Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 12 of 29
Found at i:1613618 original size:20 final size:19
Alignment explanation
Indices: 1613570--1613620 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1613560 TATATATAAT
1613570 ATTTATTT-AATATTAAAA
1 ATTTATTTAAATATTAAAA
1613588 ATATT-TTTAAATATGTAAAA
1 AT-TTATTTAAATAT-TAAAA
1613608 ATTTATTTAAATA
1 ATTTATTTAAATA
1613621 AACCAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 15 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTATTTAAATATTAAAA
Found at i:1615685 original size:2 final size:2
Alignment explanation
Indices: 1615678--1615706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1615668 AACGTAAAAT
1615678 TA 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 TA T
1615707 TCTGATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1617486 original size:31 final size:29
Alignment explanation
Indices: 1617451--1617516 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
1617441 TATTTTTTTA
*
1617451 ATTAATTTTGTAAATATAAATTATTAA-ATAT
1 ATTAAATTT-TAAATATAAA-TA-TAATATAT
1617482 ATTAAAATTTTAAATATAAATATAATATAT
1 ATT-AAATTTTAAATATAAATATAATATAT
1617512 ATTAA
1 ATTAA
1617517 GTATTATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 5 0.16
30 9 0.28
31 13 0.41
32 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTAAATTTTAAATATAAATATAATATAT
Found at i:1618065 original size:26 final size:30
Alignment explanation
Indices: 1618003--1618067 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 30
1617993 CTTAGTTTAA
*
1618003 TATAATTATTAATAATATATAAAATGATAT
1 TATATTTATTAATAATATATAAAATGATAT
*
1618033 TAT-TTTATTAA-AA-ATA-AAAATTAT-T
1 TATATTTATTAATAATATATAAAATGATAT
1618058 TATATTTATT
1 TATATTTATT
1618068 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 13 0.41
27 3 0.09
28 2 0.06
29 7 0.22
30 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
TATATTTATTAATAATATATAAAATGATAT
Found at i:1618595 original size:17 final size:19
Alignment explanation
Indices: 1618552--1618595 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1618542 AATATAAATA
*
1618552 TAAATATATCATAAATTAT
1 TAAATATGTCATAAATTAT
*
1618571 TAATTATGTCA-AAATT-T
1 TAAATATGTCATAAATTAT
1618588 TAAATATG
1 TAAATATG
1618596 AATATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
19 9 0.41
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAATATGTCATAAATTAT
Found at i:1621698 original size:5 final size:5
Alignment explanation
Indices: 1621688--1621796 Score: 55
Period size: 5 Copynumber: 21.4 Consensus size: 5
1621678 AATAATTAAA
* * *
1621688 AATAT AATAT AATAT AA-A- AAAAT AACAT AAATAT ATTA- AATAT AACTAT
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AA-TAT
* * * ** *
1621737 ATTAA AATTT ATATAT AATAT TTTA- AATAT AACTAT AATAT AAAACT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AA-TAT AATAT AATA-T
1621784 AATAAT AATAT AA
1 AAT-AT AATAT AA
1621797 ATACATGAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
3 2 0.03
4 7 0.09
5 44 0.56
6 24 0.31
7 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:1621701 original size:20 final size:21
Alignment explanation
Indices: 1621677--1621727 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
1621667 TAATATTAAA
* *
1621677 AAATAATTAAAAATATAATAT
1 AAATAATTAAAAAAATAACAT
1621698 -AAT-A-TAAAAAAATAACAT
1 AAATAATTAAAAAAATAACAT
1621716 AAATATATTAAA
1 AAATA-ATTAAA
1621728 TATAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 3 0.12
21 1 0.04
22 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAATTAAAAAAATAACAT
Found at i:1621822 original size:2 final size:2
Alignment explanation
Indices: 1621815--1621846 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1621805 ATTATCATTC
1621815 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
1621847 TGATCAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1623518 original size:3 final size:3
Alignment explanation
Indices: 1623512--1623544 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1623502 GACCACATGA
1623512 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1623545 TTCGGTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1625146 original size:20 final size:19
Alignment explanation
Indices: 1625106--1625142 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1625096 TAAAACAATT
1625106 TTTAAATTTTATCATTTTA
1 TTTAAATTTTATCATTTTA
1625125 TTTAAATCTTTAT-ATTTT
1 TTTAAAT-TTTATCATTTT
1625143 TATTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAAATTTTATCATTTTA
Found at i:1625222 original size:29 final size:29
Alignment explanation
Indices: 1625180--1625256 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
1625170 TTAATTTGTA
1625180 TTAAATAAA-CTCTTAATTGTTAACATATATC
1 TTAAATAAATCT-TTAATT-TTAACATAT-TC
* *
1625211 -TAAATAAATCTTTACTTTTAATATATTC
1 TTAAATAAATCTTTAATTTTAACATATTC
*
1625239 TTAAATAAATTTTTAATT
1 TTAAATAAATCTTTAATT
1625257 ATTTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 13 0.32
31 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (29 bp):
TTAAATAAATCTTTAATTTTAACATATTC
Found at i:1625607 original size:14 final size:13
Alignment explanation
Indices: 1625586--1625638 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 13
1625576 TAATATGTAT
1625586 ATAATAAAAAATA
1 ATAATAAAAAATA
*
1625599 ATAATTAAAATATA
1 ATAA-TAAAAAATA
1625613 AT-ATAAAAAAT-
1 ATAATAAAAAATA
1625624 AT--TAAAAAATA
1 ATAATAAAAAATA
1625635 ATAA
1 ATAA
1625639 AAATATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.24
11 4 0.12
12 7 0.21
13 5 0.15
14 10 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAATAAAAAATA
Found at i:1625630 original size:22 final size:23
Alignment explanation
Indices: 1625584--1625647 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
1625574 CATAATATGT
1625584 ATATAATAAAAAATAATAATTAAA
1 ATATAAT-AAAAATAATAATTAAA
1625608 ATATAATATAAAA-AAT-ATTAAA
1 ATATAATA-AAAATAATAATTAAA
*
1625630 AAATAATAAAAAT-ATAAT
1 ATATAATAAAAATAATAAT
1625648 ACGAATACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 6 0.17
22 15 0.42
23 4 0.11
24 11 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATAATAAAAATAATAATTAAA
Found at i:1625631 original size:11 final size:10
Alignment explanation
Indices: 1625586--1625648 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 10
1625576 TAATATGTAT
1625586 ATAATAAAAA
1 ATAATAAAAA
1625596 ATAATAATTAAAA
1 ATAAT-A--AAAA
1625609 TATAATATAAAAA
1 -AT-A-ATAAAAA
*
1625622 ATATTAAAAA
1 ATAATAAAAA
1625632 ATAATAAAAA
1 ATAATAAAAA
1625642 TATAATA
1 -ATAATA
1625649 CGAATACATA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
10 20 0.45
11 8 0.18
12 2 0.05
13 8 0.18
14 2 0.05
15 2 0.05
16 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:1627557 original size:16 final size:15
Alignment explanation
Indices: 1627536--1627565 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1627526 GAATGTCTCT
1627536 TTTTTCCTTCCTTTTC
1 TTTTTCCTT-CTTTTC
1627552 TTTTTCCTTCTTTT
1 TTTTTCCTTCTTTT
1627566 GAATCAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCCTTCTTTTC
Found at i:1628669 original size:2 final size:2
Alignment explanation
Indices: 1628662--1628689 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1628652 GCAAATGTTT
1628662 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
1628690 AAGGGAGAGA
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):
