Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 10 of 26
Found at i:1652891 original size:24 final size:23
Alignment explanation
Indices: 1652846--1652903 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
1652836 TAATATTTTA
1652846 AATATATAAAAAAAATATAAATAC
1 AATATA-AAAAAAAATATAAATAC
* *
1652870 GATATAAAAAAATAAT-TAAAATAT
1 AATATAAAAAAA-AATAT-AAATAC
1652894 AATATAAAAA
1 AATATAAAAA
1652904 TAATTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AATATAAAAAAAAATATAAATAC
Found at i:1652902 original size:22 final size:23
Alignment explanation
Indices: 1652849--1652937 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 23
1652839 TATTTTAAAT
* *
1652849 ATATAAAAA-AAATATAAATACGA
1 ATATAAAAATAATTA-AAATATGA
*
1652872 TATAAAAAAATAATTAAAATAT-A
1 -ATATAAAAATAATTAAAATATGA
**
1652895 ATATAAAAATAATTATGATATGA
1 ATATAAAAATAATTAAAATATGA
*
1652918 ATATAAAAAT-ATAAAAATAT
1 ATATAAAAATAATTAAAATAT
1652938 TTACTAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
22 25 0.46
23 12 0.22
24 13 0.24
25 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (23 bp):
ATATAAAAATAATTAAAATATGA
Found at i:1652906 original size:11 final size:11
Alignment explanation
Indices: 1652845--1652907 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
1652835 TTAATATTTT
1652845 AAAT-ATATAA
1 AAATAATATAA
*
1652855 AAAAAATATAA
1 AAATAATATAA
*
1652866 ATACGAT-ATAAAA
1 A-A--ATAATATAA
1652879 AAATAAT-TAA
1 AAATAATATAA
1652889 AATATAATATAA
1 AA-ATAATATAA
1652901 AAATAAT
1 AAATAAT
1652908 TATGATATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
10 9 0.21
11 19 0.45
12 7 0.17
13 6 0.14
14 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (11 bp):
AAATAATATAA
Found at i:1653206 original size:5 final size:5
Alignment explanation
Indices: 1653132--1653204 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 5
1653122 TTGTCTCGTC
* *
1653132 TCTTT T-TTT T-TTT T-TTT TCTCTT TC-TT TCTCTC TCTTT TCGTT TCGTTT
1 TCTTT TCTTT TCTTT TCTTT TCT-TT TCTTT TCT-TT TCTTT TCTTT TC-TTT
*
1653181 CCTTT TCTTT TC-TT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
1653205 TTCCTTTCCC
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
4 24 0.43
5 21 0.38
6 11 0.20
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:1660535 original size:17 final size:19
Alignment explanation
Indices: 1660501--1660562 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
1660491 AATTGATAAT
* *
1660501 ATTATTTTTATATTATTAT
1 ATTATTTTTATATAATTAA
1660520 A-TATTTTT-TATAATTAA
1 ATTATTTTTATATAATTAA
*
1660537 ATTATTTTTAT-TAAATAA
1 ATTATTTTTATATAATTAA
1660555 ATTATTTT
1 ATTATTTT
1660563 AACATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
17 8 0.21
18 28 0.74
19 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATTTTTATATAATTAA
Found at i:1660841 original size:3 final size:3
Alignment explanation
Indices: 1660827--1660857 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1660817 CTAATATTAC
*
1660827 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1660858 TTATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1660862 original size:3 final size:3
Alignment explanation
Indices: 1660856--1660900 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1660846 ATAATAATAA
* *
1660856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1660901 GGCCCCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1662326 original size:13 final size:13
Alignment explanation
Indices: 1662310--1662335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1662300 CATCACCTAC
1662310 AAATAATAAAATA
1 AAATAATAAAATA
1662323 AAATAATAAAATA
1 AAATAATAAAATA
1662336 TATTTCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:1666133 original size:15 final size:15
Alignment explanation
Indices: 1666113--1666142 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1666103 ACTCTTATAT
*
1666113 TACTTGGATTTAGGA
1 TACTTGGATTCAGGA
1666128 TACTTGGATTCAGGA
1 TACTTGGATTCAGGA
1666143 GTGAGTATAG
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:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (15 bp):
TACTTGGATTCAGGA
Found at i:1669669 original size:14 final size:14
Alignment explanation
Indices: 1669641--1669678 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1669631 TATTTAAATT
*
1669641 TAAATATAA-AATA
1 TAAAAATAATAATA
*
1669654 TATAAATAATAATA
1 TAAAAATAATAATA
1669668 TAAAAATAATA
1 TAAAAATAATA
1669679 TTTTAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATAATAATA
Found at i:1669675 original size:11 final size:11
Alignment explanation
Indices: 1669643--1669679 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1669633 TTTAAATTTA
1669643 AATAT-AAAAT
1 AATATAAAAAT
1669653 -ATATAAATAAT
1 AATATAAA-AAT
1669664 AATATAAAAAT
1 AATATAAAAAT
1669675 AATAT
1 AATAT
1669680 TTTAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 2 0.08
11 11 0.46
12 7 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1672298 original size:51 final size:52
Alignment explanation
Indices: 1672232--1672342 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 52
1672222 ATTAAAATTT
* * * * *
1672232 TATTTTAAATCAATTTGATGATTTAAAATA-ATAATTATAAATTTAAATAAT-A
1 TATTTTAAATCAATTTAATCA--TAAAATATATAAATATAAATTAAAAAAATAA
* *
1672284 TATTTTATAT-AATTTAATCATAAAATATATAAATATTAATTAAAAAAATAA
1 TATTTTAAATCAATTTAATCATAAAATATATAAATATAAATTAAAAAAATAA
1672335 TATTTTAA
1 TATTTTAA
1672343 TTAAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
49 7 0.14
50 17 0.35
51 16 0.33
52 9 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (52 bp):
TATTTTAAATCAATTTAATCATAAAATATATAAATATAAATTAAAAAAATAA
Found at i:1672361 original size:20 final size:19
Alignment explanation
Indices: 1672292--1672362 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
1672282 TATATTTTAT
* *
1672292 ATAATTTAATCATAAAATA
1 ATAATTTAATTAAAAAATA
1672311 TATAAATATTAATTAAAAAAATA
1 -AT-AAT-TTAATT-AAAAAATA
*
1672334 ATATTTTAATTAAATAAATA
1 ATAATTTAATTAAA-AAATA
1672354 ATAATTTAA
1 ATAATTTAA
1672363 ACTTAATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.07
20 21 0.49
21 5 0.12
22 7 0.16
23 7 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATTTAATTAAAAAATA
Found at i:1673008 original size:2 final size:2
Alignment explanation
Indices: 1673001--1673034 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1672991 CATTCTAGAA
1673001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1673035 GGCCGTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1675747 original size:16 final size:18
Alignment explanation
Indices: 1675715--1675747 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1675705 AAAATTTTAA
1675715 TTTTAATATTTATAATTT
1 TTTTAATATTTATAATTT
1675733 TTTTAAT-TTTA-AATT
1 TTTTAATATTTATAATT
1675748 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATATTTATAATTT
Found at i:1675749 original size:22 final size:24
Alignment explanation
Indices: 1675709--1675757 Score: 84
Period size: 22 Copynumber: 2.1 Consensus size: 24
1675699 ATAATTAAAA
1675709 TTTTAATTTTAATATTTATAATTT
1 TTTTAATTTTAATATTTATAATTT
1675733 TTTTAATTTTAA-A-TTATAATTT
1 TTTTAATTTTAATATTTATAATTT
1675755 TTT
1 TTT
1675758 AAATAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTAATTTTAATATTTATAATTT
