Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 13 of 196
Found at i:3775129 original size:30 final size:30
Alignment explanation
Indices: 3775094--3775152 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3775084 CCGCCATTAG
*
3775094 GAAAGTTCCTCTAAACTACTGAAAATAAAA
1 GAAAGTTCCTCTAAACTACAGAAAATAAAA
* *
3775124 GAAAGTTCCTCTAAAGTACAGGAAATAAA
1 GAAAGTTCCTCTAAACTACAGAAAATAAA
3775153 CGGTTCAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (30 bp):
GAAAGTTCCTCTAAACTACAGAAAATAAAA
Found at i:3778761 original size:25 final size:25
Alignment explanation
Indices: 3778695--3778781 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
3778685 GTATGCCATA
3778695 TGAG-CATGTAATCGGGAAGCTC-TT
1 TGAGCCATGTAAT-GGGAAGCTCATT
* * *
3778719 TCAAGCCATATAACGGGAAGCTCATT
1 T-GAGCCATGTAATGGGAAGCTCATT
* *
3778745 TGAGCTATGTAATGGGAAGCTCATG
1 TGAGCCATGTAATGGGAAGCTCATT
3778770 TGAGCCATGTAA
1 TGAGCCATGTAA
3778782 CTAGAAGCTC
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.02
25 41 0.80
26 9 0.18
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (25 bp):
TGAGCCATGTAATGGGAAGCTCATT
Found at i:3778776 original size:50 final size:50
Alignment explanation
Indices: 3778695--3778791 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 50
3778685 GTATGCCATA
* *
3778695 TGAGCATGTAATCGGGAAGCTCTTTCAAGCCATATAACGGGAAGCTCATT
1 TGAGCATGTAATCGGGAAGCTCTGTCAAGCCATATAACGAGAAGCTCATT
* * *
3778745 TGAGCTATGTAAT-GGGAAGCTCATGT-GAGCCATGTAACTAGAAGCTC
1 TGAGC-ATGTAATCGGGAAGCTC-TGTCAAGCCATATAACGAGAAGCTC
3778792 TAGAGAGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 31 0.77
51 9 0.22
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (50 bp):
TGAGCATGTAATCGGGAAGCTCTGTCAAGCCATATAACGAGAAGCTCATT
Found at i:3778788 original size:25 final size:25
Alignment explanation
Indices: 3778735--3778791 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3778725 CATATAACGG
* * *
3778735 GAAGCTCATTTGAGCTATGTAATGG
1 GAAGCTCATGTGAGCCATGTAATGA
3778760 GAAGCTCATGTGAGCCATGTAACT-A
1 GAAGCTCATGTGAGCCATGTAA-TGA
3778785 GAAGCTC
1 GAAGCTC
3778792 TAGAGAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (25 bp):
GAAGCTCATGTGAGCCATGTAATGA
Found at i:3778812 original size:24 final size:24
Alignment explanation
Indices: 3778771--3778874 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 24
3778761 AAGCTCATGT
3778771 GAGCCATGTAACTA-GAAGCTCTAGA
1 GAGCCAT-TAAC-AGGAAGCTCTAGA
* *
3778796 GAGCCATTAACAGGAAGTTCAAGCA
1 GAGCCATTAACAGGAAGCTCTAG-A
* *
3778821 -AGCCAATATC-GAGAAGCTC-AGA
1 GAGCCATTAACAG-GAAGCTCTAGA
*
3778843 GAGCCATTAACAGGAATCTCATA-A
1 GAGCCATTAACAGGAAGCTC-TAGA
3778867 GAGCCATT
1 GAGCCATT
3778875 TATCGAGAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 18 0.28
24 36 0.56
25 9 0.14
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (24 bp):
GAGCCATTAACAGGAAGCTCTAGA
Found at i:3778872 original size:47 final size:48
Alignment explanation
Indices: 3778784--3778887 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 48
3778774 CCATGTAACT
3778784 AGAAGCTCTAGAGAGCCATTAACAGGAAGTTCAAGCAAGCCA-ATATCG
1 AGAAGCTCTAGAGAGCCATTAACAGGAAGTTCAAG-AAGCCATATATCG
*
3778832 AGAAGCTC-AGAGAGCCATTAACAGGAA-TCTCATA-AGAGCCATTTATCG
1 AGAAGCTCTAGAGAGCCATTAACAGGAAGT-TCA-AGA-AGCCATATATCG
3778880 AGAAGCTC
1 AGAAGCTC
3778888 CGAAGAGCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
46 2 0.04
47 27 0.53
48 22 0.43
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (48 bp):
AGAAGCTCTAGAGAGCCATTAACAGGAAGTTCAAGAAGCCATATATCG
Found at i:3780351 original size:18 final size:19
Alignment explanation
Indices: 3780312--3780352 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3780302 AATTACAAAA
*
3780312 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
3780331 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
3780349 AAAA
1 AAAA
3780353 AATCCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:3781577 original size:40 final size:40
Alignment explanation
Indices: 3781533--3781618 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
3781523 ACGACTAATG
* * * **
3781533 TTTTTATTAGTTTATTGCATATAAATTGTTGAAA-TATTAA
1 TTTTTATTAATTCATTGCAGATAAATAATT-AAATTATTAA
3781573 TTTTTATTAATTCATTGCAGATAAATAATTAAATTATTAA
1 TTTTTATTAATTCATTGCAGATAAATAATTAAATTATTAA
3781613 TTTTTA
1 TTTTTA
3781619 ACAATAAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.08
40 37 0.93
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.52
Consensus pattern (40 bp):
TTTTTATTAATTCATTGCAGATAAATAATTAAATTATTAA
Found at i:3784643 original size:3 final size:3
Alignment explanation
Indices: 3784637--3784665 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3784627 ATTGTTGTTG
3784637 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3784666 TGCCTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3785807 original size:23 final size:26
Alignment explanation
Indices: 3785780--3785834 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 26
3785770 TGATTTAAAC
3785780 AAATATTCATATTTT-TA-TA-ATTA
1 AAATATTCATATTTTATACTAGATTA
3785803 AAATATTCATATTTTATACTAGATTA
1 AAATATTCATATTTTATACTAGATTA
3785829 AAATAT
1 AAATAT
3785835 GTGATAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.52
24 2 0.07
25 2 0.07
26 10 0.34
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATATTCATATTTTATACTAGATTA
Found at i:3795933 original size:6 final size:7
Alignment explanation
Indices: 3795914--3795958 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
3795904 TATTTTTCTC
3795914 ATAAAAA
1 ATAAAAA
3795921 ATAAAAA
1 ATAAAAA
3795928 ATAAAAAA
1 AT-AAAAA
**
3795936 ATATTAA
1 ATAAAAA
3795943 ATAAAAA
1 ATAAAAA
*
3795950 ATTAAAA
1 ATAAAAA
3795957 AT
1 AT
3795959 GGATATAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
ATAAAAA
Found at i:3795936 original size:15 final size:15
Alignment explanation
Indices: 3795916--3795957 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3795906 TTTTTCTCAT
3795916 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
**
3795931 AAAAAATATTAAATA
1 AAAAAATAAAAAATA
*
3795946 AAAAATTAAAAA
1 AAAAAATAAAAA
3795958 TGGATATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:3796095 original size:19 final size:20
Alignment explanation
Indices: 3796071--3796117 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3796061 TATTATAATT
3796071 ATTTTAAAAAAATA-AAAAA
1 ATTTTAAAAAAATATAAAAA
* *
3796090 ATTTTACAAAAATATTAAAA
1 ATTTTAAAAAAATATAAAAA
3796110 A-TTTAAAA
1 ATTTTAAAA
3796118 GTATTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTTTAAAAAAATATAAAAA
Found at i:3796117 original size:30 final size:31
Alignment explanation
Indices: 3796037--3796117 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 31
3796027 GCGCTTACTT
* *
3796037 AAAATATTTAAAATTAAAAAAATGTATTATA
1 AAAATATTAAAAATTAAAAAAATGTATTACA
** * *
3796068 ATTATTTTAAAAAAATAAAAAAAT-T-TTACA
1 AAAATATT-AAAAATTAAAAAAATGTATTACA
*
3796098 AAAATATTAAAAATTTAAAA
1 AAAATATTAAAAATTAAAAA
3796118 GTATTAAAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
29 10 0.26
30 9 0.24
31 6 0.16
32 13 0.34
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (31 bp):
AAAATATTAAAAATTAAAAAAATGTATTACA
Found at i:3796604 original size:21 final size:21
Alignment explanation
Indices: 3796579--3796627 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3796569 GTTTATATCT
**
3796579 ATTTTAATAAATTTTTATGGA
1 ATTTTAATAAATTTTTATAAA
*
3796600 ATTTTAATACATTTTTATAAA
1 ATTTTAATAAATTTTTATAAA
3796621 ATTTTAA
1 ATTTTAA
3796628 ATATGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTTTAATAAATTTTTATAAA
Found at i:3796701 original size:18 final size:17
Alignment explanation
Indices: 3796681--3796758 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 17
3796671 ATTTATTAGG
3796681 TTTTTATATTTTTATAA
1 TTTTTATATTTTTATAA
* * *
3796698 GTTTATATCAATTTTCATAC
1 -TTTTTAT--ATTTTTATAA
*
3796718 TTTTT-TAATATTTAATAA
1 TTTTTAT-AT-TTTTATAA
3796736 TTTTTATATTTTTGATAA
1 TTTTTATATTTTT-ATAA
3796754 TTTTT
1 TTTTT
3796759 TTCTGATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
17 6 0.12
18 29 0.60
19 5 0.10
20 8 0.17
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTATATTTTTATAA
Found at i:3796756 original size:10 final size:9
Alignment explanation
Indices: 3796653--3796758 Score: 67
Period size: 10 Copynumber: 11.6 Consensus size: 9
3796643 TTTCTTAATT
*
3796653 TTTTTAGAA
1 TTTTTATAA
3796662 CTTTTTATAA
1 -TTTTTATAA
**
3796672 TTTATTA-GG
1 TTT-TTATAA
3796681 TTTTTAT-A
1 TTTTTATAA
3796689 TTTTTATAA
1 TTTTTATAA
*
3796698 GTTTATATCAA
1 -TTTTTAT-AA
* *
3796709 TTTTCATAC
1 TTTTTATAA
3796718 TTTTT-TAA
1 TTTTTATAA
*
3796726 TATTTAATAA
1 T-TTTTATAA
3796736 TTTTTAT-A
1 TTTTTATAA
3796744 TTTTTGATAA
1 TTTTT-ATAA
3796754 TTTTT
1 TTTTT
3796759 TTCTGATTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
8 19 0.25
9 22 0.29
10 32 0.43
11 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3796760 original size:21 final size:19
Alignment explanation
Indices: 3796736--3796802 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 19
3796726 TATTTAATAA
*
3796736 TTTTTATATTTTTGATAATT
1 TTTTTTTATTTTTGAT-ATT
* *
3796756 TTTTTCTGATTTTTGATTTTT
1 TTTTT-TTATTTTTGA-TATT
3796777 TTTTCTTCTGATTTTTGATATT
1 TTTT-TT-T-ATTTTTGATATT
3796799 TTTT
1 TTTT
3796803 ATGATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 5 0.14
21 15 0.41
22 9 0.24
23 8 0.22
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTTTTATTTTTGATATT
Found at i:3796785 original size:23 final size:22
Alignment explanation