TA
Found at i:1630649 original size:7 final size:7
Alignment explanation
Indices: 1630609--1630645 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
1630599 ATGTTCCAAT
1630609 AACTGTC
1 AACTGTC
1630616 AACTGTC
1 AACTGTC
1630623 AACTGTC
1 AACTGTC
1630630 AACTGTC
1 AACTGTC
*
1630637 AAATGTC
1 AACTGTC
1630644 AA
1 AA
1630646 ATGTAGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (7 bp):
AACTGTC
Found at i:1633981 original size:19 final size:19
Alignment explanation
Indices: 1633954--1634015 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 19
1633944 TTAAATCACA
*
1633954 ATAACAAATAATATAAAAT
1 ATAAAAAATAATATAAAAT
1633973 ATAAAAAAT-AT-TAAAAT
1 ATAAAAAATAATATAAAAT
1633990 ATAATCCAAACATAATATAAAA-
1 ATAA---AAA-ATAATATAAAAT
1634012 ATAA
1 ATAA
1634016 TTAAACCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 10 0.28
18 2 0.06
19 8 0.22
20 3 0.08
21 2 0.06
22 6 0.17
23 5 0.14
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAATAATATAAAAT
Found at i:1634231 original size:14 final size:14
Alignment explanation
Indices: 1634190--1634232 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1634180 AAAATGAATT
1634190 TTTAAATATTAAAA
1 TTTAAATATTAAAA
* **
1634204 TTTTAATAAAAAAA
1 TTTAAATATTAAAA
*
1634218 TTTAAATTTTAAAA
1 TTTAAATATTAAAA
1634232 T
1 T
1634233 AAACAATCAG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAATATTAAAA
Found at i:1634567 original size:21 final size:23
Alignment explanation
Indices: 1634515--1634568 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
1634505 AGTTAAATTT
*
1634515 AAATTTTTT-TAATATTTGATTC
1 AAATTTTTTATAATATTTGAATC
**
1634537 AAATAATTTATAA-ATTT-AATC
1 AAATTTTTTATAATATTTGAATC
1634558 AAATTTTTTAT
1 AAATTTTTTAT
1634569 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 12 0.46
22 11 0.42
23 3 0.12
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
AAATTTTTTATAATATTTGAATC
Found at i:1634602 original size:12 final size:12
Alignment explanation
Indices: 1634585--1634614 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1634575 TTAAATCAAA
1634585 AAATTTTAATTC
1 AAATTTTAATTC
*
1634597 AAATTTTAATTT
1 AAATTTTAATTC
1634609 AAATTT
1 AAATTT
1634615 AAGCGTGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATTTTAATTC
Found at i:1634767 original size:17 final size:17
Alignment explanation
Indices: 1634741--1634785 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1634731 TTAATCACCC
*
1634741 AAATATAAAATAATTAA
1 AAATAAAAAATAATTAA
*
1634758 AAATAAAAAATCATTAA
1 AAATAAAAAATAATTAA
1634775 AAATAAAAAAT
1 AAATAAAAAAT
1634786 TCAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAAATAATTAA
Found at i:1634793 original size:18 final size:17
Alignment explanation
Indices: 1634741--1634793 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1634731 TTAATCACCC
*
1634741 AAATATAAAAT-AATTAA
1 AAATAAAAAATCAA-TAA
*
1634758 AAATAAAAAATCATTAA
1 AAATAAAAAATCAATAA
1634775 AAATAAAAAATTCAATAA
1 AAATAAAAAA-TCAATAA
1634793 A
1 A
1634794 TTAAAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 23 0.74
18 8 0.26
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAAAATCAATAA
Found at i:1635178 original size:17 final size:17
Alignment explanation
Indices: 1635158--1635191 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1635148 AATATTTTTT
1635158 AATTTTAATAAAAAATA
1 AATTTTAATAAAAAATA
* *
1635175 AATTTTATTAAATAATA
1 AATTTTAATAAAAAATA
1635192 TTTATTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTTAATAAAAAATA
Found at i:1636507 original size:12 final size:12
Alignment explanation
Indices: 1636477--1636514 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1636467 CAACATAAAT
*
1636477 AAAAAT-ATTTA
1 AAAAATAATATA
*
1636488 AAATATAATATA
1 AAAAATAATATA
1636500 AAAAATAATATA
1 AAAAATAATATA
1636512 AAA
1 AAA
1636515 CGATGCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:1636617 original size:20 final size:20
Alignment explanation
Indices: 1636544--1636617 Score: 52
Period size: 18 Copynumber: 4.0 Consensus size: 20
1636534 TTTCAAAATG
1636544 TATATAAAAAATAAT-T-AA
1 TATATAAAAAATAATATAAA
* *
1636562 TATATAAAAATTTATATAAA
1 TATATAAAAAATAATATAAA
** * *
1636582 T-T-T--TTAATACTTTAAA
1 TATATAAAAAATAATATAAA
1636598 TATATAAAAAATAATATAAA
1 TATATAAAAAATAATATAAA
1636618 CAAGACATGA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 15 0.39
19 2 0.05
20 12 0.32
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAAAAAATAATATAAA
Found at i:1636633 original size:22 final size:22
Alignment explanation
Indices: 1636605--1636655 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1636595 AAATATATAA
1636605 AAAATAA-TATAAACA-AGACATG
1 AAAATAATTA-AAACATA-ACATG
*
1636627 AAAATAATTAAAACATAATATG
1 AAAATAATTAAAACATAACATG
1636649 AAAATAA
1 AAAATAA
1636656 ATATGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATAATTAAAACATAACATG
Found at i:1636672 original size:17 final size:16
Alignment explanation
Indices: 1636652--1636701 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
1636642 TAATATGAAA
1636652 ATAAATATGATATAAAT
1 ATAAATAT-ATATAAAT
* *
1636669 ATAAAAATATAAAAAAT
1 ATAAATATAT-ATAAAT
*
1636686 ATAAATTTATATAAAT
1 ATAAATATATATAAAT
1636702 TTATAATACT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAAATATATATAAAT
Found at i:1637320 original size:16 final size:17
Alignment explanation
Indices: 1637299--1637331 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1637289 TAAATTTAAA
1637299 AATTAAA-ATAAAATTT
1 AATTAAATATAAAATTT
*
1637315 AATTAAATTTAAAATTT
1 AATTAAATATAAAATTT
1637332 CAACTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATATAAAATTT
Found at i:1637652 original size:20 final size:22
Alignment explanation
Indices: 1637614--1637655 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1637604 ATTTAAAATA
1637614 TTATATTTTTAATATAAAAAAG
1 TTATATTTTTAATATAAAAAAG
*
1637636 TTATATTTTAAATA-AAAAAA
1 TTATATTTTTAATATAAAAAA
1637656 TAGATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTATATTTTTAATATAAAAAAG
Found at i:1637814 original size:25 final size:26
Alignment explanation
Indices: 1637786--1637848 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
1637776 TAAGTTAATA
*
1637786 ATTTATATTATAT-AAATTTTAACAT
1 ATTTATATTATATCAAATTATAACAT
* *
1637811 ATTTATA-TAT-TCAAGTTATATCAT
1 ATTTATATTATATCAAATTATAACAT
1637835 ATTTTATATTATAT
1 A-TTTATATTATAT
1637849 TTTTCTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 13 0.42
25 13 0.42
26 3 0.10
27 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTATATTATATCAAATTATAACAT
Found at i:1639143 original size:2 final size:2
Alignment explanation
Indices: 1639136--1639161 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1639126 TCATCTAAAT
1639136 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
1639162 GAAATTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1644413 original size:2 final size:2
Alignment explanation
Indices: 1644408--1644455 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1644398 TCTCTCTCTC
* * *
1644408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA CA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1644450 TA TA TA
1 TA TA TA
1644456 AAGTTTGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1647742 original size:2 final size:2
Alignment explanation