Found at i:1677566 original size:16 final size:15
Alignment explanation
Indices: 1677499--1677572 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 15
1677489 TTACTATATT
1677499 TTTTAAATATTTTAA
1 TTTTAAATATTTTAA
**
1677514 TATTTATTTA-TTTAA
1 T-TTTAAATATTTTAA
1677529 TGTTTAAA-ATTTTGAA
1 T-TTTAAATATTTT-AA
*
1677545 TATTAAATATTTATAA
1 TTTTAAATATTT-TAA
*
1677561 TTTTAAAAATTT
1 TTTTAAATATTT
1677573 ATATTTGTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
14 1 0.02
15 19 0.41
16 25 0.54
17 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTAAATATTTTAA
Found at i:1679275 original size:1 final size:1
Alignment explanation
Indices: 1679269--1679299 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1679259 TCTTCAATTT
*
1679269 GGGGGGGGGGGGGGGGGGGGGGGGGTGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1679300 AGAAGAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:1681790 original size:3 final size:3
Alignment explanation
Indices: 1681782--1681819 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1681772 GATTGAAATT
1681782 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1681820 TTTAAATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1682406 original size:15 final size:15
Alignment explanation
Indices: 1682388--1682433 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1682378 ATTTATTATA
*
1682388 TTAAATATTTAAATT
1 TTAAATAATTAAATT
1682403 TTAAATTAAATTAAATT
1 TTAAA-T-AATTAAATT
*
1682420 TAAAATAATTAAAT
1 TTAAATAATTAAAT
1682434 ACTTGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATAATTAAATT
Found at i:1682418 original size:17 final size:16
Alignment explanation
Indices: 1682390--1682433 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1682380 TTATTATATT
*
1682390 AAATATTTAAATTTTA
1 AAATAATTAAATTTTA
*
1682406 AATTAAATTAAA-TTTA
1 AAAT-AATTAAATTTTA
1682422 AAATAATTAAAT
1 AAATAATTAAAT
1682434 ACTTGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAATTAAATTTTA
Found at i:1682860 original size:17 final size:17
Alignment explanation
Indices: 1682809--1682861 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1682799 GTATATTTTT
1682809 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
*
1682824 AAA-TTAT-TAATGTATCA
1 AAATTTATATAA-ATAT-A
1682841 AAATTTATATAAATATA
1 AAATTTATATAAATATA
1682858 AAAT
1 AAAT
1682862 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 6 0.20
17 8 0.27
18 7 0.23
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:1684752 original size:16 final size:16
Alignment explanation
Indices: 1684731--1684763 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1684721 GGGATCTGCA
1684731 ACATTGTCAATGGCGT
1 ACATTGTCAATGGCGT
1684747 ACATTGTCAATGGCGT
1 ACATTGTCAATGGCGT
1684763 A
1 A
1684764 AGTATTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (16 bp):
ACATTGTCAATGGCGT
Found at i:1688412 original size:27 final size:27
Alignment explanation
Indices: 1688382--1688443 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1688372 TTTATGTTTG
1688382 TCAAAAAT-GATGATTACTTTGTATTTA
1 TCAAAAATAG-TGATTACTTTGTATTTA
** * *
1688409 TCAAAAATAGTGATTTTTTTTTATTTG
1 TCAAAAATAGTGATTACTTTGTATTTA
1688436 TCAAAAAT
1 TCAAAAAT
1688444 TATGGCTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (27 bp):
TCAAAAATAGTGATTACTTTGTATTTA
Found at i:1700577 original size:17 final size:18
Alignment explanation
Indices: 1700552--1700589 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1700542 TTTTTTTATT
* *
1700552 TTATTAAATAA-ATTTAA
1 TTATAAAATAATATGTAA
1700569 TTATAAAATAATATGTAA
1 TTATAAAATAATATGTAA
1700587 TTA
1 TTA
1700590 ATATAATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TTATAAAATAATATGTAA
Found at i:1702059 original size:27 final size:29
Alignment explanation
Indices: 1702029--1702090 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1702019 ATATTCATTT
* *
1702029 TATTTTAT-A-TATTTTATCTTTTTATAA
1 TATTTTATAAGTATTTTATATTTATATAA
*
1702056 TATTTTTTAAGTATTTTATATTTATATAA
1 TATTTTATAAGTATTTTATATTTATATAA
1702085 -ATTTTA
1 TATTTTA
1702091 ATACATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.24
28 6 0.21
29 16 0.55
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTATAAGTATTTTATATTTATATAA
Found at i:1703026 original size:21 final size:22
Alignment explanation
Indices: 1702997--1703042 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1702987 AAAAATATTT
*
1702997 ATATTTAAAT-TTAAT-TATAAA
1 ATATATAAATATTAATGTA-AAA
1703018 ATATATAAATATTAATGTAAAA
1 ATATATAAATATTAATGTAAAA
1703040 ATA
1 ATA
1703043 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 11 0.50
23 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATATAAATATTAATGTAAAA
Found at i:1704379 original size:2 final size:2
Alignment explanation
Indices: 1704372--1704421 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1704362 TGAATAAAAG
* *
1704372 AT AT AT AT AT AT GT AT AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1704414 AT AT AT AT
1 AT AT AT AT
1704422 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1710432 original size:19 final size:20
Alignment explanation
Indices: 1710400--1710437 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1710390 TTATATTATT
1710400 TCATATAAAATTAATAATAA
1 TCATATAAAATTAATAATAA
*
1710420 TCAT-TAAATTTAATAATA
1 TCATATAAAATTAATAATA
1710438 TAATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TCATATAAAATTAATAATAA
Found at i:1712250 original size:14 final size:14
Alignment explanation
Indices: 1712233--1712301 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
1712223 TAATTGTAAT
1712233 TAATTATTAAAAAA
1 TAATTATTAAAAAA
*
1712247 TAATT-TGATAAAAA
1 TAATTATTA-AAAAA
***
1712261 TAATATATT-AATTG
1 TAAT-TATTAAAAAA
1712275 TAATTATTAAAAAA
1 TAATTATTAAAAAA
*
1712289 TAATAATTAAAAA
1 TAATTATTAAAAA
1712302 TAAATTTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
13 6 0.14
14 34 0.81
15 1 0.02
16 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAATTATTAAAAAA
Found at i:1712272 original size:46 final size:45
Alignment explanation
Indices: 1712210--1712296 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 45
1712200 TTAAAATGAA
*
1712210 AAAAATATATAATTAATTGTAATTAATTATTAAAA-AATAATTTGAT
1 AAAAATATATAATTAATTGTAATT-ATTA-AAAAATAATAATTTGAT
1712256 AAAAATA-ATATATTAATTGTAATTATTAAAAAATAATAATT
1 AAAAATATATA-ATTAATTGTAATTATTAAAAAATAATAATT
1712297 AAAAATAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
44 4 0.11
45 14 0.37
46 20 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (45 bp):
AAAAATATATAATTAATTGTAATTATTAAAAAATAATAATTTGAT
Found at i:1712827 original size:24 final size:26
Alignment explanation
Indices: 1712794--1712843 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
1712784 TTTTTCATTC
*
1712794 ATTATCATTT-TTAATATAA-TTTTA
1 ATTATCATTTATAAATATAACTTTTA
*
1712818 ATTATTATTTATAAATATAACTTTTA
1 ATTATCATTTATAAATATAACTTTTA
1712844 TAAATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTATCATTTATAAATATAACTTTTA
Found at i:1713054 original size:14 final size:15
Alignment explanation
Indices: 1713032--1713064 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1713022 AAAAAAATAT
