Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 15 of 126
Found at i:4948610 original size:17 final size:17
Alignment explanation
Indices: 4948588--4948621 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4948578 TATAGTTTTA
4948588 CTCTCT-TCT-TTTTCT
1 CTCTCTCTCTCTTTTCT
4948603 CTCTCTCTCTCTTTTCT
1 CTCTCTCTCTCTTTTCT
4948620 CT
1 CT
4948622 TATTTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
CTCTCTCTCTCTTTTCT
Found at i:4949004 original size:5 final size:6
Alignment explanation
Indices: 4948991--4949020 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
4948981 GGAACTTTCC
4948991 TTTATT TTTATT TTTATT TTTATT ATTTAT
1 TTTATT TTTATT TTTATT TTTATT -TTTAT
4949021 CAAGTTCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:4949101 original size:19 final size:19
Alignment explanation
Indices: 4949077--4949115 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4949067 TGAGGATATA
*
4949077 ATCGAAACTAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
*
4949096 ATCGAAGCCAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
4949115 A
1 A
4949116 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (19 bp):
ATCGAAACCAAATTAAAAT
Found at i:4949856 original size:220 final size:220
Alignment explanation
Indices: 4949472--4949897 Score: 771
Period size: 220 Copynumber: 1.9 Consensus size: 220
4949462 GTATTAGTTC
* *
4949472 TTACGGTAAAAAATAAATTGATGTTTGATATTTGTTAAGGAGAAATTGACTCTTTTTTAAAAAGT
1 TTACGGTAAAAAACAAATTGATGTTTGATATTTGTTAAGGAGAAATTGACTCCTTTTTAAAAAGT
* * *
4949537 TATTGGTATATCGTTTGTTCAAAGTTGTCGGACTTCTCAATGAGTCAGTATTGTCTCTCAATCTA
66 TATTGGTATATCGTCTGTTCAAAGTTGTCGGACTCCTCAATGAGTCAGTATTGTCTCTCAATCGA
*
4949602 GTCGAAATTTGGTCTCCTAACATCTTGACTCTACGAAAAGCTCAAATGACTGGGGCAACAAGTTC
131 GTCAAAATTTGGTCTCCTAACATCTTGACTCTACGAAAAGCTCAAATGACTGGGGCAACAAGTTC
4949667 AATAAAGTGAGATTGACTCTTGACT
196 AATAAAGTGAGATTGACTCTTGACT
*
4949692 TTACGGTAAAAAACAAATTGATGTTTGATATTTGTTAAGGAGAGATTGACTCCTTTTTAAAAAGT
1 TTACGGTAAAAAACAAATTGATGTTTGATATTTGTTAAGGAGAAATTGACTCCTTTTTAAAAAGT
4949757 TATTGGTATATCGTCTGTTCAAAGTTGTCGGACTCCTCAATGAGTCAGTATTGTCTCTCAATCGA
66 TATTGGTATATCGTCTGTTCAAAGTTGTCGGACTCCTCAATGAGTCAGTATTGTCTCTCAATCGA
* *
4949822 GTCAAAATTTGGTCTCCTAACCTCTTGCCTCTACGAAAAGCTCAAATGACTGGGGCAACAAGTTC
131 GTCAAAATTTGGTCTCCTAACATCTTGACTCTACGAAAAGCTCAAATGACTGGGGCAACAAGTTC
4949887 AATAAAGTGAG
196 AATAAAGTGAG
4949898 TTCAAATAGT
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
220 197 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (220 bp):
TTACGGTAAAAAACAAATTGATGTTTGATATTTGTTAAGGAGAAATTGACTCCTTTTTAAAAAGT
TATTGGTATATCGTCTGTTCAAAGTTGTCGGACTCCTCAATGAGTCAGTATTGTCTCTCAATCGA
GTCAAAATTTGGTCTCCTAACATCTTGACTCTACGAAAAGCTCAAATGACTGGGGCAACAAGTTC
AATAAAGTGAGATTGACTCTTGACT
Found at i:4950747 original size:29 final size:29
Alignment explanation
Indices: 4950688--4950747 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
4950678 CATTTATTTA
* * *
4950688 AATTATTATATTTATAATTTTTTTTGAAT
1 AATTATTATATTTATAATTTGTATGGAAT
*
4950717 AATTATTATATTTATAATTTGTATGGTAT
1 AATTATTATATTTATAATTTGTATGGAAT
4950746 AA
1 AA
4950748 ATTTTACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (29 bp):
AATTATTATATTTATAATTTGTATGGAAT
Found at i:4951221 original size:14 final size:15
Alignment explanation
Indices: 4951202--4951234 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4951192 AAAATAAAAT
*
4951202 ATTAATT-TTTTTAA
1 ATTAATTATCTTTAA
4951216 ATTAATTATCTTTAA
1 ATTAATTATCTTTAA
4951231 ATTA
1 ATTA
4951235 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATTATCTTTAA
Found at i:4954028 original size:15 final size:16
Alignment explanation
Indices: 4953992--4954031 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
4953982 ATAGTAAAAA
4953992 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
4954009 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
4954024 TATAATTT
1 TATAATTT
4954032 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:4955145 original size:21 final size:21
Alignment explanation
Indices: 4955120--4955163 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4955110 ACAACATTTG
4955120 AACTTCTT-TAAATATATTTTT
1 AACTTCTTGTAAATA-ATTTTT
* *
4955141 AACTTTTTGTCAATAATTTTT
1 AACTTCTTGTAAATAATTTTT
4955162 AA
1 AA
4955164 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (21 bp):
AACTTCTTGTAAATAATTTTT
Found at i:4955231 original size:16 final size:16
Alignment explanation
Indices: 4955210--4955240 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4955200 CGGAGAGAAT
*
4955210 AATATAAATTATCATA
1 AATATAAATAATCATA
4955226 AATATAAATAATCAT
1 AATATAAATAATCAT
4955241 GGTGTTTTTA
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:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAATAATCATA
Found at i:4955738 original size:2 final size:2
Alignment explanation
Indices: 4955731--4955755 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4955721 TCTTTAAAGA
4955731 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4955756 AGAGTAAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4959643 original size:27 final size:28
Alignment explanation
Indices: 4959613--4959677 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
4959603 CCAATTCAAT
*
4959613 TAATTAAAAATATATT-TATT-TAAAAAG
1 TAATTAAAAAT-TATTCTATTATAAAAAA
* *