Indices: 3796743--3796802 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
3796733 TAATTTTTAT
*
3796743 ATTTTTGATA-ATTTTTTTCTG
1 ATTTTTGATATTTTTTTTTCTG
*
3796764 ATTTTTGATTTTTTTTTCTTCTG
1 ATTTTTGATATTTTTTT-TTCTG
3796787 ATTTTTGATATTTTTT
1 ATTTTTGATATTTTTT
3796803 ATGATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 9 0.26
22 5 0.15
23 20 0.59
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (22 bp):
ATTTTTGATATTTTTTTTTCTG
Found at i:3800609 original size:41 final size:41
Alignment explanation
Indices: 3800552--3800676 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
3800542 GTTTGGAGAA
3800552 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
1 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
**
3800593 TTGAAATTTAATTCATTTTATCCAATTTGTGAGTAAAACCT
1 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
*
3800634 TTGAAATTTAATTCATTCCATCCAGTTTGTGAGTAAAACCT
1 TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
3800675 TT
1 TT
3800677 AGTACAAAAG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (41 bp):
TTGAAATTTAATTCATTCCATCCAATTTGTGAGTAAAACCT
Found at i:3814029 original size:21 final size:22
Alignment explanation
Indices: 3814003--3814043 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3813993 CAACCTCTGG
3814003 TAAAAA-AATGCACTGAAAATC
1 TAAAAATAATGCACTGAAAATC
*
3814024 TAAAAATAATGCATTGAAAA
1 TAAAAATAATGCACTGAAAA
3814044 ATTTGGTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAAATAATGCACTGAAAATC
Found at i:3814275 original size:21 final size:21
Alignment explanation
Indices: 3814251--3814300 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
3814241 AATTTTACAT
3814251 CTAAAAAAAT-TATAAAAAAAC
1 CTAAAAAAATATAT-AAAAAAC
*
3814272 CT-AAAGAATATATAAAAAAC
1 CTAAAAAAATATATAAAAAAC
*
3814292 TTAAAAAAA
1 CTAAAAAAA
3814301 AACCTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.20
Consensus pattern (21 bp):
CTAAAAAAATATATAAAAAAC
Found at i:3816384 original size:3 final size:3
Alignment explanation
Indices: 3816376--3816418 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3816366 CCCTGTTTCT
3816376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3816419 ATCTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3822762 original size:3 final size:3
Alignment explanation
Indices: 3822754--3822782 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3822744 TAAATCCATT
3822754 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3822783 TTTCGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3826900 original size:46 final size:46
Alignment explanation
Indices: 3826777--3826901 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 46
3826767 AATATTCCTA
* * **
3826777 TATTCTCAAGTCAACAACACATGTAGAAGCTTGGAACCTAAACATG
1 TATTCTCAAGTCCACAACATATGTAGAAGCTCAGAACCTAAACATG
* * *
3826823 TATTCTCGAGTCCGCAACACT-TGCTAG-AGCTCAGAACCTATAC-TGG
1 TATTCTCAAGTCCACAACA-TATG-TAGAAGCTCAGAACCTAAACAT-G
3826869 TATTCTCAAGTCCACAACATATGTAGAAGCTCA
1 TATTCTCAAGTCCACAACATATGTAGAAGCTCA
3826902 AACTTGGGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
45 5 0.08
46 57 0.88
47 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (46 bp):
TATTCTCAAGTCCACAACATATGTAGAAGCTCAGAACCTAAACATG
Found at i:3826992 original size:15 final size:15
Alignment explanation
Indices: 3826964--3826996 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3826954 GGATTTAACC
3826964 TCACACAATACCATT
1 TCACACAATACCATT
3826979 TCACAACAAT-CCATT
1 TCAC-ACAATACCATT
3826994 TCA
1 TCA
3826997 ATTTGATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.27
Consensus pattern (15 bp):
TCACACAATACCATT
Found at i:3834834 original size:29 final size:30
Alignment explanation
Indices: 3834785--3834843 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
3834775 AAAATTTTTA
* * *
3834785 ATTTATTTTTACTATTTTAAATA-TAAAAT
1 ATTTATTTTTACTACTATAAAAATTAAAAT
3834814 ATTTATTTCTTAC-ACTATAAAAATTAAAAT
1 ATTTATTT-TTACTACTATAAAAATTAAAAT
3834844 TAATAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTATTTTTACTACTATAAAAATTAAAAT
Found at i:3842396 original size:18 final size:18
Alignment explanation
Indices: 3842373--3842407 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3842363 TTTCTCATAA
3842373 AAAAAACTATAAAAAATT
1 AAAAAACTATAAAAAATT
*
3842391 AAAAAACTTTAAAAAAT
1 AAAAAACTATAAAAAAT
3842408 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAACTATAAAAAATT
Found at i:3842428 original size:15 final size:16
Alignment explanation
Indices: 3842403--3842432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3842393 AAAACTTTAA
3842403 AAAATATATTAAAAAT
1 AAAATATATTAAAAAT
3842419 AAAA-ATATTAAAAA
1 AAAATATATTAAAAA
3842433 CTTTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATATTAAAAAT
Found at i:3842474 original size:22 final size:21
Alignment explanation
Indices: 3842449--3842495 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
3842439 ATAAACTTTT
3842449 AAAAAATATAAAAGATTCATA
1 AAAAAATATAAAAGATTCATA
* *
3842470 AAAAAGT-TATAAGATTCATA
1 AAAAAATATAAAAGATTCATA
3842490 AAAAAA
1 AAAAAA
3842496 AGTATACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAAATATAAAAGATTCATA
Found at i:3842887 original size:19 final size:20
Alignment explanation
Indices: 3842862--3842900 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3842852 AATTGAACCG
**
3842862 TTTTTTTTTTAATTTTTAAA
1 TTTTTTTTGAAATTTTTAAA
3842882 TTTTTTTTGAAATTTTTAA
1 TTTTTTTTGAAATTTTTAA
3842901 TGATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTTTGAAATTTTTAAA
Found at i:3850030 original size:25 final size:25
Alignment explanation
Indices: 3849993--3850048 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3849983 CATATATGAA
* *
3849993 ATAATCTTGTTGTTTAATGTATTGG
1 ATAATCTTATTGTTTAATGTATAGG
*
3850018 ATAATCTTATTGTTTGATGTATAGG
1 ATAATCTTATTGTTTAATGTATAGG
3850043 ATAATC
1 ATAATC
3850049 ATTTCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (25 bp):
ATAATCTTATTGTTTAATGTATAGG
Found at i:3853941 original size:17 final size:17
Alignment explanation
Indices: 3853904--3853942 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3853894 TTATTTGTTC
*
3853904 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
3853921 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
3853938 TATTG
1 TATTG
3853943 AATTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:3854107 original size:21 final size:21
Alignment explanation
Indices: 3854081--3854187 Score: 110
Period size: 21 Copynumber: 5.2 Consensus size: 21
3854071 GTGTTTTACT
3854081 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
3854102 TTCTGTTCAACTCTAATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
3854123 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
3854144 TTCTATTAAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
3854163 TTCTATTCAGCTTTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
3854184 TTCT
1 TTCT
3854188 ATTAAGCTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
19 16 0.22
20 4 0.06
21 52 0.72
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:3854163 original size:19 final size:19
Alignment explanation
Indices: 3854139--3854206 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
3854129 TTAGCTCTTA
3854139 CGAGCTTCTATTAAGCTTT
1 CGAGCTTCTATTAAGCTTT
*
3854158 CGAGCTTCTATTCAGCTTTT
1 CGAGCTTCTATTAAGC-TTT
*
3854178 ATGAGCTTCTATTAAGCTTT
1 -CGAGCTTCTATTAAGCTTT
*
3854198 CAAGCTTCT
1 CGAGCTTCT
3854207 GTTGGCATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 22 0.52
20 6 0.14
21 14 0.33
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (19 bp):
CGAGCTTCTATTAAGCTTT
Found at i:3854187 original size:40 final size:40
Alignment explanation
Indices: 3854131--3854206 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3854121 GTTTCTGTTT
*
3854131 AGCTCTTACGAGCTTCTATTAAGCTTTCGAGCTTCTATTC
1 AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCTATTC
* *
3854171 AGCTTTTATGAGCTTCTATTAAGCTTTCAAGCTTCT
1 AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCT
3854207 GTTGGCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.42
Consensus pattern (40 bp):
AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCTATTC
Found at i:3857517 original size:21 final size:20
Alignment explanation
Indices: 3857490--3857538 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3857480 AATAGAACTT
*
3857490 ATGAATGACAGGAAATTGTC
1 ATGAATGACAGGAAATTGAC
*
3857510 AGTGAATGACAGGGAATTGAC
1 A-TGAATGACAGGAAATTGAC
3857531 ATGAATGA
1 ATGAATGA
3857539 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.22
Consensus pattern (20 bp):
ATGAATGACAGGAAATTGAC
Found at i:3859798 original size:21 final size:22
Alignment explanation
Indices: 3859770--3859833 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
3859760 CAGAAACAGT
*
3859770 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
3859792 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
3859812 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
3859834 TCGACAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:3862641 original size:17 final size:18
Alignment explanation
Indices: 3862607--3862642 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3862597 TGAACTTTTA
3862607 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
3862625 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
3862642 T
1 T
3862643 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:3866584 original size:90 final size:89
Alignment explanation
Indices: 3866478--3866767 Score: 364
