243104 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
54243058 AATTATTATT
54243068 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
54243084 AAATATATGATTTAATA
1 AAATATATGATTTAATA
54243101 AAAT
1 AAAT
54243105 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:54243114 original size:120 final size:120
Alignment explanation
Indices: 54242696--54243105 Score: 741
Period size: 120 Copynumber: 3.4 Consensus size: 120
54242686 ATATTTTAAC
*
54242696 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
54242761 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
54242815 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
54242880 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
54242936 ATAATTATTATTAAATAAAATTTAATTAAAATATATGATTTAATAAAATTTTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
54243001 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
54243056 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
54243106 TAAAATAATT
Statistics
Matches: 281, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
120 279 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:54243189 original size:15 final size:15
Alignment explanation
Indices: 54243146--54243199 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
54243136 TATGAATTTG
54243146 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
54243160 -ATTA-TTATTAA-A
1 TATAATTTAATAATA
54243172 TATAATTTAATAATA
1 TATAATTTAATAATA
*
54243187 TATAATTTCATAA
1 TATAATTTAATAA
54243200 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 6 0.19
15 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:54243232 original size:71 final size:73
Alignment explanation
Indices: 54243151--54243286 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 73
54243141 ATTTGTATAA
*
54243151 TTTAAAATAATTATTATTAAATATAATTTAAT-A-ATATATAATTTCATAAAATTCTTGATAATA
1 TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
54243214 AATTTTCT
66 AATTTTCT
*
54243222 TTTAGAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAAT
1 TTTAAAATAATTAATATTAAATATAATTTAATAA-GATATATAATTTCATAAAATTCTTGATAAT
54243287 TTAATCATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 30 0.50
72 1 0.02
74 29 0.48
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (73 bp):
TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
AATTTTCT
Found at i:54249269 original size:17 final size:18
Alignment explanation
Indices: 54249247--54249282 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
54249237 TTCATTTTTA
*
54249247 TATAAAATAA-TTTATTT
1 TATAAAACAATTTTATTT
54249264 TATAAAACAATTTTATTT
1 TATAAAACAATTTTATTT
54249282 T
1 T
54249283 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAAAACAATTTTATTT
Found at i:54250496 original size:16 final size:17
Alignment explanation
Indices: 54250472--54250514 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54250462 TGATATTATA
*
54250472 AAATCAAAAAAT-AATT
1 AAATAAAAAAATAAATT
54250488 AAATAAAAAAATCAAATT
1 AAATAAAAAAAT-AAATT
*
54250506 AATTAAAAA
1 AAATAAAAA
54250515 TTCGTCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAAAAATAAATT
Found at i:54252562 original size:12 final size:13
Alignment explanation
Indices: 54252544--54252573 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
54252534 GGACGTGAAT
54252544 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
54252557 -AAAAAAGAAAAA
1 GAAAAAAGAAAAA
54252569 GAAAA
1 GAAAA
54252574 GGGAGATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:54260791 original size:25 final size:26
Alignment explanation
Indices: 54260743--54260796 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
54260733 GGTTGCTACC
*
54260743 ATTGTTCAATTTATAATTAGAAAG-A