Indices: 1647735--1647767 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1647725 GCATTTTGAA
*
1647735 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1647768 AACGTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1648417 original size:12 final size:12
Alignment explanation
Indices: 1648402--1648436 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1648392 TTTTTAACTA
*
1648402 TGGATCCCACTG
1 TGGATTCCACTG
*
1648414 TGGATTCCACTT
1 TGGATTCCACTG
1648426 TGGATTCCACT
1 TGGATTCCACT
1648437 ACCTTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.34
Consensus pattern (12 bp):
TGGATTCCACTG
Found at i:1650803 original size:19 final size:19
Alignment explanation
Indices: 1650765--1650807 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1650755 TTAAAATAAG
1650765 TAAAAAATTGAATTAAATTT
1 TAAAAAATTGAATTAAA-TT
**
1650785 TAAAAAATT-AATTTTATT
1 TAAAAAATTGAATTAAATT
1650803 TAAAA
1 TAAAA
1650808 TATTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAAATTGAATTAAATT
Found at i:1650860 original size:17 final size:19
Alignment explanation
Indices: 1650838--1650876 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1650828 TTTAAATATT
1650838 TATTTTTTTA-TTATTT-A
1 TATTTTTTTATTTATTTAA
1650855 TA-TTTTTTATTTATTTAA
1 TATTTTTTTATTTATTTAA
1650873 TATT
1 TATT
1650877 AAAGTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 3 0.16
19 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTTATTTATTTAA
Found at i:1650908 original size:21 final size:21
Alignment explanation
Indices: 1650864--1650910 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1650854 ATATTTTTTA
* *
1650864 TTTATTTAATATTAAAGTTAT
1 TTTAATTAATATTAAAATTAT
1650885 TTTAATTAATATTATAAATT-T
1 TTTAATTAATATTA-AAATTAT
1650906 TTTAA
1 TTTAA
1650911 ATTTATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATTAATATTAAAATTAT
Found at i:1653218 original size:22 final size:22
Alignment explanation
Indices: 1653187--1653237 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1653177 TTTTTTTATT
* *
1653187 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATAAAAAAATATA
*
1653208 TAAATATTAATAAAAAAATATT
1 TAAATATTAATAAAAAAATATA
*
1653230 TTAATATT
1 TAAATATT
1653238 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTAATAAAAAAATATA
Found at i:1653224 original size:21 final size:20
Alignment explanation
Indices: 1653187--1653228 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1653177 TTTTTTTATT
*
1653187 TAAATTTAATTATAAAATATA
1 TAAATTTAATTA-AAAAAATA
1653208 TAAATATTAA-TAAAAAAATA
1 TAAAT-TTAATTAAAAAAATA
1653228 T
1 T
1653229 TTTAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAAAATA
Found at i:1657311 original size:2 final size:2
Alignment explanation
Indices: 1657304--1657331 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1657294 CAAAAATTAA
1657304 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
1657332 TTACCGAGTG
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:1658293 original size:21 final size:22
Alignment explanation
Indices: 1658266--1658316 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1658256 CGTCTCTAAA
1658266 ATTTTTAAAAATAATTTATT-AT
1 ATTTTTAAAAATAA-TTATTAAT
*
1658288 -TTTTTAAAGATAATTATTAAT
1 ATTTTTAAAAATAATTATTAAT
1658309 ATTTTTAA
1 ATTTTTAA
1658317 TTCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 14 0.54
22 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTTAAAAATAATTATTAAT
Found at i:1659850 original size:3 final size:3
Alignment explanation
Indices: 1659842--1659876 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1659832 TACAATAACC
1659842 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1659877 TAACTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1660021 original size:23 final size:23
Alignment explanation
Indices: 1659969--1660021 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1659959 TAAATTTTTT
1659969 AACTTTTAATTTATATTTAAATA
1 AACTTTTAATTTATATTTAAATA
* *
1659992 AATTTTTAATTTGTATTTAAATA
1 AACTTTTAATTTATATTTAAATA
*
1660015 AGCTTTT
1 AACTTTT
1660022 GATATGTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
AACTTTTAATTTATATTTAAATA
Found at i:1660091 original size:90 final size:92
Alignment explanation
Indices: 1659992--1660160 Score: 243
Period size: 90 Copynumber: 1.9 Consensus size: 92
1659982 TATTTAAATA
* ** * * *
1659992 AATTTTTAATTTGTATTTAAATAAGCTTTTGATATGTTTGAAATAAAAACTTATTTGATTATAAA
1 AATTTTTAATTCGTATTTAAATAAAATTTTGATATATTTAAAACAAAAACTTATTTGATTATAAA
1660057 TAAA-AA-AATAATAAATAAATTTTTT
66 TAAATAATAATAATAAATAAATTTTTT
* * *
1660082 AATTTTTAATTCGTATTTAAATAAAATTTTTATATATTTAAAACAAAGATTTATTTGATTATAAA
1 AATTTTTAATTCGTATTTAAATAAAATTTTGATATATTTAAAACAAAAACTTATTTGATTATAAA
1660147 TAAATAATAATAAT
66 TAAATAATAATAAT
1660161 TTTTTGAGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 60 0.88
91 2 0.03
92 6 0.09
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (92 bp):
AATTTTTAATTCGTATTTAAATAAAATTTTGATATATTTAAAACAAAAACTTATTTGATTATAAA
TAAATAATAATAATAAATAAATTTTTT
Found at i:1660422 original size:23 final size:25
Alignment explanation
Indices: 1660395--1660442 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1660385 TTACATTTTA
1660395 ATATT-TAACTTAATAA-ATAATAT
1 ATATTATAACTTAATAATATAATAT
* *
1660418 ATATTATTATTTAATAATATAATAT
1 ATATTATAACTTAATAATATAATAT
1660443 TAATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATTATAACTTAATAATATAATAT
Found at i:1660431 original size:24 final size:24
Alignment explanation
Indices: 1660404--1660450 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1660394 AATATTTAAC
*
1660404 TTAATAA-ATAATATATATTATTAT
1 TTAATAATATAATAT-TAATATTAT
1660428 TTAATAATATAATATTAATATTA
1 TTAATAATATAATATTAATATTA
1660451 AAATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATAATATAATATTAATATTAT
Found at i:1660435 original size:20 final size:21
Alignment explanation
Indices: 1660410--1660449 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1660400 TAACTTAATA
*
1660410 AATAATAT-ATATTATTATTT
1 AATAATATAATATTAATATTT
1660430 AATAATATAATATTAATATT
1 AATAATATAATATTAATATT
1660450 AAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATATAATATTAATATTT
Found at i:1660823 original size:3 final size:3
Alignment explanation
Indices: 1660817--1660865 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1660807 AAAAATACAT
1660817 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1660865 A
1 A
1660866 AGCGTAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1661251 original size:19 final size:21
Alignment explanation
Indices: 1661202--1661255 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
1661192 ATTTTTTATT
1661202 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1661223 TAAATATTAATATAAAA-A-A
1 TAAATTTTAATATAAAATATA
*
1661242 TAATTTTTAATATA
1 TAAATTTTAATATA
1661256 TTTTTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 13 0.45
20 1 0.03
21 11 0.38
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1663023 original size:28 final size:27
Alignment explanation
Indices: 1662992--1663072 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
1662982 TAAGACTTAA
* *
1662992 GGTTTAAGTTTCGAGATTTAATATTTAG
1 GGTTTAAGTTT-AAGATTTAAAATTTAG
*
1663020 GGTTTAAGTTTAAGATTTAAAATTTTG
1 GGTTTAAGTTTAAGATTTAAAATTTAG
** * *
1663047 AATTTTGAGTTTAACATTTAAAATTT
1 -GGTTTAAGTTTAAGATTTAAAATTT