Period size: 90 Copynumber: 3.1 Consensus size: 89
3866468 TGAATTTTTT
*
3866478 TAATTTTTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAGATTGTTTGTATTTAGTTT
1 TAATTTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATA-ATTGTTTGTATTTAGTTT
3866543 AGTGTTTTGTGATTTTTTATGAATG
65 AGTGTTTTGTGATTTTTTATGAATG
* * *
3866568 TAATTTTTTCAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATTAATCGTTTGTGTTTAGTTT
1 TAATTTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTA-TAATTGTTTGTATTTAGTTT
* *
3866633 AGTGTTTTGTGATTTGTTATGAATA
65 AGTGTTTTGTGATTTTTTATGAATG
* * *
3866658 TATTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTAT
1 TA-----AT-TT-TTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTAT-AATTGTTTGTAT
* *
3866723 TTAGTTTAATGTTTATTGTGATTTTTTATAAATG
58 TTAGTTTAGTG-TT-TTGTGATTTTTTATGAATG
3866757 TAAATTTTTTT
1 T-AATTTTTTT
3866768 GTTTTTTTAT
Statistics
Matches: 172, Mismatches: 16, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
90 83 0.48
91 2 0.01
93 4 0.02
94 2 0.01
95 4 0.02
96 3 0.02
97 54 0.31
98 2 0.01
99 17 0.10
100 1 0.01
ACGTcount: A:0.26, C:0.01, G:0.16, T:0.58
Consensus pattern (89 bp):
TAATTTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAATTGTTTGTATTTAGTTTA
GTGTTTTGTGATTTTTTATGAATG
Found at i:3866708 original size:97 final size:103
Alignment explanation
Indices: 3866568--3866848 Score: 324
Period size: 112 Copynumber: 2.7 Consensus size: 103
3866558 TTTATGAATG
* *
3866568 TAATT-TTTTCAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATTAATCGTTTGTGTTTAGTT
1 TAATTATTTT-AAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTT
*
3866632 TAGTGTTTTGTGA-TTTGT-T-ATG-AA-TATATTTTTA
65 TAATGTTTTGTGATTTTGTATAATGAAATTATATTTTTA
* * * *
3866666 T-ATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTATTTAGTTT
1 TAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
* * *
3866730 AATGTTTATTGTGATTTTTTATAAATGTAAATTTTTTTGTTTTTTTA
66 AATG-TT-TTGTGATTTTGTAT-AATG-AAA-----TTATATTTTTA
*
3866777 TAATTATTTTAAAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
1 TAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
3866842 AATGTTT
66 AATGTTT
3866849 ATTGTGAATT
Statistics
Matches: 152, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
97 55 0.36
98 7 0.05
99 6 0.04
100 4 0.03
101 1 0.01
103 3 0.02
105 2 0.01
110 1 0.01
111 11 0.07
112 62 0.41
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (103 bp):
TAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
AATGTTTTGTGATTTTGTATAATGAAATTATATTTTTA
Found at i:3866797 original size:112 final size:112
Alignment explanation
Indices: 3866660--3866888 Score: 361
Period size: 112 Copynumber: 2.0 Consensus size: 112
3866650 TATGAATATA
* *
3866660 TTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTATTT
1 TTTTTATATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATTT
* * *
3866725 AGTTTAATGTTTATTGTGATTTTTTATAAATGTAAATTTTTTTGT-T
66 AGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTTGTAT
* * *
3866771 TTTTTATAATTATTTTAAAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTTGTGTT
1 TTTTTAT-ATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATT
*
3866836 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAATTTTTTTTGTAT
65 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTTGTAT
3866884 TTTTT
1 TTTTT
3866889 GTTAGTAATT
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
111 7 0.07
112 94 0.88
113 6 0.06
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.59
Consensus pattern (112 bp):
TTTTTATATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATTT
AGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTTGTAT
Found at i:3866944 original size:89 final size:90
Alignment explanation
Indices: 3866794--3866963 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 90
3866784 TTTAAAGTTA
* **
3866794 TTTTGTTAATAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTAATGTTTATTGTGAATT
1 TTTTGTTAATAATTTATGATTAGGTTATAAATTGATTGTGTTTAGTTTAATGTAAATTGTGAATT
*
3866859 GTCATAAATGTAATTTTTTTTGTATT
66 GTCAT-AACGTAATTTTTTTTGTATT
* *
3866885 TTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTTTAGTTTAATGTAAATTGTGATTT
1 TTTTGTTAATAATTTATGATTAGGTTATAAATTGATTGTGTTTAGTTTAATGTAAATTGTGAATT
*
3866948 GTTATAACGTAATTTT
66 GTCATAACGTAATTTT
3866964 ATTTATTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
88 10 0.14
89 28 0.39
90 2 0.03
91 32 0.44
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (90 bp):
TTTTGTTAATAATTTATGATTAGGTTATAAATTGATTGTGTTTAGTTTAATGTAAATTGTGAATT
GTCATAACGTAATTTTTTTTGTATT
Found at i:3867532 original size:21 final size:21
Alignment explanation
Indices: 3867506--3867561 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3867496 CACCATTGTT
*
3867506 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
3867527 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
3867548 ACTAATCTCACCGC
1 TCTAATCTCACCGC
3867562 CACTGCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:3872021 original size:54 final size:54
Alignment explanation
Indices: 3871873--3872023 Score: 143
Period size: 54 Copynumber: 2.9 Consensus size: 54
3871863 AACTAATAAT
* * * *
3871873 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATT-AAAATAAACAAA
* * * *
3871928 -AATTTATATTAATAACCTAAC-AAATCAC---AATAA-ACATTAAACTAAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAA-AATAAATTAAAATAAACAAA
* *
3871978 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAA
3872024 ACAACATAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
50 14 0.19
51 25 0.33
52 2 0.03
53 2 0.03
54 27 0.36
55 5 0.07
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (54 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAATAAACAAA
Found at i:3872026 original size:51 final size:51
Alignment explanation
Indices: 3871873--3872032 Score: 137
Period size: 51 Copynumber: 3.1 Consensus size: 51
3871863 AACTAATAAT
* * *
3871873 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAA--CA-AA
* * * ** *
3871927 AAATTTATATTAATAACCTAAC-AAATCACAATAAACATTAAACT--AAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAAA-A-TAAATTAAAAACAAA
* *
3871978 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAAACAACA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAA-A
3872030 TAA
1 TAA
3872033 AAACAACAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
49 5 0.06
50 6 0.07
51 31 0.37
52 5 0.06
54 25 0.30
55 6 0.07
56 5 0.06
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (51 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAAA
Found at i:3872154 original size:18 final size:17
Alignment explanation
Indices: 3872125--3872166 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
3872115 TACATTATCC
3872125 TTCTTTTTTCTTC-TCA
1 TTCTTTTTTCTTCTTCA
3872141 TTTCTTTCTTTCTTCTTCA
1 -TTCTTT-TTTCTTCTTCA
3872160 TTCTTTT
1 TTCTTTT
3872167 CTCCTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 13 0.57
19 3 0.13
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTTTTTCTTCTTCA
Found at i:3875698 original size:6 final size:6
Alignment explanation
Indices: 3875687--3875721 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3875677 TGATGAGGAG
* *
3875687 GATGAA GATGAA GATGAA GATGAT GATGAT GATGA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGA
3875722 TTATGGGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (6 bp):
GATGAA
Found at i:3881399 original size:17 final size:19
Alignment explanation
Indices: 3881361--3881400 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
3881351 TTAAAACGTG
3881361 AATTAATGTTATGTTTAAA
1 AATTAATGTTATGTTTAAA
*
3881380 AATT-ATGTTAT-TTTACA
1 AATTAATGTTATGTTTAAA
3881397 AATT
1 AATT
3881401 TTAAAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (19 bp):
AATTAATGTTATGTTTAAA
Found at i:3887939 original size:21 final size:22
Alignment explanation
Indices: 3887913--3887954 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3887903 CACTATTTCA
*
3887913 TTAAAAA-ATAATTTTAATCCC
1 TTAAAAAGATAATTTCAATCCC
*
3887934 TTAAAAAGTTAATTTCAATCC
1 TTAAAAAGATAATTTCAATCC
3887955 TACATTGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAAAGATAATTTCAATCCC
Found at i:3888212 original size:68 final size:67
Alignment explanation
Indices: 3888099--3888225 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
3888089 ATAAATAAGT
* * ** *
3888099 ACATTGACTAAAGAATACTCTTATTGCTCACTTATCACTATTTTCATTTAAAAGTTAATTTTAAT
1 ACATTAACTAAAGAATACTCTCATAACTCACTTATCACTATTTTCA-TTAAAAATTAATTTTAAT
3888164 CTC
65 CTC
* *
3888167 ACATTAACTAGAGAATACTCTCATAACTCACTTCTTCACTA-TTTCATTAAAAATTAATT
1 ACATTAACTAAAGAATACTCTCATAACTCACTT-ATCACTATTTTCATTAAAAATTAATT
3888226 AAATTTGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 12 0.24
68 33 0.65
69 6 0.12
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (67 bp):
ACATTAACTAAAGAATACTCTCATAACTCACTTATCACTATTTTCATTAAAAATTAATTTTAATC
TC
Found at i:3890766 original size:65 final size:64
Alignment explanation
Indices: 3890629--3890835 Score: 163
Period size: 65 Copynumber: 3.1 Consensus size: 64
3890619 CACTCACATG
* * * * *
3890629 CTCACACTTACTCT-ATAAATAAGTGTCAGTTTCTTAACTATTTTCTTTAACAACTTAGTTTTAA
1 CTCACATTTA-TCTGATAAATAAGTGT-AATTTCTTAACTATTTTCATTAAAAACTTAATTTTAA
3890693 T
64 T
* *
3890694 C-CTACATTTATCTGATAAATAAGTGATAATTTCTTCACTATTTTCATTAAAAATTTAATTTTAA
1 CTC-ACATTTATCTGATAAATAAGTG-TAATTTCTTAACTATTTTCATTAAAAACTTAATTTTAA
3890758 T
64 T
* * * * *
3890759 CTCACATTGAT-TAGAGAATACTCTCATAG-CTAACTTT-TTTACTATTTTCATTAAAAAGTTAA