4959640 TAA-TAAATATTATTCTTTTATAAAAAA
1 TAATTAAAAATTATTCTATTATAAAAAA
*
4959667 TAATTTAAAAT
1 TAATTAAAAAT
4959678 CAAAATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 4 0.13
26 9 0.30
27 12 0.40
28 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TAATTAAAAATTATTCTATTATAAAAAA
Found at i:4961226 original size:23 final size:21
Alignment explanation
Indices: 4961189--4961264 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 21
4961179 AACAGTAAGC
4961189 GCACACAAGTGCAATCCAGTAG
1 GCACACAAGTGCAAT-CAGTAG
4961211 GCACACACAGTGCAATCAGTAG
1 GCACACA-AGTGCAATCAGTAG
* *
4961233 GCGCACATAGCGCAAATCAGTAG
1 GCACACA-AGTGC-AATCAGTAG
4961256 GCACACAAG
1 GCACACAAG
4961265 GTGCGAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
22 25 0.52
23 23 0.48
ACGTcount: A:0.37, C:0.28, G:0.24, T:0.12
Consensus pattern (21 bp):
GCACACAAGTGCAATCAGTAG
Found at i:4968031 original size:17 final size:17
Alignment explanation
Indices: 4968009--4968047 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4967999 CTCCACCTTG
* *
4968009 ACAAGAATTCTCTACAA
1 ACAAGAACTCTCAACAA
*
4968026 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACAA
4968043 ACAAG
1 ACAAG
4968048 TTCACCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:4975252 original size:3 final size:3
Alignment explanation
Indices: 4975244--4975278 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4975234 AGGGAATTGC
4975244 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4975279 TAAACTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4975840 original size:27 final size:28
Alignment explanation
Indices: 4975779--4975840 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
4975769 ATTACTTTAT
* *
4975779 TATTATTT-AATTTATCTATAAAAAATA
1 TATTATTTAAAATTATATATAAAAAATA
4975806 -ACTT-TTTAAAATTATAT-TAAAAAATA
1 TA-TTATTTAAAATTATATATAAAAAATA
4975832 TATTATTTA
1 TATTATTTA
4975841 TAAGAAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTATTTAAAATTATATATAAAAAATA
Found at i:4984604 original size:30 final size:31
Alignment explanation
Indices: 4984560--4984625 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
4984550 TAGTAAAGAT
*
4984560 AAAATTGTACTTTAACTCC-CTAAAAA-TGATA
1 AAAATTGTAATTTAA-TCCTCTAAAAACT-ATA
*
4984591 AAAATT-TAATTTAATCCTTTAAAAACTATA
1 AAAATTGTAATTTAATCCTCTAAAAACTATA
4984621 AAAAT
1 AAAAT
4984626 ATAAGCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 21 0.68
31 7 0.23
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAATTGTAATTTAATCCTCTAAAAACTATA
Found at i:4985036 original size:31 final size:31
Alignment explanation
Indices: 4984998--4985068 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
4984988 TTATATATAG
4984998 AAAATTATATTTTAATAC-CCTAAAAATAAAT
1 AAAATTATA-TTTAATACTCCTAAAAATAAAT
* ** *
4985029 AAAATTATATTTAATTCTTTTAAAAATTAAT
1 AAAATTATATTTAATACTCCTAAAAATAAAT
4985060 AAAATTATA
1 AAAATTATA
4985069 AATTAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATTATATTTAATACTCCTAAAAATAAAT
Found at i:4985083 original size:15 final size:16
Alignment explanation
Indices: 4985051--4985096 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
4985041 AATTCTTTTA
*
4985051 AAAATTAATAAAATTAT
1 AAAATTAAT-ATATTAT
4985068 -AAATTAATATATTAT
1 AAAATTAATATATTAT
4985083 AAAATT-ATATATTA
1 AAAATTAATATATTA
4985097 GCATCTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTAATATATTAT
Found at i:4985089 original size:32 final size:31
Alignment explanation
Indices: 4985018--4985086 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4985008 TTTAATACCC
* * * *
4985018 TAAAAATAAATAAAATTATATTTAATTCTTT
1 TAAAAATTAATAAAATTATAATTAATTATTA
4985049 TAAAAATTAATAAAATTATAAATTAATATATTA
1 TAAAAATTAATAAAATTAT-AATTAAT-TATTA
4985082 TAAAA
1 TAAAA
4985087 TTATATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 18 0.56
32 6 0.19
33 8 0.25
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
TAAAAATTAATAAAATTATAATTAATTATTA
Found at i:4992003 original size:14 final size:14
Alignment explanation
Indices: 4991984--4992010 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4991974 TTTAGAAAAT
4991984 TATTTATATATATA
1 TATTTATATATATA
4991998 TATTTATATATAT
1 TATTTATATATAT
4992011 TTCATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTATATATATA
Found at i:5013117 original size:23 final size:21
Alignment explanation
Indices: 5013058--5013117 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
5013048 GATTATTTTT
*
5013058 ATATAAAAATAAATTTTAAAA
1 ATATAAAAATAAATTCTAAAA
5013079 ATATAATAAATCAAATTGACTAAAA
1 ATATAA-AAAT-AAATT--CTAAAA
*
5013104 ATATTAAAATAAAT
1 ATATAAAAATAAAT
5013118 ATTTTGCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.18
22 4 0.12
23 9 0.27
24 4 0.12
25 10 0.30
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATAAAAATAAATTCTAAAA
Found at i:5013269 original size:11 final size:11
Alignment explanation
Indices: 5013255--5013300 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
5013245 ATATCTAAAC
*
5013255 AATAATAATAA
1 AATAATAACAA
5013266 AATAATAACAA
1 AATAATAACAA
* *
5013277 TATAATAACGA
1 AATAATAACAA
*
5013288 AATAATAGCAA
1 AATAATAACAA
5013299 AA
1 AA
5013301 CAAAAACATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (11 bp):
AATAATAACAA
Found at i:5023353 original size:70 final size:70
Alignment explanation
Indices: 5023236--5023370 Score: 218