1713032 AAATAATAAATATTA
1 AAATAATAAATATTA
*
1713047 AAAT-ATAAATTTTA
1 AAATAATAAATATTA
1713061 AAAT
1 AAAT
1713065 CGAAGGCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAATAAATATTA
Found at i:1713598 original size:32 final size:32
Alignment explanation
Indices: 1713561--1713621 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1713551 CGTAAAATAT
*
1713561 TTTAAATTAATTTGATA-TTTTAAT-TATATCGA
1 TTTAAAAT-ATTT-ATATTTTTAATATATATCGA
1713593 TTTAAAATATTTATATTTTTAATATATAT
1 TTTAAAATATTTATATTTTTAATATATAT
1713622 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 11 0.42
32 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTAAAATATTTATATTTTTAATATATATCGA
Found at i:1713795 original size:24 final size:25
Alignment explanation
Indices: 1713768--1713815 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1713758 ATTAATTTAA
1713768 TTTATATCAA-TATAAATAA-ATTTT
1 TTTATATCAATTA-AAATAATATTTT
*
1713792 TTTATATTAATTAAAATAATATTT
1 TTTATATCAATTAAAATAATATTT
1713816 AAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATATCAATTAAAATAATATTTT
Found at i:1713863 original size:26 final size:25
Alignment explanation
Indices: 1713834--1713889 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1713824 TTTAATATTT
1713834 TAATTTGATAAAAATAATATATAAAA
1 TAATTTGATAAAAATAAT-TATAAAA
** *
1713860 TAATTTTTTAAAAATAATTATTAAA
1 TAATTTGATAAAAATAATTATAAAA
1713885 TAATT
1 TAATT
1713890 CTTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTTGATAAAAATAATTATAAAA
Found at i:1713885 original size:25 final size:26
Alignment explanation
Indices: 1713842--1713904 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
1713832 TTTAATTTGA
1713842 TAAAAATAATATATAAAATAATT-TTT
1 TAAAAATAAT-TATAAAATAATTCTTT
*
1713868 TAAAAATAATTATTAAATAATTCTTT
1 TAAAAATAATTATAAAATAATTCTTT
* *
1713894 CAAAAACAATT
1 TAAAAATAATT
1713905 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 11 0.33
26 22 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAAAATAATTATAAAATAATTCTTT
Found at i:1719852 original size:36 final size:36
Alignment explanation
Indices: 1719729--1719850 Score: 155
Period size: 36 Copynumber: 3.5 Consensus size: 36
1719719 TTTAAAAATT
* *
1719729 AATAAAAT-AA-A-AAAATATTAAGTAAAATTTCAG
1 AATAAAATAAATATAAAATATCAAGTAAAATTTTAG
* *
1719762 AATAAAACAAATATAAAGTATCAAGTAAAATTTTAG
1 AATAAAATAAATATAAAATATCAAGTAAAATTTTAG
*
1719798 AATAAGATAAATATAAAATATCAAGTAAAATTTT-G
1 AATAAAATAAATATAAAATATCAAGTAAAATTTTAG
1719833 AAATAAAATAAAT-TAAAA
1 -AATAAAATAAATATAAAA
1719851 ATTTATTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
33 7 0.09
34 2 0.03
35 7 0.09
36 61 0.79
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (36 bp):
AATAAAATAAATATAAAATATCAAGTAAAATTTTAG
Found at i:1723475 original size:21 final size:21
Alignment explanation
Indices: 1723451--1723490 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1723441 TATTGATTAT
1723451 GAATT-TTTATTTATTATTTTA
1 GAATTATTTATTTA-TATTTTA
*
1723472 GAATTATTTTTTTATATTT
1 GAATTATTTATTTATATTT
1723491 AATATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
GAATTATTTATTTATATTTTA
Found at i:1724019 original size:17 final size:16
Alignment explanation
Indices: 1723988--1724035 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1723978 TCATCGAATC
*
1723988 AAAATTAATACTTTAAT
1 AAAA-TAATATTTTAAT
1724005 AAAATAATTATTTTAAT
1 AAAATAA-TATTTTAAT
* *
1724022 ATAATTATATTTTA
1 AAAATAATATTTTA
1724036 TTATAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATAATATTTTAAT
Found at i:1724034 original size:16 final size:17
Alignment explanation
Indices: 1723999--1724044 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1723989 AAATTAATAC
*
1723999 TTTAATAAAATAATTAT
1 TTTAATATAATAATTAT
*
1724016 TTTAATATAATTA-TAT
1 TTTAATATAATAATTAT
*
1724032 TTTATTATAATAA
1 TTTAATATAATAA
1724045 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATAATAATTAT
Found at i:1725319 original size:2 final size:2
Alignment explanation
Indices: 1725312--1725341 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1725302 ACATACATAC
1725312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1725342 TCAGTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1726033 original size:21 final size:21
Alignment explanation
Indices: 1726007--1726048 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1725997 ATCGGATATA
1726007 TTACTTGTATTTGACTCACAC
1 TTACTTGTATTTGACTCACAC
1726028 TTACTTGTATTTGACTCACAC
1 TTACTTGTATTTGACTCACAC
1726049 GGGAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (21 bp):
TTACTTGTATTTGACTCACAC
Found at i:1728038 original size:2 final size:2
Alignment explanation
Indices: 1728028--1728069 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1728018 TTATATAGAA
* *
1728028 AT AT GT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1728070 TCATGCAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1730584 original size:11 final size:11
Alignment explanation
Indices: 1730570--1730604 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1730560 GATATATTTA
1730570 AAAATTAAAAT
1 AAAATTAAAAT
1730581 AAAATTAAAAT
1 AAAATTAAAAT
*
1730592 AATAAATAAAAT
1 AA-AATTAAAAT
1730604 A
1 A
1730605 TGTAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:1733095 original size:2 final size:2
Alignment explanation
Indices: 1733088--1733131 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1733078 ACCTTAAAAC
*
1733088 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1733130 AT
1 AT
1733132 CCTTTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1733260 original size:7 final size:7
Alignment explanation
Indices: 1733250--1733287 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1733240 GTTTGAATTT
*
1733250 AATTTGA
1 AATTTAA
1733257 AATTTAA
1 AATTTAA
*
1733264 AATTTGA
1 AATTTAA
1733271 AATTTAA
1 AATTTAA
1733278 AATTTAA
1 AATTTAA
1733285 AAT
1 AAT
1733288 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:1733269 original size:14 final size:14
Alignment explanation
Indices: 1733250--1733287 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1733240 GTTTGAATTT
1733250 AATTTGAAATTTAA
1 AATTTGAAATTTAA
1733264 AATTTGAAATTTAA
1 AATTTGAAATTTAA
*
1733278 AATTTAAAAT
1 AATTTGAAAT
1733288 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTTGAAATTTAA
Found at i:1733301 original size:6 final size:6
Alignment explanation
Indices: 1733245--1733330 Score: 54
Period size: 7 Copynumber: 13.8 Consensus size: 6
1733235 CTTAAGTTTG
*
1733245 AATTT- AATTTGA AATTTAA AATTTGA AATTTAA AATTTA AA-ATA TAATTTA
1 AATTTA AATTT-A AATTT-A AATTT-A AATTT-A AATTTA AATTTA -AATTTA
**
1733296 AATTT- AA-TTA AATTTTA TTTTTAA AATTTA AATTT
1 AATTTA AATTTA AA-TTTA AATTT-A AATTTA AATTT
1733331 GATTCAAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.03
5 11 0.17
6 19 0.30
7 32 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:1734369 original size:14 final size:15
Alignment explanation
Indices: 1734350--1734387 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1734340 AATATTAATA
1734350 TTAAATATA-TTTAT
1 TTAAATATATTTTAT
*
1734364 TTAAATTTATTTTAT
1 TTAAATATATTTTAT
*
1734379 TAAAATATA
1 TTAAATATA