1 CTCACATTTATCT-GATAA-A---T-A-AGTGTAA-TTTCTTAACTATTTTCATTAAAAACTTAA
3890821 TTTTAAT
58 TTTTAAT
3890828 CTCACATT
1 CTCACATT
3890836 AACTAAAATA
Statistics
Matches: 118, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
64 5 0.04
65 62 0.53
66 3 0.03
69 42 0.36
70 4 0.03
71 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (64 bp):
CTCACATTTATCTGATAAATAAGTGTAATTTCTTAACTATTTTCATTAAAAACTTAATTTTAAT
Found at i:3890811 original size:69 final size:68
Alignment explanation
Indices: 3890727--3890904 Score: 234
Period size: 69 Copynumber: 2.6 Consensus size: 68
3890717 TGATAATTTC
* *
3890727 TTCACTATTTTCATTAAAAATTTAATTTTAATCTCACATTGATTAGAGA-ATACTCTCATAGCTA
1 TTCACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTA-AAATATACTCTCATAGCTA
* *
3890791 ACTTT
64 ACGTA
* * *
3890796 TTTACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTAACTAAAATATACTCTCATAGCTCA
1 TTCACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAA
3890861 CGTA
65 CGTA
*
3890865 TTCACAATTTTCATTAAAAATTAATTTTAAT-TCCACATTG
1 TTCACTATTTTCATTAAAAATTAATTTTAATCT-CACATTG
3890905 GCTAGACAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
67 1 0.01
68 19 0.20
69 76 0.79
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAAC
GTA
Found at i:3894119 original size:69 final size:69
Alignment explanation
Indices: 3894031--3894179 Score: 192
Period size: 69 Copynumber: 2.2 Consensus size: 69
3894021 AAGTGACAAT
* ** * * *
3894031 TTCTTCACTATTTTTATTAAAAAATTAATTTTAATCCTATATTGACTAGAGAATACTCTCATAGA
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATA-A
3894096 -TAAC
65 CTAAC
* * *
3894100 TTCTTCACTATATCCATTAAAAAGTCAATTTTAATCCCAAATTGACTAGAGACTACTTTCATAAC
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
*
3894165 TCAC
66 TAAC
3894169 TTCTTCACTAT
1 TTCTTCACTAT
3894180 TAAAAATTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
68 1 0.01
69 68 0.99
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (69 bp):
TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
TAAC
Found at i:3894200 original size:21 final size:22
Alignment explanation
Indices: 3894176--3894219 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3894166 CACTTCTTCA
3894176 CTATTAAAAATT-AATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
*
3894197 CTATTAAAACTTAAATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
3894219 C
1 C
3894220 CCACATTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
CTATTAAAAATTAAATTTTAAT
Found at i:3904220 original size:23 final size:23
Alignment explanation
Indices: 3904193--3904312 Score: 159
Period size: 23 Copynumber: 5.2 Consensus size: 23
3904183 TGTTATTGAT
* **
3904193 CAGTGGTAGCTTCGGCTACGTTT
1 CAGTGGTAGCTTCGGCTACATAA
*
3904216 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
* **
3904239 CAGTGGTAGCTTCAGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
*
3904262 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
3904285 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
3904308 CAGTG
1 CAGTG
3904313 TTGCACTTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:3904246 original size:46 final size:46
Alignment explanation
Indices: 3904193--3904305 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
3904183 TGTTATTGAT
*
3904193 CAGTGGTAGCTTCGGCTACGTTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
*
3904239 CAGTGGTAGCTTCAGCTACATTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
3904285 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
3904306 ATCAGTGTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
Found at i:3907026 original size:46 final size:46
Alignment explanation
Indices: 3906959--3907212 Score: 379
Period size: 46 Copynumber: 5.6 Consensus size: 46
3906949 TTTGAGTACT
* * **
3906959 TCTGATCAAGAGATAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
3907005 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
3907051 TCTGATCAAGTGACAAAGTGATAACTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
3907097 TTTGATCAAGTAACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
3907143 CCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
3907188 TCTGAT-TAGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
3907213 ATCATACGTA
Statistics
Matches: 191, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 17 0.09
46 157 0.82
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:3919547 original size:9 final size:9
Alignment explanation
Indices: 3919530--3919605 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
3919520 TTTGGTTAAA
3919530 AATTAACCG
1 AATTAACCG
*
3919539 AATTGACCG
1 AATTAACCG
3919548 AATT-ACCTG
1 AATTAACC-G
3919557 AATTAACCG
1 AATTAACCG
3919566 AATT-ACTCG
1 AATTAAC-CG
*
3919575 AATT-ACCTA
1 AATTAACC-G
3919584 AATTAACCG
1 AATTAACCG
*
3919593 AATTAACCA
1 AATTAACCG
3919602 AATT
1 AATT
3919606 GAATCACTAC
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
8 6 0.10
9 46 0.79
10 6 0.10
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:3919605 original size:27 final size:26
Alignment explanation
Indices: 3919529--3919597 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 26
3919519 TTTTGGTTAA
3919529 AAATTAACCGAATTGACCGAATTACCT
1 AAATTAACCGAATT-ACCGAATTACCT
*
3919556 GAATTAACCGAATTACTCGAATTACCT
1 AAATTAACCGAATTAC-CGAATTACCT
3919583 AAATTAACCGAATTA
1 AAATTAACCGAATTA
3919598 ACCAAATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (26 bp):
AAATTAACCGAATTACCGAATTACCT
Found at i:3919752 original size:18 final size:18
Alignment explanation
Indices: 3919712--3919755 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3919702 TAATTTTATG
*
3919712 ATTGGGTTGGGTTAGGTA
1 ATTGGGTTGGGTTAGATA
3919730 ATTGGGTTGGGTT-GAATA
1 ATTGGGTTGGGTTAG-ATA
*
3919748 CTTGGGTT
1 ATTGGGTT
3919756 TAAATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTAGATA
Found at i:3922402 original size:20 final size:20
Alignment explanation
Indices: 3922380--3922416 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3922370 AATTTTAGGT
3922380 TTTTTAAG-AATATTTTATA
1 TTTTTAAGAAATATTTTATA
*
3922399 TTTTTATGAAATATTTTA
1 TTTTTAAGAAATATTTTA
3922417 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTAAGAAATATTTTATA
Found at i:3922426 original size:21 final size:20
Alignment explanation
Indices: 3922388--3922426 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3922378 GTTTTTTAAG
*
3922388 AATATTTTATATTTTTATGA
1 AATATTTTATAATTTTATGA
3922408 AATATTTTAATAATTTTAT
1 AATATTTT-ATAATTTTAT
3922427 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AATATTTTATAATTTTATGA
Found at i:3923420 original size:9 final size:9
Alignment explanation
Indices: 3923406--3923587 Score: 55
Period size: 10 Copynumber: 18.9 Consensus size: 9
3923396 ATATCAGGAC
3923406 AAAATTATA
1 AAAATTATA
3923415 AAAATTATTA
1 AAAATTA-TA
*
3923425 AATATTA-A
1 AAAATTATA
* *
3923433 AATATTATT
1 AAAATTATA
* *
3923442 ATACTTAATA
1 AAAATT-ATA
*
3923452 TAAGATTATA
1 -AAAATTATA
3923462 AAAATGT-TA
1 AAAAT-TATA
* *
3923471 ATAGTTAT-
1 AAAATTATA
*
3923479 AAAATTTTA
1 AAAATTATA
3923488 TAAAATTAATA
1 -AAAATT-ATA
*
3923499 AAACATATTTA
1 AAA-AT-TATA
3923510 AAATATTATAA
1 AAA-ATTAT-A
*
3923521 AAAACGTATA
1 AAAA-TTATA
*
3923531 AAAATTCTTA
1 AAAATT-ATA
3923541 AAAACTTATAA
1 AAAA-TTAT-A
* *
3923552 AAAATAAAA
1 AAAATTATA
* *
3923561 AAAATAATTG
1 AAAATTA-TA
3923571 AAAATTATA
1 AAAATTATA
*
3923580 AAAGTTAT
1 AAAATTAT
3923588 TCAAAATATT
Statistics
Matches: 126, Mismatches: 30, Indels: 34
0.66 0.16 0.18
Matches are distributed among these distances:
8 14 0.11
9 37 0.29
10 46 0.37
11 28 0.22
12 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:3924307 original size:27 final size:25
Alignment explanation
Indices: 3924267--3924316 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
3924257 ATATTTTTAA
*
3924267 TTTTTTATAATTTTTATACTTTTCT
1 TTTTTTATAATTTTAATACTTTTCT
*
3924292 TTTTTTATATATTTTTAATATTTTT
1 TTTTTTATA-A-TTTTAATACTTTT
3924317 ATGAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 1 0.05
27 11 0.52
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTTATAATTTTAATACTTTTCT
Found at i:3930707 original size:24 final size:24
Alignment explanation
Indices: 3930673--3930718 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3930663 TATATGAAAT
* *
3930673 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
3930697 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
3930719 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:3934021 original size:240 final size:241
Alignment explanation
Indices: 3933538--3934026 Score: 854
Period size: 243 Copynumber: 2.0 Consensus size: 241
3933528 ATCTTCTTGT
*
3933538 CATTCCAGTGGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
* *
3933603 CCCAGCTGCAATTTCTTCAGGAAGACTCCGCTGAAATGTTTTGGGGAGATCCTTTCCAACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
*
3933668 TACAAGGAGAATGAAAGAAAGGATAGTGCTGTTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
131 TAC-A-GAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
3933733 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
194 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
*
3933781 CATTCCAGTAGATGGGGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
** * * *
3933846 CTGAGCTGCAATTTCTTCAGGAAGATTCCACTGAAGTGTTTCGGGGAGATCCTTTCCGACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
3933911 TAC-GAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGAAG
131 TACAGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGAAG
*