1663073 CATATTTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 13 0.29
28 32 0.71
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.48
Consensus pattern (27 bp):
GGTTTAAGTTTAAGATTTAAAATTTAG
Found at i:1665585 original size:21 final size:22
Alignment explanation
Indices: 1665561--1665619 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1665551 ATTTAAATAT
1665561 AAATATAAAATATAATTTTT-A
1 AAATATAAAATATAATTTTTCA
*
1665582 AAATATATAAAT-T-TTTTTTCA
1 AAATATA-AAATATAATTTTTCA
* *
1665603 AAAAATTAAATATAATT
1 AAATATAAAATATAATT
1665620 AAATTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 9 0.30
21 15 0.50
22 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATAAAATATAATTTTTCA
Found at i:1665612 original size:20 final size:20
Alignment explanation
Indices: 1665576--1665613 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1665566 TAAAATATAA
*
1665576 TTTTTAAAATATATAAATTT
1 TTTTTAAAAAATATAAATTT
1665596 TTTTTCAAAAAAT-TAAAT
1 TTTTT-AAAAAATATAAAT
1665614 ATAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTAAAAAATATAAATTT
Found at i:1671621 original size:1 final size:1
Alignment explanation
Indices: 1671615--1671643 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1671605 AGGTTTGAGC
1671615 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1671644 CCCTCAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1672284 original size:26 final size:26
Alignment explanation
Indices: 1672248--1672299 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1672238 TGAATTGATA
1672248 GAAACTAGTTTAATCAGTACAAAACT
1 GAAACTAGTTTAATCAGTACAAAACT
1672274 GAAACTAGTTTAATCAGTACAAAACT
1 GAAACTAGTTTAATCAGTACAAAACT
1672300 ACTAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (26 bp):
GAAACTAGTTTAATCAGTACAAAACT
Found at i:1673126 original size:21 final size:20
Alignment explanation
Indices: 1673086--1673126 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1673076 ATGTTTATTA
*
1673086 ATTATAATTATATTTAAAAT
1 ATTATAATTATATATAAAAT
*
1673106 ATTATATATTTTATATAAAAT
1 ATTATA-ATTATATATAAAAT
1673127 TTAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATAATTATATATAAAAT
Found at i:1673161 original size:16 final size:16
Alignment explanation
Indices: 1673117--1673162 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1673107 TTATATATTT
1673117 TATATAAAATTTAAAA
1 TATATAAAATTTAAAA
*
1673133 TAT-TAATAATTTATAA
1 TATATAA-AATTTAAAA
*
1673149 TATATAAATTTTAA
1 TATATAAAATTTAA
1673163 TATTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATAAAATTTAAAA
Found at i:1673162 original size:32 final size:29
Alignment explanation
Indices: 1673097--1673159 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 29
1673087 TTATAATTAT
1673097 ATTTAAAATATT-ATATATTTTATATAAA
1 ATTTAAAATATTAATATATTTTATATAAA
1673125 ATTTAAAATATTAATA-ATTTATAATATATAA
1 ATTTAAAATATTAATATATTT-T-ATATA-AA
1673156 ATTT
1 ATTT
1673160 TAATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 16 0.52
29 4 0.13
30 5 0.16
31 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTAAAATATTAATATATTTTATATAAA
Found at i:1674185 original size:15 final size:14
Alignment explanation
Indices: 1674161--1674192 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1674151 TAAAATTAAT
1674161 TTAAAATATTAAAA
1 TTAAAATATTAAAA
1674175 TTAAAATTATTAAAA
1 TTAAAA-TATTAAAA
1674190 TTA
1 TTA
1674193 CATAACGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATATTAAAA
Found at i:1674257 original size:20 final size:21
Alignment explanation
Indices: 1674225--1674265 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1674215 CTGTTGAATA
1674225 TTAAAATATAATAAA-AAAAT
1 TTAAAATATAATAAATAAAAT
1674245 TTAATAATA-AATAAATAAAAT
1 TTAA-AATATAATAAATAAAAT
1674266 AAATAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAAATATAATAAATAAAAT
Found at i:1675338 original size:122 final size:120
Alignment explanation
Indices: 1675169--1675399 Score: 426
Period size: 122 Copynumber: 1.9 Consensus size: 120
1675159 CCGTAGAATT
1675169 CATTTCACAGCTTGCCAATGTTTTTTTTCAGGATCATGCATGTACCTACTCACAACTTCAACTGC
1 CATTTCACAGCTTGCCAATGTTTTTTTTCAGGATCATGCATGTACCTACTCACAACTTCAACTGC
*
1675234 TTGTGAAATATCAAACTGCGTACATACCATTACATACATCAAGCCGCGTACATAC
66 TTGTGAAATATCAAACCGCGTACATACCATTACATACATCAAGCCGCGTACATAC
1675289 CATTTCACAGCTTGCCAATGTTTTTTTTTTCAGGATCATGCATGTACCTACTCACAACTTCAACT
1 CATTTCACAGCTTGCCAATG--TTTTTTTTCAGGATCATGCATGTACCTACTCACAACTTCAACT
*
1675354 GCTTGTGAAATATCAAGCCGCGTACATACCATTACATACATCAAGC
64 GCTTGTGAAATATCAAACCGCGTACATACCATTACATACATCAAGC
1675400 TCCCAACTGC
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 20 0.19
122 87 0.81
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (120 bp):
CATTTCACAGCTTGCCAATGTTTTTTTTCAGGATCATGCATGTACCTACTCACAACTTCAACTGC
TTGTGAAATATCAAACCGCGTACATACCATTACATACATCAAGCCGCGTACATAC
Found at i:1682293 original size:78 final size:78
Alignment explanation
Indices: 1682188--1682331 Score: 243
Period size: 78 Copynumber: 1.8 Consensus size: 78
1682178 AGGTGCAATT
* *
1682188 CCCTTAATTAAATCAGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTTGCAATCAGAGCA
1 CCCTCAATTAAATCAGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCA
1682253 ATAAGAAAGCATC
66 ATAAGAAAGCATC
* * *
1682266 CCCTCAATTAAATTAGAGAAAGATCTGCTTCCTGATACTGGGGTCCATGCTTCGCAATCAGAGCA
1 CCCTCAATTAAATCAGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCA
1682331 A
66 A
1682332 CGATGAAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (78 bp):
CCCTCAATTAAATCAGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCA
ATAAGAAAGCATC
Found at i:1682497 original size:261 final size:258
Alignment explanation
Indices: 1682007--1682514 Score: 788
Period size: 261 Copynumber: 2.0 Consensus size: 258
1681997 GAGGAGGAAC
*
1682007 CCCCTCAATTAAATTAGAGAAAGATCTAGTTCCTGATATTAGGGTACATACTTCGCAATCAGAGC
1 CCCCTCAATTAAATTAGAGAAAGATCTAGTTCCTGATACTAGGGTACATACTTCGCAATCAGAGC
* *
1682072 AACGAGAAAATGCTTCCTCTATGATATCCAAGAAAACATCGCTGACTCCATTGCATGGTATCGAA
66 AACGAGAAAATGCTTCCTCTATAATATCCAAGAAAACATCACTGACTCCATTGCATGGTATCGAA
* ** *
1682137 GGGAGCAGTAGTAAAATTTGCTCATCACAATCTGATCAAGGAGGTGCAATTCCCTTAATTAAATC
131 GGGAGCAGTAGTAAAATTTGCTCATCACAATCTGATCAAGGAGGAGCAACCCCCTCAATTAAATC
*
1682202 AGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTTGCAATCAGAGCAATAAGAAAGCAT
196 AGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCAATAAGAAAGCAT
* * *
1682265 CCCCTCAATTAAATTAGAGAAAGATCT-GCTTCCTGATACTGGGGTCCATGCTTCGCAATCAGAG
1 CCCCTCAATTAAATTAGAGAAAGATCTAG-TTCCTGATACTAGGGTACATACTTCGCAATCAGAG
1682329 CAACGATG-AAATGCTTCCTCTATAATATCCAAGAAAACATCACTGACTCCTCCATTG-ACTGGT
65 CAACGA-GAAAATGCTTCCTCTATAATATCCAAGAAAACATCACTGA---CTCCATTGCA-TGGT
* * * *
1682392 CTTGAAGGGAGCAGTAGTACAATTTGCTCATCACAATCTGATCAAGGAGGAGGAACCCCCTCAAT
125 ATCGAAGGGAGCAGTAGTAAAATTTGCTCATCACAATCTGATCAAGGAGGAGCAACCCCCTCAAT
* *
1682457 TAAATCAGAGAAAGATCTTCTTCCTGATACTGGGGTCCATACTTCGCAATCAGAGCAA
190 TAAATCAGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCAA
1682515 CAAGGAAATG
Statistics
Matches: 227, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
257 1 0.00
258 100 0.44
259 1 0.00
260 1 0.00
261 124 0.55
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (258 bp):
CCCCTCAATTAAATTAGAGAAAGATCTAGTTCCTGATACTAGGGTACATACTTCGCAATCAGAGC
AACGAGAAAATGCTTCCTCTATAATATCCAAGAAAACATCACTGACTCCATTGCATGGTATCGAA
