Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:1147793 original size:26 final size:28
Alignment explanation
Indices: 1147764--1147821 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 28
1147754 TAATAACATT
1147764 TAAAATTTTATGT-A-ATTTTATAATA-A
1 TAAAATTTTATGTAATATTTTA-AATATA
*
1147790 T-AAATTTTATTTAATATTTTAAATATA
1 TAAAATTTTATGTAATATTTTAAATATA
1147817 TAAAA
1 TAAAA
1147822 AAATAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 10 0.37
26 6 0.22
27 8 0.30
28 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TAAAATTTTATGTAATATTTTAAATATA
Found at i:1147808 original size:27 final size:25
Alignment explanation
Indices: 1147766--1147820 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
1147756 ATAACATTTA
1147766 AAATTTTATGTAATTTTATAATA-AT
1 AAATTTTATGTAATTTTA-AATATAT
*
1147791 AAATTTTATTTAATATTTTAAATATAT
1 AAATTTTATGT-A-ATTTTAAATATAT
1147818 AAA
1 AAA
1147821 AAAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
26 5 0.19
27 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATTTTATGTAATTTTAAATATAT
Found at i:1150002 original size:2 final size:2
Alignment explanation
Indices: 1149995--1150045 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1149985 TCAAAGACTT
1149995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1150037 TA TA TA TA T
1 TA TA TA TA T
1150046 GAACCAAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1151732 original size:20 final size:20
Alignment explanation
Indices: 1151709--1151748 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1151699 TAATATTATT
1151709 TATTTATTCTTTATATGATA
1 TATTTATTCTTTATATGATA
* *
1151729 TATTTGTTTTTTATATGATA
1 TATTTATTCTTTATATGATA
1151749 AAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (20 bp):
TATTTATTCTTTATATGATA
Found at i:1155436 original size:7 final size:8
Alignment explanation
Indices: 1155419--1155443 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1155409 GCGAGAAGAG
1155419 AAAATTAA
1 AAAATTAA
1155427 AAAATTAA
1 AAAATTAA
1155435 AAAATTAA
1 AAAATTAA
1155443 A
1 A
1155444 TGAATAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:1155687 original size:22 final size:22
Alignment explanation
Indices: 1155657--1155716 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1155647 TTTTTAAATT
*
1155657 ATTTGAATTTATTTAAATAAAA
1 ATTTAAATTTATTTAAATAAAA
**
1155679 ATTTAAATTTAATTT-AATAATT
1 ATTTAAATTT-ATTTAAATAAAA
1155701 A-TTAAATTTTATTTAA
1 ATTTAAA-TTTATTTAA
1155717 GTTAATGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 9 0.28
22 19 0.59
23 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTAAATTTATTTAAATAAAA
Found at i:1155895 original size:50 final size:44
Alignment explanation
Indices: 1155774--1155895 Score: 113
Period size: 45 Copynumber: 2.6 Consensus size: 44
1155764 ATTTGTAAAT
*
1155774 TTTAATTTGTTTTAAAATTTAAATAAAAATAATTAAATATAAAAA
1 TTTAATTT-TTTTAAAATTTAAATAAAAATAATCAAATATAAAAA
* *
1155819 -TTATATTTTTTTACTAAA-ATAAATAAAATTAATCAAATTATTTTAAATAA
1 TTTA-ATTTTTTTA--AAATTTAAATAAAAATAATCAAA-TA---TAAA-AA
1155869 TTTAATTTTTTTAAAATTTAATATAAA
1 TTTAATTTTTTTAAAATTTAA-ATAAA
1155896 TTTTTAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
44 8 0.13
45 20 0.32
46 5 0.08
48 3 0.05
49 7 0.11
50 16 0.26
51 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (44 bp):
TTTAATTTTTTTAAAATTTAAATAAAAATAATCAAATATAAAAA
Found at i:1155899 original size:21 final size:21
Alignment explanation
Indices: 1155866--1155905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1155856 TTATTTTAAA
* * *
1155866 TAATTTAATTTTTTTAAAATT
1 TAATATAAATTTTTAAAAATT
1155887 TAATATAAATTTTTAAAAA
1 TAATATAAATTTTTAAAAA
1155906 ATAAAATTTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATAAATTTTTAAAAATT
Found at i:1155918 original size:21 final size:21
Alignment explanation
Indices: 1155867--1155918 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
1155857 TATTTTAAAT
** **
1155867 AATTTAATTTTTTTAAAATTT
1 AATTTAATTTTTAAAAAATAA
*
1155888 AATATAAATTTTTAAAAAATAA
1 AAT-TTAATTTTTAAAAAATAA
1155910 AATTTAATT
1 AATTTAATT
1155919 AAACTCTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTAATTTTTAAAAAATAA
Found at i:1156725 original size:14 final size:15
Alignment explanation
Indices: 1156708--1156738 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1156698 TTTTAAAATC
1156708 AATTTTAAT-TTAAA
1 AATTTTAATCTTAAA
1156722 AATTTTAATCTTAAA
1 AATTTTAATCTTAAA
1156737 AA
1 AA
1156739 AATTCAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAATCTTAAA
Found at i:1158885 original size:43 final size:45
Alignment explanation
Indices: 1158823--1158910 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 45
1158813 CTTTCCACTT
*
1158823 GATTTGGTATAATTTTGGATATGAT-AAAAAAATTGATACAAATA
1 GATTTGGTATAATTTTGGATATAATAAAAAAAATTGATACAAATA
*
1158867 GATTTGGT-TTATTTTGGATATAATAAAAAAAATTGATACAAATA
1 GATTTGGTATAATTTTGGATATAATAAAAAAAATTGATACAAATA
1158911 TGATAAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 14 0.34
44 27 0.66
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (45 bp):
GATTTGGTATAATTTTGGATATAATAAAAAAAATTGATACAAATA
Found at i:1159149 original size:19 final size:21
Alignment explanation
Indices: 1159115--1159156 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1159105 GTGAATAATT
1159115 TTTTAAACTGATTATTA-AAA
1 TTTTAAACTGATTATTATAAA
*
1159135 TTTTAAA-TTATTATTATAAA
1 TTTTAAACTGATTATTATAAA
1159155 TT
1 TT
1159157 ATTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTAAACTGATTATTATAAA
Found at i:1159154 original size:13 final size:13
Alignment explanation
Indices: 1159138--1159162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1159128 ATTAAAATTT
1159138 TAAATTATTATTA
1 TAAATTATTATTA
1159151 TAAATTATTATT
1 TAAATTATTATT
1159163 TATATTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTATTATTA
Found at i:1159574 original size:5 final size:5
Alignment explanation
Indices: 1159564--1159610 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
1159554 TTTTGTGCTT
* *
1159564 TAAAA TAAAA TAAAA TAAAA T--AA TATAA TATAA TAAAA T-AAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1159611 AGATGTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 31 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:1159593 original size:18 final size:18
Alignment explanation
Indices: 1159567--1159608 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1159557 TGTGCTTTAA
*
1159567 AATAAAATAAAATAAAAT
1 AATATAATAAAATAAAAT
*
1159585 AATATAATATAATAAAAT
1 AATATAATAAAATAAAAT
1159603 AA-ATAA
1 AATATAA
1159609 AAAGATGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAATAAAATAAAAT
Found at i:1159936 original size:19 final size:20
Alignment explanation
Indices: 1159912--1159954 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1159902 CACTTGATAA
1159912 AATAATAAAATAT-AAATAT
1 AATAATAAAATATAAAATAT
*
1159931 AATAATATAATATAAAATAT
1 AATAATAAAATATAAAATAT
1159951 AATA
1 AATA
1159955 TAATTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAAAATATAAAATAT
Found at i:1159951 original size:12 final size:12
Alignment explanation
Indices: 1159916--1159957 Score: 66
Period size: 12 Copynumber: 3.3 Consensus size: 12
1159906 TGATAAAATA
1159916 ATAAAATATAAAT