1 ATTGTTCAATTTAAAATTAGAAAGTA
*
54260768 ATTGTTCCATATTAAAATTA-AAAGTA
1 ATTGTTCAAT-TTAAAATTAGAAAGTA
54260794 ATT
1 ATT
54260797 CAAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (26 bp):
ATTGTTCAATTTAAAATTAGAAAGTA
Found at i:54262139 original size:25 final size:25
Alignment explanation
Indices: 54262111--54262159 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
54262101 ATTCAAAATA
* *
54262111 TTTATAAATATTAAAAAAATTATAT
1 TTTAAAAAAATTAAAAAAATTATAT
*
54262136 TTTAAAAAAATTATAAAAATTATA
1 TTTAAAAAAATTAAAAAAATTATA
54262160 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTAAAAAAATTAAAAAAATTATAT
Found at i:54268538 original size:20 final size:20
Alignment explanation
Indices: 54268513--54268556 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
54268503 TCTTAAAAAG
54268513 TATACAAAAATAGAGGAAAT
1 TATACAAAAATAGAGGAAAT
54268533 TATACAAAAATAGAGGAAAT
1 TATACAAAAATAGAGGAAAT
54268553 TATA
1 TATA
54268557 AACAATCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.23
Consensus pattern (20 bp):
TATACAAAAATAGAGGAAAT
Found at i:54271649 original size:31 final size:31
Alignment explanation
Indices: 54271614--54271680 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
54271604 AATATCCCAG
* ** *
54271614 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTCTCAAATAATTCAA
*
54271645 TGACTTAAATGAAAACTCTCAAATAATTCAA
1 TGACTTAAATAAAAACTCTCAAATAATTCAA
54271676 TGACT
1 TGACT
54271681 ATTTTGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTCTCAAATAATTCAA
Found at i:54275064 original size:19 final size:19
Alignment explanation
Indices: 54275042--54275081 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54275032 TAAATATCTT
54275042 TTAAAATAA-TCCATTTTTA
1 TTAAAA-AATTCCATTTTTA
*
54275061 TTAAAAAATTCTATTTTTA
1 TTAAAAAATTCCATTTTTA
54275080 TT
1 TT
54275082 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAAAATTCCATTTTTA
Found at i:54277362 original size:18 final size:19
Alignment explanation
Indices: 54277339--54277377 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54277329 TAAAATGATG
54277339 AAAATT-GAAAATTTTAAA
1 AAAATTAGAAAATTTTAAA
*
54277357 AAAATTAGAACATTTTAAA
1 AAAATTAGAAAATTTTAAA
54277376 AA
1 AA
54277378 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATTAGAAAATTTTAAA
Found at i:54294920 original size:16 final size:16
Alignment explanation
Indices: 54294896--54294929 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54294886 TAATACTAAT
*
54294896 TAATTTTTGATATTAA
1 TAATGTTTGATATTAA
*
54294912 TAATGTTTGATTTTAA
1 TAATGTTTGATATTAA
54294928 TA
1 TA
54294930 TTTAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TAATGTTTGATATTAA
Found at i:54295123 original size:43 final size:42
Alignment explanation
Indices: 54295062--54295251 Score: 263
Period size: 43 Copynumber: 4.5 Consensus size: 42
54295052 CGTTTGTTAG
*
54295062 GGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
1 GGTCTTGATCTATAGCGGCGTTTGT-GGAAAAGCGCCGCTAAA
* *
54295105 GGTCTTGATCTATAGCGGCATTTGTGGAAAAAGCGTCGCTAAA
1 GGTCTTGATCTATAGCGGCGTTTGTGG-AAAAGCGCCGCTAAA
* * * *
54295148 GATCTTGAGCTATAGCGGCGTTTGTGTAAAAGCGCTGCTAAA
1 GGTCTTGATCTATAGCGGCGTTTGTGGAAAAGCGCCGCTAAA
* *
54295190 GGTCCTGATTTATAGCGGCGTTTGTGGAAAAGGCGCCGCTAAA
1 GGTCTTGATCTATAGCGGCGTTTGTGGAAAA-GCGCCGCTAAA
*
54295233 GGTCATGATCTATAGCGGC
1 GGTCTTGATCTATAGCGGC
54295252 ATTTATTTCT
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 41 0.32
43 87 0.68
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (42 bp):
GGTCTTGATCTATAGCGGCGTTTGTGGAAAAGCGCCGCTAAA
Found at i:54295208 original size:85 final size:86
Alignment explanation
Indices: 54295064--54295251 Score: 279
Period size: 85 Copynumber: 2.2 Consensus size: 86