1734388 AATATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATATATTTTAT
Found at i:1734384 original size:29 final size:28
Alignment explanation
Indices: 1734348--1734404 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1734338 ATAATATTAA
**
1734348 TATTAAATATATTTATTTAAA-TTTATTT
1 TATTAAATATAAATA-TTAAATTTTATTT
1734376 TATTAAAATATAAATATTAAATTTTATTT
1 TATT-AAATATAAATATTAAATTTTATTT
1734405 AAATTTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTAAATATAAATATTAAATTTTATTT
Found at i:1736639 original size:18 final size:18
Alignment explanation
Indices: 1736616--1736764 Score: 61
Period size: 18 Copynumber: 7.9 Consensus size: 18
1736606 CCTCACTAGA
1736616 TATTATATTTATATATTT
1 TATTATATTTATATATTT
* *
1736634 TATTATATTAAAATTATATT
1 TATTATATTTATA-TAT-TT
* *
1736654 TAATATATATTATAT-TTAA
1 TATTATAT-TTATATATT-T
* *
1736673 TATAAATTTTTATATATTAAT
1 TAT-TATATTTATATATT--T
* * *
1736694 AATTTATATTAAATAAATTT
1 TA-TTATATT-TATATATTT
**
1736714 TAAAATATTTATATA-TT
1 TATTATATTTATATATTT
* *
1736731 TATTTTATTTTTATATTT
1 TATTATATTTATATATTT
*
1736749 TAATTAT-TTTTTATAT
1 T-ATTATATTTATATAT
1736765 AATGTAATAT
Statistics
Matches: 95, Mismatches: 25, Indels: 22
0.67 0.18 0.15
Matches are distributed among these distances:
17 13 0.14
18 28 0.29
19 21 0.22
20 17 0.18
21 9 0.09
22 7 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATTTATATATTT
Found at i:1736665 original size:16 final size:16
Alignment explanation
Indices: 1736615--1736676 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
1736605 TCCTCACTAG
1736615 ATATTATATTT-ATAT
1 ATATTATATTTAATAT
*
1736630 AT-TT-TATTATATTA-
1 ATATTATATT-TAATAT
*
1736644 AAATTATATTTAATAT
1 ATATTATATTTAATAT
1736660 ATATTATATTTAATAT
1 ATATTATATTTAATAT
1736676 A
1 A
1736677 AATTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 10 0.26
16 20 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTATATTTAATAT
Found at i:1736669 original size:50 final size:50
Alignment explanation
Indices: 1736615--1736739 Score: 120
Period size: 48 Copynumber: 2.6 Consensus size: 50
1736605 TCCTCACTAG
*
1736615 ATATTATATTTATATATTTTATTATATTAA-AA-TTATATTTAAT--A-T
1 ATATTATATTTATATATTTTATTATATTAATAATTTATATTAAATAAATT
1736660 ATATTATATTTAATATAAATTTT-TATATATTAATAATTTATATTAAATAAATT
1 ATATTATATTT-ATAT--ATTTTAT-TATATTAATAATTTATATTAAATAAATT
* ** *
1736713 TTAAAATATTTATATA-TTTATTTTATT
1 ATATTATATTTATATATTTTATTATATT
1736740 TTTATATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
45 11 0.17
46 4 0.06
47 1 0.02
48 13 0.20
49 10 0.15
50 12 0.18
52 5 0.08
53 9 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (50 bp):
ATATTATATTTATATATTTTATTATATTAATAATTTATATTAAATAAATT
Found at i:1736680 original size:32 final size:31
Alignment explanation
Indices: 1736617--1736712 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 31
1736607 CTCACTAGAT
*
1736617 ATTATATTT-ATATATTT-TATTATATTA-AA
1 ATTATATTTAATATATTTATATT-TAATATAA
1736646 ATTATATTTAATATATATTATATTTAATATAA
1 ATTATATTTAATATAT-TTATATTTAATATAA
1736678 ATTTTTATATATTAATA-ATTTATA-TTAA-ATAA
1 A---TTATAT-TTAATATATTTATATTTAATATAA
1736710 ATT
1 ATT
1736713 TTAAAATATT
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
29 11 0.19
30 6 0.10
31 6 0.10
32 12 0.21
33 4 0.07
34 5 0.09
35 8 0.14
36 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTATATTTAATATATTTATATTTAATATAA
Found at i:1736691 original size:48 final size:47
Alignment explanation
Indices: 1736615--1736739 Score: 123
Period size: 50 Copynumber: 2.6 Consensus size: 47
1736605 TCCTCACTAG
*
1736615 ATATTATATTTATATATTTTATTATATTAA-AA-TTATATTTAATAT
1 ATATTATATTTATATATTTTATTATATTAATAATTTATATTAAATAT
*
1736660 ATATTATATTTAATATAAATTTT-TATATATTAATAATTTATATTAAATAA
1 ATATTATATTT-ATAT--ATTTTAT-TATATTAATAATTTATATTAAATAT
* *
1736710 ATTTTAAAATATTTATATA-TTTATTTTATT
1 ATATT---ATATTTATATATTTTATTATATT
1736740 TTTATATTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
45 11 0.17
46 4 0.06
47 1 0.02
48 13 0.20
49 10 0.15
50 17 0.26
52 4 0.06
53 6 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
ATATTATATTTATATATTTTATTATATTAATAATTTATATTAAATAT
Found at i:1736722 original size:32 final size:35
Alignment explanation
Indices: 1736653--1736737 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 35
1736643 AAAATTATAT
* *
1736653 TTAATATATATTATATTTAATATAAATTTTTATATA
1 TTAATATAT-TTATATTTAATATAAATTTTAAAATA
1736689 TTAATA-ATTTATA-TTAA-ATAAATTTTAAAATA
1 TTAATATATTTATATTTAATATAAATTTTAAAATA
*
1736721 TTTATATATTTAT-TTTA
1 TTAATATATTTATATTTA
1736738 TTTTTATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 18 0.41
33 13 0.30
34 5 0.11
35 2 0.05
36 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TTAATATATTTATATTTAATATAAATTTTAAAATA
Found at i:1738826 original size:43 final size:43
Alignment explanation
Indices: 1738776--1738861 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
1738766 AATATGAGTC
* *
1738776 TCAAATTTTTATTTAAATTCATTTATA-TTTATAAATAAATAAG
1 TCAAA-TTTTATCTAAATTCATTTATATTTTATAAAAAAATAAG
* * *
1738819 TCAAATTTTGTCTAAGTTCATTTATATTTTTTAAAAAAATAAG
1 TCAAATTTTATCTAAATTCATTTATATTTTATAAAAAAATAAG
1738862 ATATGTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 18 0.49
43 19 0.51
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (43 bp):
TCAAATTTTATCTAAATTCATTTATATTTTATAAAAAAATAAG
Found at i:1740958 original size:30 final size:30
Alignment explanation
Indices: 1740924--1741014 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
1740914 GCTTTTTGAG
*
1740924 AATATAAATTTATATATTATTAATGTATTA
1 AATATAAATTTATATATTATTAATATATTA
* * *
1740954 AATATAAA--T-CA-ATT-TTGATTTATTA
1 AATATAAATTTATATATTATTAATATATTA
*
1740979 AGA-ATAAATTTATATATTATTAATATATCA
1 A-ATATAAATTTATATATTATTAATATATTA
1741009 AATATA
1 AATATA
1741015 TATAAAGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
25 15 0.32
26 4 0.09
27 2 0.04
28 2 0.04
29 4 0.09
30 20 0.43
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (30 bp):
AATATAAATTTATATATTATTAATATATTA
Found at i:1744910 original size:16 final size:17
Alignment explanation
Indices: 1744881--1744914 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1744871 AACAATAAAA
1744881 TATATTTAAATATTTAT
1 TATATTTAAATATTTAT
1744898 TATATTT-AATATTTAT
1 TATATTTAAATATTTAT
1744914 T
1 T
1744915 CGTTAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTAAATATTTAT
Found at i:1746048 original size:27 final size:27
Alignment explanation
Indices: 1745983--1746050 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1745973 TGATTATAAT
* *
1745983 ATTAATTAATGATAAGTGATCGATACA
1 ATTAATTAATTATAAGTGATCAATACA
* *
1746010 ATTAAGTAATTATAAGTGATCAATATA
1 ATTAATTAATTATAAGTGATCAATACA
*
1746037 ATTAATTGATTATA
1 ATTAATTAATTATA
1746051 TTATTTTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (27 bp):
ATTAATTAATTATAAGTGATCAATACA
Found at i:1746315 original size:25 final size:25
Alignment explanation
Indices: 1746287--1746341 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1746277 ATTAATTATG
*
1746287 AAAATTATATTTATAAATAAT-AATT
1 AAAAATATA-TTATAAATAATGAATT
* *
1746312 AAAAATATATTATAAGTGATGAATT
1 AAAAATATATTATAAATAATGAATT
1746337 AAAAA
1 AAAAA
1746342 GTAAGGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