1 ATAAAATAT-AAT
1159929 ATAATAATATAAT
1 ATAA-AATATAAT
1159942 ATAAAATATAAT
1 ATAAAATATAAT
1159954 ATAA
1 ATAA
1159958 TTATGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.43
13 11 0.39
14 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:1159974 original size:26 final size:26
Alignment explanation
Indices: 1159912--1160009 Score: 85
Period size: 26 Copynumber: 3.7 Consensus size: 26
1159902 CACTTGATAA
*
1159912 AATAATAAAATATAAATATAATAATAT
1 AATAATAAAATAT-AATATAATTATAT
1159939 AAT-ATAAAATATAATATAATTATGAT
1 AATAATAAAATATAATATAATTAT-AT
* * * *
1159965 TATAAT-AAATAGAATAAAATTTTTAT
1 AATAATAAAATATAATATAA-TTATAT
*
1159991 AA-AATAAATTATTAATATA
1 AATAATAAAATA-TAATATA
1160010 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
25 13 0.23
26 31 0.54
27 13 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AATAATAAAATATAATATAATTATAT
Found at i:1160043 original size:17 final size:17
Alignment explanation
Indices: 1159996--1160045 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1159986 TTTATAAAAT
*
1159996 AAATTATTAATATATTA
1 AAATTATTAAAATATTA
1160013 AAATT-TATATAAAT-TTA
1 AAATTAT-TA-AAATATTA
1160030 AAATATATTAAAATAT
1 AAAT-TATTAAAATAT
1160046 AATAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 1 0.04
17 18 0.67
18 7 0.26
19 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATTAAAATATTA
Found at i:1165742 original size:17 final size:17
Alignment explanation
Indices: 1165722--1165764 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1165712 GTAATATTAT
1165722 TTATTAAATATTTAAAC
1 TTATTAAATATTTAAAC
* *
1165739 TTATTAAAAATTTAAAT
1 TTATTAAATATTTAAAC
*
1165756 TTAATAAAT
1 TTATTAAAT
1165765 TGTTAACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATTAAATATTTAAAC
Found at i:1166511 original size:16 final size:18
Alignment explanation
Indices: 1166481--1166513 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1166471 CTTTGAAACT
1166481 AAATAGAAAATTAGAGAC
1 AAATAGAAAATTAGAGAC
1166499 AAATA-AAAA-TAGAGA
1 AAATAGAAAATTAGAGA
1166514 GGAATGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (18 bp):
AAATAGAAAATTAGAGAC
Found at i:1167755 original size:15 final size:15
Alignment explanation
Indices: 1167703--1167756 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
1167693 ACCTAAACTT
*
1167703 GAAATAACTCGAACCC
1 GAAATGACT-GAACCC
*
1167719 GAAATGACCTGAATCC
1 GAAATGA-CTGAACCC
1167735 -AGAATGACTGAACCC
1 GA-AATGACTGAACCC
1167750 GAAATGA
1 GAAATGA
1167757 TCCAAATCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 13 0.41
16 17 0.53
17 2 0.06
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (15 bp):
GAAATGACTGAACCC
Found at i:1167770 original size:47 final size:47
Alignment explanation
Indices: 1167717--1167838 Score: 124
Period size: 48 Copynumber: 2.6 Consensus size: 47
1167707 TAACTCGAAC
** *
1167717 CCGAAATGACCTGAATCC-AGAATGA-CTGAACCCGAAATGATCCAAAT
1 CCGAAATGACC-GAATCCGA-AATGATCCAAACCCAAAATGATCCAAAT
* *
1167764 CTGAAATGATCCGAATCCGAAATGATCCAAACCCAAAATGATCTAAAT
1 CCGAAATGA-CCGAATCCGAAATGATCCAAACCCAAAATGATCCAAAT
* *
1167812 CCAAAATGACCCGAACCCGAAAT-ATCC
1 CCGAAATGA-CCGAATCCGAAATGATCC
1167839 TGAATAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
47 23 0.37
48 40 0.63
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (47 bp):
CCGAAATGACCGAATCCGAAATGATCCAAACCCAAAATGATCCAAAT
Found at i:1167771 original size:16 final size:16
Alignment explanation
Indices: 1167748--1167838 Score: 94
Period size: 16 Copynumber: 5.8 Consensus size: 16
1167738 ATGACTGAAC
1167748 CCGAAATGATCCAAAT
1 CCGAAATGATCCAAAT
* *
1167764 CTGAAATGATCCGAAT
1 CCGAAATGATCCAAAT
*
1167780 CCGAAATGATCCAAAC
1 CCGAAATGATCCAAAT
* *
1167796 CCAAAATGATCTAAAT
1 CCGAAATGATCCAAAT
* * * *
1167812 CCAAAATGACCCGAAC
1 CCGAAATGATCCAAAT
1167828 CCGAAAT-ATCC
1 CCGAAATGATCC
1167839 TGAATAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
15 3 0.05
16 58 0.95
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (16 bp):
CCGAAATGATCCAAAT
Found at i:1167803 original size:32 final size:32
Alignment explanation
Indices: 1167748--1167843 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 32
1167738 ATGACTGAAC
* *
1167748 CCGAAATGATCCAAATCTGAAATGATCCGAAT
1 CCGAAATGATCCAAACCCGAAATGATCCGAAT
* **
1167780 CCGAAATGATCCAAACCCAAAATGATCTAAAT
1 CCGAAATGATCCAAACCCGAAATGATCCGAAT
* * *
1167812 CCAAAATGACCCGAACCCGAAAT-ATCCTGAAT
1 CCGAAATGATCCAAACCCGAAATGATCC-GAAT
1167844 AATTAATTCG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 3 0.06
32 49 0.94
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (32 bp):
CCGAAATGATCCAAACCCGAAATGATCCGAAT
Found at i:1167812 original size:48 final size:47
Alignment explanation
Indices: 1167745--1167838 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 47
1167735 AGAATGACTG
* ** * *
1167745 AACCCGAAATGATCCAAATCTGAAATGATCCGAATCCGAAATGATCCA
1 AACCCAAAATGATCCAAATCCAAAATGACCCGAACCCGAAAT-ATCCA
*
1167793 AACCCAAAATGATCTAAATCCAAAATGACCCGAACCCGAAATATCC
1 AACCCAAAATGATCCAAATCCAAAATGACCCGAACCCGAAATATCC
1167839 TGAATAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.17
Consensus pattern (47 bp):
AACCCAAAATGATCCAAATCCAAAATGACCCGAACCCGAAATATCCA
Found at i:1168922 original size:16 final size:15
Alignment explanation
Indices: 1168903--1169017 Score: 50
Period size: 16 Copynumber: 7.2 Consensus size: 15
1168893 CCTGAACTCG
1168903 AAATGACCCGAATCCA
1 AAATGACCCGAA-CCA
* * * *
1168919 AAATAACTCAAACCTG
1 AAATGACCCGAACC-A
* *
1168935 AAATAACCCGAACTCG
1 AAATGACCCGAAC-CA
* *
1168951 AAATGATCTGAATCCA
1 AAATGACCCGAA-CCA
* * *
1168967 AAGTAACCCGAACTCG
1 AAATGACCCGAAC-CA
*
1168983 AAATGACCTGAACCCA
1 AAATGACCCGAA-CCA
*
1168999 AAATGACCTGAACCCA
1 AAATGACCCGAA-CCA
1169015 AAA
1 AAA
1169018 ACAACCTGAA
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
15 3 0.04
16 69 0.92
17 3 0.04
ACGTcount: A:0.45, C:0.28, G:0.12, T:0.15
Consensus pattern (15 bp):
AAATGACCCGAACCA
Found at i:1168954 original size:48 final size:48
Alignment explanation
Indices: 1168896--1169017 Score: 138
Period size: 48 Copynumber: 2.5 Consensus size: 48
1168886 CGATTGACCT
* *
1168896 GAACTCGAAATGACCCGAATCCAAAATAACTCAAAC-CTGAAATAACCC
1 GAACTCGAAATGACCTGAATCCAAAATAACCCAAACTC-GAAATAACCC
* * * * *
1168944 GAACTCGAAATGATCTGAATCCAAAGTAACCCGAACTCGAAATGACCT
1 GAACTCGAAATGACCTGAATCCAAAATAACCCAAACTCGAAATAACCC
* * *
1168992 GAACCCAAAATGACCTGAACCCAAAA
1 GAACTCGAAATGACCTGAATCCAAAA
1169018 ACAACCTGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (48 bp):
GAACTCGAAATGACCTGAATCCAAAATAACCCAAACTCGAAATAACCC
Found at i:1168974 original size:32 final size:32
Alignment explanation
Indices: 1168938--1169000 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1168928 AAACCTGAAA
* *
1168938 TAACCCGAACTCGAAATGATCTGAATCCAAAG
1 TAACCCGAACTCGAAATGACCTGAACCCAAAG
1168970 TAACCCGAACTCGAAATGACCTGAACCCAAA
1 TAACCCGAACTCGAAATGACCTGAACCCAAA
1169001 ATGACCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (32 bp):
TAACCCGAACTCGAAATGACCTGAACCCAAAG
Found at i:1169024 original size:17 final size:16
Alignment explanation
Indices: 1168988--1169027 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1168978 ACTCGAAATG
**
1168988 ACCTGAACCCAAAATG
1 ACCTGAACCCAAAACA
1169004 ACCTGAACCCAAAAACA