GGGAGCAGTAGTAAAATTTGCTCATCACAATCTGATCAAGGAGGAGCAACCCCCTCAATTAAATC
AGAGAAAGATCTGCTTCCTGATACTGCGGTCCATACTTCGCAATCAGAGCAATAAGAAAGCAT
Found at i:1683845 original size:28 final size:28
Alignment explanation
Indices: 1683809--1683867 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1683799 CAAGGTACCT
* *
1683809 TTGCTTAGGGTTCTTAGCATTGAGATGG
1 TTGCATAGGGTCCTTAGCATTGAGATGG
* *
1683837 TTGCATAGGGTCCTTCGCATTGAGATTG
1 TTGCATAGGGTCCTTAGCATTGAGATGG
1683865 TTG
1 TTG
1683868 TTCATTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.39
Consensus pattern (28 bp):
TTGCATAGGGTCCTTAGCATTGAGATGG
Found at i:1684318 original size:2 final size:2
Alignment explanation
Indices: 1684313--1684344 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1684303 TTGTGTGTAC
1684313 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
1684345 GTATGTCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1684828 original size:6 final size:5
Alignment explanation
Indices: 1684803--1684836 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
1684793 TTGTATGATC
1684803 ATTCA ATTCA ATTCA ATTCAA ATTCAA ATTCA AT
1 ATTCA ATTCA ATTCA ATTC-A ATTC-A ATTCA AT
1684837 GCTTGCAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:1685009 original size:23 final size:23
Alignment explanation
Indices: 1684983--1685027 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1684973 GAATTATACG
*
1684983 TCTGATAATTTTTAACTTGTATA
1 TCTGATAATTTTTAACATGTATA
1685006 TCTGATAATTTTTAACATGTAT
1 TCTGATAATTTTTAACATGTAT
1685028 GAAAACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (23 bp):
TCTGATAATTTTTAACATGTATA
Found at i:1685176 original size:2 final size:2
Alignment explanation
Indices: 1685163--1685209 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1685153 TAGATCTAAC
* *
1685163 AT AT AA AT AT AT AT AT AT AA AT AT AT A- 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
1685204 AT AT AT
1 AT AT AT
1685210 GCTATCCCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1685195 original size:19 final size:19
Alignment explanation
Indices: 1685171--1685208 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1685161 ACATATAAAT
1685171 ATATATATATAAATATATA
1 ATATATATATAAATATATA
*
1685190 ATATATATATATATATATA
1 ATATATATATAAATATATA
1685209 TGCTATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATATATAAATATATA
Found at i:1686757 original size:52 final size:53
Alignment explanation
Indices: 1686697--1686826 Score: 253
Period size: 52 Copynumber: 2.5 Consensus size: 53
1686687 CGTGAAACTC
1686697 TCAAGCAGATATCCACATTAGCCAAGCCTAGTCTTAAATC-TTCTAGAAATGT
1 TCAAGCAGATATCCACATTAGCCAAGCCTAGTCTTAAATCTTTCTAGAAATGT
1686749 TCAAGCAGATATCCACATTAGCCAAGCCTAGTCTTAAATCTTTCTAGAAATGT
1 TCAAGCAGATATCCACATTAGCCAAGCCTAGTCTTAAATCTTTCTAGAAATGT
1686802 TCAAGCAGATATCCACATTAGCCAA
1 TCAAGCAGATATCCACATTAGCCAA
1686827 ACATAATAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 40 0.52
53 37 0.48
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (53 bp):
TCAAGCAGATATCCACATTAGCCAAGCCTAGTCTTAAATCTTTCTAGAAATGT
Found at i:1686893 original size:59 final size:59
Alignment explanation
Indices: 1686778--1686929 Score: 162
Period size: 59 Copynumber: 2.5 Consensus size: 59
1686768 AGCCAAGCCT
* * * * * *
1686778 AGTCTTAAATCTTTCTAGAAATGTTCAAGCAGATATCCACATTAGCCAAACATAATAAGC
1 AGTCATAAATCTGTCTTGAAAT-CTCAAGCAGATATCCACATCAGCAAAACATAATAAGC
* * *
1686838 AGTCATAAATCTGTCTTGAAATCTCAGGCAGTTATCCACATCAGCAAAACCTAATAAGC
1 AGTCATAAATCTGTCTTGAAATCTCAAGCAGATATCCACATCAGCAAAACATAATAAGC
* * *
1686897 AATCCTAAATCTGAT-TTGAAACTCTCAAACAGA
1 AGTCATAAATCTG-TCTTGAAA-TCTCAAGCAGA
1686930 CTAAACCACA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 48 0.63
60 28 0.37
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (59 bp):
AGTCATAAATCTGTCTTGAAATCTCAAGCAGATATCCACATCAGCAAAACATAATAAGC
Found at i:1690057 original size:24 final size:26
Alignment explanation
Indices: 1690012--1690059 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
1690002 AACATAAATA
**
1690012 ATTTTATTTGTATTTATTATAATTAT
1 ATTTTATTTGTATTTAAGATAATTAT
1690038 ATTTTATTT-T-TTTAAGATAATT
1 ATTTTATTTGTATTTAAGATAATT
1690060 TTATGTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 1 0.05
26 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
ATTTTATTTGTATTTAAGATAATTAT
Found at i:1693622 original size:193 final size:194
Alignment explanation
Indices: 1693269--1693654 Score: 509
Period size: 194 Copynumber: 2.0 Consensus size: 194
1693259 TAATTAAATC
*
1693269 TTAAATTTTAGGACAAATCTCCGAAAGCTAAGCCTATCCACGTGTCAACTATTTTTTTTTTCATT
1 TTAAATTTTAGGACAAATCTCCGAAAGCTAAGCCCATCCACGTGTCAACTATTTTTTTTTTCATT
* * * *
1693334 TTTTCTTTGATTGCCGTGTAGTTATTTCTATTGCTTTTTCTCCATTTCTTTGTACCTAGCTTATT
66 TTTCCTTTGATTGCCGTGTAGTTATTTCTATTGCTTTTCCTCCAATTCTTTGTACCTAGCCTATT
*
1693399 TGACTAGGTTAAAAAGCTAATAAGTTTAGAAAAGA-TTTAC-GAAGATATTAAAAGATTTTATGT
131 TGACTAAGTTAAAAAGCTAATAAGTTTAGAAAAGATTTTACAGAA-ATATTAAAAGATTTTATGT
* * * * *
1693462 TTAAATTTTA-GACAAATC-CTTGAAAGTTGAGCCCATCCATGTGTCAGCTATTATTTTTTTTTC
1 TTAAATTTTAGGACAAATCTC-CGAAAGCTAAGCCCATCCACGTGTCAACTA-T-TTTTTTTTTC
*
1693525 ATTTTTCCTTTGGTTGCCGTGTA-TTCATTTCTATTGCTTTTCCT-CAATTCTTTGTA-CTCAGC
63 ATTTTTCCTTTGATTGCCGTGTAGTT-ATTTCTATTGCTTTTCCTCCAATTCTTTGTACCT-AGC
** * *
1693587 CTATTTGTTTAAGTTAAAAAGTTGATGAA-TTTAGAAAAGATTTTACAGAAATATTAAAAGATTT
126 CTATTTGACTAAGTTAAAAAGCTAAT-AAGTTTAGAAAAGATTTTACAGAAATATTAAAAGATTT
1693651 TATG
190 TATG
1693655 CATTATTTAA
Statistics
Matches: 169, Mismatches: 16, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
191 1 0.01
192 34 0.20
193 58 0.34
194 73 0.43
195 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (194 bp):
TTAAATTTTAGGACAAATCTCCGAAAGCTAAGCCCATCCACGTGTCAACTATTTTTTTTTTCATT
TTTCCTTTGATTGCCGTGTAGTTATTTCTATTGCTTTTCCTCCAATTCTTTGTACCTAGCCTATT
TGACTAAGTTAAAAAGCTAATAAGTTTAGAAAAGATTTTACAGAAATATTAAAAGATTTTATGT
Found at i:1708404 original size:16 final size:15
Alignment explanation
Indices: 1708385--1708459 Score: 66
Period size: 16 Copynumber: 4.9 Consensus size: 15
1708375 ATTTATACTA
1708385 TTTAATTAAATATATT
1 TTTAATTAAATAT-TT
1708401 TTT-ATTAAATATTT
1 TTTAATTAAATATTT
**
1708415 ACTATATTAAATATTT
1 TTTA-ATTAAATATTT
*
1708431 TTTAATATTAAA-ATTA
1 TTT-A-ATTAAATATTT
1708447 TTT-ATTAAATATT
1 TTTAATTAAATATT
1708460 AATATTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
13 6 0.12
14 6 0.12
15 9 0.18
16 21 0.42
17 8 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATTAAATATTT
Found at i:1708453 original size:30 final size:30
Alignment explanation
Indices: 1708383--1708459 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
1708373 AAATTTATAC
*
1708383 TATTTAATTAAATATATTTTTATTAAATATT
1 TATTT-ATTAAATATTTTTTTATTAAATATT
*
1708414 TACTATATTAAATATTTTTTAATATTAAA-A-T
1 TA-TTTATTAAATATTTTTT--TATTAAATATT
1708445 TATTTATTAAATATT
1 TATTTATTAAATATT
1708460 AATATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 12 0.30
31 18 0.45
32 3 0.08
33 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTATTAAATATTTTTTTATTAAATATT
Found at i:1708459 original size:20 final size:18
Alignment explanation
Indices: 1708418--1708470 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
1708408 AATATTTACT
*
1708418 ATATT-AAATATTTTTTA
1 ATATTAAAATATTTTTAA
1708435 ATATTAAAATTATTTATTAA
1 ATATTAAAA-TATTT-TTAA