Period size: 70 Copynumber: 1.9 Consensus size: 70
5023226 TAACGGTTAT
* *
5023236 TAACTGTTGATGTGATAGGTGACGTGTTAAGCTAACGTGATAAATGATATGACAAAAATGATGTG
1 TAACTGTTGATGTGATAGGTGACATGCTAAGCTAACGTGATAAATGATATGACAAAAATGATGTG
5023301 GCAGC
66 GCAGC
* *
5023306 TAACTGTTGATGT-AGTAGGTGACATGCTAAGCTAACGTGATACATGATGTGACAAAAATGATGT
1 TAACTGTTGATGTGA-TAGGTGACATGCTAAGCTAACGTGATAAATGATATGACAAAAATGATGT
5023370 G
65 G
5023371 ACAATTAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 1 0.02
70 59 0.98
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (70 bp):
TAACTGTTGATGTGATAGGTGACATGCTAAGCTAACGTGATAAATGATATGACAAAAATGATGTG
GCAGC
Found at i:5023641 original size:8 final size:9
Alignment explanation
Indices: 5023614--5023716 Score: 54
Period size: 10 Copynumber: 11.4 Consensus size: 9
5023604 CATTTTTTAG
5023614 AAAAATTAT
1 AAAAATTAT
5023623 CAAAAATTAT
1 -AAAAATTAT
5023633 AAAAA-TAT
1 AAAAATTAT
*
5023641 AGGAAATGT-T
1 A-AAAAT-TAT
**
5023651 AAATGTTAT
1 AAAAATTAT
*
5023660 AAAAA-TAG
1 AAAAATTAT
*
5023668 AATAATATAT
1 AAAAAT-TAT
5023678 AAAAATT-T
1 AAAAATTAT
*
5023686 -TAAATTAT
1 AAAAATTAT
*
5023694 TAAAATTAT
1 AAAAATTAT
*
5023703 ATAAAAATAT
1 A-AAAATTAT
5023713 AAAA
1 AAAA
5023717 TTACTTATCA
Statistics
Matches: 70, Mismatches: 14, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.07
8 13 0.19
9 25 0.36
10 26 0.37
11 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5034511 original size:21 final size:20
Alignment explanation
Indices: 5034487--5034547 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
5034477 GAAATTGTTA
5034487 AAAAATCATTAAAAAATTAAT
1 AAAAAT-ATTAAAAAATTAAT
**
5034508 AAAAAT-TGTAAAAAAAAAATT
1 AAAAATAT-TAAAAAATTAA-T
* *
5034529 AAAATTATAAAAAAATTAA
1 AAAAATATTAAAAAATTAA
5034548 ATAACTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.03
20 9 0.29
21 20 0.65
22 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATATTAAAAAATTAAT
Found at i:5034519 original size:20 final size:20
Alignment explanation
Indices: 5034496--5034547 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5034486 AAAAAATCAT
*
5034496 TAAAAAATTAATAAAAATTG
1 TAAAAAATTAATAAAAATTA
** *
5034516 TAAAAAAAAAATTAAAATTA
1 TAAAAAATTAATAAAAATTA
5034536 TAAAAAAATTAA
1 T-AAAAAATTAA
5034548 ATAACTGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAAATTAATAAAAATTA
Found at i:5034542 original size:17 final size:19
Alignment explanation
Indices: 5034520--5034567 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
5034510 AAATTGTAAA
*
5034520 AAAAAAATTAAAATTA-T-
1 AAAAAAATTAAAATAACTG
5034537 AAAAAAATT-AAATAACTG
1 AAAAAAATTAAAATAACTG
5034555 AAAAAAATTAAAA
1 AAAAAAATTAAAA
5034568 AATGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 5 0.19
17 10 0.37
18 9 0.33
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAAAATTAAAATAACTG
Found at i:5054920 original size:22 final size:22
Alignment explanation
Indices: 5054892--5054944 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
5054882 TGTGTTTGGT
5054892 TCGTTTATGTTCACGAACAAGC
1 TCGTTTATGTTCACGAACAAGC
5054914 TCGTTTATGTTCACGAACAAGC
1 TCGTTTATGTTCACGAACAAGC
5054936 TCGTTTATG
1 TCGTTTATG
5054945 ACTTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (22 bp):
TCGTTTATGTTCACGAACAAGC
Found at i:5055033 original size:23 final size:23
Alignment explanation
Indices: 5054990--5055035 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5054980 ACATTGTTCG
*
5054990 TGAACATGTTCGTTTAAATTAAA
1 TGAACATGTTCGTTGAAATTAAA
*
5055013 TGAATATGTTCG-TGAACATTAAA
1 TGAACATGTTCGTTGAA-ATTAAA
5055036 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (23 bp):
TGAACATGTTCGTTGAAATTAAA
Found at i:5059284 original size:3 final size:3
Alignment explanation
Indices: 5059276--5059309 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5059266 GGAATCAAAG
*
5059276 AGA AGA AGA TGA AGA AGA AGA AGA AGA AG- AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
5059310 TGTGTGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:5061274 original size:52 final size:52
Alignment explanation
Indices: 5061038--5061271 Score: 387
Period size: 52 Copynumber: 4.5 Consensus size: 52
5061028 ATTTCATTTC
*
5061038 ATTCATATACTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCACCAGACCTCATAATCCGTAAAGG
* *
5061090 ATTCATATACTCACAATGACACATAGCCATCAGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCACCAGACCTCATAATCCGTAAAGG
* * *
5061142 ATTCATATACTCACGATGATACATAGCCATCAGACCTCATAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCACCAGACCTCATAATCCGTAAAGG
* *
5061194 ATTCATATACTCACGATGACACATAGTCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCACCAGACCTCATAATCCGTAAAGG
*
5061246 ATTAATATACTCACGATGACACATAG
1 ATTCATATACTCACGATGACACATAG
5061272 TCATCGAACC
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 170 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCACCAGACCTCATAATCCGTAAAGG
Found at i:5074677 original size:15 final size:16
Alignment explanation
Indices: 5074652--5074683 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5074642 CAAGATTATT
5074652 TTTTATTTAAAAATAA
1 TTTTATTTAAAAATAA
5074668 TTTT-TTTAAAAATAA
1 TTTTATTTAAAAATAA
5074683 T
1 T
5074684 ACACTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTATTTAAAAATAA
Found at i:5079613 original size:16 final size:16