54295054 TTTGTTAGGG
*
54295064 TCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCATTTG
1 TCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
*
54295129 TGGAAAAAGCGTCGCTAAAGA
66 TGGAAAAAGCGCCGCTAAAGA
* * * *
54295150 TCTTGAGCTATAGCGGCGTTTGT-GTAAAAGCGCTGCTAAAGGTCCTGATTTATAGCGGCGTTTG
1 TCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* *
54295214 TGGAAAAGGCGCCGCTAAAGG
66 TGGAAAAAGCGCCGCTAAAGA
* *
54295235 TCATGATCTATAGCGGC
1 TCTTGAGCTATAGCGGC
54295252 ATTTATTTCT
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 69 0.75
86 23 0.25
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (86 bp):
TCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
TGGAAAAAGCGCCGCTAAAGA
Found at i:54296996 original size:19 final size:19
Alignment explanation
Indices: 54296928--54296998 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
54296918 GAATATATTT
*
54296928 ATATATATTATAAAGTTGTAA
1 ATATATATTATAAA-TT-TAC
* ** *
54296949 ATAGATATT-TATGTTCAC
1 ATATATATTATAAATTTAC
*
54296967 ATTATAAATTATAAATTTAC
1 A-TATATATTATAAATTTAC
54296987 ATATATATTATA
1 ATATATATTATA
54296999 TTACAAGATT
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
18 2 0.05
19 18 0.49
20 9 0.24
21 8 0.22
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (19 bp):
ATATATATTATAAATTTAC
Found at i:54297454 original size:19 final size:19
Alignment explanation
Indices: 54297430--54297475 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
54297420 GACTTCAACC
54297430 GACTAACTAAAACAGTTAT
1 GACTAACTAAAACAGTTAT
*
54297449 GACTAACTAAAACGGTTAT
1 GACTAACTAAAACAGTTAT
54297468 GAGCTAAC
1 GA-CTAAC
54297476 CATCTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (19 bp):
GACTAACTAAAACAGTTAT
Found at i:54297598 original size:77 final size:77
Alignment explanation
Indices: 54297471--54297625 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
54297461 CGGTTATGAG
54297471 CTAACCATCTTATTAACCACTAACAACTAACCGTTGACTGGTCAACTGACCATACTGTAACAGTA
1 CTAACCATCTTATTAACCACTAACAACTAACCGTTGACTGGTCAACTGACCATACTGTAACAGTA
54297536 GGCTAATACTGC
66 GGCTAATACTGC
54297548 CTAACCATCTTATTAACCACTAACAACTAACCGTTGACTGGTCAACTGACCATACTGTAACAGTA
1 CTAACCATCTTATTAACCACTAACAACTAACCGTTGACTGGTCAACTGACCATACTGTAACAGTA
54297613 GGCTAATACTGC
66 GGCTAATACTGC
54297625 C
1 C
54297626 CCTGCTAATC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (77 bp):
CTAACCATCTTATTAACCACTAACAACTAACCGTTGACTGGTCAACTGACCATACTGTAACAGTA
GGCTAATACTGC
Found at i:54315808 original size:20 final size:20
Alignment explanation
Indices: 54315750--54315810 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
54315740 TAGTTTTAAT
* *
54315750 ATTTTTTTGTAATTTTTAAAA
1 ATTTTTTAG-AATTTTTACAA
* * *
54315771 AATTATTATAATTTTTACAA
1 ATTTTTTAGAATTTTTACAA
54315791 ATTTTTTAGAATTTTTACAA
1 ATTTTTTAGAATTTTTACAA
54315811 CTTCAAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTTTAGAATTTTTACAA
Found at i:54322879 original size:13 final size:13
Alignment explanation
Indices: 54322861--54322889 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54322851 TGATCATATG
54322861 TGGTCCATCACAA
1 TGGTCCATCACAA
54322874 TGGTCCATCACAA
1 TGGTCCATCACAA
54322887 TGG
1 TGG
54322890 AAGCAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (13 bp):
TGGTCCATCACAA
Found at i:54324343 original size:5 final size:5
Alignment explanation
Indices: 54324335--54324366 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
54324325 CTAAATCTAG
54324335 ATATT ATATT ATATT ATATT -TATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
54324367 CATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:54324360 original size:14 final size:15
Alignment explanation
Indices: 54324335--54324366 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