3933975 AGATGAATTCATCAACAGTGGATATCTTCAGGGTATGGGATTTGGA
196 AGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
3934021 CATTCC
1 CATTCC
3934027 GGATGAGGAA
Statistics
Matches: 235, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
240 111 0.47
243 124 0.53
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (241 bp):
CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
TACAGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGAAG
AGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
Found at i:3935389 original size:31 final size:31
Alignment explanation
Indices: 3935354--3935413 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3935344 AAGTAGTCCG
*
3935354 ATGACTTAAATAAAAACTTTCGACTAGTTCA
1 ATGACTTAAATAAAAACTTTCGAATAGTTCA
*
3935385 ATGACTTAAATGAAAACTTTCGAATAGTT
1 ATGACTTAAATAAAAACTTTCGAATAGTT
3935414 TAGTGATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (31 bp):
ATGACTTAAATAAAAACTTTCGAATAGTTCA
Found at i:3935880 original size:21 final size:21
Alignment explanation
Indices: 3935842--3935881 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3935832 AAATTTCTAG
*
3935842 ATTTTTAATTTTGAAAATCGA
1 ATTTTTAATTTGGAAAATCGA
* *
3935863 ATTTTTAGTTTGGTAAATC
1 ATTTTTAATTTGGAAAATC
3935882 ATGCGATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
ATTTTTAATTTGGAAAATCGA
Found at i:3950983 original size:12 final size:13
Alignment explanation
Indices: 3950966--3950999 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3950956 TAAATTGAAA
3950966 TAAAATAAAA-AC
1 TAAAATAAAACAC
*
3950978 TAAAATAAAACCC
1 TAAAATAAAACAC
3950991 TAAAATAAA
1 TAAAATAAA
3951000 CTAAGTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAATAAAACAC
Found at i:3955810 original size:12 final size:11
Alignment explanation
Indices: 3955793--3955826 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
3955783 ACCTTGTGTG
3955793 TGTTCTTTCTGT
1 TGTTCTTT-TGT
3955805 TGTTCTTTTGT
1 TGTTCTTTTGT
3955816 TGCTTCTTTTG
1 TG-TTCTTTTG
3955827 GCATAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.68
Consensus pattern (11 bp):
TGTTCTTTTGT
Found at i:3962608 original size:21 final size:20
Alignment explanation
Indices: 3962572--3962610 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3962562 CTTTGACCGA
*
3962572 TCATTGACTAGTGTTGACTG
1 TCATTGACTAGCGTTGACTG
3962592 TCATTGACTACGCGTTGAC
1 TCATTGACTA-GCGTTGAC
3962611 CAACCACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
TCATTGACTAGCGTTGACTG
Found at i:3962758 original size:23 final size:23
Alignment explanation
Indices: 3962697--3962766 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
3962687 AAAAATAATC
* *
3962697 ATATATAATATATAAAAATTT-AA
1 ATATATAAT-TTTAAAATTTTAAA
* **
3962720 ATATTTTTTTTATAAAATTTTAAA
1 ATATATAATTT-TAAAATTTTAAA
3962744 ATATATAATTTT-AAATTTTAAA
1 ATATATAATTTTAAAATTTTAAA
3962766 A
1 A
3962767 AGTTAAAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
22 12 0.32
23 15 0.41
24 10 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATAATTTTAAAATTTTAAA
Found at i:3963047 original size:21 final size:17
Alignment explanation
Indices: 3963012--3963071 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
3963002 TATATGTTTT
**
3963012 TTTTTCTAGATTATATA
1 TTTTTCTATTTTATATA
3963029 -TTTTCTGAATTTTTATATA
1 TTTTTCT--A-TTTTATATA
3963048 TTTATTTCTATTTTATATA
1 -TT-TTTCTATTTTATATA
3963067 TTTTT
1 TTTTT
3963072 AATGTGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 6 0.17
17 3 0.09
18 3 0.09
19 16 0.46
20 1 0.03
21 1 0.03
22 5 0.14
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTCTATTTTATATA
Found at i:3967175 original size:13 final size:13
Alignment explanation
Indices: 3967157--3967186 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3967147 TATTTGGTAG
3967157 TACAAATTGTAAT
1 TACAAATTGTAAT
3967170 TACAAATTGTAAT
1 TACAAATTGTAAT
3967183 TACA
1 TACA
3967187 CAGTTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (13 bp):
TACAAATTGTAAT
Found at i:3971295 original size:15 final size:16
Alignment explanation
Indices: 3971265--3971297 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3971255 TAGTTACTTA
*
3971265 TTTGGGTCATTTCGAG
1 TTTGGATCATTTCGAG
3971281 TTTGGATCA-TTCGAG
1 TTTGGATCATTTCGAG
3971296 TT
1 TT
3971298 AGCTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.45
Consensus pattern (16 bp):
TTTGGATCATTTCGAG
Found at i:3972963 original size:18 final size:18
Alignment explanation
Indices: 3972942--3973180 Score: 84
Period size: 18 Copynumber: 13.6 Consensus size: 18
3972932 AAATACGAGA
3972942 ATTTTTAAAAACACGAAG
1 ATTTTTAAAAACACGAAG
* ****
3972960 ATTTTT-GAAACA-TTTT
1 ATTTTTAAAAACACGAAG
* * *
3972976 TTTTTTGAAAACACGAAAA
1 ATTTTTAAAAACACG-AAG
3972995 ATTTTT-AAAACACG-AG
1 ATTTTTAAAAACACGAAG
* * * * *
3973011 AATTTTAGAGACAAGAAA
1 ATTTTTAAAAACACGAAG
* * * *
3973029 ATTCTTAAAAATATGAAA
1 ATTTTTAAAAACACGAAG
*
3973047 ATTTTTGAAAACACGGAA-
1 ATTTTTAAAAACAC-GAAG
*
3973065 ATTTTT-AAAACACG-GG
1 ATTTTTAAAAACACGAAG
* *
3973081 AATTTTTAAAAACATGAAA
1 -ATTTTTAAAAACACGAAG
*
3973100 ATTTTT-GAAACACCG--G
1 ATTTTTAAAAACA-CGAAG
* * * *
3973116 AATTTTGAAAATACGAGG
1 ATTTTTAAAAACACGAAG
* *
3973134 ATTCTTGAAAACACGAAG
1 ATTTTTAAAAACACGAAG
* * *
3973152 ATTTTTTAAAACACAAAA
1 ATTTTTAAAAACACGAAG
3973170 ATTTTTTAAAA
1 A-TTTTTAAAA
3973181 TACGGAAATT
Statistics
Matches: 159, Mismatches: 47, Indels: 29
0.68 0.20 0.12
Matches are distributed among these distances:
16 19 0.12
17 37 0.23
18 87 0.55
19 16 0.10
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
ATTTTTAAAAACACGAAG
Found at i:3973029 original size:35 final size:34
Alignment explanation
Indices: 3972992--3973125 Score: 110
Period size: 35 Copynumber: 3.9 Consensus size: 34
3972982 GAAAACACGA
*
3972992 AAAATTTTTAAAACACGAGAATTTTAGAGACAAG
1 AAAATTTTTAAAACACGAGAATTTTAGAAACAAG
* * * * * *
3973026 AAAATTCTTAAAAATATGAAAATTTTTGAAAACACG
1 AAAATT-TTTAAAACACGAGAATTTTAG-AAACAAG
* * * *
3973062 GAAATTTTTAAAACACGGGAATTTTTAAAAACATG
1 AAAATTTTTAAAACACGAGAA-TTTTAGAAACAAG
*
3973097 AAAATTTTTGAAACACCG-GAATTTT-GAAA
1 AAAATTTTTAAAACA-CGAGAATTTTAGAAA
3973126 ATACGAGGAT
Statistics
Matches: 77, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
33 3 0.04
34 10 0.13
35 48 0.62
36 16 0.21
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (34 bp):
AAAATTTTTAAAACACGAGAATTTTAGAAACAAG
Found at i:3973047 original size:53 final size:50
Alignment explanation
Indices: 3972983--3973165 Score: 150
Period size: 53 Copynumber: 3.5 Consensus size: 50
3972973 TTTTTTTTTG
* *
3972983 AAAACACGAAAAATTTTTAAAACACGAGAATTTTAGAGACAAGAAAATTCTTA
1 AAAACATG-AAAATTTTTAAAACACG-GAATTTTA-AAACAAGAAAATTCTTA
* * ** *
3973036 AAAATATGAAAATTTTTGAAAACACGGAAATTTTTAAAACACGGGAATTTTTA
1 AAAACATGAAAATTTTT-AAAACACGG-AA-TTTTAAAACAAGAAAATTCTTA
* * * ** *
3973089 AAAACATGAAAATTTTTGAAACACCGGAATTTTGAAAATACGAGGATTCTTG
1 AAAACATGAAAATTTTTAAAACA-CGGAATTTT-AAAACAAGAAAATTCTTA
* *
3973141 AAAACACGAAGATTTTTTAAAACAC
1 AAAACATGAA-AATTTTTAAAACAC
3973166 AAAAATTTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
51 4 0.04
52 40 0.37
53 58 0.54
54 5 0.05
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (50 bp):
AAAACATGAAAATTTTTAAAACACGGAATTTTAAAACAAGAAAATTCTTA
Found at i:3973189 original size:18 final size:18
Alignment explanation
Indices: 3973045--3973191 Score: 99
Period size: 18 Copynumber: 8.3 Consensus size: 18
3973035 AAAAATATGA
*
3973045 AAATTTTTGAAAACACGG
1 AAATTTTTTAAAACACGG
3973063 AAA-TTTTTAAAACACGG
1 AAATTTTTTAAAACACGG
* * *
3973080 GAATTTTTAAAAACA-TG
1 AAATTTTTTAAAACACGG
* *
3973097 AAAATTTTTGAAACACCGG
1 AAATTTTTTAAAACA-CGG
* *
3973116 -AA-TTTTGAAAATAC-G
1 AAATTTTTTAAAACACGG
* * *
3973131 AGGATTCTTGAAAACAC-G
1 A-AATTTTTTAAAACACGG
**
3973149 AAGATTTTTTAAAACACAA
1 AA-ATTTTTTAAAACACGG
*
3973168 AAATTTTTTAAAATACGG
1 AAATTTTTTAAAACACGG
3973186 AAATTT
1 AAATTT
3973192 GAAATACGGA
Statistics
Matches: 99, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
15 1 0.01
16 1 0.01
17 36 0.36
18 58 0.59
19 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (18 bp):
AAATTTTTTAAAACACGG
Found at i:3973808 original size:22 final size:21
Alignment explanation
Indices: 3973773--3973814 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3973763 GCAATTCGGG
* *
3973773 CCTTTTTTCTTTTTTGTTTTTT
1 CCTTTTCTCCTTTTT-TTTTTT
3973795 CCTTTTCTCCTTTTTTTTTT
1 CCTTTTCTCCTTTTTTTTTT
3973815 GTGCAGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (21 bp):
CCTTTTCTCCTTTTTTTTTTT
Found at i:3973971 original size:19 final size:20
Alignment explanation
Indices: 3973949--3973986 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3973939 TGGGCCTGGC
*
3973949 CTGCTGCTGTTT-TTTTTTG
1 CTGCTGCTATTTCTTTTTTG
3973968 CTGCTGCTATTTCTTTTTT
1 CTGCTGCTATTTCTTTTTT
3973987 TTTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.03, C:0.18, G:0.16, T:0.63
Consensus pattern (20 bp):
CTGCTGCTATTTCTTTTTTG
Found at i:3973993 original size:11 final size:11
Alignment explanation
Indices: 3973977--3974008 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
3973967 GCTGCTGCTA
3973977 TTTCTTTTTTT
1 TTTCTTTTTTT
3973988 TTTC-TTTTTT
1 TTTCTTTTTTT
3973998 TTTCTTTTTTT
1 TTTCTTTTTTT
3974009 GGGCTGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3974133 original size:8 final size:7
Alignment explanation
Indices: 3974120--3974168 Score: 53
Period size: 8 Copynumber: 6.3 Consensus size: 7
3974110 ATTTGTTTAT
3974120 TTTTTTC
1 TTTTTTC
3974127 TTCTTTTTC
1 -T-TTTTTC
3974136 TTTCTTTC
1 TTT-TTTC
3974144 TTTTTCTC
1 TTTTT-TC
3974152 TTTTTTC