Alignment explanation
Indices: 5079589--5079627 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5079579 TCATAATTAG
*
5079589 TTTTTTAGATTA-TTT
1 TTTTTTAGAGTAGTTT
5079604 TTTATTTAGAGTAGTTT
1 TTT-TTTAGAGTAGTTT
5079621 TTTTTTA
1 TTTTTTA
5079628 AAAATAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (16 bp):
TTTTTTAGAGTAGTTT
Found at i:5089789 original size:20 final size:20
Alignment explanation
Indices: 5089764--5089804 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5089754 AAATTAATAA
* *
5089764 TAATAAAATTTTATTTTAAT
1 TAATAAAAATTTAATTTAAT
5089784 TAATAAAAATTTAATTTAAT
1 TAATAAAAATTTAATTTAAT
5089804 T
1 T
5089805 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAAAAATTTAATTTAAT
Found at i:5089799 original size:26 final size:27
Alignment explanation
Indices: 5089748--5089806 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
5089738 ATAATTTATA
*
5089748 AATTTTAAATTAATAATAATAAAATTT
1 AATTTTAAATTAATAAAAATAAAATTT
* **
5089775 TATTTT-AATTAATAAAAATTTAATTT
1 AATTTTAAATTAATAAAAATAAAATTT
5089801 AATTTT
1 AATTTT
5089807 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTAAATTAATAAAAATAAAATTT
Found at i:5091844 original size:19 final size:19
Alignment explanation
Indices: 5091807--5091845 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5091797 ATTGAAGTAA
*
5091807 TTTTATATTTTTTAAATTT
1 TTTTATATTATTTAAATTT
5091826 TTTTATA-TATTTAATATTT
1 TTTTATATTATTTAA-ATTT
5091845 T
1 T
5091846 AATAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATATTATTTAAATTT
Found at i:5093340 original size:18 final size:20
Alignment explanation
Indices: 5093317--5093353 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5093307 GTTTTTGGTG
5093317 TTTT-GGGGG-TGATTTTTT
1 TTTTGGGGGGTTGATTTTTT
5093335 TTTTGGGGGGTTGATTTTT
1 TTTTGGGGGGTTGATTTTT
5093354 CATCTGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.05, C:0.00, G:0.35, T:0.59
Consensus pattern (20 bp):
TTTTGGGGGGTTGATTTTTT
Found at i:5095033 original size:17 final size:18
Alignment explanation
Indices: 5094993--5095033 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5094983 GTCATATATA
5094993 AAACAAAATGAAGAGTTG
1 AAACAAAATGAAGAGTTG
* *
5095011 -ATCAAATTGAA-AGTTG
1 AAACAAAATGAAGAGTTG
5095027 AAACAAA
1 AAACAAA
5095034 GACCTTTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (18 bp):
AAACAAAATGAAGAGTTG
Found at i:5100023 original size:4 final size:4
Alignment explanation
Indices: 5100014--5100043 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
5100004 TATAATGTAA
5100014 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5100044 TCGGTGCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:5107772 original size:10 final size:10
Alignment explanation
Indices: 5107757--5107782 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5107747 AAATTTTAAC
5107757 TTTTTATATA
1 TTTTTATATA
5107767 TTTTTATATA
1 TTTTTATATA
5107777 TTTTTA
1 TTTTTA
5107783 AATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATATA
Found at i:5108855 original size:19 final size:20
Alignment explanation
Indices: 5108819--5108860 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
5108809 TATATATATG
** *
5108819 AATATTTTTTATTTTTTTTA
1 AATATTTTTTATAATTTTAA
5108839 AATA-TTTTTATAATTTTAA
1 AATATTTTTTATAATTTTAA
5108858 AAT
1 AAT
5108861 TACTTATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATATTTTTTATAATTTTAA
Found at i:5120264 original size:39 final size:39
Alignment explanation
Indices: 5120210--5120289 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
5120200 GAGATTTCAA
* * *
5120210 ATGATATAGACGAGGAAGGCTTGAATGAAGAGGTCTCGG
1 ATGATATAGAAGAGGAAGGCCTGAATGAAGAGGTCCCGG
*
5120249 ATGATATCGAAGAGGAAGGCCTGAATGAAGAGGTCCCGG
1 ATGATATAGAAGAGGAAGGCCTGAATGAAGAGGTCCCGG
5120288 AT
1 AT
5120290 AGTCGACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.35, T:0.19
Consensus pattern (39 bp):
ATGATATAGAAGAGGAAGGCCTGAATGAAGAGGTCCCGG
Found at i:5122415 original size:26 final size:26
Alignment explanation
Indices: 5122386--5122446 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5122376 ATGAATTTGG
*
5122386 AATTAATTA-TATTTAAATTTATATTT
1 AATTAATTAGT-TTTAAATTTATAATT
* * *
5122412 AATTAATAAGTTTTATATTTGTAATT
1 AATTAATTAGTTTTAAATTTATAATT
5122438 AATTAATTA
1 AATTAATTA
5122447 ATCTCTGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
AATTAATTAGTTTTAAATTTATAATT
Found at i:5122628 original size:21 final size:20
Alignment explanation
Indices: 5122590--5122657 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
5122580 TAGTTTTTTA
5122590 TTTAAAATTTTAGGGTTTAAGG
1 TTTAAAA-TTTA-GGTTTAAGG
5122612 TTTAAAATTTAGTGTTT-AGAG
1 TTTAAAATTTAG-GTTTAAG-G
* *
5122633 TTCAAGATTTAGGATTTAAGG
1 TTTAAAATTTAGG-TTTAAGG
5122654 TTTA
1 TTTA
5122658 CAGTTTTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.10
21 26 0.67
22 9 0.23
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (20 bp):
TTTAAAATTTAGGTTTAAGG
Found at i:5122804 original size:6 final size:6
Alignment explanation
Indices: 5122793--5122857 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
5122783 GCCTATACCC
* * *
5122793 TAAACA TAAACA -AAAGCA TAAATA TAATTA-A TTAAATA CAAACA TAAACA
1 TAAACA TAAACA TAAA-CA TAAACA TAA--ACA -TAAACA TAAACA TAAACA
5122843 TAAACA TAAACA TAA
1 TAAACA TAAACA TAA