1708455 ATATT--AATATTTTTAA
1 ATATTAAAATATTTTTAA
1708471 TTATATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
18 5 0.16
19 5 0.16
20 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTAAAATATTTTTAA
Found at i:1708473 original size:20 final size:20
Alignment explanation
Indices: 1708418--1708461 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1708408 AATATTTACT
*
1708418 ATATT-AAA-TATTT-TTTA
1 ATATTAAAATTATTTATTAA
1708435 ATATTAAAATTATTTATTAA
1 ATATTAAAATTATTTATTAA
1708455 ATATTAA
1 ATATTAA
1708462 TATTTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 5 0.22
20 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTAAAATTATTTATTAA
Found at i:1717952 original size:84 final size:84
Alignment explanation
Indices: 1717808--1717964 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
1717798 CCATCGAAGT
* * * ** * *
1717808 TTTTATACTCCCTAAACAAGGCTAGAAGGGTGACACCTCTTAAGTCAGATTTGTTGTTGTTTACA
1 TTTTATAATCACTAAACAAGGCTAGAAAGGTGACACCTCTTAAGAAAAATTTGTTATTGTTTACA
1717873 AGATCATTGTGGATGAAAA
66 AGATCATTGTGGATGAAAA
*
1717892 TTTTATAATCACTGAACAAGGCTAGAAAGGTGACACCTCTTAAGAAAAATTTGTTATTGTTTACA
1 TTTTATAATCACTAAACAAGGCTAGAAAGGTGACACCTCTTAAGAAAAATTTGTTATTGTTTACA
*
1717957 AGGTCATT
66 AGATCATT
1717965 CTGGTGATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (84 bp):
TTTTATAATCACTAAACAAGGCTAGAAAGGTGACACCTCTTAAGAAAAATTTGTTATTGTTTACA
AGATCATTGTGGATGAAAA
Found at i:1719707 original size:3 final size:3
Alignment explanation
Indices: 1719699--1719743 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1719689 ATTTGTAAAA
1719699 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1719744 GGCACCTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1730895 original size:2 final size:2
Alignment explanation
Indices: 1730888--1730920 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1730878 CACAATGGCA
1730888 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1730921 AATGAAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1731805 original size:23 final size:23
Alignment explanation
Indices: 1731771--1731815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1731761 ACATATGAAC
1731771 AATATTAAATTTATTAATATAAA
1 AATATTAAATTTATTAATATAAA
* *
1731794 AATA-TAATATTTTTTATTATAA
1 AATATTAA-ATTTATTAATATAA
1731816 TATAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTAAATTTATTAATATAAA
Found at i:1732729 original size:21 final size:22
Alignment explanation
Indices: 1732703--1732753 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1732693 ATAAATATTT
1732703 ATAATTTAAT-TTAAATAAAAA
1 ATAATTTAATATTAAATAAAAA
* * **
1732724 ATAATTTTATATTATATAAATG
1 ATAATTTAATATTAAATAAAAA
1732746 ATAATTTA
1 ATAATTTA
1732754 GATGAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATTTAATATTAAATAAAAA
Found at i:1733331 original size:22 final size:22
Alignment explanation
Indices: 1733306--1733384 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 22
1733296 AAAAATATTT
1733306 ATATATTTAAATTTAAATAAAA
1 ATATATTTAAATTTAAATAAAA
* * *
1733328 ATAT-TTTTATTATTAAATAATA
1 ATATATTTAAAT-TTAAATAAAA
* * *
1733350 ATTTAAATT-AATTTTAATAAAAA
1 ATAT-ATTTAAATTTAAAT-AAAA
1733373 ATTATATTTAAA
1 A-TATATTTAAA
1733385 ATCTAAACCA
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
21 5 0.12
22 21 0.51
23 9 0.22
24 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATTTAAATTTAAATAAAA
Found at i:1733853 original size:18 final size:20
Alignment explanation
Indices: 1733832--1733877 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
1733822 CAAATTAGAC
1733832 AAAAATAG-A-AAATAAATA
1 AAAAATAGTATAAATAAATA
* *
1733850 AAAAAAAGTATTAAATTAATA
1 AAAAATAGTA-TAAATAAATA
1733871 AAAAATA
1 AAAAATA
1733878 TTTTTTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
21 14 0.64
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAATAGTATAAATAAATA
Found at i:1734694 original size:17 final size:18
Alignment explanation
Indices: 1734665--1734698 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1734655 TTTTATTATC
1734665 AATAATATAATTTTTTAA
1 AATAATATAATTTTTTAA
1734683 AATAAT-TAATTTTTTA
1 AATAATATAATTTTTTA
1734699 TATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAATATAATTTTTTAA
Found at i:1734705 original size:28 final size:30
Alignment explanation
Indices: 1734669--1734724 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1734659 ATTATCAATA
*
1734669 ATATAATTTTTTAAAAT-AATTAATTTTTT
1 ATATAATTTTATAAAATAAATTAATTTTTT
1734698 ATAT-ATTTTATAAAATAAATTAATTTT
1 ATATAATTTTATAAAATAAATTAATTTT
1734725 AAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
ATATAATTTTATAAAATAAATTAATTTTTT
Found at i:1734725 original size:27 final size:28
Alignment explanation
Indices: 1734669--1734724 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1734659 ATTATCAATA
*
1734669 ATATAATTTTTTAAAATAATTAATTTTT
1 ATATAATTTTATAAAATAATTAATTTTT
1734697 -TATATATTTTATAAAATAAATTAATTTT
1 ATATA-ATTTTATAAAAT-AATTAATTTT
1734725 AAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATAATTTTATAAAATAATTAATTTTT
Found at i:1735286 original size:18 final size:17
Alignment explanation
Indices: 1735251--1735312 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 17
1735241 GATGCAATAA
1735251 TTATAT-AATAT-AAA-
1 TTATATAAATATAAAAT
1735265 TTAT-TAATATATTAAAAT
1 TTATATAA-ATA-TAAAAT
1735283 TTATATAAATATAAAAT
1 TTATATAAATATAAAAT
1735300 ATT-T-TAAATATAA
1 -TTATATAAATATAA
1735313 TTACGATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 3 0.07
16 10 0.24
17 10 0.24
18 9 0.22
19 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATATAAATATAAAAT
Found at i:1735381 original size:132 final size:133
Alignment explanation
Indices: 1735239--1735497 Score: 448
Period size: 132 Copynumber: 1.9 Consensus size: 133
1735229 AATCTATAAA
1735239 TAGATGCAATAATTATATAATATAAATTATTAATATATTAAAATTTATATAAATATAAAATATTT
1 TAGATGCAATAATTATATAATATAAATTATTAATATATTAAAATTTATATAAATATAAAATATTT
* *
1735304 TAAATATAATTACGATAAAATAAATATATAAATATATATATACA-CATCAATTGTTCAATCTATC
66 TAAATATAATTACAATAAAATAAATATATAAATATATATATACACCATCAATTGTTAAATCTATC
1735368 TTT
131 TTT
* *
1735371 TAGATTCAATAATTATATAATATAAGTTATTAATATATTAAAATTTATATAAATATAAAATATTT
1 TAGATGCAATAATTATATAATATAAATTATTAATATATTAAAATTTATATAAATATAAAATATTT
* *
1735436 TAAATATAATTATAATAAAATAAATATATATATATATATATACACGCATCAATTGTTAAATC
66 TAAATATAATTACAATAAAATAAATATATAAATATATATATACAC-CATCAATTGTTAAATC
1735498 AATATATAAA
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
132 104 0.87
134 15 0.13
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (133 bp):
TAGATGCAATAATTATATAATATAAATTATTAATATATTAAAATTTATATAAATATAAAATATTT
TAAATATAATTACAATAAAATAAATATATAAATATATATATACACCATCAATTGTTAAATCTATC
TTT
Found at i:1735463 original size:14 final size:15
Alignment explanation
Indices: 1735419--1735477 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 15
1735409 TAAAATTTAT
*
1735419 ATAAATATAAAATATT
1 ATAAATAT-AAATATA
* *
1735435 TTAAATATAATTATA
1 ATAAATATAAATATA
1735450 ATAAA-ATAAATAT-
1 ATAAATATAAATATA
* *
1735463 ATATATATATATATA
1 ATAAATATAAATATA
1735478 CACGCATCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 4 0.12
14 14 0.41
15 9 0.26
16 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAATATAAATATA
Found at i:1735502 original size:40 final size:40
Alignment explanation