AAAAATATATTATAAATAATGAATT
Found at i:1749937 original size:21 final size:20
Alignment explanation
Indices: 1749911--1749972 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
1749901 ATTTCATAAT
1749911 ATATAAAATATT-ATATATTTA
1 ATAT-AAATATTAATATA-TTA
*
1749932 ATATAAATTTTAATATATTA
1 ATATAAATATTAATATATTA
**
1749952 ATAATTTATATT-ATATATTA
1 AT-ATAAATATTAATATATTA
1749972 A
1 A
1749973 AAAATTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATATTAATATATTA
Found at i:1749967 original size:20 final size:20
Alignment explanation
Indices: 1749944--1750001 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1749934 ATAAATTTTA
1749944 ATATATTAATAATTTATATT
1 ATATATTAATAATTTATATT
* *
1749964 ATATATTAAAAAATTATATT
1 ATATATTAATAATTTATATT
* *
1749984 TTTTATT-AT-ATTTATATT
1 ATATATTAATAATTTATATT
1750002 TTTATGTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 8 0.25
19 1 0.03
20 23 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTAATAATTTATATT
Found at i:1750450 original size:19 final size:19
Alignment explanation
Indices: 1750428--1750484 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1750418 TATATAATAC
*
1750428 TTAATTTAATAAATTTTCA
1 TTAATTTAATAAATTATCA
**
1750447 TTAATTTAATAAGAAAATCA
1 TTAATTTAATAA-ATTATCA
1750467 TTAATTTAATAAATTATC
1 TTAATTTAATAAATTATC
1750485 CAAGGTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAATTTAATAAATTATCA
Found at i:1750709 original size:2 final size:2
Alignment explanation
Indices: 1750702--1750737 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1750692 TCGTTATTTA
*
1750702 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1750738 CTTTCGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1758051 original size:16 final size:15
Alignment explanation
Indices: 1758030--1758066 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1758020 CATTAAATGT
1758030 TTTAAATTTAATATTA
1 TTTAAATTTAAT-TTA
*
1758046 TTTAAATTTAATTTT
1 TTTAAATTTAATTTA
1758061 TTTAAA
1 TTTAAA
1758067 AATAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAATTTAATTTA
Found at i:1758090 original size:23 final size:23
Alignment explanation
Indices: 1758050--1758131 Score: 55
Period size: 23 Copynumber: 3.7 Consensus size: 23
1758040 ATATTATTTA
* * *
1758050 AATTTAATTTTTTTAAAAATAAT
1 AATTTAAATTATTAAAAAATAAT
*
1758073 AATTTAAATTATTAAAAATTTAA-
1 AATTTAAATTATTAAAAA-ATAAT
* *
1758096 AATTTAAGATT-TTGAAATATAAT
1 AATTTAA-ATTATTAAAAAATAAT
*
1758119 --TTTAAGTTATTAA
1 AATTTAAATTATTAA
1758132 TGTCAAATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 2 0.04
21 8 0.17
22 3 0.07
23 27 0.59
24 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTTAAATTATTAAAAAATAAT
Found at i:1758551 original size:12 final size:12
Alignment explanation
Indices: 1758534--1758558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1758524 AATTCTTATT
1758534 ATTAAAAAAAAA
1 ATTAAAAAAAAA
1758546 ATTAAAAAAAAA
1 ATTAAAAAAAAA
1758558 A
1 A
1758559 CTATTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
ATTAAAAAAAAA
Found at i:1759232 original size:6 final size:6
Alignment explanation
Indices: 1759223--1759253 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1759213 AGATGGAAAC
1759223 GGAACA GGAACA GGAACA GGAACA GGAACA G
1 GGAACA GGAACA GGAACA GGAACA GGAACA G
1759254 CTTCTAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.35, T:0.00
Consensus pattern (6 bp):
GGAACA
Found at i:1761378 original size:18 final size:17
Alignment explanation
Indices: 1761320--1761416 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 17
1761310 ATTTTTAACA
1761320 TATTTAAAT-AAATTTT
1 TATTTAAATAAAATTTT
* *
1761336 TATTT--AT-TAATTTA
1 TATTTAAATAAAATTTT
1761350 TATTT---TAAAATTTT
1 TATTTAAATAAAATTTT
1761364 TATATTAAATAAAATATATT
1 TAT-TTAAATAAAAT-T-TT
* *
1761384 TATTTAAGTTAAAA-ATT
1 TATTTAA-ATAAAATTTT
1761401 TATTTAAATATAAATT
1 TATTTAAATA-AAATT
1761417 AAAAGTTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 20 0.32
15 2 0.03
16 7 0.11
17 12 0.19
18 6 0.10
19 5 0.08
20 10 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TATTTAAATAAAATTTT
Found at i:1761425 original size:30 final size:30
Alignment explanation
Indices: 1761389--1761451 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1761379 ATATTTATTT
*
1761389 AAGTTAAAAATTTATTTAAATATAAATTAA
1 AAGTTAAAAATTTATTTAAATAAAAATTAA
* * *
1761419 AAGTTAAAAGTTTATTTGATTAAAAATTAA
1 AAGTTAAAAATTTATTTAAATAAAAATTAA
1761449 AAG
1 AAG
1761452 CTTATTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (30 bp):
AAGTTAAAAATTTATTTAAATAAAAATTAA
Found at i:1761440 original size:23 final size:23
Alignment explanation
Indices: 1761414--1761458 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1761404 TTAAATATAA
* *
1761414 ATTAAAAGTTAAAAGTTTATTTG
1 ATTAAAAATTAAAAGCTTATTTG
1761437 ATTAAAAATTAAAAGCTTATTT
1 ATTAAAAATTAAAAGCTTATTT
1761459 AACTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (23 bp):
ATTAAAAATTAAAAGCTTATTTG
Found at i:1761845 original size:20 final size:20
Alignment explanation
Indices: 1761820--1761863 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1761810 AAAAAAGTAA
1761820 TTTTTACTAATTAAATTAAT
1 TTTTTACTAATTAAATTAAT
* *
1761840 TTTTTACTAATTTATTTAAT
1 TTTTTACTAATTAAATTAAT
1761860 TTTT
1 TTTT
1761864 AAATGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTACTAATTAAATTAAT
Found at i:1766173 original size:25 final size:22
Alignment explanation
Indices: 1766113--1766174 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 22
1766103 CGTTTTATAA
*
1766113 TTAAATTTAAATAAAAATATTAT
1 TTAAATTTATA-AAAAATATTAT
*
1766136 TTTAA-TTATTAAAAAATAATTCAAT
1 TTAAATTTA-TAAAAAAT-ATT--AT
1766161 TTAAATTTATAAAA
1 TTAAATTTATAAAA
1766175 TTTTTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 9 0.29
23 8 0.26
25 11 0.35
26 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATTTATAAAAAATATTAT
Found at i:1769525 original size:26 final size:24
Alignment explanation
Indices: 1769476--1769528 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
1769466 TTAATTAATT
* *
1769476 TATTAAAAATAAAATAAGTCTTAA
1 TATTAAAAATAAAATAAATATTAA
1769500 TATTAAATAATAAAATTAAATATTAA
1 TATTAAA-AATAAAA-TAAATATTAA
1769526 TAT
1 TAT
1769529 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 7 0.28
26 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTAAAAATAAAATAAATATTAA
Found at i:1770528 original size:21 final size:22
Alignment explanation
Indices: 1770475--1770529 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1770465 ATATTTTATT
*
1770475 TAAATTTAAT-TATAAAATATG
1 TAAATTTAATATATAAAATATA
1770496 TAAATATTAATATA-AAAATATA
1 TAAAT-TTAATATATAAAATATA
*
1770518 TATATTTAATAT
1 TAAATTTAATAT
1770530 TTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 16 0.53
23 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAATTTAATATATAAAATATA
Found at i:1770617 original size:12 final size:12
Alignment explanation
Indices: 1770583--1770620 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1770573 AACTGAGTCA
1770583 AAAATA-AATTT
1 AAAATATAATTT
*
1770594 AAATAAATAATTT
1 AAA-ATATAATTT
1770607 AAAATATAATTT
1 AAAATATAATTT
1770619 AA
1 AA
1770621 TTTGATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 12 0.52