5122858 TTAATTCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 37 0.76
7 5 0.10
8 4 0.08
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (6 bp):
TAAACA
Found at i:5125356 original size:60 final size:59
Alignment explanation
Indices: 5125187--5125357 Score: 215
Period size: 60 Copynumber: 2.8 Consensus size: 59
5125177 TTTCTTATTA
5125187 TTTTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTT
1 TTTTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAATTT
* *
5125247 TTATTTATTTATTTATT-TATTATTG--TATGAATATAAATAAATGTAAAATAATATTAATTT
1 TT-TTTATTTATTTATTATTTTA-TGAATAT-AA-ATAAATAAATATAAAATAATATTAATTT
* *
5125307 TGTTTTA-TTATTTATTATTTTATGAATATAGATAAATAAATAAATAAATAA
1 T-TTTTATTTATTTATTATTTTATGAATATAAATAAATAAATATA-AAATAA
5125358 CAAATCCAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
58 3 0.03
59 28 0.29
60 47 0.49
61 18 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (59 bp):
TTTTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTT
Found at i:5125677 original size:11 final size:11
Alignment explanation
Indices: 5125661--5125686 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5125651 TTCTCTCTAG
5125661 CATTTCCCTTC
1 CATTTCCCTTC
5125672 CATTTCCCTTC
1 CATTTCCCTTC
5125683 CATT
1 CATT
5125687 CCTTTGCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.46
Consensus pattern (11 bp):
CATTTCCCTTC
Found at i:5127538 original size:33 final size:34
Alignment explanation
Indices: 5127501--5127566 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
5127491 TTAAATTTTC
* *
5127501 TTTTTGTTTAATTAAATACTTGAATTTA-ATTTA
1 TTTTTATTTAATTAAATACTTAAATTTATATTTA
*
5127534 TTTTTATTTAATTAAATATTTAAATTTATATTT
1 TTTTTATTTAATTAAATACTTAAATTTATATTT
5127567 TGATTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (34 bp):
TTTTTATTTAATTAAATACTTAAATTTATATTTA
Found at i:5129191 original size:19 final size:19
Alignment explanation
Indices: 5129167--5129206 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5129157 ATTAATTTTG
5129167 ATCAAATGAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
5129186 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
5129205 AT
1 AT
5129207 AAGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:5129644 original size:56 final size:58
Alignment explanation
Indices: 5129575--5129703 Score: 174
Period size: 56 Copynumber: 2.3 Consensus size: 58
5129565 TTCAAAAATA
* * *
5129575 ATATTATTTTAATATATTTAATATTAAATTTAATTTAATACTTAAT-TTG-TAA-TATT
1 ATATTAATTTAATATATTTAATATTAAATTTAATCTAATA-TTAATCTTGAAAAGTATT
* * *
5129631 TTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGAAAAGTATT
1 ATATTAATTTAATATATTTAATATTAAATTTAATCTAATATTAATCTTGAAAAGTATT
5129689 ATATTAATTTAATAT
1 ATATTAATTTAATAT
5129704 TAAAGTGATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
55 4 0.06
56 39 0.63
57 2 0.03
58 17 0.27
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (58 bp):
ATATTAATTTAATATATTTAATATTAAATTTAATCTAATATTAATCTTGAAAAGTATT
Found at i:5129669 original size:17 final size:18
Alignment explanation
Indices: 5129590--5129672 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 18
5129580 ATTTTAATAT
5129590 ATTTAATATTAAATT-TA
1 ATTTAATATTAAATTATA
* *
5129607 ATTTAATACTTAATTTGTA
1 ATTTAATA-TTAAATTATA
* *
5129626 ATATT-TTATTAATTTAATA
1 AT-TTAATATTAAATT-ATA
5129645 GATTTAATATTAAATT-TA
1 -ATTTAATATTAAATTATA
*
5129663 ATCTAATATT
1 ATTTAATATT
5129673 TATCTTGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
17 17 0.31
18 15 0.28
19 10 0.19
20 12 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTAATATTAAATTATA
Found at i:5135981 original size:17 final size:16
Alignment explanation
Indices: 5135934--5135984 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 16
5135924 TAAAGTGTTA
**
5135934 AAAAATTTAATTAATT
1 AAAAATTTAATTTTTT
*
5135950 AAAAA-TTAATATTTT
1 AAAAATTTAATTTTTT
5135965 AAGAAATTTAATTTTTT
1 AA-AAATTTAATTTTTT
5135982 AAA
1 AAA
5135985 TAAGTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.31
16 9 0.31
17 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAAAATTTAATTTTTT
Found at i:5136529 original size:49 final size:50
Alignment explanation
Indices: 5136451--5136583 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 50
5136441 GTCTTGGTTC
* * * * * *
5136451 ACAGTGATTATACAGTTATGGGTTGAAGTATAACTTAG-GCTCTCAATTG
1 ACAGTGGTTATGCAGTCACGGGTTCAAGTATAACTTAGAGCTCCCAATTG
* *
5136500 ACAGTGGTTATGCAGTCACGGGTTCAAGTATAAC-TCGAGCTCCCAGTTG
1 ACAGTGGTTATGCAGTCACGGGTTCAAGTATAACTTAGAGCTCCCAATTG
* *
5136549 ATAGTGGTTATGCAATCACGGGTTCAAGTATAACT
1 ACAGTGGTTATGCAGTCACGGGTTCAAGTATAACT
5136584 CGGGGCTCCA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
48 2 0.03
49 70 0.97
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (50 bp):
ACAGTGGTTATGCAGTCACGGGTTCAAGTATAACTTAGAGCTCCCAATTG
Found at i:5136584 original size:49 final size:50
Alignment explanation
Indices: 5136470--5136609 Score: 169
Period size: 49 Copynumber: 2.9 Consensus size: 50
5136460 ATACAGTTAT
* * * *
5136470 GGGTTGAAGTATAACT-TAGGCTCTCAATTGACAGTGGTTATGCAGTCAC
1 GGGTTCAAGTATAACTCGAGGCTCCCAATTGACAGTGGTTATGCAATCAC
* *
5136519 GGGTTCAAGTATAACTCGA-GCTCCCAGTTGATAGTGGTTATGCAATCAC
1 GGGTTCAAGTATAACTCGAGGCTCCCAATTGACAGTGGTTATGCAATCAC
* * **
5136568 GGGTTCAAGTATAACTCGGGGCT-CCAATAGATGGTGGTTATG
1 GGGTTCAAGTATAACTCGAGGCTCCCAATTGACAGTGGTTATG