1 TTTTTTC
3974159 TTTCTTTC
1 TTT-TTTC
3974167 TT
1 TT
3974169 CTTCTTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 9 0.24
8 22 0.59
9 6 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:3974141 original size:4 final size:4
Alignment explanation
Indices: 3974132--3974168 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3974122 TTTTCTTCTT
3974132 TTTC TTTC TTTC TTT- TTCTC TTT- TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TT
3974169 CTTCTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 5 0.17
4 23 0.77
5 2 0.07
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3974146 original size:14 final size:14
Alignment explanation
Indices: 3974119--3974161 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3974109 TATTTGTTTA
3974119 TTTT-TTTC-TTCT
1 TTTTCTTTCTTTCT
3974131 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
*
3974145 TTTTCTCTTTTTTCT
1 TTTTCT-TTCTTTCT
3974160 TT
1 TT
3974162 CTTTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 10 0.37
15 9 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:3974156 original size:23 final size:22
Alignment explanation
Indices: 3974096--3974174 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
3974086 CTGTGATGTA
*
3974096 TTTCTTTTTCTTTTATTTGTTT-
1 TTTCTTTTTCTTTT-TTTCTTTC
*
3974118 ATT-TTTTTCTTCTTTTTCTTTC
1 TTTCTTTTTCTT-TTTTTCTTTC
3974140 TTTCTTTTTCTCTTTTTTCTTTC
1 TTTCTTTTTCT-TTTTTTCTTTC
*
3974163 TTTCTTCTTCTT
1 TTTCTTTTTCTT
3974175 CCTTCCCTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 14 0.29
22 7 0.14
23 27 0.55
24 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (22 bp):
TTTCTTTTTCTTTTTTTCTTTC
Found at i:3974475 original size:23 final size:23
Alignment explanation
Indices: 3974431--3974475 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3974421 GCCCTTTGGC
* *
3974431 TTGCTGCTTTTTGTTTGATTTTT
1 TTGCTGCTTTTTCTTAGATTTTT
3974454 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
3974476 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.04, C:0.11, G:0.18, T:0.67
Consensus pattern (23 bp):
TTGCTGCTTTTTCTTAGATTTTT
Found at i:3974841 original size:30 final size:29
Alignment explanation
Indices: 3974796--3974878 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
3974786 AAAGTCTAAC
* **
3974796 GGTCGAAATGT-AATTTTAGAAATTTTTGG
1 GGTCAAAATGTAAATTTTAGAAAAGTTT-G
*
3974825 GGTTAAAATGTAAATTTTAGAAAAGTTTG
1 GGTCAAAATGTAAATTTTAGAAAAGTTTG
3974854 GGTCAAAATGTAAATTTT-GAAAAGT
1 GGTCAAAATGTAAATTTTAGAAAAGT
3974879 ATAGGGGTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 7 0.15
29 27 0.56
30 14 0.29
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
GGTCAAAATGTAAATTTTAGAAAAGTTTG
Found at i:3974890 original size:29 final size:28
Alignment explanation
Indices: 3974801--3974890 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
3974791 CTAACGGTCG
**
3974801 AAATGT-AATTTTAGAAATTTTTGGGGTTA
1 AAATGTAAATTTTAGAAA-AGTTGGGG-TA
*
3974830 AAATGTAAATTTTAGAAAAGTTTGGGTCA
1 AAATGTAAATTTTAGAAAAGTTGGGGT-A
3974859 AAATGTAAATTTT-GAAAAGTATAGGGGTA
1 AAATGTAAATTTTAGAAAAGT-T-GGGGTA
3974888 AAA
1 AAA
3974891 ATGCAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.15
29 30 0.57
30 15 0.28
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (28 bp):
AAATGTAAATTTTAGAAAAGTTGGGGTA
Found at i:3975488 original size:79 final size:74
Alignment explanation
Indices: 3975089--3976202 Score: 1104
Period size: 74 Copynumber: 14.6 Consensus size: 74
3975079 CTCGGCGTGC
* * * ** *
3975089 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGA-TCTTCGAAAAAC--AAATATCAAAAA
1 GACCCGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTAAAAAAACATAAAT-TAAAAAA
3975151 TACCTC-GACATGT
64 TACCTCAG-C--GT
* * ** * * *
3975164 GCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTT-GAAAAACATGAATTGAAAAAT
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAACATAAATTAAAAAAT
*
3975228 ACCTCGGCGT
65 ACCTCAGCGT
* * * * *
3975238 GACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAACAGAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAACATAAA-TT-AAA-A
* * *
3975302 AACACCTCGGCAT
62 AATACCTCAGCGT
** * * * **
3975315 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAACATAAA-TT-AAA-A
* *
3975380 AATACCTCGGCAT
62 AATACCTCAGCGT
** * * * **
3975393 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTTAAAAG
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTAAAAAAACATAAA-TT-AAA-
* *
3975458 AAATACCTCGGCAT
61 AAATACCTCAGCGT
** * * * *
3975472 GGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAACAGAAATTTA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTTT---AAAAAAACATAAA-TT-
3975537 AAAGAAATACCTCAGCGT
58 AAA-AAATACCTCAGCGT
* * * *
3975555 GACCTGAGGCACAACTCACCTCTCATATTATGAGTTGA-TTTAAAAAAATACATAAATT-AAAAA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAA-ACATAAATTAAAAAA
3975618 TACCTCAGCGT
64 TACCTCAGCGT
*
3975629 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAGACTGAAATT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAACA-T-AAATTAAAAAA
3975692 TACCTCAGCGT
64 TACCTCAGCGT
*
3975703 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAAAATAGAAATTTAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT-AAAAAAACAT--AAA-TTAAA
3975768 AAATACCTCAGCGT
61 AAATACCTCAGCGT
* *
3975782 GACCCCAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACATAAATT-AAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAA-ACATAAATTAAAAAAT
3975846 ACCTCAGCGT
65 ACCTCAGCGT
* *
3975856 GACCCGAGGCTTAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACATAAATT-AAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAA-ACATAAATTAAAAAAT
3975920 ACCTCAGCGT
65 ACCTCAGCGT
* * **
3975930 GAGCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACCGAAATT-AAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAA-ACATAAATTAAAAAAT
3975994 ACCTCAGCGT
65 ACCTCAGCGT
** *
3976004 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTTCTTTTTTAAAAAAAAGCAGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAG-TTGATTTTT-AAAAAAA-CATAAA-TTAAAA
3976069 AATACCTCAGCGT
62 AATACCTCAGCGT
*
3976082 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAATT-A
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT--AAAAA-A-ACA-TAAATTAA
3976146 AAAATACCTCAGCGT
60 AAAATACCTCAGCGT
3976161 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
3976203 TTGAAAAAAA
Statistics
Matches: 942, Mismatches: 63, Indels: 65
0.88 0.06 0.06
Matches are distributed among these distances:
72 2 0.00
73 23 0.02
74 336 0.36
75 51 0.05
76 37 0.04
77 85 0.09
78 144 0.15
79 187 0.20
80 13 0.01
81 4 0.00
83 60 0.06
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (74 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAACATAAATTAAAAAATA
CCTCAGCGT
Found at i:3975930 original size:301 final size:305
Alignment explanation
Indices: 3975165--3976201 Score: 1230
Period size: 301 Copynumber: 3.4 Consensus size: 305
3975155 TCGACATGTG
* * *
3975165 CCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTG---AAAA-ACATGAATTGAAAA
1 CCCC-AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGACATAAATTAAAAA
* * * * *
3975226 ATACCTCGGCGTGACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGA
65 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT-AAAAAAAGA
* * * * * ** * * *
3975291 AATTTAAA--AGAAACACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
128 CA--TAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT
*** * * ** *
3975354 TTTTTGAAAA-ACAT-AAATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTC
190 TTTAAAAAAAGAC-TGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-
* * ** * * * *
3975417 GCAATATGAGTTGATTTTTTTGAAAAACAT--AAATTTAAAAGAAATACCTCGGCATGG
249 GTATTATGAGTTGATTTTTTAAAAAAAAATAGAAATTT-AAA-AAATACCTCAGCGTGA
* * * * *
3975474 TCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAACAGAAATTTAAA
1 CCCCAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAAGACATAAA-TT-AA
* * *
3975539 AGAAATACCTCAGCGTGACCTGAGGCACAACTCACCTCTCATATTATGAGTTGA-TTTAAAAAAA
62 A-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAA
*
3975603 TACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
126 GACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
3975668 TTAAAAAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTAT
191 TTAAAAAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTAT
3975733 GAGTTGATTTTTTAAAAAAAAAATAGAAATTTAAAAAATACCTCAGCGTGA
256 GAGTTGATTTTTT-AAAAAAAAATAGAAATTTAAAAAATACCTCAGCGTGA
* *
3975784 CCCCAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTT-AAAAAAAGACATAAATT-AAAAA
1 CCCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGACATAAATTAAAAAA
*
3975845 TACCTCAGCGTGACCCGAGGCTTAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAGACAT
66 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAGACAT
*
3975909 AAATTAAAAATACCTCAGCGTGAGCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
131 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
*
3975974 AAAAGACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
196 AAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
** **
3976039 TCTTTTTTAAAAAAAAGCAGAAATTTAAAAAATACCTCAGCGTGA
261 GATTTTTTAAAAAAAAATAGAAATTTAAAAAATACCTCAGCGTGA
* * * *
3976084 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAATT-AA
1 CCCCAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAA-AGACA-TAAATTAAA
3976147 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTT
63 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTT
3976202 TTTGAAAAAA
Statistics
Matches: 643, Mismatches: 63, Indels: 48
0.85 0.08 0.06
Matches are distributed among these distances:
300 82 0.13
301 182 0.28
302 6 0.01
303 6 0.01
304 6 0.01
305 75 0.12
306 4 0.01
308 30 0.05
309 32 0.05
310 76 0.12
311 5 0.01
312 10 0.02
313 27 0.04
314 50 0.08
315 5 0.01
316 2 0.00
317 45 0.07
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (305 bp):
CCCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGACATAAATTAAAAAA
TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAGACAT
AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
AAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTTTAAAAAAAAATAGAAATTTAAAAAATACCTCAGCGTGA
Found at i:3977110 original size:9 final size:10
Alignment explanation
Indices: 3977096--3977176 Score: 68
Period size: 10 Copynumber: 8.7 Consensus size: 10
3977086 TTCATCTTGA
3977096 TTTTTTTCT-
1 TTTTTTTCTG
**
3977105 TTTTTTTCCA
1 TTTTTTTCTG
3977115 TTTTTTT-TG
1 TTTTTTTCTG
3977124 --TTTTT-TG
1 TTTTTTTCTG
*
3977131 -TTTTGTCTG
1 TTTTTTTCTG
3977140 TTTTTTTCTG
1 TTTTTTTCTG
*
3977150 TTTTTTCTCTA
1 TTTTTT-TCTG
3977161 TTTTTTT-TG
1 TTTTTTTCTG
3977170 TTTTTTT
1 TTTTTTT
3977177 AAGCATAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
7 7 0.12
8 4 0.07
9 18 0.30
10 22 0.37
11 9 0.15
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTG
Found at i:3977118 original size:11 final size:9
Alignment explanation
Indices: 3977096--3977176 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
3977086 TTCATCTTGA
3977096 TTTTTTTCT
1 TTTTTTTCT
*
3977105 TTTTTTTCC
1 TTTTTTTCT
*
3977114 ATTTTTT-T
1 TTTTTTTCT
*
3977122 TGTTTTT-T
1 TTTTTTTCT
* *
3977130 GTTTTGTCT
1 TTTTTTTCT
3977139 GTTTTTTTCT
1 -TTTTTTTCT
3977149 GTTTTTTCTCT
1 -TTTTTT-TCT
3977160 ATTTTTTT-T
1 -TTTTTTTCT
3977169 GTTTTTTT
1 -TTTTTTT
3977177 AAGCATAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
8 10 0.18
9 23 0.40
10 15 0.26
11 9 0.16
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:3977146 original size:19 final size:20
Alignment explanation
Indices: 3977124--3977173 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3977114 ATTTTTTTTG
*
3977124 TTTTTTGTTTTGTCTGT-TT
1 TTTTTTGTTTTGTCTCTATT
* *
3977143 TTTTCTGTTTTTTCTCTATT
1 TTTTTTGTTTTGTCTCTATT
3977163 TTTTTTGTTTT
1 TTTTTTGTTTT
3977174 TTTAAGCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTTTGTTTTGTCTCTATT
Found at i:3982772 original size:18 final size:17
Alignment explanation
Indices: 3982745--3982959 Score: 164
Period size: 18 Copynumber: 12.2 Consensus size: 17
3982735 GAAACATTTT
3982745 TTTTTGAAAACACGAAAAA
1 TTTTT-AAAACACG-AAAA
*
3982764 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
3982781 -TTTTAGAGACACGAAAA
1 TTTTTA-AAACACGAAAA
* *
3982798 TTCTTAAAAATACGAAAA
1 TT-TTTAAAACACGAAAA
*
3982816 TTTTTGAAAACACGGAAA
1 TTTTT-AAAACACGAAAA
**
3982834 TTTTTAAAACACGGGAA
1 TTTTTAAAACACGAAAA
*
3982851 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
* * *
3982869 TTTTTGAGACACCG-GAA
1 TTTTTAAAACA-CGAAAA
* * **
3982886 TTTTGAAAATACGAGGA
1 TTTTTAAAACACGAAAA
* *
3982903 TTCTTGAAAACACGAAGAT
1 TT-TTTAAAACACGAA-AA
3982922 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
3982939 TTTTTAAAAATACGAAAA
1 TTTTT-AAAACACGAAAA
3982957 TTT
1 TTT
3982960 GAAATACGGA
Statistics
Matches: 157, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
16 7 0.04
17 53 0.34
18 87 0.55
19 10 0.06
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:3982818 original size:35 final size:35
Alignment explanation
Indices: 3982745--3982959 Score: 148
Period size: 35 Copynumber: 6.1 Consensus size: 35
3982735 GAAACATTTT
* * *
3982745 TTTTTGAAAACACGAAAAATTTTTAAAACACGAGAA
1 TTTTAGAAAACACG-AAAATTTTAAAAACACGAAAA
* *
3982781 TTTTAG-AGACACGAAAATTCTTAAAAATACGAAAA
1 TTTTAGAAAACACGAAAATT-TTAAAAACACGAAAA
* * * **
3982816 TTTTTGAAAACACGGAAATTTTTAAAACACGGGAA
1 TTTTAGAAAACACGAAAATTTTAAAAACACGAAAA
* * ** * *
3982851 TTTTTGAAAACATGAAAATTTTTGAGACACCG-GAA
1 TTTTAGAAAACACGAAAATTTTAAAAACA-CGAAAA
* ** * *
3982886 TTTT-GAAAATACGAGGATTCTTGAAAACACGAAGA
1 TTTTAGAAAACACGAAAATT-TTAAAAACACGAAAA
** *
3982921 TTTTTTAAAACACGAAAATTTTTAAAAATACGAAAA
1 TTTTAGAAAACACGAAAA-TTTTAAAAACACGAAAA
3982957 TTT
1 TTT
3982960 GAAATACGGA
Statistics
Matches: 140, Mismatches: 32, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
34 19 0.14
35 77 0.55
36 42 0.30
37 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTAGAAAACACGAAAATTTTAAAAACACGAAAA
Found at i:3982828 original size:53 final size:52
Alignment explanation
Indices: 3982748--3982934 Score: 184
Period size: 53 Copynumber: 3.6 Consensus size: 52
3982738 ACATTTTTTT
* *
3982748 TTGAAAACACGAAAAATTTTT-AAAACACGAGAATTTTAGAGACACGAAAATTC
1 TTGAAAACACG-AAAATTTTTGAAAACACG-GAATTTTAGAAACACGAGAATTC
* * * *
3982801 TTAAAAATACGAAAATTTTTGAAAACACGGAAATTTTTA-AAACACGGGAATTT
1 TTGAAAACACGAAAATTTTTGAAAACACGG-AA-TTTTAGAAACACGAGAATTC
* * * *
3982854 TTGAAAACATGAAAATTTTTG-AGACACCGGAATTTT-GAAAATACGAGGATTC
1 TTGAAAACACGAAAATTTTTGAAAACA-CGGAATTTTAG-AAACACGAGAATTC
* *
3982906 TTGAAAACACGAAGATTTTTTAAAACACG
1 TTGAAAACACGAAAATTTTTGAAAACACG
3982935 AAAATTTTTA
Statistics
Matches: 109, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
51 4 0.04
52 46 0.42
53 54 0.50
54 5 0.05
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (52 bp):
TTGAAAACACGAAAATTTTTGAAAACACGGAATTTTAGAAACACGAGAATTC
Found at i:3983561 original size:6 final size:7
Alignment explanation
Indices: 3983543--3983576 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3983533 CAATTCGGGC
3983543 CTTTTTT
1 CTTTTTT
3983550 CTTTTTT
1 CTTTTTT
3983557 CTTTTTT
1 CTTTTTT
*
3983564 GTTTTTT
1 CTTTTTT
3983571 CCTTTT
1 -CTTTT
3983577 CTCCTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
CTTTTTT
Found at i:3983748 original size:18 final size:19
Alignment explanation
Indices: 3983725--3983760 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3983715 TGGGCCTGGC
*
3983725 CTGCTGCTGTTT-TTTTTG
1 CTGCTGCTATTTCTTTTTG
3983743 CTGCTGCTATTTCTTTTT
1 CTGCTGCTATTTCTTTTT
3983761 TTTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.03, C:0.19, G:0.17, T:0.61
Consensus pattern (19 bp):
CTGCTGCTATTTCTTTTTG
Found at i:3983870 original size:8 final size:8
Alignment explanation
Indices: 3983857--3983919 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
3983847 TTTCTTTTTC
*
3983857 TTTTATTT
1 TTTTCTTT
*
3983865 TTTTATTT
1 TTTTCTTT
3983873 TTTTCTTCT
1 TTTTCTT-T
3983882 TTTTCTTT
1 TTTTCTTT
*
3983890 CTTTCTTT
1 TTTTCTTT
*
3983898 TTCTC-TT
1 TTTTCTTT
3983905 TTTTCTTT
1 TTTTCTTT
*
3983913 CTTTCTT
1 TTTTCTT
3983920 CTTCTTCCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
7 6 0.13
8 33 0.70
9 8 0.17
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:3983892 original size:4 final size:4
Alignment explanation
Indices: 3983883--3983919 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3983873 TTTTCTTCTT
3983883 TTTC TTTC TTTC TTT- TTCTC TTT- TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TT
3983920 CTTCTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 5 0.17
4 23 0.77
5 2 0.07
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3983897 original size:14 final size:14
Alignment explanation
Indices: 3983870--3983912 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3983860 TATTTTTTTA
3983870 TTTT-TTTC-TTCT
1 TTTTCTTTCTTTCT
3983882 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
*
3983896 TTTTCTCTTTTTTCT
1 TTTTCT-TTCTTTCT
3983911 TT
1 TT
3983913 CTTTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 10 0.37
15 9 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:3983907 original size:23 final size:22
Alignment explanation
Indices: 3983847--3983925 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 22
3983837 CTGTGATGTA
3983847 TTTCTTTTTCTTTTATTT-TTT-
1 TTTCTTTTTCTTTT-TTTCTTTC
3983868 TATT-TTTTTCTTCTTTTTCTTTC
1 T-TTCTTTTTCTT-TTTTTCTTTC
3983891 TTTCTTTTTCTCTTTTTTCTTTC
1 TTTCTTTTTCT-TTTTTTCTTTC
*
3983914 TTTCTTCTTCTT
1 TTTCTTTTTCTT
3983926 CCTTCCCTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
21 12 0.24
22 10 0.20
23 28 0.55
24 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTCTTTTTTTCTTTC
Found at i:3984225 original size:22 final size:22
Alignment explanation
Indices: 3984182--3984225 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3984172 GCCCTTTGGC
* *
3984182 TTGCTGCTTTTTGTTTGATTTT
1 TTGCTGCTTTTTCTTAGATTTT
3984204 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
3984226 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.05, C:0.11, G:0.18, T:0.66
Consensus pattern (22 bp):
TTGCTGCTTTTTCTTAGATTTT
Found at i:3984576 original size:29 final size:29
Alignment explanation
Indices: 3984458--3984643 Score: 119
Period size: 30 Copynumber: 6.2 Consensus size: 29
3984448 GCTTCTAGGG
* * *
3984458 CAAAAGTGTAATTTTAGCAAAAATAT-GGGC
1 CAAAA-TGTAATTTTAG-AAAAGTTTGGGGT
* *
3984488 CAAAATGTAATTTCTTG-AGAGTTTAGGGGT
1 CAAAATGTAATTT-TAGAAAAGTTT-GGGGT
* * **
3984518 CAAAGTGCAATTTT-GAGAAAGTCTAAGGGT
1 CAAAATGTAATTTTAGA-AAAGT-TTGGGGT
* **
3984548 CGAAATGTAATTTTAGAAATTTTTGGGGT
1 CAAAATGTAATTTTAGAAAAGTTTGGGGT
*
3984577 TAAAATGTAAATTTTAGAAAAGTTTGGGGT
1 CAAAATGT-AATTTTAGAAAAGTTTGGGGT
* *
3984607 CAAAATGTAAAATTT-GAAAAGTATAGGGGT
1 CAAAATGT-AATTTTAGAAAAGT-TTGGGGT
*
3984637 AAAAATG
1 CAAAATG
3984644 CAAAAAAATA
Statistics
Matches: 122, Mismatches: 25, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
28 5 0.04
29 27 0.22
30 87 0.71