13 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATATAATTT
Found at i:1772937 original size:2 final size:2
Alignment explanation
Indices: 1772932--1772961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1772922 TATATATATA
1772932 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1772962 ATATTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1776611 original size:27 final size:27
Alignment explanation
Indices: 1776561--1776668 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 27
1776551 ATAATATAAA
* *
1776561 AAATAATATAA-ATATTATATAATATAT
1 AAAT-ATATAATATATTAAAAAATATAT
* * *
1776588 AAATTTTTAATATTTTAAAAAATATAT
1 AAATATATAATATATTAAAAAATATAT
1776615 AAATATATAATATATTAAATATAAT-TAT
1 AAATATATAATATATTAAA-A-AATATAT
* *
1776643 -AATATA-AATATAATATAAATATATAT
1 AAATATATAATATATTA-AAAAATATAT
1776669 TATTAAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
25 2 0.03
26 16 0.24
27 41 0.62
28 4 0.06
29 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATATATAATATATTAAAAAATATAT
Found at i:1776636 original size:22 final size:22
Alignment explanation
Indices: 1776611--1776686 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 22
1776601 TTTAAAAAAT
1776611 ATATAAATATATAATATATTAA
1 ATATAAATATATAATATATTAA
*
1776633 ATAT-AAT-TATAATATAAATATA
1 ATATAAATATATAATAT-ATTA-A
1776655 ATATAAATATAT-AT-TATTAA
1 ATATAAATATATAATATATTAA
* *
1776675 ATTTAATTATAT
1 ATATAAATATAT
1776687 TTTAATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
20 19 0.41
21 9 0.20
22 10 0.22
23 5 0.11
24 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAAATATATAATATATTAA
Found at i:1776665 original size:42 final size:42
Alignment explanation
Indices: 1776563--1776685 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 42
1776553 AATATAAAAA
* *
1776563 ATAATATAAATATTATATAATATATAA-ATTTTTAATAT--TT
1 ATAATATAAATA-TATATAATATATAATATATTAAATATAATT
1776603 -TAA-A-AAATATATA-AATATATAATATATTAAATATAATT
1 ATAATATAAATATATATAATATATAATATATTAAATATAATT
*
1776641 ATAATATAAATATAATATAA-ATAT-ATATTATTAAATTTAATT
1 ATAATATAAATAT-ATATAATATATAATA-TATTAAATATAATT
1776683 ATA
1 ATA
1776686 TTTTAATTAA
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
35 9 0.13
36 13 0.18
37 5 0.07
38 3 0.04
39 6 0.08
40 1 0.01
41 9 0.13
42 23 0.32
43 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
ATAATATAAATATATATAATATATAATATATTAAATATAATT
Found at i:1776973 original size:10 final size:10
Alignment explanation
Indices: 1776960--1777003 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
1776950 CCACAATTAC
*
1776960 TTATTATTAA
1 TTATTATTTA
1776970 TTATTATTTA
1 TTATTATTTA
*
1776980 -TAATATTTA
1 TTATTATTTA
1776989 TTATTATTTA
1 TTATTATTTA
1776999 TTATT
1 TTATT
1777004 TATGAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATTTA
Found at i:1778662 original size:16 final size:16
Alignment explanation
Indices: 1778641--1778704 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
1778631 TAATATTTAT
1778641 TAAAATTATATAAATA
1 TAAAATTATATAAATA
*
1778657 TAAAA-TATTTTAAATA
1 TAAAATTA-TATAAATA
* *
1778673 TAATTATAATATAAATA
1 TAA-AATTATATAAATA
1778690 TATAAATTAT-TAAAT
1 TA-AAATTATATAAAT
1778705 TTAAGTATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.05
16 20 0.53
17 14 0.37
18 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTATATAAATA
Found at i:1778687 original size:33 final size:33
Alignment explanation
Indices: 1778648--1778713 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1778638 TATTAAAATT
* *
1778648 ATATAAATATA-AAATATTTTAAATATAATTATA
1 ATATAAATATATAAAT-TATTAAATATAAGTATA
*
1778681 ATATAAATATATAAATTATTAAATTTAAGTATA
1 ATATAAATATATAAATTATTAAATATAAGTATA
1778714 CATTTATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (33 bp):
ATATAAATATATAAATTATTAAATATAAGTATA
Found at i:1778697 original size:50 final size:46
Alignment explanation
Indices: 1778554--1778704 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 46
1778544 CTCTGTAATT
* ** *
1778554 ATATATAATTATATAAATAT-AATAGTGATAAA--AATA-ATTA-AA
1 ATATAAAATTATATAAATATAAATA-TTTTAAATTAATATAATATAA
* **
1778596 ATATAAAATTA-A-AAA-ATAAATATTTTAAATTTATATAATATTT
1 ATATAAAATTATATAAATATAAATATTTTAAATTAATATAATATAA
1778639 AT-TAAAATTATATAAATATAAAATATTTTAAATATAATTATAATATAA
1 ATATAAAATTATATAAATAT-AAATATTTTAAAT-TAA-TATAATATAA
1778687 ATATATAAATTAT-TAAAT
1 ATATA-AAATTATATAAAT
1778705 TTAAGTATAC
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
39 7 0.08
40 7 0.08
41 4 0.05
42 21 0.24
43 3 0.03
44 3 0.03
45 2 0.02
46 13 0.15
47 2 0.02
48 10 0.12
49 7 0.08
50 7 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (46 bp):
ATATAAAATTATATAAATATAAATATTTTAAATTAATATAATATAA
Found at i:1779511 original size:16 final size:17
Alignment explanation
Indices: 1779480--1779516 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1779470 TTTATTTGTA
1779480 ATAAAATCAGTTAATTT
1 ATAAAATCAGTTAATTT
*
1779497 ATAAAATTA-TTAATTT
1 ATAAAATCAGTTAATTT
1779513 -TAAA
1 ATAAA
1779517 TATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 7 0.37
17 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
ATAAAATCAGTTAATTT
Found at i:1780071 original size:2 final size:2
Alignment explanation
Indices: 1780066--1780092 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1780056 TGTGTGTTTG
1780066 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1780093 GTATGTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1788634 original size:30 final size:30
Alignment explanation
Indices: 1788574--1788636 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1788564 AATATAATTT
*
1788574 TTATATAATTAAATTTATAATTTCATTAAA
1 TTATATAATTAAATTTATAATTTCAATAAA
* * * *
1788604 TTATATAATTAATTTTTTATTTTTAATAAA
1 TTATATAATTAAATTTATAATTTCAATAAA
1788634 TTA
1 TTA
1788637 AATTATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATATAATTAAATTTATAATTTCAATAAA
Found at i:1794282 original size:23 final size:24
Alignment explanation
Indices: 1794233--1794283 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1794223 TTAACATATT
*
1794233 TTTTTAAAAAATTATTTATTTAAA
1 TTTTTAAAAAATTAATTATTTAAA
*
1794257 TTTTTAAAATA-TAATT-TTTAATA
1 TTTTTAAAAAATTAATTATTTAA-A
1794280 TTTT
1 TTTT
1794284 GTATTGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTTAAAAAATTAATTATTTAAA
Found at i:1794431 original size:24 final size:23
Alignment explanation
Indices: 1794404--1794460 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
1794394 TGTACTTATT
1794404 TATTTAATATTTAAAAATTTTAGA
1 TATTTAATATTTAAAAATTTTA-A
* * *
1794428 TATTAAATATTTATAATTTTTAA
1 TATTTAATATTTAAAAATTTTAA
1794451 -ATTT-ATATTT
1 TATTTAATATTT
1794461 GTATATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 3 0.10
23 1 0.03
24 19 0.66
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTTAATATTTAAAAATTTTAA
Found at i:1798934 original size:115 final size:115
Alignment explanation
Indices: 1798798--1799029 Score: 410
Period size: 115 Copynumber: 2.0 Consensus size: 115
1798788 TATCTCTGGG
* *
1798798 GACTTTCTTAGCATCTTCTTCAAGGGAGCTAAATAATGCTCTCATAAAATAAGTTGGATCCGAAT
1 GACTTTCTCAGCATCTTCTTCAAGGGAGCTAAATAATGCTATCATAAAATAAGTTGGATCCGAAT
*
1798863 ATCTCTTTCAAGCAATATCATGGGTCACCAGGATCATATCTAATTGCAAA