54324325 CTAAATCTAG
54324335 ATATTATATTATATT
1 ATATTATATTATATT
54324350 ATATT-TATTATATT
1 ATATTATATTATATT
54324364 ATA
1 ATA
54324367 CATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATATTATATT
Found at i:54325914 original size:23 final size:23
Alignment explanation
Indices: 54325888--54325932 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54325878 CTATGTACCT
54325888 TGAAGGAAATAAATTTA-TAAATG
1 TGAAGG-AATAAATTTATTAAATG
*
54325911 TGAAGGATTAAATTTATTAAAT
1 TGAAGGAATAAATTTATTAAAT
54325933 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (23 bp):
TGAAGGAATAAATTTATTAAATG
Found at i:54334937 original size:14 final size:15
Alignment explanation
Indices: 54334913--54334942 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54334903 AATTATAAGT
54334913 AATAGTAATATATTA
1 AATAGTAATATATTA
54334928 AATA-TAATATATTA
1 AATAGTAATATATTA
54334942 A
1 A
54334943 TCATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATAGTAATATATTA
Found at i:54335722 original size:28 final size:29
Alignment explanation
Indices: 54335691--54335769 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 29
54335681 ATATATATCC
*
54335691 TAAAATATGTATGTATATATTC-AGATAA
1 TAAAATATGTATGTATATATACAAGATAA
* * *
54335719 T-AAA-ATGCATGCATATATACATAGATTA
1 TAAAATATGTATGTATATATACA-AGATAA
54335747 TAAAATATAGATATGTATATATA
1 TAAAATAT-G-TATGTATATATA
54335770 TATGTATATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
26 13 0.33
27 3 0.08
28 7 0.18
29 3 0.08
30 2 0.05
31 1 0.03
32 10 0.26
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (29 bp):
TAAAATATGTATGTATATATACAAGATAA
Found at i:54336027 original size:11 final size:11
Alignment explanation
Indices: 54336011--54336125 Score: 78
Period size: 11 Copynumber: 10.7 Consensus size: 11
54336001 ATTTTTTTAA
54336011 TTTTAAAATAT
1 TTTTAAAATAT
54336022 TTTTAAAATACT
1 TTTTAAAATA-T
** *
54336034 TTTTTTAATTT
1 TTTTAAAATAT
**
54336045 TTTTTTAA-A-
1 TTTTAAAATAT
54336054 TTTTAAAATAT
1 TTTTAAAATAT
54336065 TTTTAAAATACT
1 TTTTAAAATA-T
** *
54336077 TTTTTTAATTT
1 TTTTAAAATAT
**
54336088 TTTTTTAA-A-
1 TTTTAAAATAT
54336097 TTTTAAAATAT
1 TTTTAAAATAT
*
54336108 TTTTAAAA-CT
1 TTTTAAAATAT
54336118 TTTTAAAA
1 TTTTAAAA
54336126 AAAATTTAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
9 12 0.14
10 11 0.13
11 46 0.54
12 16 0.19
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54336063 original size:43 final size:42
Alignment explanation
Indices: 54335963--54336115 Score: 240
Period size: 43 Copynumber: 3.7 Consensus size: 42
54335953 AATATATTTA
* * *
54335963 TTTTTTTAATTTTAAAATATTTTTTACATAC-TGTTTTAA--
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATT
54336002 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATT
54336044 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATT
1 TTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTAATT
54336087 TTTTTTTAAATTTTAAAATATTTTTAAAA
1 TTTTTTT-AATTTTAAAATATTTTTAAAA
54336116 CTTTTTAAAA
Statistics
Matches: 107, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
39 29 0.27
40 7 0.07
42 7 0.07
43 64 0.60
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (42 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATT
Found at i:54336080 original size:32 final size:32
Alignment explanation
Indices: 54336022--54336089 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
54336012 TTTAAAATAT
** *
54336022 TTTTAAAATACTTTTTTTAATTTTTTTTTAAA
1 TTTTAAAATACTTTTTAAAATCTTTTTTTAAA
*
54336054 TTTTAAAATA-TTTTTAAAATACTTTTTTTAAT
1 TTTTAAAATACTTTTTAAAAT-CTTTTTTTAAA
54336086 TTTT
1 TTTT
54336090 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTTAAAATACTTTTTAAAATCTTTTTTTAAA
Done.