31 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAAGTTTGGGGT
Found at i:3985007 original size:74 final size:76
Alignment explanation
Indices: 3984820--3985493 Score: 581
Period size: 79 Copynumber: 8.7 Consensus size: 76
3984810 AGAAATCGAG
* * * * * * *
3984820 AATAGCTCGGCGTGCGACCCGAGACTCAATTCACCTCTTGGATTATGAGTTGATCTTCGAAAAAC
1 AATACCTCGGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
* *
3984885 ---AAATATCAAA
64 ATGAAATTTAAAA
* * **
3984895 AATACCTCGACATGTGCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTGAAAAAC
1 AATACCTCGGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
*
3984960 ATG-AA-TTGAAA
64 ATGAAATTTAAAA
*
3984971 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA-
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAT
3985035 GAAATTTAAAAGA
66 GAAATTT-AAA-A
* * ** * *
3985048 AACACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAC
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAAAAC
3985113 AT-AAATTTAAAAGA
64 ATGAAATTT-AAA-A
* ** * *
3985127 AATACCTCGGCATGGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAA
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTG-----A
3985192 AAAACA-GAAATTTAAAAGA
59 AAAACATGAAATTT-AAA-A
* * * * ** ***
3985211 AATACCTCAGCGTGACCTGAGGCACAATTCACCTCTCATATTATGAGTTGATTTAAAAAAATACA
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAA-ACA
3985276 T-AAA-TT-AAA
65 TGAAATTTAAAA
* * ** *
3985285 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAAGA
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT-TGAAAAACA
3985349 CTGAAA-TT-AAA
65 -TGAAATTTAAAA
* *
3985360 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAA-A
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAACA
*
3985423 TAGAAATTAAATTAAA
65 T-GAAATT---TAAAA
* *
3985439 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT
1 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
3985494 TTGAAAAAAA
Statistics
Matches: 522, Mismatches: 47, Indels: 57
0.83 0.08 0.09
Matches are distributed among these distances:
73 20 0.04
74 99 0.19
75 118 0.23
76 20 0.04
77 57 0.11
78 12 0.02
79 134 0.26
82 3 0.01
84 59 0.11
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (76 bp):
AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAT
GAAATTTAAAA
Found at i:3986454 original size:19 final size:20
Alignment explanation
Indices: 3986432--3986469 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3986422 TGGGCCTGGC
*
3986432 CTGCTGCTGTTT-TTTTTTG
1 CTGCTGCTATTTCTTTTTTG
3986451 CTGCTGCTATTTCTTTTTT
1 CTGCTGCTATTTCTTTTTT
3986470 TTTCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.03, C:0.18, G:0.16, T:0.63
Consensus pattern (20 bp):
CTGCTGCTATTTCTTTTTTG
Found at i:3986594 original size:8 final size:9
Alignment explanation
Indices: 3986567--3986606 Score: 62
Period size: 9 Copynumber: 4.2 Consensus size: 9
3986557 TTGTGATGTA
3986567 TTTATTTTTCT
1 TTTA-TTTT-T
3986578 TTTATTTTT
1 TTTATTTTT
3986587 TTTATTTTT
1 TTTATTTTT
3986596 TTTATTTTT
1 TTTATTTTT
3986605 TT
1 TT
3986607 CTTTCTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 21 0.72
10 4 0.14
11 4 0.14
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:3986611 original size:4 final size:4
Alignment explanation
Indices: 3986604--3986656 Score: 61
Period size: 4 Copynumber: 12.5 Consensus size: 4
3986594 TTTTTATTTT
* *
3986604 TTTC TTTC TCTTT TTTC TTTC TTTTC TTTC TCTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC T-TTC TTTC TTTC -TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
3986655 TT
1 TT
3986657 CTTCCTTCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 32 0.76
5 10 0.24
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3986617 original size:13 final size:13
Alignment explanation
Indices: 3986601--3986656 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
3986591 TTTTTTTTAT
3986601 TTTTTTCTTTCTC
1 TTTTTTCTTTCTC
3986614 TTTTTTC-TT-TC
1 TTTTTTCTTTCTC
3986625 --TTTTCTTTCTC
1 TTTTTTCTTTCTC
3986636 TTTTTTCTTTCT-
1 TTTTTTCTTTCTC
*
3986648 TTCTTTCTT
1 TTTTTTCTT
3986657 CTTCCTTCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 4 0.11
12 10 0.26
13 17 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTCTC
Found at i:3986617 original size:22 final size:21
Alignment explanation
Indices: 3986571--3986655 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 21
3986561 GATGTATTTA
*
3986571 TTTTTCTTTTATTTTT-TTTAT-
1 TTTTT-TTTT-TTTTTCTTTCTC
3986592 TTTTTTTATTTTTTTCTTTCTC
1 TTTTTTT-TTTTTTTCTTTCTC
*
3986614 TTTTTTCTTTCTTTTCTTTCTC
1 TTTTTT-TTTTTTTTCTTTCTC
* *
3986636 TTTTTTCTTTCTTTCTTTCT
1 TTTTTTTTTTTTTTCTTTCT
3986656 TCTTCCTTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.13
21 22 0.40
22 25 0.45
23 1 0.02
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTTTTTCTTTCTC
Found at i:3986659 original size:22 final size:21
Alignment explanation
Indices: 3986593--3986655 Score: 99
Period size: 22 Copynumber: 3.0 Consensus size: 21
3986583 TTTTTTTATT
* *
3986593 TTTTTTATTTTTTTCTTTCTC
1 TTTTTTCTTTCTTTCTTTCTC
3986614 TTTTTTCTTTCTTTTCTTTCTC
1 TTTTTTCTTTC-TTTCTTTCTC
3986636 TTTTTTCTTTCTTTCTTTCT
1 TTTTTTCTTTCTTTCTTTCT
3986656 TCTTCCTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 18 0.46
22 21 0.54
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTCTTTCTTTCTC
Found at i:3987324 original size:30 final size:29
Alignment explanation
Indices: 3987189--3987347 Score: 119
Period size: 30 Copynumber: 5.4 Consensus size: 29
3987179 CAAAGCTTCT
*
3987189 GGGG-CAAAAGTGTAATTTTAGCAAA--ATA
1 GGGGTCAAAA-TGTAATTTTAG-AAAGTTTA
* * * *
3987217 TGGGCCAAAATGTAATTTCTTGAGAGTTTA
1 GGGGTCAAAATGTAATTT-TAGAAAGTTTA
* * *
3987247 GGGGTCAAAGTGCAATTTTGAGAAAGTCTA
1 GGGGTCAAAATGTAATTTT-AGAAAGTTTA
* *
3987277 AGGGTCAAAATGTAATTTTAGAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAGTTTA
**
3987306 GGGGTCAAAATGTAAATTTT-GAAAAGTACA
1 GGGGTCAAAATGT-AATTTTAG-AAAGTTTA
*
3987336 GGGGTAAAAATG
1 GGGGTCAAAATG
3987348 CAAAAAAAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
28 13 0.13
29 29 0.28
30 61 0.59
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.30
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAGAAAGTTTA
Found at i:3987346 original size:59 final size:60
Alignment explanation
Indices: 3987223--3987347 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 60
3987213 AATATGGGCC
* * * * *
3987223 AAAATGTAATTTCTTGAGAGTTTAGGGGTCAAAGTGCAATTTTGAGAAAGTCTAAGGGTC
1 AAAATGTAATTTCTAGAAAGTTTAGGGGTCAAAATGAAATTTTGAGAAAGTCTAAGGGTA
* *
3987283 AAAATGTAATTT-TAGAAAGTTTTGGGGTCAAAATGTAAATTTTGA-AAAGTAC-AGGGGTA
1 AAAATGTAATTTCTAGAAAGTTTAGGGGTCAAAATG-AAATTTTGAGAAAGT-CTAAGGGTA
3987342 AAAATG
1 AAAATG
3987348 CAAAAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
59 35 0.62
60 21 0.38
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (60 bp):
AAAATGTAATTTCTAGAAAGTTTAGGGGTCAAAATGAAATTTTGAGAAAGTCTAAGGGTA
Found at i:3987682 original size:26 final size:24
Alignment explanation
Indices: 3987653--3987733 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 24
3987643 ATTATAGAAT
*
3987653 AATATAATAAAATAATTTAAGTTTG
1 AATATAATAAAATAATTTAA-ATTG
*
3987678 AAATATAA-AAATTAAATTTAAATTG
1 -AATATAATAAAAT-AATTTAAATTG
* *
3987703 AATAT-ATAACATAATTTATAACT-
1 AATATAATAAAATAATTTA-AATTG
3987726 AATATAAT
1 AATATAAT
3987734 GAGAAGCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
23 12 0.26
24 13 0.28
25 7 0.15
26 14 0.30
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
AATATAATAAAATAATTTAAATTG
Found at i:3987688 original size:24 final size:23
Alignment explanation
Indices: 3987653--3987720 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 23
3987643 ATTATAGAAT
*
3987653 AATATAATAAAATAATTTAAGTTTG
1 AATAT-ATAAAATAATTTAA-ATTG
3987678 AA-ATATAAAAATTAAATTTAAATTG
1 AATATAT-AAAA-T-AATTTAAATTG
*
3987703 AATATATAACATAATTTA
1 AATATATAAAATAATTTA
3987721 TAACTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 8 0.22
24 7 0.19
25 11 0.30
26 11 0.30
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (23 bp):
AATATATAAAATAATTTAAATTG
Found at i:3989614 original size:10 final size:10
Alignment explanation
Indices: 3989595--3989624 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3989585 ACGAAACAAC
3989595 TTTA-AAAAT
1 TTTATAAAAT
3989604 TTTATAAAAT
1 TTTATAAAAT
3989614 TTTATAAAAT
1 TTTATAAAAT
3989624 T
1 T
3989625 AGTAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:3989680 original size:21 final size:20
Alignment explanation
Indices: 3989656--3989694 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3989646 TTTAAACTTT
3989656 ATTTAAAAATATATAAAAATA
1 ATTTAAAAATAT-TAAAAATA
3989677 ATTTAAAAATATTAAAAA
1 ATTTAAAAATATTAAAAA
3989695 GTTGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAAATATTAAAAATA
Found at i:3989702 original size:19 final size:18
Alignment explanation
Indices: 3989659--3989776 Score: 80
Period size: 19 Copynumber: 6.2 Consensus size: 18
3989649 AAACTTTATT
*
3989659 TAAAAATATATAAAAATAATT
1 TAAAAATAT-TAAAAAT--TG
3989680 TAAAAATATTAAAAAGTTG
1 TAAAAATATTAAAAA-TTG
* * *
3989699 TAAAAGTTCTTAAAAATGG
1 TAAAA-ATATTAAAAATTG
3989718 TAAAAA-AGTATAAAAATTG
1 TAAAAATA-T-TAAAAATTG
* *
3989737 TAAAAAAATTTAAAA-TG
1 TAAAAATATTAAAAATTG
3989754 TAAAAACTATTAAATAATT-
1 TAAAAA-TATTAAA-AATTG
3989773 TAAA
1 TAAA
3989777 TTTTTTTTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
17 8 0.10
18 11 0.14
19 34 0.43
20 16 0.20
21 10 0.13
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (18 bp):
TAAAAATATTAAAAATTG
Done.