66 ATCTCTTTCAAACAATATCATGGGTCACCAGGATCATATCTAATTGCAAA
* * *
1798913 GACTTTCTCAGCATCTTCTTCAATGGAGCTAAATAATGCTATCATAAAGTAAGTTGGATCTGAAT
1 GACTTTCTCAGCATCTTCTTCAAGGGAGCTAAATAATGCTATCATAAAATAAGTTGGATCCGAAT
1798978 ATCTCTTTCAAACAATATCATGGGTCACCAGGATCATATCTAATTGCAAA
66 ATCTCTTTCAAACAATATCATGGGTCACCAGGATCATATCTAATTGCAAA
1799028 GA
1 GA
1799030 AGTGAGAATC
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (115 bp):
GACTTTCTCAGCATCTTCTTCAAGGGAGCTAAATAATGCTATCATAAAATAAGTTGGATCCGAAT
ATCTCTTTCAAACAATATCATGGGTCACCAGGATCATATCTAATTGCAAA
Found at i:1799054 original size:2 final size:2
Alignment explanation
Indices: 1799047--1799074 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1799037 ATCCAAAACA
1799047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1799075 CAAATCACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1802286 original size:19 final size:21
Alignment explanation
Indices: 1802248--1802288 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1802238 TTATATTTGA
1802248 TATATTAATAATATATAAATT
1 TATATTAATAATATATAAATT
*
1802269 TATA-TAATATTA-ATAAATT
1 TATATTAATAATATATAAATT
1802288 T
1 T
1802289 GATGATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 7 0.37
21 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAATAATATATAAATT
Found at i:1802987 original size:10 final size:10
Alignment explanation
Indices: 1802972--1802998 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1802962 CTTACAAAAG
1802972 ATTTTGTCTA
1 ATTTTGTCTA
1802982 ATTTTGTCTA
1 ATTTTGTCTA
1802992 ATTTTGT
1 ATTTTGT
1802999 ATCGAATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.11, T:0.63
Consensus pattern (10 bp):
ATTTTGTCTA
Found at i:1803607 original size:18 final size:18
Alignment explanation
Indices: 1803585--1803634 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1803575 AAAAATTTTA
1803585 AAATTAAATAAATTAATT
1 AAATTAAATAAATTAATT
*
1803603 GAATTTAAA-AAATTAATT
1 -AAATTAAATAAATTAATT
* *
1803621 AAAATAATTAAATT
1 AAATTAAATAAATT
1803635 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTAAATAAATTAATT
Found at i:1803614 original size:27 final size:29
Alignment explanation
Indices: 1803584--1803649 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1803574 TAAAAATTTT
* *
1803584 AAAATTAAATAAATTAATTGAA-TTTA-A
1 AAAATTAAATAAAATAATTAAATTTTATA
*
1803611 AAAATTAATTAAAATAATTAAATTTTTATA
1 AAAATTAAATAAAATAATTAAA-TTTTATA
1803641 AAAATTAAA
1 AAAATTAAA
1803650 ATTAATCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 19 0.59
29 4 0.12
30 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTAAATAAAATAATTAAATTTTATA
Found at i:1805252 original size:30 final size:30
Alignment explanation
Indices: 1805216--1805290 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
1805206 ATGTTAGATG
1805216 ATTTATTTAAATATAAATTAAAAATTAAGA-
1 ATTTATTTAAATATAAATTAAAAATTAA-AT
* * *
1805246 ATTTATTTGAGTATAAATTAAATATTAAAT
1 ATTTATTTAAATATAAATTAAAAATTAAAT
1805276 ATTTATTTAAATATA
1 ATTTATTTAAATATA
1805291 TTAAAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
ATTTATTTAAATATAAATTAAAAATTAAAT
Found at i:1805678 original size:13 final size:13
Alignment explanation
Indices: 1805643--1805752 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 13
1805633 TAAACTTACA
1805643 ATAATAT-TAAAT
1 ATAATATATAAAT
1805655 ATAATTATATAAAT
1 ATAA-TATATAAAT
*
1805669 TTAATATATAAA-
1 ATAATATATAAAT
1805681 A-AAT-TATTAAGAT
1 ATAATATA-TAA-AT
1805694 ATAATAT-T-AAT
1 ATAATATATAAAT
*
1805705 A-AATATTTTAAA-
1 ATAATA-TATAAAT
*
1805717 AT-TTATAT-AAT
1 ATAATATATAAAT
*
1805728 ATAA-ATAT-GAT
1 ATAATATATAAAT
1805739 ATAAATATATAAAT
1 AT-AATATATAAAT
1805753 TTTTAAATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 30
0.67 0.06 0.27
Matches are distributed among these distances:
10 8 0.11
11 22 0.29
12 12 0.16
13 19 0.25
14 13 0.17
15 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:1805687 original size:25 final size:24
Alignment explanation
Indices: 1805644--1805744 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 24
1805634 AAACTTACAA
1805644 TAATATTAAATATAATTATATAAATT
1 TAATATTAAA-A-AATTATATAAATT
*
1805670 TAATATATAAAAAATTAT-TAAGATA
1 TAATAT-TAAAAAATTATATAA-ATT
*
1805695 TAATATTAATAAATATTTTA-AAATT
1 TAATATTAA-AAA-ATTATATAAATT
* * *
1805720 TATATAATATAAATATGATATAAAT
1 TA-ATATTA-AAAAATTATATAAAT
1805745 ATATAAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
24 6 0.10
25 25 0.42
26 24 0.40
27 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATATTAAAAAATTATATAAATT
Found at i:1807945 original size:2 final size:2
Alignment explanation
Indices: 1807938--1807975 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1807928 GTCCTTCTTG
1807938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1807976 CATAGTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1810149 original size:2 final size:2
Alignment explanation
Indices: 1810142--1810175 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1810132 TAGCAAGTTA
*
1810142 AT AT AT AT AT AT AT AT AT AG AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1810176 ACCTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1810312 original size:19 final size:19
Alignment explanation
Indices: 1810254--1810312 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1810244 TAATACATTA
1810254 ATTTTA-TATAAATAAA--T
1 ATTTTATTA-AAATAAAGTT
* * * *
1810271 ATATTATTCAAATAATGTC
1 ATTTTATTAAAATAAAGTT
1810290 ATTTTATTAAAATAAAGTT
1 ATTTTATTAAAATAAAGTT
1810309 ATTT
1 ATTT
1810313 GCATTCTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 19 0.61
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTATTAAAATAAAGTT
Found at i:1810986 original size:22 final size:21
Alignment explanation
Indices: 1810946--1810986 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1810936 ATATTATATC
1810946 ATTAAATTTTATTATTAATAA
1 ATTAAATTTTATTATTAATAA
1810967 ATTAAATCATTTA-TATTAAT
1 ATTAAAT--TTTATTATTAAT
1810987 TTTGTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAAATTTTATTATTAATAA
Found at i:1811179 original size:13 final size:14
Alignment explanation
Indices: 1811150--1811183 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1811140 ACTTAATTTA
1811150 TTAATAATATAAAT
1 TTAATAATATAAAT
*
1811164 TTAATGATAT-AAT
1 TTAATAATATAAAT
1811177 TTAATAA
1 TTAATAA
1811184 AATTAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TTAATAATATAAAT
Found at i:1813048 original size:2 final size:2
Alignment explanation
Indices: 1813041--1813085 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1813031 ACTTATGCTT
1813041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1813083 TA T
1 TA T
1813086 CTTAGGTCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1813145 original size:2 final size:2
Alignment explanation
Indices: 1813138--1813167 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1813128 GTTCAACAAG
1813138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1813168 TCACAATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1819160 original size:3 final size:3
Alignment explanation
Indices: 1819146--1819179 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1819136 TTAAGGTACT
*