Indices: 1735453--1735532 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1735443 AATTATAATA
* *
1735453 AAATAAATATATATATATATATATACACGCATCAATTGTT
1 AAATAAATATATAAATATATATATACACACATCAATTGTT
* *
1735493 AAATCAATATATAAATATATATATATACACATCAATTGTT
1 AAATAAATATATAAATATATATATACACACATCAATTGTT
1735533 CGATCTATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.38
Consensus pattern (40 bp):
AAATAAATATATAAATATATATATACACACATCAATTGTT
Found at i:1737742 original size:2 final size:2
Alignment explanation
Indices: 1737731--1737765 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1737721 TTATTTTGCT
1737731 TA TA -A 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
1737766 AAAGTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1738760 original size:2 final size:2
Alignment explanation
Indices: 1738753--1738791 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1738743 ATTTGATTAT
* * *
1738753 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1738792 TGTTTTACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1738955 original size:2 final size:2
Alignment explanation
Indices: 1738948--1738988 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1738938 GAAAAAGACA
1738948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
1738989 TCTGGTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1742171 original size:52 final size:49
Alignment explanation
Indices: 1742115--1742224 Score: 116
Period size: 50 Copynumber: 2.2 Consensus size: 49
1742105 TATATATTAT
* *
1742115 TATTTTTTAATTAATAATTAATAATATTA-ATTAATAT-AAATATTTTTAATAA
1 TATTTTTTAATT--TAATTAA-AAT-TTATATAAATATAAAATATTTTAAAT-A
* *
1742167 TATTTTTAAATTTTATTAAAATTTATATAAATATAAAATATTTTAAATA
1 TATTTTTTAATTTAATTAAAATTTATATAAATATAAAATATTTTAAATA
1742216 TAATTTTTT
1 T-ATTTTTT
1742225 TAAAAATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
48 3 0.06
49 12 0.24
50 24 0.48
52 11 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (49 bp):
TATTTTTTAATTTAATTAAAATTTATATAAATATAAAATATTTTAAATA
Found at i:1748240 original size:25 final size:24
Alignment explanation
Indices: 1748167--1748235 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
1748157 ATATAATTTT
*
1748167 TTAATATTTAAATA-TATATTAAATA
1 TTAA-ATTTAAATATTAAATTAAA-A
*
1748192 ATAAATTTAAATCATTAAATTAAAA
1 TTAAATTTAAAT-ATTAAATTAAAA
1748217 TTAAATTTAAAT-TTAAATT
1 TTAAATTTAAATATTAAATT
1748236 TTAAATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.18
24 8 0.21
25 16 0.41
26 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAATTTAAATATTAAATTAAAA
Found at i:1748244 original size:7 final size:6
Alignment explanation
Indices: 1748166--1748243 Score: 61
Period size: 6 Copynumber: 12.5 Consensus size: 6
1748156 AATATAATTT
* * *
1748166 TTTAATA TTTAAA TATATA -TTAAA TAATAAA TTTAAA TCATTAAA -TTAAA
1 TTTAA-A TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA T--TTAAA TTTAAA
*
1748216 ATTAAA TTTAAA TTTAAA TTTTAAA TTT
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTT
1748244 TTTGAAACAG
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.14
6 29 0.50
7 16 0.28
8 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:1748881 original size:13 final size:13
Alignment explanation
Indices: 1748857--1748890 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1748847 TAAACTAAAA
*
1748857 TATAATAACAAAT
1 TATAATATCAAAT
*
1748870 TTTAATATCAAAT
1 TATAATATCAAAT
1748883 TATAATAT
1 TATAATAT
1748891 AATGATGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
TATAATATCAAAT
Found at i:1753189 original size:11 final size:12
Alignment explanation
Indices: 1753165--1753192 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1753155 ATTAAAAATA
1753165 TTTAAAATTTTT
1 TTTAAAATTTTT
1753177 TTTAAAATTTTT
1 TTTAAAATTTTT
1753189 TTTA
1 TTTA
1753193 CTAATCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAAATTTTT
Found at i:1754216 original size:15 final size:15
Alignment explanation
Indices: 1754189--1754222 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1754179 AATTAAAAGA
1754189 TTAATATATATATAT
1 TTAATATATATATAT
1754204 TTAAT-TATAATATAT
1 TTAATATAT-ATATAT
1754219 TTAA
1 TTAA
1754223 AATAATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATATATATAT
Found at i:1757970 original size:16 final size:17
Alignment explanation
Indices: 1757949--1757986 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1757939 ATACGAATTT
*
1757949 ATTAATT-TTTAAAAAA
1 ATTAATTATATAAAAAA
*
1757965 ATTAATTATATAAATAA
1 ATTAATTATATAAAAAA
1757982 ATTAA
1 ATTAA
1757987 ATTAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATTATATAAAAAA
Found at i:1758020 original size:2 final size:2
Alignment explanation
Indices: 1758009--1758042 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1757999 TTTTATATGC
*
1758009 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1758043 AGCTGCAACC
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1758295 original size:3 final size:3
Alignment explanation
Indices: 1758287--1758320 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1758277 GAAAGCATAC
1758287 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1758321 TCATTAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1758458 original size:17 final size:17
Alignment explanation
Indices: 1758430--1758551 Score: 58
Period size: 18 Copynumber: 6.9 Consensus size: 17
1758420 CATATATCTA
1758430 TATTATATTTATATATTT
1 TATTATA-TTATATATTT
1758448 TATTATATTATAATTATTT
1 TATTATATTAT-A-TATTT
1758467 T-TTAT-TTATAATAAATTT
1 TATTATATTAT-AT--ATTT
* *
1758485 AAATATATTA-ATAATTT
1 TATTATATTATAT-ATTT
*
1758502 ATATTATA-TATAAAATATT
1 -TATTATATTAT-ATAT-TT
1758521 TATATATATTATAT-TTT
1 TAT-TATATTATATATTT
* *
1758538 AATTTTATT-TATAT
1 TATTATATTATATAT
1758552 CGTACTTATG
Statistics
Matches: 83, Mismatches: 8, Indels: 28
0.70 0.07 0.24
Matches are distributed among these distances:
15 3 0.04
16 7 0.08
17 21 0.25
18 29 0.35
19 17 0.20
20 6 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATATTATATATTT
Found at i:1758459 original size:15 final size:15
Alignment explanation
Indices: 1758428--1758538 Score: 55
Period size: 16 Copynumber: 6.9 Consensus size: 15
1758418 AGCATATATC
1758428 TATATTATA-TTTA-
1 TATATTATATTTTAT
* *
1758441 TATATTTTATTATAT
1 TATATTATATTTTAT
*
1758456 TATAATTATTTTTTATT
1 TAT-ATTATATTTTA-T
* * * *
1758473 TATAATAAATTTAAA
1 TATATTATATTTTAT
1758488 TATATTAATAATTTATAT
1 TATATT-AT-ATTT-TAT
*
1758506 TATATATAAAATATTTAT
1 TATAT-T-ATAT-TTTAT
1758524 ATATATTATATTTTA
1 -TATATTATATTTTA
1758539 ATTTTATTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
13 8 0.11
14 3 0.04
15 8 0.11
16 20 0.28
17 11 0.15
18 12 0.17
19 10 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTATATTTTAT
Found at i:1762002 original size:23 final size:24
Alignment explanation
Indices: 1761976--1762022 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1761966 ATTTATGAAT
*
1761976 AAGCTAATTT-GTAAATTGATTAA
1 AAGCTAATTTAATAAATTGATTAA
* *
1761999 AAGCTCATTTAATAAATTGTTTAA
1 AAGCTAATTTAATAAATTGATTAA
1762023 TGTTCTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (24 bp):
AAGCTAATTTAATAAATTGATTAA
Found at i:1762276 original size:29 final size:29
Alignment explanation
Indices: 1762244--1762300 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1762234 ACAAGTTCAT
1762244 TTAA-TTTAAAAAAATAAACACAAACACAC