5136610 TGGTCTCGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 75 0.95
50 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (50 bp):
GGGTTCAAGTATAACTCGAGGCTCCCAATTGACAGTGGTTATGCAATCAC
Found at i:5138609 original size:23 final size:23
Alignment explanation
Indices: 5138537--5138639 Score: 99
Period size: 23 Copynumber: 4.5 Consensus size: 23
5138527 ACGAAACAAA
* *
5138537 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
5138558 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
5138583 CAGAGAGCACACACAA-TGCTAAT
1 CAGAGAGCACACA-AAGTGCTAAT
5138606 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
5138629 CAGAGAGCACA
1 CAGAGAGCACA
5138640 TGACGTACTA
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
21 15 0.22
22 4 0.06
23 31 0.45
25 13 0.19
26 4 0.06
27 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:5138650 original size:23 final size:23
Alignment explanation
Indices: 5138537--5138659 Score: 85
Period size: 23 Copynumber: 5.3 Consensus size: 23
5138527 ACGAAACAAA
*
5138537 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTACTAAT
* *
5138558 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTACT----AAT
*
5138583 CAGAGAGCACACACAA-TGCTAAT
1 CAGAGAGCACACA-AAGTACTAAT
*
5138606 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTACTAAT
** * *
5138629 CAGAGAGCACATGACGTACTAAA
1 CAGAGAGCACACAAAGTACTAAT
5138652 CAGAGAGC
1 CAGAGAGC
5138660 GCGTTAGTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
21 15 0.18
22 4 0.05
23 46 0.55
25 13 0.15
26 4 0.05
27 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTACTAAT
Found at i:5143660 original size:18 final size:20
Alignment explanation
Indices: 5143639--5143684 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
5143629 AATGTTTGAA
5143639 TTTTATATAAA-AAAAT-AT
1 TTTTATATAAATAAAATAAT
5143657 TTTTAT-TAAATAAAATAAT
1 TTTTATATAAATAAAATAAT
5143676 TTTTA-ATAA
1 TTTTATATAA
5143685 TTGAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTATATAAATAAAATAAT
Found at i:5162570 original size:27 final size:27
Alignment explanation
Indices: 5162522--5162633 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 27
5162512 AAATTTTGTA
**
5162522 AAAAAAATTTTGGGCCCC-TAAAAACT
1 AAAAAAATTTTGAACCCCTTAAAAACT
* **
5162548 AAAAAAATTTTAAACCCCTTAAAAGTT
1 AAAAAAATTTTGAACCCCTTAAAAACT
* *
5162575 GATAAAAAACTTTG-A-CCTTTAAAAA-T
1 -A-AAAAAATTTTGAACCCCTTAAAAACT
* *
5162601 TAAAAAATTTTGAGCCCCTTAAAAACT
1 AAAAAAATTTTGAACCCCTTAAAAACT
*
5162628 AGAAAA
1 AAAAAA
5162634 TAATATTTTG
Statistics
Matches: 65, Mismatches: 15, Indels: 11
0.71 0.16 0.12
Matches are distributed among these distances:
24 10 0.15
26 25 0.38
27 19 0.29
28 2 0.03
29 9 0.14
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAAAAATTTTGAACCCCTTAAAAACT
Found at i:5172241 original size:11 final size:11
Alignment explanation
Indices: 5172225--5172249 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5172215 AAAACTTTTA
5172225 AATAATTTAAT
1 AATAATTTAAT
5172236 AATAATTTAAT
1 AATAATTTAAT
5172247 AAT
1 AAT
5172250 TTTTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:5174768 original size:7 final size:7
Alignment explanation
Indices: 5174756--5174794 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5174746 ATTCGATTTG
5174756 GATTCAA
1 GATTCAA
5174763 GATTCAA
1 GATTCAA
5174770 GATTC-A
1 GATTCAA
*
5174776 GAGTTCAT
1 GA-TTCAA
5174784 GATTCAA
1 GATTCAA
5174791 GATT
1 GATT
5174795 TAGGATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.11
7 23 0.82
8 2 0.07
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (7 bp):
GATTCAA
Found at i:5174801 original size:14 final size:14
Alignment explanation
Indices: 5174755--5174801 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5174745 AATTCGATTT
5174755 GGATTCAAGATTCA
1 GGATTCAAGATTCA
*
5174769 AGATTC-AGAGTTCA
1 GGATTCAAGA-TTCA
* *
5174783 TGATTCAAGATTTA
1 GGATTCAAGATTCA
5174797 GGATT
1 GGATT
5174802 TTAGGTTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (14 bp):
GGATTCAAGATTCA
Found at i:5175038 original size:38 final size:38
Alignment explanation
Indices: 5174995--5175075 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
5174985 TTTTTTTTCG
*
5174995 TATTTTAGTTTAATTTCATATTATCGTTGATATTAGTT
1 TATTTTAGTTTAATTTCATATTATCATTGATATTAGTT
* *
5175033 TATTTTAGTTTGATTTCTTATTATCATTGATATTAGTT
1 TATTTTAGTTTAATTTCATATTATCATTGATATTAGTT
*
5175071 GATTT
1 TATTT
5175076 AATTATGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (38 bp):
TATTTTAGTTTAATTTCATATTATCATTGATATTAGTT
Found at i:5179879 original size:18 final size:17
Alignment explanation
Indices: 5179858--5179909 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
5179848 GGTGAAGATT
5179858 ACGATGACGATGAAGACG
1 ACGATGA-GATGAAGACG
* *
5179876 ACGAT-A-TTGAAGAAG
1 ACGATGAGATGAAGACG
5179891 ACGATGAAGATGAAGACG
1 ACGATG-AGATGAAGACG
5179909 A
1 A
5179910 AGAAGACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.13
Consensus pattern (17 bp):
ACGATGAGATGAAGACG
Found at i:5179905 original size:15 final size:15
Alignment explanation
Indices: 5179858--5179921 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
5179848 GGTGAAGATT
*
5179858 ACGATGACGATGAAG
1 ACGATGAAGATGAAG
* *
5179873 ACGACGATATTGAAGAAG
1 ACGATGA-A--GATGAAG
5179891 ACGATGAAGATGAAG
1 ACGATGAAGATGAAG
* *
5179906 ACGAAGAAGACGAAG