1 ACCTGAACCC-AAAACA
1169021 ACCTGAA
1 ACCTGAA
1169028 AATTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.47, C:0.33, G:0.10, T:0.10
Consensus pattern (16 bp):
ACCTGAACCCAAAACA
Found at i:1172691 original size:52 final size:52
Alignment explanation
Indices: 1172608--1172736 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1172598 CGAAATATGA
1172608 AAATTTGCCTGTATGTATCGATACATGTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGTATGTATCGATACATGTCATAGTGTATCGATACATCTGGGC
* *
1172660 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGTATGTATCGATACATGTCATAGTGTATCGATACATCTGGGC
**
1172712 AAATTTGCCTGCGTGTATCGATACA
1 AAATTTGCCTGTATGTATCGATACA
1172737 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGTATGTATCGATACATGTCATAGTGTATCGATACATCTGGGC
Found at i:1172747 original size:52 final size:52
Alignment explanation
Indices: 1172608--1172756 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 52
1172598 CGAAATATGA
1172608 AAATTTGCCTGTATGTATCGATAC-ATG-TCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGTATGTATCGATACAATGATC--AGTGTATCGATACATCTGGGC
* * *
1172660 AAATTTGCCTGTATGTATCGATACATTTCAT-AGTGTATCGATACATTTGGGC
1 AAATTTGCCTGTATGTATCGATACA-ATGATCAGTGTATCGATACATCTGGGC
** *
1172712 AAATTTGCCTGCGTGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGTATGTATCGATACAATGATCAGTGTATCGATACA
1172757 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
54 1 0.01
55 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGTATGTATCGATACAATGATCAGTGTATCGATACATCTGGGC
Found at i:1172763 original size:13 final size:13
Alignment explanation
Indices: 1172745--1172769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1172735 CAAAGATCAG
1172745 TGTATCGATACAA
1 TGTATCGATACAA
1172758 TGTATCGATACA
1 TGTATCGATACA
1172770 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1172835 original size:19 final size:19
Alignment explanation
Indices: 1172811--1172876 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1172801 AGTAGCTTCA
1172811 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
1172830 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
*
1172844 T-TGTATCGATACAATACT
1 TATGTATCGATACAACACT
1172862 TATGTATCGATACAA
1 TATGTATCGATACAA
1172877 ATCGTTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 5 0.12
18 1 0.03
19 24 0.60
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:1172850 original size:13 final size:13
Alignment explanation
Indices: 1172832--1172856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1172822 ACAACACTTA
1172832 TGTATCGATACAT
1 TGTATCGATACAT
1172845 TGTATCGATACA
1 TGTATCGATACA
1172857 ATACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1172854 original size:32 final size:32
Alignment explanation
Indices: 1172813--1172875 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1172803 TAGCTTCATA
1172813 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
1172845 TGTATCGATACAATACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
1172876 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:1173164 original size:52 final size:52
Alignment explanation
Indices: 1173078--1173206 Score: 168
Period size: 52 Copynumber: 2.5 Consensus size: 52
1173068 CGAAATATGA
* *
1173078 AAATTTGCCTGCATGCATCGATACATGTCGTAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGCATCGATACATGTCATAGTGTATCGATACATCTGGGC
* * * *
1173130 AAATTTACCTGTATGTATTGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGCATCGATACATGTCATAGTGTATCGATACATCTGGGC
* * * *
1173182 AAATTTGCCTACGTGTATCGATACA
1 AAATTTACCTGCATGCATCGATACA
1173207 AATATCAGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTACCTGCATGCATCGATACATGTCATAGTGTATCGATACATCTGGGC
Found at i:1173217 original size:52 final size:52
Alignment explanation
Indices: 1173078--1173226 Score: 156
Period size: 52 Copynumber: 2.9 Consensus size: 52
1173068 CGAAATATGA
* * * ** *
1173078 AAATTTGCCTGCATGCATCGATACATGTCGTAGTGTATCGATACATCTGGGC
1 AAATTTACCTACATGTATCGATACAAATCATAGTGTATCGATACATCTGGGC
** * **
1173130 AAATTTACCTGTATGTATTGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTACCTACATGTATCGATACAAATCATAGTGTATCGATACATCTGGGC
* * *
1173182 AAATTTGCCTACGTGTATCGATACAAAT-ATCAGTGTATTGATACA
1 AAATTTACCTACATGTATCGATACAAATCAT-AGTGTATCGATACA
1173227 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTACCTACATGTATCGATACAAATCATAGTGTATCGATACATCTGGGC
Found at i:1174718 original size:5 final size:5
Alignment explanation
Indices: 1174689--1174777 Score: 51
Period size: 5 Copynumber: 17.4 Consensus size: 5
1174679 TTGTGAAAAT
* * *
1174689 TTATA TTCTA TTATTA TTATATA TTCTA TTATA TTA-A -TATA TTCTA
1 TTATA TTATA TTA-TA -T-TATA TTATA TTATA TTATA TTATA TTATA
* *
1174735 TTATA TTA-A TTCTA TTA-A ATATA TTAATA TATATA TATATA TT
1 TTATA TTATA TTATA TTATA TTATA TT-ATA T-TATA T-TATA TT
1174778 CTAATTTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 8 0.12
5 32 0.49
6 17 0.26
7 4 0.06
8 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:1174743 original size:18 final size:18
Alignment explanation
Indices: 1174690--1174766 Score: 95
Period size: 18 Copynumber: 4.3 Consensus size: 18
1174680 TGTGAAAATT
1174690 TATATTCTATTATTATT-A
1 TATATTCTATTA-TATTAA
1174708 TATATTCTATTATATTAA
1 TATATTCTATTATATTAA
1174726 TATATTCTATTATATTAA
1 TATATTCTATTATATTAA
* * *
1174744 TTCTATT-AAATATATTAA
1 -TATATTCTATTATATTAA
1174762 TATAT
1 TATAT
1174767 ATATATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
17 8 0.15
18 40 0.75
19 5 0.09
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTCTATTATATTAA
Found at i:1174768 original size:10 final size:10
Alignment explanation
Indices: 1174700--1174777 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 10
1174690 TATATTCTAT
*
1174700 TATTATTATA
1 TATTAATATA
*
1174710 TATT-CTATTA
1 TATTAATA-TA
1174720 TATTAATATA
1 TATTAATATA
1174730 T-TCT-AT-TA
1 TAT-TAATATA
*
1174738 TATTAAT-TC
1 TATTAATATA
1174747 TATTAA-ATA
1 TATTAATATA
1174756 TATTAATATA
1 TATTAATATA
1174766 TA-T-ATATA
1 TATTAATATA
1174774 TATT
1 TATT
1174778 CTAATTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
8 11 0.20
9 24 0.43
10 19 0.34
11 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (10 bp):
TATTAATATA
Found at i:1174774 original size:18 final size:18
Alignment explanation
Indices: 1174718--1174777 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1174708 TATATTCTAT
*
1174718 TATATTAATATAT-TCTA
1 TATATTAATATATATATA
* *
1174735 TTATATTAAT-TCTATTAAA
1 -TATATTAATATATA-TATA
1174754 TATATTAATATATATATA
1 TATATTAATATATATATA
1174772 TATATT
1 TATATT
1174778 CTAATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.06
18 27 0.79
19 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTAATATATATATA
Found at i:1174803 original size:46 final size:44
Alignment explanation
Indices: 1174702--1174803 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 44
1174692 TATTCTATTA
* *
1174702 TTATTATATAT-TCTATTATATTAATATATTCTATTATATTAAT
1 TTATTATATATATCTAATATATTAATATATTCTATTATAATAAT
*
1174745 TCTATTAAATATAT-TAATATATATATATATATTCTAATT-TAATAAT
1 T-TATTATATATATCTAATATAT-TA-ATATATTCT-ATTATAATAAT
1174791 TTATCTATATATA
1 TTAT-TATATATA
1174804 ATTTATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