1819146 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
1819180 TAAAGGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1819429 original size:18 final size:17
Alignment explanation
Indices: 1819388--1819446 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 17
1819378 TTTTGATATA
*
1819388 TTTATA-TA-ATTATAT
1 TTTATATTATATTTTAT
1819403 TTTA-ATTATATTTTAT
1 TTTATATTATATTTTAT
1819419 TTTATAGTTATATTTTAT
1 TTTATA-TTATATTTTAT
* *
1819437 CTTATTTTAT
1 TTTATATTAT
1819447 CTCATATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 10 0.27
17 5 0.14
18 15 0.41
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTATATTATATTTTAT
Found at i:1819539 original size:15 final size:15
Alignment explanation
Indices: 1819506--1819554 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
1819496 AAAATTAAAT
1819506 TATTACATATATTATA
1 TATTA-ATATATTATA
1819522 TATTAATATAATTA-A
1 TATTAATAT-ATTATA
1819537 TA-TAA-ATATTATA
1 TATTAATATATTATA
1819550 T-TTAA
1 TATTAA
1819555 AATTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 3 0.10
15 7 0.23
16 9 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAATATATTATA
Found at i:1820237 original size:2 final size:2
Alignment explanation
Indices: 1820230--1820265 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1820220 CCACTTAGCG
1820230 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1820266 GCGCCGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1821913 original size:19 final size:17
Alignment explanation
Indices: 1821893--1821949 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
1821883 TATTACATTA
1821893 AAATATATAATCATAATT
1 AAATATATAATCAT-ATT
*
1821911 AAATATTATAATTATATTT
1 AAATA-TATAATCATA-TT
**
1821930 AAATATA-AAAAATATT
1 AAATATATAATCATATT
1821946 AAAT
1 AAAT
1821950 TATTACTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 8 0.24
19 15 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATAATCATATT
Found at i:1821935 original size:37 final size:37
Alignment explanation
Indices: 1821878--1821961 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
1821868 TTGTTTTTAA
**
1821878 ATTACT-ATTACATTAAAATATATAATCATAATTAAA-T
1 ATTACTAATTACATTAAAATATA-AAAAAT-ATTAAATT
* *
1821915 ATTA-TAATTATATTTAAATATAAAAAATATTAAATT
1 ATTACTAATTACATTAAAATATAAAAAATATTAAATT
1821951 ATTACTAATTA
1 ATTACTAATTA
1821962 AATAAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 6 0.15
36 10 0.25
37 24 0.60
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (37 bp):
ATTACTAATTACATTAAAATATAAAAAATATTAAATT
Found at i:1822873 original size:139 final size:137
Alignment explanation
Indices: 1822728--1823063 Score: 494
Period size: 139 Copynumber: 2.4 Consensus size: 137
1822718 TATAATTGTA
*
1822728 AATTATTATTTAACATAAATAAATAATTTTATTTATAATTTATAATGTAATATAATTATAATTTT
1 AATTATTATTTAACATAAAT-AATAATTTTATTTATAATTTATTATGTAATATAATTATAATTTT
* * * * * * *
1822793 AGTATTTCTAATATAAATATAATTTTAGTTGTTTTTAATTATTATCCACTATAAATATAATTTTA
65 AGTATTTCTAATATAAATACAATTATA-TGGTTGTTAATTACTATCCAATATAAATAAAATTTTA
1822858 TTAATTTTT
129 TTAATTTTT
* *
1822867 AATTATTATTTAACATAAATATATAATTTTATATATAATTTATTATGCAATATAATTATAATTTT
1 AATTATTATTTAACATAAATA-ATAATTTTATTTATAATTTATTATGTAATATAATTATAATTTT
*
1822932 AGTATTTCTAATATAAATACAATTATATGGTTGTTAATTACTATCCAATATAAATAAAATTTTGT
65 AGTATTTCTAATATAAATACAATTATATGGTTGTTAATTACTATCCAATATAAATAAAATTTTAT
1822997 TAATTTTT
130 TAATTTTT
* * * * *
1823005 AATTACTATTCAACATAAAT-ATAATTTTATTTATATTTTATTATTTAATATAAATATAA
1 AATTATTATTTAACATAAATAATAATTTTATTTATAATTTATTATGTAATATAATTATAA
1823064 ATATAAATTT
Statistics
Matches: 178, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
136 34 0.19
138 59 0.33
139 85 0.48
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (137 bp):
AATTATTATTTAACATAAATAATAATTTTATTTATAATTTATTATGTAATATAATTATAATTTTA
GTATTTCTAATATAAATACAATTATATGGTTGTTAATTACTATCCAATATAAATAAAATTTTATT
AATTTTT
Found at i:1822885 original size:38 final size:37
Alignment explanation
Indices: 1822804--1823063 Score: 123
Period size: 38 Copynumber: 7.3 Consensus size: 37
1822794 GTATTTCTAA
* *
1822804 TATAAATATAATTTTAGTTGTTTTTAATTATTATCCAC
1 TATAAATATAATTTTA-TTATTTTTAATTATTATCAAC
*
1822842 TATAAATATAATTTTATTAATTTTTAATTATTATTTAAC
1 TATAAATATAATTTTATT-ATTTTTAATTATTA-TCAAC
*
1822881 -ATAAATATATAATTTTA-TA--TATAATTTATTATGCAA-
1 TAT-AA-ATATAATTTTATTATTTTTAA-TTATTAT-CAAC
* * *
1822917 TATAATTATAATTTTAGTATTTCTAA-TA-TA--AA-
1 TATAAATATAATTTTATTATTTTTAATTATTATCAAC
* ** * *
1822949 TA-CAAT-T-A---TATGGTTGTTAATTACTATCCAA-
1 TATAAATATAATTTTATTATTTTTAATTATTAT-CAAC
* * *
1822980 TATAAATAAAATTTTGTTAATTTTTAATTACTATTCAAC
1 TATAAATATAATTTTATT-ATTTTTAATTATTA-TCAAC
1823019 -ATAAATATAATTTTATTTATATTTT-ATTATT-T-AA-
1 TATAAATATAATTTTA-TTAT-TTTTAATTATTATCAAC
1823053 TATAAATATAA
1 TATAAATATAA
1823064 ATATAAATTT
Statistics
Matches: 172, Mismatches: 23, Indels: 57
0.68 0.09 0.23
Matches are distributed among these distances:
26 7 0.04
27 2 0.01
28 2 0.01
29 1 0.01
30 1 0.01
31 6 0.03
32 7 0.04
34 1 0.01
35 24 0.14
36 12 0.07
37 14 0.08
38 71 0.41
39 13 0.08
40 11 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (37 bp):
TATAAATATAATTTTATTATTTTTAATTATTATCAAC
Found at i:1824376 original size:12 final size:12
Alignment explanation
Indices: 1824359--1824387 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1824349 TTAATTTTAA
1824359 AATTATTAATTT
1 AATTATTAATTT
1824371 AATTATTAATTT
1 AATTATTAATTT
1824383 AATTA
1 AATTA
1824388 GAAATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTATTAATTT
Found at i:1825470 original size:2 final size:2
Alignment explanation
Indices: 1825463--1825507 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
1825453 TCAAAAACAA
1825463 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1825502 -T AT AT A
1 AT AT AT A
1825508 ATTGGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1826178 original size:4 final size:4
Alignment explanation
Indices: 1826169--1826195 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1826159 GAATGATATA
1826169 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1826196 TATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1826368 original size:28 final size:27
Alignment explanation
Indices: 1826315--1826368 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
1826305 TATTATACAC
1826315 TATGAAAAAAAATTTAAATATGATATTT
1 TATGAAAAAAAATTTAAATA-GATATTT
*
1826343 TATGAAAAATAATATTAAGATA-ATAT
1 TATGAAAAAAAAT-TTAA-ATAGATAT
1826369 GAATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 16 0.70
29 4 0.17
30 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (27 bp):
TATGAAAAAAAATTTAAATAGATATTT
Found at i:1826424 original size:35 final size:36
Alignment explanation
Indices: 1826384--1826457 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
1826374 TATATATTTT
*
1826384 TAAAATATATTTTAA-ATTATTAATAA-AT-TAAAATA
1 TAAAATAT-TTTAAATATTATT-ATAATATATAAAATA
1826419 TAAAATATTTTAAATATTATTATAATATAATAAAATA
1 TAAAATATTTTAAATATTATTATAATAT-ATAAAATA
1826456 TA
1 TA
1826458 GGAAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
34 9 0.26
35 16 0.47
37 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
TAAAATATTTTAAATATTATTATAATATATAAAATA
Done.