1 TTAATTTTAAAAAAATAAA-ACAAACACAC
*
1762273 TTAATTTTAAACAAATAAAACAAACACA
1 TTAATTTTAAAAAAATAAAACAAACACA
1762301 AATTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (29 bp):
TTAATTTTAAAAAAATAAAACAAACACAC
Found at i:1767477 original size:27 final size:27
Alignment explanation
Indices: 1767445--1767513 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1767435 AGCAATATTA
1767445 ATCATTTGATCTT-ATTCTGAATTGTTC
1 ATCATTTGAT-TTCATTCTGAATTGTTC
*
1767472 ATCATTTGATTTCATTTTGAATTGTTC
1 ATCATTTGATTTCATTCTGAATTGTTC
1767499 ATCATTTGATTTCAT
1 ATCATTTGATTTCAT
1767514 ATCATTAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (27 bp):
ATCATTTGATTTCATTCTGAATTGTTC
Found at i:1769929 original size:34 final size:33
Alignment explanation
Indices: 1769881--1770099 Score: 267
Period size: 34 Copynumber: 6.5 Consensus size: 33
1769871 TGGTAAAAAC
* *
1769881 CACCATTTAATCAACAATGGCAATCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* *
1769914 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1769948 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
** *
1769982 TTCTCATTTAATCAACAATGGTAAGCTACAAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
1770016 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1770050 CATCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1770084 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1770100 GTTAGCAGTA
Statistics
Matches: 159, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
33 17 0.11
34 141 0.89
35 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:1769997 original size:68 final size:68
Alignment explanation
Indices: 1769883--1770099 Score: 294
Period size: 68 Copynumber: 3.2 Consensus size: 68
1769873 GTAAAAACCA
* * * *
1769883 CCATTTAATCAACAATGGCAATCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
1769948 CAC
66 CAC
* * * *
1769951 CCATTTAATCAATAATGGTAAGCTACCAAAT-TTCTCATTTAATCAACAATGGTAAGCTACAAAA
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTC-CATTTAATCAACAATGGTAAGCTACCAAA
*
1770015 TCTC
65 TCAC
* * * *
1770019 CCATTTAGTCAACAATGGCAAACCACCAAATCATCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
1770084 CA-
66 CAC
1770086 CCATTTAATCAACA
1 CCATTTAATCAACA
1770100 GTTAGCAGTA
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 112 0.87
69 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:1770026 original size:102 final size:101
Alignment explanation
Indices: 1769881--1770099 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
1769871 TGGTAAAAAC
* * * *
1769881 CACCATTTAATCAACAATGGCAATCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAGCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1769946 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
1769982 TTCTCATTTAATCAACAATGGTAAGCTACAAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAAGCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
1770047 AATCATCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1770084 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1770100 GTTAGCAGTA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 14 0.13
102 90 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAAGCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1770912 original size:77 final size:76
Alignment explanation
Indices: 1770787--1770940 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 76
1770777 ATATATACAC
1770787 ACACGTAATGTTACTTAATTCTAAAAAAAAAAAAAAAACCTAAAAATAGAGTACATGAGAAGACA
1 ACACGTAATGTTACTTAATTCTAAAAAAAAAAAAAAAACCTAAAAATAGAGTACATGAGAAGACA
1770852 CCCTAGCAATT
66 CCCTAGCAATT
*
1770863 ACACGTAATGTTACCTTAATTCTAAAAAAAAAAAGAAAACCTAAAAATAGAGTACATGAGAAGAC
1 ACACGTAATGTTA-CTTAATTCTAAAAAAAAAAAAAAAACCTAAAAATAGAGTACATGAGAAGAC
1770928 ACCCTAGCAATT
65 ACCCTAGCAATT
1770940 A
1 A
1770941 AAATTTAATT
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 13 0.17
77 63 0.83
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (76 bp):
ACACGTAATGTTACTTAATTCTAAAAAAAAAAAAAAAACCTAAAAATAGAGTACATGAGAAGACA
CCCTAGCAATT
Found at i:1771005 original size:14 final size:14
Alignment explanation
Indices: 1770986--1771012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1770976 ACGTAAATAG
1770986 ATAAAAAATTATGA
1 ATAAAAAATTATGA
1771000 ATAAAAAATTATG
1 ATAAAAAATTATG
1771013 TTTCTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAAAAAATTATGA
Found at i:1771162 original size:3 final size:3
Alignment explanation
Indices: 1771154--1771188 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1771144 TCATACAAAT
*
1771154 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1771189 GCTTATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1771699 original size:5 final size:5
Alignment explanation
Indices: 1771660--1771711 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
1771650 TTTATTTGTT
* *
1771660 ATTAA ATTTAAA ATTAA ATCAA ATTCA ATTAAA ATTAA ATTAAA ATTAA
1 ATTAA A-TT-AA ATTAA ATTAA ATTAA ATT-AA ATTAA ATT-AA ATTAA
1771709 ATT
1 ATT
1771712 GAACATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 23 0.59
6 13 0.33
7 3 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:1771700 original size:11 final size:11
Alignment explanation
Indices: 1771660--1771711 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
1771650 TTTATTTGTT
1771660 ATTAAATTTAAA
1 ATTAAA-TTAAA
*
1771672 ATTAAA-TCAA
1 ATTAAATTAAA
*
1771682 ATTCAATTAAA
1 ATTAAATTAAA
1771693 ATTAAATTAAA
1 ATTAAATTAAA
1771704 ATTAAATT
1 ATTAAATT
1771712 GAACATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.23
11 21 0.60
12 6 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAATTAAA
Found at i:1772023 original size:18 final size:17
Alignment explanation
Indices: 1771998--1772044 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
1771988 GTTATTTAAT
1771998 TTATTAAATATAAAAAA
1 TTATTAAATATAAAAAA
*
1772015 TTATATAAATATATAAAA
1 TTAT-TAAATATAAAAAA
1772033 TT-TTAAATATAA
1 TTATTAAATATAA
1772045 TTATGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATTAAATATAAAAAA
Found at i:1772287 original size:42 final size:43
Alignment explanation
Indices: 1772240--1772321 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
1772230 TAATTAAAAA
* *
1772240 ATTAAT-TTTATTATTTAAAATATATTAAAAA-ATTATTTTCAT
1 ATTAATATTTA-TAATTAAAATAAATTAAAAATATTATTTTCAT
* *
1772282 ATTAATATTTATAATTAAATTAAATTAAAAATATTTTTTT
1 ATTAATATTTATAATTAAAATAAATTAAAAATATTATTTT
1772322 AATACTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 23 0.68
43 11 0.32
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
ATTAATATTTATAATTAAAATAAATTAAAAATATTATTTTCAT
Found at i:1772941 original size:16 final size:18
Alignment explanation
Indices: 1772920--1772957 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1772910 AATTCAATTT
1772920 ATTTTT-TA-ATTATATA
1 ATTTTTATATATTATATA
*
1772936 ATTTTTATATATTATGTA
1 ATTTTTATATATTATATA
1772954 ATTT
1 ATTT
1772958 ATATCGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTTATATATTATATA
Found at i:1773886 original size:15 final size:15
Alignment explanation
Indices: 1773856--1773885 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1773846 GTTCATGTTT
1773856 TAAATTTAATAAAAA
1 TAAATTTAATAAAAA
1773871 TAAATCTTAATAAAA
1 TAAAT-TTAATAAAA
1773886 TTTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATTTAATAAAAA
Done.