43 1 0.02
44 16 0.33
45 6 0.12
46 23 0.47
47 3 0.06
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (44 bp):
TTATTATATATATCTAATATATTAATATATTCTATTATAATAAT
Found at i:1177180 original size:2 final size:2
Alignment explanation
Indices: 1177173--1177197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1177163 TTGCTAGTAT
1177173 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 T
1177198 GAAAGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1177834 original size:9 final size:10
Alignment explanation
Indices: 1177809--1177833 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1177799 AAATTAAAAA
1177809 TTTTTTAATT
1 TTTTTTAATT
1177819 TTTTTTAATT
1 TTTTTTAATT
1177829 TTTTT
1 TTTTT
1177834 ATATTCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:1178848 original size:20 final size:20
Alignment explanation
Indices: 1178819--1178863 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1178809 ACTATTAAGC
* *
1178819 ATTTATTATAT-TTAATACTT
1 ATTTAATATATATTAA-AATT
1178839 ATTTAATATATATTAAAATT
1 ATTTAATATATATTAAAATT
1178859 ATTTA
1 ATTTA
1178864 TTTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAATATATATTAAAATT
Found at i:1178874 original size:11 final size:11
Alignment explanation
Indices: 1178822--1178880 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1178812 ATTAAGCATT
1178822 TATTATATTTAA
1 TATT-TATTTAA
*
1178834 TACTTATTTAA
1 TATTTATTTAA
* *
1178845 TATATATTAAAA
1 TATTTATT-TAA
1178857 TTATTTATTTAA
1 -TATTTATTTAA
*
1178869 TATTTAATTAA
1 TATTTATTTAA
1178880 T
1 T
1178881 TAACATAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 24 0.63
12 7 0.18
13 7 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:1179670 original size:14 final size:14
Alignment explanation
Indices: 1179653--1179691 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1179643 AATTTTAACT
*
1179653 TTTTTTAAATATTA
1 TTTTTTAAATATAA
*
1179667 TTTTTTAAAAATAA
1 TTTTTTAAATATAA
*
1179681 TTATTTAAATA
1 TTTTTTAAATA
1179692 AATATAGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTTAAATATAA
Found at i:1180163 original size:17 final size:18
Alignment explanation
Indices: 1180143--1180184 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
1180133 TAAAATTTTT
1180143 TAATATCTTAAAAT-A-TA
1 TAATAT-TTAAAATAATTA
1180160 TAATTATTTAAAATAATTA
1 TAA-TATTTAAAATAATTA
1180179 TAATAT
1 TAATAT
1180185 AATAAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.45
18 7 0.32
19 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATTTAAAATAATTA
Found at i:1180170 original size:25 final size:25
Alignment explanation
Indices: 1180100--1180171 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
1180090 TATAATATAA
* *
1180100 TATAAATATATAAATATTTCAAATTT
1 TATAAATATATAATTATTT-AAATCT
*
1180126 TATATAATA-A-AATTTTTTAATATCT
1 TATA-AATATATAATTATTTAA-ATCT
1180151 TA-AAATATATAATTATTTAAA
1 TATAAATATATAATTATTTAAA
1180172 ATAATTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
23 4 0.11
24 5 0.13
25 20 0.53
26 5 0.13
27 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
TATAAATATATAATTATTTAAATCT
Found at i:1181992 original size:32 final size:33
Alignment explanation
Indices: 1181954--1182049 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 33
1181944 AAAAAAATTA
1181954 AATTAAATTATTATTATTTAATTAATAAAATAT
1 AATTAAATTATTATTATTTAATTAATAAAATAT
1181987 -ATTAAATT-TTA--ATTTAATT-ATAAAA-AT
1 AATTAAATTATTATTATTTAATTAATAAAATAT
* *
1182014 AATTTATAA-TATTATTA--TAAATAATAAAATAA
1 AA-TTA-AATTATTATTATTTAATTAATAAAATAT
1182046 AATT
1 AATT
1182050 TTACATCAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 12 0.23
30 9 0.17
31 11 0.21
32 12 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTAAATTATTATTATTTAATTAATAAAATAT
Found at i:1182023 original size:24 final size:24
Alignment explanation
Indices: 1181991--1182040 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1181981 AAATATATTA
1181991 AATTTTAAT-TTAATTATAAA-AAT
1 AATTTTAATATT-ATTATAAATAAT
1182014 AATTTATAATATTATTATAAATAAT
1 AATTT-TAATATTATTATAAATAAT
1182039 AA
1 AA
1182041 AATAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTTAATATTATTATAAATAAT
Found at i:1182802 original size:11 final size:11
Alignment explanation
Indices: 1182786--1182830 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1182776 TATGCTTATG
1182786 TATTTATATTA
1 TATTTATATTA
1182797 TATTTATATT-
1 TATTTATATTA
1182807 T-TTT-TATTA
1 TATTTATATTA
*
1182816 TTTTTCATATTA
1 TATTT-ATATTA
1182828 TAT
1 TAT
1182831 CTACATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 4 0.14
11 10 0.34
12 7 0.24
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1184543 original size:17 final size:17
Alignment explanation
Indices: 1184518--1184556 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1184508 AGTAACAAAA
1184518 TATTATAATTATTTTT-T
1 TATTATAATT-TTTTTAT
*
1184535 TATTTTAATTTTTTTAT
1 TATTATAATTTTTTTAT
1184552 TATTA
1 TATTA
1184557 ATATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATAATTTTTTTAT
Found at i:1184549 original size:15 final size:15
Alignment explanation
Indices: 1184528--1184558 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1184518 TATTATAATT
1184528 ATTTTTTTATT-TTA
1 ATTTTTTTATTATTA
1184542 ATTTTTTTATTATTA
1 ATTTTTTTATTATTA
1184557 AT
1 AT
1184559 ATTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTTATTATTA
Found at i:1184562 original size:17 final size:17
Alignment explanation
Indices: 1184518--1184562 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
1184508 AGTAACAAAA
1184518 TATTA-TAATTATTTTTT
1 TATTATTAA-TATTTTTT
1184535 TATT-TT-A-ATTTTTT
1 TATTATTAATATTTTTT
1184549 TATTATTAATATTT
1 TATTATTAATATTT
1184563 ATAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 2 0.08
17 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTAATATTTTTT
Found at i:1184585 original size:14 final size:13
Alignment explanation
Indices: 1184547--1184579 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1184537 TTTTAATTTT
*
1184547 TTTATTATTAATA
1 TTTATAATTAATA
1184560 TTTATAATTAATA
1 TTTATAATTAATA
1184573 TTT-TAAT
1 TTTATAAT
1184580 CGTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:1185968 original size:12 final size:13
Alignment explanation
Indices: 1185910--1185973 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 13
1185900 TTTATTTTTA
1185910 TTTAAAT-TTAAT
1 TTTAAATATTAAT
*
1185922 TATAAATATTAAT
1 TTTAAATATTAAT
*
1185935 TTTGATAA-AATAAT
1 TTT-A-AATATTAAT
*
1185949 TTTTAATATT-AT
1 TTTAAATATTAAT
*
1185961 TTTAAATAATAAT
1 TTTAAATATTAAT
1185974 ATATGCTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
12 18 0.45
13 11 0.28
14 9 0.22
15 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TTTAAATATTAAT
Found at i:1186120 original size:22 final size:21
Alignment explanation
Indices: 1186095--1186136 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1186085 ATCCAACCTA
1186095 ATTC-ATCAATTATGAAAAATAC
1 ATTCTATCAATT-T-AAAAATAC
*
1186117 ATTCTATTAATTTAAAAATA
1 ATTCTATCAATTTAAAAATA
1186137 TTAAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTCTATCAATTTAAAAATAC
Found at i:1187480 original size:44 final size:44
Alignment explanation