1 ACGATGAAGATGAAG
5179921 A
1 A
5179922 TGAAAACGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 26 0.67
17 1 0.03
18 12 0.31
ACGTcount: A:0.47, C:0.11, G:0.31, T:0.11
Consensus pattern (15 bp):
ACGATGAAGATGAAG
Found at i:5179920 original size:21 final size:21
Alignment explanation
Indices: 5179887--5179935 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5179877 CGATATTGAA
* * *
5179887 GAAGACGATGAAGATGAAGAC
1 GAAGAAGACGAAGATGAAAAC
5179908 GAAGAAGACGAAGATGAAAAC
1 GAAGAAGACGAAGATGAAAAC
*
5179929 GACGAAG
1 GAAGAAG
5179936 TTCTGTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.33, T:0.06
Consensus pattern (21 bp):
GAAGAAGACGAAGATGAAAAC
Found at i:5181507 original size:28 final size:28
Alignment explanation
Indices: 5181467--5181521 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
5181457 AGCATTAATG
*
5181467 GTGCAATTGACTGCTAGATGGAAGTTTA
1 GTGCAATTGACTGCCAGATGGAAGTTTA
5181495 GTGCAATTGACTGCCAGATGGAAGTTT
1 GTGCAATTGACTGCCAGATGGAAGTTT
5181522 GGGTATTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
GTGCAATTGACTGCCAGATGGAAGTTTA
Found at i:5185190 original size:2 final size:2
Alignment explanation
Indices: 5185185--5185211 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5185175 TTTTTATTCT
5185185 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5185212 TATTTCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5189305 original size:15 final size:17
Alignment explanation
Indices: 5189275--5189308 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5189265 CAAAATTAAA
5189275 TTATAATTTTTAATAAT
1 TTATAATTTTTAATAAT
5189292 TTAT-ATTTTT-ATAAT
1 TTATAATTTTTAATAAT
5189307 TT
1 TT
5189309 TTAAAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATTTTTAATAAT
Found at i:5189702 original size:6 final size:7
Alignment explanation
Indices: 5189682--5189715 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
5189672 CTTGGTAGAG
5189682 ATGAAAA
1 ATGAAAA
5189689 ATGAAAA
1 ATGAAAA
5189696 ATGAAAA
1 ATGAAAA
5189703 ATGAAAA
1 ATGAAAA
5189710 AT-AAAA
1 ATGAAAA
5189716 CATTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:5207291 original size:6 final size:6
Alignment explanation
Indices: 5207280--5207309 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5207270 GCTTTCCACT
5207280 CCAACC CCAACC CCAACC CCAACC CCAACC
1 CCAACC CCAACC CCAACC CCAACC CCAACC
5207310 ATGCCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAACC
Found at i:5209496 original size:22 final size:21
Alignment explanation
Indices: 5209450--5209496 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
5209440 TAACTGTCGC
*
5209450 TTCAACCGATTTTTTAACCTA
1 TTCAACCGATCTTTTAACCTA
*
5209471 -TCAACCGATCTTTTAACTTAA
1 TTCAACCGATCTTTTAACCT-A
5209492 TTCAA
1 TTCAA
5209497 TCGGTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 17 0.77
21 1 0.05
22 4 0.18
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.40
Consensus pattern (21 bp):
TTCAACCGATCTTTTAACCTA
Found at i:5227484 original size:13 final size:13
Alignment explanation
Indices: 5227466--5227506 Score: 68
Period size: 12 Copynumber: 3.3 Consensus size: 13
5227456 ACTCGACCTG
5227466 TTTATATTAATTT
1 TTTATATTAATTT
5227479 TTTATATT-ATTT
1 TTTATATTAATTT
5227491 TTTATA-TAATTT
1 TTTATATTAATTT
5227503 TTTA
1 TTTA
5227507 AAAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.67
13 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATTAATTT
Found at i:5234924 original size:3 final size:3
Alignment explanation
Indices: 5234918--5234958 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5234908 CTAATAATTG
5234918 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5234959 TCATACTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5237544 original size:12 final size:12
Alignment explanation
Indices: 5237527--5237551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5237517 TATTAGATTC
5237527 ACTTTGATAAAT
1 ACTTTGATAAAT
5237539 ACTTTGATAAAT
1 ACTTTGATAAAT
5237551 A
1 A
5237552 AAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ACTTTGATAAAT
Found at i:5238113 original size:32 final size:33
Alignment explanation
Indices: 5238077--5238138 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
5238067 ATAATGCATC
5238077 AAAATTAAAATTT-TATAAAATAAAT-AGGTTAT
1 AAAATT-AAATTTCTATAAAATAAATCAGGTTAT
* *
5238109 AAAATTTAATTTCTATATAATAAATCAGGT
1 AAAATTAAATTTCTATAAAATAAATCAGGT
5238139 AGACCTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 17 0.65
33 4 0.15
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (33 bp):
AAAATTAAATTTCTATAAAATAAATCAGGTTAT
Found at i:5245402 original size:11 final size:11
Alignment explanation
Indices: 5245388--5245412 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5245378 TAAATATTTT
5245388 AAAAATTATAA
1 AAAAATTATAA
5245399 AAAAATTATAA
1 AAAAATTATAA
5245410 AAA
1 AAA
5245413 TTCAACAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:5261365 original size:19 final size:20
Alignment explanation
Indices: 5261330--5261372 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5261320 AAATTACACA
5261330 AAAAAATCAAAATTATTT-T
1 AAAAAATCAAAATTATTTAT
*
5261349 AAAAAATACAACA-TATTTAT
1 AAAAAAT-CAAAATTATTTAT
5261369 AAAA
1 AAAA
5261373 TATTTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATCAAAATTATTTAT
Found at i:5268094 original size:33 final size:33