Indices: 1187423--1187506 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
1187413 AACTACTCTT
*
1187423 TAAAATTCAACTAACATTT-TTA-GTAATTTAATTTTTAAAAAAAA
1 TAAAATTCAACTAACATTTCTCACGTAATTT--TTTTTAAAAAAAA
1187467 TAAATATTC-ACTAACATTTCTCACGTAATTTTTTTTAAAA
1 TAAA-ATTCAACTAACATTTCTCACGTAATTTTTTTTAAAA
1187507 TACGATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
44 23 0.64
45 6 0.17
46 7 0.19
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (44 bp):
TAAAATTCAACTAACATTTCTCACGTAATTTTTTTTAAAAAAAA
Found at i:1190314 original size:2 final size:2
Alignment explanation
Indices: 1190309--1190342 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1190299 TATATGTGTG
1190309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1190343 ATGTGGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1193221 original size:13 final size:14
Alignment explanation
Indices: 1193199--1193235 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1193189 CTTAAAAAAA
1193199 TTTA-TTATTTA-T
1 TTTATTTATTTATT
1193211 TTTATTTATTTATT
1 TTTATTTATTTATT
1193225 TTTATTT-TTTA
1 TTTATTTATTTA
1193236 ATATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:1193543 original size:20 final size:20
Alignment explanation
Indices: 1193478--1193544 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1193468 TTAAATTGGA
*
1193478 TTATTATTTAATAAAATTATTT
1 TTATTAATTAA-AAAA-TATTT
* * **
1193500 TAATT-ATAAAAAAATATAA
1 TTATTAATTAAAAAATATTT
*
1193519 ATATTAATTAAAAAATATTT
1 TTATTAATTAAAAAATATTT
1193539 TTATTA
1 TTATTA
1193545 TTTTTAATAT
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 6 0.18
20 20 0.61
21 3 0.09
22 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTAATTAAAAAATATTT
Found at i:1195111 original size:2 final size:2
Alignment explanation
Indices: 1195106--1195135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1195096 AATATATGTG
1195106 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
1195136 ATGTGGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1198014 original size:13 final size:14
Alignment explanation
Indices: 1197992--1198028 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1197982 CTTAAAAAAA
1197992 TTTA-TTATTTA-T
1 TTTATTTATTTATT
1198004 TTTATTTATTTATT
1 TTTATTTATTTATT
1198018 TTTATTT-TTTA
1 TTTATTTATTTA
1198029 ATATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:1198336 original size:20 final size:20
Alignment explanation
Indices: 1198313--1198352 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1198303 AAAATATAAA
1198313 TATTAATTTAAAAATATTTT
1 TATTAATTTAAAAATATTTT
* * *
1198333 TATTATTTTTAATATATTTT
1 TATTAATTTAAAAATATTTT
1198353 AAACAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTAATTTAAAAATATTTT
Found at i:1203955 original size:27 final size:30
Alignment explanation
Indices: 1203916--1203982 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
1203906 AACAAATAAA
1203916 TTTTAATTCAA-TTT-AAA-TTATATTTATT
1 TTTTAATTCAATTTTAAAATTTAT-TTTATT
1203944 TTTTAATT-AATTTTTAAAATTTATTTTATT
1 TTTTAATTCAA-TTTTAAAATTTATTTTATT
1203974 TATTTAATT
1 T-TTTAATT
1203983 TTATAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 3 0.09
30 10 0.29
31 11 0.32
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTAATTCAATTTTAAAATTTATTTTATT
Found at i:1204158 original size:3 final size:3
Alignment explanation
Indices: 1204150--1204177 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1204140 TTTTGAAAAC
1204150 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1204178 TAATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1204423 original size:19 final size:18
Alignment explanation
Indices: 1204384--1204424 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1204374 TCATTCCCAA
* *
1204384 TTTTGCATTACTTTATTT
1 TTTTGCATTAATTCATTT
1204402 TTTTGCATTAATTCACTTT
1 TTTTGCATTAATTCA-TTT
1204421 TTTT
1 TTTT
1204425 AAATTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTGCATTAATTCATTT
Found at i:1204541 original size:20 final size:22
Alignment explanation
Indices: 1204498--1204548 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1204488 AAATTTTATT
1204498 TTAATTTAATTATAAAAATATA
1 TTAATTTAATTATAAAAATATA
1204520 TTAATATTAA-TA-AAAAAT-TA
1 TTAAT-TTAATTATAAAAATATA
1204540 TT--TTTAATT
1 TTAATTTAATT
1204549 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.15
18 2 0.07
20 4 0.15
21 6 0.22
22 7 0.26
23 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTTAATTATAAAAATATA
Found at i:1205487 original size:34 final size:36
Alignment explanation
Indices: 1205435--1205501 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
1205425 ATTTAATAAT
*
1205435 TAAAAATATTTTTAATTAAAT-TTAATTATAAAATA
1 TAAAAATATTTTTAATTAAATATTAATAATAAAATA
*
1205470 TAAAAATA-TTTTAATTAATTATTAATAATAAA
1 TAAAAATATTTTTAATTAAATATTAATAATAAA
1205502 TATGAGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TAAAAATATTTTTAATTAAATATTAATAATAAAATA
Found at i:1205503 original size:34 final size:34
Alignment explanation
Indices: 1205428--1205504 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
1205418 AATTAATATT
1205428 TAAT-AAT-TAAAAATATTTTTAATTAAATTTAA
1 TAATAAATATAAAAATATTTTTAATTAAATTTAA
* *
1205460 TTATAAAATATAAAAATA-TTTTAATTAATTATTAA
1 TAAT-AAATATAAAAATATTTTTAATTAAAT-TTAA
1205495 TAATAAATAT
1 TAATAAATAT
1205505 GAGTAATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 3 0.08
34 20 0.53
35 15 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
TAATAAATATAAAAATATTTTTAATTAAATTTAA
Found at i:1206583 original size:5 final size:5
Alignment explanation
Indices: 1206573--1206599 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1206563 GACACATGAC
1206573 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1206600 TTAATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1208219 original size:22 final size:22
Alignment explanation
Indices: 1208157--1208228 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
1208147 TTATTTAAAG
*
1208157 TATT-ATATATTTATATATATA
1 TATTAATAAATTTATATATATA
*
1208178 TATTAATAACTTATATTATATATA
1 TATTAATAAATT-TA-TATATATA
* *
1208202 TTTTAA-AAGATTTATATATTTA
1 TATTAATAA-ATTTATATATATA
1208224 TATTA
1 TATTA
1208229 TATTTATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 6 0.15
24 15 0.37
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
TATTAATAAATTTATATATATA
Found at i:1209771 original size:43 final size:43
Alignment explanation
Indices: 1209723--1209813 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
1209713 ATAAATGTGA
*
1209723 TTAATTATTTACATAAATTAATTTAATTTAATAAATTTAAAGC
1 TTAATTATTTACATAAATTAATTTAATTTAATAAATTCAAAGC
* *
1209766 TTAATTATTTATATAAATTTATTTAATTTAATAAATTCAAAGC
1 TTAATTATTTACATAAATTAATTTAATTTAATAAATTCAAAGC
1209809 TTAAT
1 TTAAT
1209814 GGAAGCTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (43 bp):
TTAATTATTTACATAAATTAATTTAATTTAATAAATTCAAAGC
Found at i:1209890 original size:17 final size:17
Alignment explanation
Indices: 1209855--1209893 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1209845 ACTTTACTAG
*
1209855 AATTATTTTAAAAGTAT
1 AATTATTTTAAAAGAAT
1209872 AATTATATTTAAAA-AAT
1 AATTAT-TTTAAAAGAAT
1209889 AATTA
1 AATTA
1209894 ACATTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTATTTTAAAAGAAT
Found at i:1210455 original size:27 final size:26
Alignment explanation
Indices: 1210416--1210473 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
1210406 TTTAAAAATA
* *
1210416 ATTTTTTAAAATTTTAAATAATATTT
1 ATTTTTTAAAATTTTAAATAAAATTC
*
1210442 ATTTTTTAAAAATTTTATATAAAATTC
1 ATTTTTT-AAAATTTTAAATAAAATTC
1210469 ATTTT
1 ATTTT
1210474 ATCATTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTTTAAAATTTTAAATAAAATTC
Found at i:1210458 original size:16 final size:18
Alignment explanation
Indices: 1210427--1210459 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1210417 TTTTTTAAAA
1210427 TTTTAAATAATATTTATT
1 TTTTAAATAATATTTATT
1210445 TTTTAAA-AAT-TTTAT
1 TTTTAAATAATATTTAT
1210460 ATAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAATAATATTTATT
Found at i:1211628 original size:2 final size:2
Alignment explanation
Indices: 1211581--1211616 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1211571 TTATACATGA
*
1211581 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1211617 TGGATCATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1211834 original size:24 final size:24
Alignment explanation
Indices: 1211807--1211853 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1211797 TATTAAATTA
1211807 TATTTAAAAGT-AATATTTAAAAAG
1 TATTTAAAA-TAAATATTTAAAAAG
*
1211831 TATTTAAAATAAATTTTTAAAAA
1 TATTTAAAATAAATATTTAAAAA
1211854 ATTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TATTTAAAATAAATATTTAAAAAG
Found at i:1211949 original size:2 final size:2
Alignment explanation
Indices: 1211937--1211981 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1211927 CTTATTTTTC
1211937 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1211978 CT CT
1 CT CT
1211982 AAGCATCCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1212426 original size:16 final size:17
Alignment explanation
Indices: 1212405--1212438 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1212395 AATTCTAAGG
1212405 TTATTTTAAATA-TAAA
1 TTATTTTAAATACTAAA
*
1212421 TTATTTTTAATACTAAA
1 TTATTTTAAATACTAAA
1212438 T
1 T
1212439 ATTATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTTAAATACTAAA
Found at i:1212886 original size:26 final size:27
Alignment explanation
Indices: 1212850--1212904 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
1212840 TAAAATTTAG
**
1212850 ATAATATATTATTTATAATAATA-ATA
1 ATAATATATTAAATATAATAATAGATA
1212876 ATAATATATTAAATATAATAATAGATA
1 ATAATATATTAAATATAATAATAGATA
1212903 AT
1 AT
1212905 TTTAACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAATATATTAAATATAATAATAGATA
Found at i:1212963 original size:22 final size:21
Alignment explanation
Indices: 1212926--1212980 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1212916 ATTTTTTAAA
1212926 AAAATATTGAGAAAAATATTATT
1 AAAATATT-A-AAAAATATTATT
* *
1212949 ATAAATTTTAAAAAATATTTTT
1 A-AAATATTAAAAAATATTATT
1212971 AAAATATTAA
1 AAAATATTAA
1212981 TTAATCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.29
22 12 0.43
23 2 0.07
24 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATATTAAAAAATATTATT
Found at i:1215295 original size:19 final size:20
Alignment explanation
Indices: 1215259--1215308 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1215249 ATAAGTTATA
**
1215259 TATTTTTATTATGTTAATTT
1 TATTTTTATTATCATAATTT
1215279 TATTTTT-TTATCATAA--T
1 TATTTTTATTATCATAATTT
1215296 TATTTTATATTAT
1 TATTTT-TATTAT
1215309 TATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 11 0.42
20 7 0.27
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTTATTATCATAATTT
Found at i:1215311 original size:22 final size:21
Alignment explanation
Indices: 1215275--1215319 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1215265 TATTATGTTA
* *
1215275 ATTTTATTTTTTTATCATAATT
1 ATTTTATATTATTAT-ATAATT
*
1215297 ATTTTATATTATTATATATTT
1 ATTTTATATTATTATATAATT
1215318 AT
1 AT
1215320 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATATTATTATATAATT
Found at i:1215319 original size:30 final size:29
Alignment explanation
Indices: 1215297--1215355 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
1215287 TATCATAATT
*
1215297 ATTTTATATTATTATATATTTATATAAAAA
1 ATTTTAAATTATTATATATTTATAT-AAAA
1215327 ATTTTAAATTATTATATATTTATATAAAA
1 ATTTTAAATTATTATATATTTATATAAAA
1215356 TTAACACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTAAATTATTATATATTTATATAAAA
Found at i:1215489 original size:24 final size:24
Alignment explanation
Indices: 1215458--1215511 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1215448 ATTATAATTT
1215458 TTATATTTTTTATCATATCTAATA
1 TTATATTTTTTATCATATCTAATA
1215482 TTATATTTTTTATCATATCTAATA
1 TTATATTTTTTATCATATCTAATA
1215506 TTATAT
1 TTATAT
1215512 GTTCAAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATTTTTTATCATATCTAATA
Found at i:1215858 original size:20 final size:20
Alignment explanation
Indices: 1215833--1215871 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1215823 ATAAGGCATA
*
1215833 TTTTAAAAAATAAAA-ATAT
1 TTTTTAAAAATAAAATATAT
1215852 TTTTTAAAAATAAAATATAT
1 TTTTTAAAAATAAAATATAT
1215872 AATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTTAAAAATAAAATATAT
Found at i:1218823 original size:22 final size:21
Alignment explanation
Indices: 1218795--1218836 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1218785 TATTAAAAAA
1218795 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1218815 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1218836 A
1 A
1218837 AATAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1219189 original size:224 final size:224
Alignment explanation
Indices: 1218786--1219228 Score: 811
Period size: 224 Copynumber: 2.0 Consensus size: 224
1218776 ATTTAAAAAT
*
1218786 ATTAAAAAAATATTTTTATATTAATATTTATATATTTTATAATTAAATTTAAATAAAAACATCTT
1 ATTAAAAAAATATCTTTATATTAATATTTATATATTTTATAATTAAATTTAAATAAAAACATCTT
1218851 TTATAAACTAAACAATAATTTGAATTAAACCGATTAGAATAAAAAAATTATGTCCAAACTTGATT
66 TTATAAACTAAACAATAATTTGAATTAAACCGATTAGAATAAAAAAATTATGTCCAAACTTGATT
1218916 AAATTTTGAAGAAATTATAAAGGAAAACATTTGATGTTCAAAAAAGTTGATTGTAATT-AAAAAA
131 AAATTTTGAAGAAATTATAAAGGAAAACATTTGATGTTCAAAAAAGTTGATTGTAATTAAAAAAA
1218980 AAAA-AGGAAAATGAGAAAGTTGATTGTA
196 AAAAGAGGAAAATGAGAAAGTTGATTGTA
*
1219008 ATTAAAAAAATTATCTTTATATTAATATTTATATATTTTTATAATTAAATTTAAATAAAAATA-C
1 ATTAAAAAAA-TATCTTTATATTAATATTTATATA-TTTTATAATTAAATTTAAATAAAAACATC
*
1219072 TTTTATAAATTAAACAATAATTTGAATTAAACCGATTAGAATAAAAAAAATTATGTCCAAACTTG
64 TTTTATAAACTAAACAATAATTTGAATTAAACCGATTAGAAT-AAAAAAATTATGTCCAAACTTG
1219137 ATTAAATTTTGAAGAAATTATAAAGGAAAACATTTGATGTTCAAAAAAGTTGATTGTAATTAAAA
128 ATTAAATTTTGAAGAAATTATAAAGGAAAACATTTGATGTTCAAAAAAGTTGATTGTAATTAAAA
1219202 AAAAAAAGAGGAAAATGAGAAAGTTGA
193 AAAAAAAGAGGAAAATGAGAAAGTTGA
1219229 GGAGTGAGGG
Statistics
Matches: 213, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
222 10 0.05
223 65 0.31
224 109 0.51
225 10 0.05
226 19 0.09
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (224 bp):
ATTAAAAAAATATCTTTATATTAATATTTATATATTTTATAATTAAATTTAAATAAAAACATCTT
TTATAAACTAAACAATAATTTGAATTAAACCGATTAGAATAAAAAAATTATGTCCAAACTTGATT
AAATTTTGAAGAAATTATAAAGGAAAACATTTGATGTTCAAAAAAGTTGATTGTAATTAAAAAAA
AAAAGAGGAAAATGAGAAAGTTGATTGTA
Found at i:1219629 original size:31 final size:32
Alignment explanation
Indices: 1219594--1219653 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
1219584 TTAAATTACT
1219594 ATTTAATAATAAAAATAATATTTT-TAATTAA
1 ATTTAATAATAAAAATAATATTTTATAATTAA
*
1219625 ATTTAATTATAAAAATAATATTTTATAAT
1 ATTTAATAATAAAAATAATATTTTATAAT
1219654 ATAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTTAATAATAAAAATAATATTTTATAATTAA
Found at i:1222166 original size:17 final size:18
Alignment explanation
Indices: 1222128--1222176 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
1222118 GAATAGATTA
*
1222128 AATAAATAATTTTAATATT
1 AATAAAT-ATTTAAATATT
1222147 AATAAATATTTAAATA-T
1 AATAAATATTTAAATATT
1222164 AATAAATATTTAA
1 AATAAATATTTAA
1222177 TAAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.48
18 8 0.28
19 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATATTTAAATATT
Found at i:1222177 original size:11 final size:10
Alignment explanation
Indices: 1222141--1222180 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 10
1222131 AAATAATTTT
1222141 AATATTAATA
1 AATATTAATA
1222151 AATATT--TA
1 AATATTAATA
1222159 AATA-TAATA
1 AATATTAATA
1222168 AATATTTAATA
1 AATA-TTAATA
1222179 AA
1 AA
1222181 AATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.04
8 6 0.23
9 6 0.23
10 6 0.23
11 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATTAATA
Found at i:1222184 original size:17 final size:17
Alignment explanation
Indices: 1222127--1222194 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1222117 TGAATAGATT
*
1222127 AAATAAATAATTTTAATAT
1 AAATAAAT-A-TTTAATAA
*
1222146 TAATAAATATTTAA-ATA
1 AAATAAATATTTAATA-A
*
1222163 TAATAAATATTTAATAA
1 AAATAAATATTTAATAA
*
1222180 AAATATATATTTAAT
1 AAATAAATATTTAAT
1222195 TAAATAGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.02
17 33 0.77
18 2 0.05
19 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATATTTAATAA
Found at i:1222190 original size:34 final size:31
Alignment explanation
Indices: 1222125--1222200 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 31
1222115 ATTGAATAGA
**
1222125 TTAAATAAATAATTTTAATATTAATAAATAT
1 TTAAATAAATAATTTTAATAAAAATAAATAT
*
1222156 TTAAATATAATAAATATTTAATAAAAATATATAT
1 TTAAATA-AAT-AAT-TTTAATAAAAATAAATAT
*
1222190 TTAATTAAATA
1 TTAAATAAATA
1222201 GTATGTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 7 0.18
32 4 0.11
33 6 0.16
34 21 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TTAAATAAATAATTTTAATAAAAATAAATAT
Found at i:1222194 original size:28 final size:28
Alignment explanation
Indices: 1222141--1222200 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1222131 AAATAATTTT
* *
1222141 AATATTAATAAATATTTAAATATAA-TA
1 AATATTAATAAAAATATAAATATAATTA
* *
1222168 AATATTTAATAAAAATATATATTTAATTA
1 AATA-TTAATAAAAATATAAATATAATTA
1222197 AATA
1 AATA
1222201 GTATGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 17 0.63
29 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATATTAATAAAAATATAAATATAATTA
Found at i:1222285 original size:11 final size:10
Alignment explanation
Indices: 1222266--1222299 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
1222256 TAATAATTTT
1222266 TTTAAAAAAA
1 TTTAAAAAAA
1222276 TTTAAAAAAA
1 TTTAAAAAAA
1222286 TTTAAAAATAA
1 TTTAAAAA-AA
1222297 TTT
1 TTT
1222300 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:1224022 original size:12 final size:13
Alignment explanation
Indices: 1223998--1224048 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 13
1223988 TAAAAAAAAA
1223998 ATTAAATTATGAT
1 ATTAAATTATGAT
1224011 ATTAAATT-TGAT
1 ATTAAATTATGAT
* * *
1224023 ATAAAATAATAAT
1 ATTAAATTATGAT
1224036 A-TAAA-TATGAT
1 ATTAAATTATGAT
1224047 AT
1 AT
1224049 ATAACATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 5 0.17
12 13 0.43
13 12 0.40
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTAAATTATGAT
Found at i:1224050 original size:13 final size:13
Alignment explanation
Indices: 1224000--1224057 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 13
1223990 AAAAAAAAAT
1224000 TAAATTATGATAT-
1 TAAA-TATGATATA
*
1224013 TAAATTTGATATA
1 TAAATATGATATA
1224026 -AAATA--ATAATA
1 TAAATATGAT-ATA
1224037 TAAATATGATATA
1 TAAATATGATATA
1224050 TAACATAT
1 TAA-ATAT
1224058 TATTAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 2 0.05
11 3 0.08
12 16 0.43
13 10 0.27
14 6 0.16
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (13 bp):
TAAATATGATATA
Found at i:1224226 original size:24 final size:24
Alignment explanation
Indices: 1224192--1224294 Score: 70
Period size: 28 Copynumber: 4.0 Consensus size: 24
1224182 CTATTTTTAA
*
1224192 ATTTT-TT-ATAAAATA-ATAATTT
1 ATTTTATTAATAAAATATA-AATAT
1224214 ATTTTATTAATAAAATATAAATAT
1 ATTTTATTAATAAAATATAAATAT
*
1224238 ATATTATTAATATATTAAATATAAATAT
1 ATTTTATT-A-ATA--AAATATAAATAT
1224266 ATATATATAATTAA-AAATATATAAATAT
1 AT-T-T-T-ATTAATAAA-ATATAAATAT
1224294 A
1 A
1224295 ATATAAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
22 5 0.08
23 2 0.03
24 19 0.29
25 2 0.03
26 3 0.05
27 2 0.03
28 25 0.38
29 1 0.02
30 2 0.03
31 2 0.03
32 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTTATTAATAAAATATAAATAT
Found at i:1224237 original size:6 final size:6
Alignment explanation
Indices: 1224222--1224304 Score: 59
Period size: 6 Copynumber: 13.8 Consensus size: 6
1224212 TTATTTTATT
* *
1224222 AATA-A AATATA AATATA TATTATTA ATATATTA AATATA AATATA TATATA
1 AATATA AATATA AATATA -AATA-TA A-ATA-TA AATATA AATATA AATATA
*
1224273 TAAT-TA AA-A-A TATATA AATAT- AATATA AATAT
1 -AATATA AATATA AATATA AATATA AATATA AATAT
1224305 TTGAATTACT
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
4 2 0.03
5 12 0.19
6 32 0.51
7 9 0.14
8 8 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
AATATA
Found at i:1224262 original size:28 final size:27
Alignment explanation
Indices: 1224219--1224299 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 27
1224209 AATTTATTTT
1224219 ATTAATAAAATATAAATATATAT-TATTA
1 ATTAA-AAAATATAAATATATATATA-TA
**
1224247 ATATATTAAATATAAATATATATATATA
1 AT-TAAAAAATATAAATATATATATATA
1224275 ATTAAAAATATATAAATATA-ATATA
1 ATTAAAAA-ATATAAATATATATATA
1224300 AATATTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.20
28 33 0.72
29 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTAAAAAATATAAATATATATATATA
Found at i:1224285 original size:20 final size:20
Alignment explanation
Indices: 1224247--1224301 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1224237 TATATTATTA
* *
1224247 ATATAT-TAAATATAAATAT
1 ATATATATAATTAAAAATAT
1224266 ATATATATAATTAAAAATAT
1 ATATATATAATTAAAAATAT
*
1224286 ATAAATATAATATAAA
1 ATATATATAAT-TAAA
1224302 TATTTGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.19
20 21 0.68
21 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATATAATTAAAAATAT
Found at i:1224605 original size:17 final size:17
Alignment explanation
Indices: 1224582--1224632 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
1224572 TTTTTAAATT
1224582 AATTTTT-ATTATTTTA
1 AATTTTTAATTATTTTA
*
1224598 AATATTTTAATTA-ATTA
1 AAT-TTTTAATTATTTTA
1224615 AATTTTATAATTATTTTA
1 AATTTT-TAATTATTTTA
1224633 TTCAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 6 0.21
17 16 0.55
18 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTAATTATTTTA
Found at i:1224859 original size:14 final size:14
Alignment explanation
Indices: 1224842--1224876 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1224832 TTAAGATATA
1224842 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
*
1224856 AAAAATAAAAATAT
1 AAAAATAAAAAAAT
*
1224870 ATAAATA
1 AAAAATA
1224877 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:1224945 original size:47 final size:45
Alignment explanation
Indices: 1224854--1224970 Score: 109
Period size: 45 Copynumber: 2.6 Consensus size: 45
1224844 AAATAAAAAA
* *
1224854 ATAA-AAATAAAAA-TATATAAATATTTTTAAAATTTATGTAATAT
1 ATAATAAATAAAAATTATATAAATA-TATTAAAATTTATATAATAT
*
1224898 ATAATAAATAAAAATTTATATAAATATATTAATTATTT-TAT-ATAT
1 ATAATAAATAAAAA-TTATATAAATATATTAA-AATTTATATAATAT
*
1224943 ATAA-ATAATATAAATATATTATAAATAT
1 ATAATA-AATAAAAAT-TA-TATAAATAT
1224971 TCAAATACTT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
44 6 0.10
45 26 0.42
46 16 0.26
47 14 0.23
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (45 bp):
ATAATAAATAAAAATTATATAAATATATTAAAATTTATATAATAT
Found at i:1224955 original size:9 final size:10
Alignment explanation
Indices: 1224894--1224970 Score: 58
Period size: 10 Copynumber: 8.2 Consensus size: 10
1224884 AATTTATGTA
1224894 ATATAT-AAT
1 ATATATAAAT
* *
1224903 AAATAAAAAT
1 ATATATAAAT
*
1224913 TTATATAAAT
1 ATATATAAAT
1224923 ATAT-T-AAT
1 ATATATAAAT
**
1224931 -TAT-TTTAT
1 ATATATAAAT
1224939 ATATATAAAT
1 ATATATAAAT
1224949 A-ATATAAAT
1 ATATATAAAT
1224958 ATATTATAAAT
1 ATA-TATAAAT
1224969 AT
1 AT
1224971 TCAAATACTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
7 4 0.08
8 5 0.09
9 17 0.32
10 18 0.34
11 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATAAAT
Found at i:1224964 original size:26 final size:26
Alignment explanation
Indices: 1224914--1224970 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1224904 AATAAAAATT
* *
1224914 TATATAAATATATTAATTATTTTATA
1 TATATAAATATATTAAATATATTATA
1224940 TATATAAATA-ATATAAATATATTATA
1 TATATAAATATAT-TAAATATATTATA
*
1224966 AATAT
1 TATAT
1224971 TCAAATACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATAAATATATTAAATATATTATA
Found at i:1225372 original size:17 final size:16
Alignment explanation
Indices: 1225323--1225403 Score: 71
Period size: 17 Copynumber: 5.2 Consensus size: 16
1225313 ATCAATAAAA
1225323 TAAA-ATAT-TTTAAT
1 TAAATATATATTTAAT
*
1225337 TAATTATAT-TTTAA-
1 TAAATATATATTTAAT
* * *
1225351 AAAATTAAATATTAAAT
1 TAAA-TATATATTTAAT
1225368 TAAATATATATTTAAT
1 TAAATATATATTTAAT
*
1225384 AAAAATATATATTTAAT
1 -TAAATATATATTTAAT
1225401 TAA
1 TAA
1225404 CTAATATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
14 5 0.10
15 13 0.25
16 16 0.31
17 18 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATATATATTTAAT
Found at i:1225396 original size:33 final size:31
Alignment explanation
Indices: 1225319--1225403 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
1225309 TTTAATCAAT
* *
1225319 AAAATAAAATATTTTAATTAATTATATTTTAAA
1 AAAAT-AAATA-TTAAATTAAATATATTTTAAA
*
1225352 AAATTAAATATTAAATTAAATATATATTTAATA
1 AAAATAAATATTAAATTAAATATAT-TTTAA-A
* *
1225385 AAAATATATATTTAATTAA
1 AAAATAAATATTAAATTAA
1225404 CTAATATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 13 0.30
32 10 0.23
33 21 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATAAATATTAAATTAAATATATTTTAAA
Found at i:1225410 original size:17 final size:17
Alignment explanation
Indices: 1225320--1225411 Score: 61
Period size: 17 Copynumber: 5.6 Consensus size: 17
1225310 TTAATCAATA
*
1225320 AAATAAAATATTTTAATT
1 AAATAATATA-TTTAATT
* *
1225338 -AATTATAT-TTTAA-A
1 AAATAATATATTTAATT
*
1225352 AAATTAA-ATATTAAATT
1 AAA-TAATATATTTAATT
1225369 AAAT-ATATATTTAA-T
1 AAATAATATATTTAATT
*
1225384 AAAAATATATATTTAATT
1 AAATA-ATATATTTAATT
*
1225402 AACTAATATA
1 AAATAATATA
1225412 ATTTTTAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
15 14 0.25
16 14 0.25
17 24 0.43
18 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATATATTTAATT
Found at i:1225503 original size:2 final size:2
Alignment explanation
Indices: 1225498--1225534 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1225488 CAAACAAAAT
1225498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1225535 AGACGAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1226318 original size:22 final size:22
Alignment explanation
Indices: 1226293--1226335 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1226283 TTATTCAGAT
1226293 TTTTTTAT-TTGATTCATTTATA
1 TTTTTTATATTGATT-ATTTATA
*
1226315 TTTTTTATATTTATTATTTAT
1 TTTTTTATATTGATTATTTAT
1226336 TATTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTTATATTGATTATTTATA
Found at i:1226339 original size:23 final size:23
Alignment explanation
Indices: 1226291--1226335 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1226281 TTTTATTCAG
1226291 ATTTTTTTATTTGATTCATTTAT
1 ATTTTTTTATTTGATTCATTTAT
1226314 ATTTTTTATATTT-ATT-ATTTAT
1 ATTTTTT-TATTTGATTCATTTAT
1226336 TATTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 10 0.48
24 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTTTTTTATTTGATTCATTTAT
Found at i:1226384 original size:19 final size:19
Alignment explanation
Indices: 1226355--1226396 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1226345 AAATTTAAAA
*
1226355 ATATATTTTATATTAATATTT
1 ATATATTATA-ATTAA-ATTT
1226376 ATATATTATAATTAAATTT
1 ATATATTATAATTAAATTT
1226395 AT
1 AT
1226397 TAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTATAATTAAATTT
Found at i:1226884 original size:6 final size:6
Alignment explanation
Indices: 1226873--1226900 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1226863 AAACAGACAT
1226873 CATGAA CATGAA CATGAA CATGAA CATG
1 CATGAA CATGAA CATGAA CATGAA CATG
1226901 TTCTCTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
CATGAA
Found at i:1227372 original size:16 final size:16
Alignment explanation
Indices: 1227351--1227381 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1227341 CAATGTATAA
1227351 GATAATTTTTGTTAAG
1 GATAATTTTTGTTAAG
*
1227367 GATAATTTTTTTTAA
1 GATAATTTTTGTTAA
1227382 TTAGCATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (16 bp):
GATAATTTTTGTTAAG
Found at i:1228866 original size:16 final size:15
Alignment explanation
Indices: 1228837--1228875 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1228827 TTAAATTTTT
*
1228837 TTATTTAAGTTTAAA
1 TTATTTAAGCTTAAA
1228852 TTATATTAAGCTTAAA
1 TTAT-TTAAGCTTAAA
1228868 TTATTTAA
1 TTATTTAA
1228876 AAATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TTATTTAAGCTTAAA
Found at i:1229759 original size:22 final size:21
Alignment explanation
Indices: 1229734--1229791 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
1229724 TATTATATAT
1229734 TTTTTAATTTAATATTTAATAA
1 TTTTTAATTTAATATTTAA-AA
* *
1229756 TTTTTTATTAAAT-TTTAAAA
1 TTTTTAATTTAATATTTAAAA
*
1229776 TATTAATAATTTAATA
1 T-TT-TTAATTTAATA
1229792 AATATTACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 3 0.11
21 7 0.25
22 18 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATTTAATATTTAAAA
Done.