Alignment explanation
Indices: 5268051--5268197 Score: 178
Period size: 33 Copynumber: 4.6 Consensus size: 33
5268041 GAACTCTTTC
* *
5268051 GGCATGTGCGAGCTGAGACTGTGAGCTCCCCTT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* *
5268084 AGCATGTGCGAGCTGATATTGTGAGCTCCCATT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
5268117 GGCA--T--GAGCTGATACTGTGAGCTCCCATT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* **
5268146 GGCATGTGCGAGCTGATATTGTGAGCTTTTC-TT
1 GGCATGTGCGAGCTGATACTGTGAGC-TCCCATT
*
5268179 GGCATGTGCGAGTTGATAC
1 GGCATGTGCGAGCTGATAC
5268198 CTCAAGCCCC
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
29 27 0.28
31 2 0.02
33 67 0.68
34 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (33 bp):
GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
Found at i:5268135 original size:29 final size:29
Alignment explanation
Indices: 5268060--5268151 Score: 112
Period size: 29 Copynumber: 3.0 Consensus size: 29
5268050 CGGCATGTGC
* * *
5268060 GAGCTGAGACTGTGAGCTCCCCTTAGCATGT
1 GAGCTGATACTGTGAGCTCCCATTGGCA--T
*
5268091 GCGAGCTGATATTGTGAGCTCCCATTGGCAT
1 --GAGCTGATACTGTGAGCTCCCATTGGCAT
5268122 GAGCTGATACTGTGAGCTCCCATTGGCAT
1 GAGCTGATACTGTGAGCTCCCATTGGCAT
5268151 G
1 G
5268152 TGCGAGCTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 29 0.54
31 1 0.02
33 24 0.44
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (29 bp):
GAGCTGATACTGTGAGCTCCCATTGGCAT
Found at i:5269571 original size:20 final size:20
Alignment explanation
Indices: 5269538--5269576 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5269528 GGTTACAGAA
*
5269538 GTTCTTTTTATTTTCTTTTC
1 GTTCTTTTTATTTTATTTTC
5269558 GTTC-TTTTAGTTTTATTTT
1 GTTCTTTTTA-TTTTATTTT
5269577 TGGTTCTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.10, G:0.08, T:0.74
Consensus pattern (20 bp):
GTTCTTTTTATTTTATTTTC
Found at i:5273774 original size:22 final size:21
Alignment explanation
Indices: 5273724--5273767 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5273714 AAACGGTCTT
*
5273724 TTCTATTAAAATTTTCATTCA
1 TTCTATTAAAAATTTCATTCA
5273745 TTCTATTAAAAATTTCATTCA
1 TTCTATTAAAAATTTCATTCA
5273766 TT
1 TT
5273768 TGTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (21 bp):
TTCTATTAAAAATTTCATTCA
Found at i:5275358 original size:15 final size:15
Alignment explanation
Indices: 5275310--5275361 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5275300 TGTTTGATAA
5275310 ATTGAAAAATTAAGT
1 ATTGAAAAATTAAGT
** *
5275325 GCT-AAAAAATAAG-
1 ATTGAAAAATTAAGT
5275338 AGTTGAAAAATTAAGT
1 A-TTGAAAAATTAAGT
5275354 ATTGAAAA
1 ATTGAAAA
5275362 TTTTATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 10 0.36
15 17 0.61
16 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (15 bp):
ATTGAAAAATTAAGT
Found at i:5276231 original size:14 final size:15
Alignment explanation
Indices: 5276206--5276234 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5276196 TCTTTTAATC
5276206 AAAATGACAGAAAAA
1 AAAATGACAGAAAAA
5276221 AAAATGA-AGAAAAA
1 AAAATGACAGAAAAA
5276235 TATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (15 bp):
AAAATGACAGAAAAA
Found at i:5278512 original size:20 final size:19
Alignment explanation
Indices: 5278457--5278512 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
5278447 ATTAAAACAT
**
5278457 TCAATCAATTCATTTTTAA
1 TCAATCAATTCATTTGCAA
5278476 TCCGAATCAA-TCGATTTGCAGA
1 T-C-AATCAATTC-ATTTGCA-A
5278498 TCAATCAATTCATTT
1 TCAATCAATTCATTT
5278513 TCTTTCTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
21 14 0.47
22 2 0.07
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (19 bp):
TCAATCAATTCATTTGCAA
Found at i:5286798 original size:18 final size:18
Alignment explanation
Indices: 5286777--5286839 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
5286767 TGCGAATTGA
5286777 TATTTTATGTGATCTGCT
1 TATTTTATGTGATCTGCT
*
5286795 TATTTTATGTGAAT-TGAT
1 TATTTTATGTG-ATCTGCT
* *
5286813 TATTATATGT-ACACTGCT
1 TATTTTATGTGA-TCTGCT
5286831 TATTTTATG
1 TATTTTATG
5286840 AGTTCTGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
18 34 0.92
19 2 0.05
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTTTATGTGATCTGCT
Found at i:5286809 original size:35 final size:36
Alignment explanation
Indices: 5286760--5286839 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
5286750 TATGAACTGA
* * *
5286760 TATTTAATGCGAATTGA-TATTTTATGTGA-TCTGCT
1 TATTTTATGCGAATTGATTATTATATGT-ACACTGCT
*
5286795 TATTTTATGTGAATTGATTATTATATGTACACTGCT
1 TATTTTATGCGAATTGATTATTATATGTACACTGCT
5286831 TATTTTATG
1 TATTTTATG
5286840 AGTTCTGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
35 16 0.41
36 23 0.59
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.51
Consensus pattern (36 bp):
TATTTTATGCGAATTGATTATTATATGTACACTGCT
Found at i:5290575 original size:27 final size:27
Alignment explanation
Indices: 5290545--5290604 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
5290535 TGGCTCAACC
*
5290545 TTCATCATCTATTTTATGTATCATCAA
1 TTCAACATCTATTTTATGTATCATCAA
5290572 TTCAACATCTATTTTATGTATCATCAA
1 TTCAACATCTATTTTATGTATCATCAA
5290599 TTCAAC
1 TTCAAC
5290605 TTTTTAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (27 bp):
TTCAACATCTATTTTATGTATCATCAA
Found at i:5292914 original size:16 final size:18
Alignment explanation
Indices: 5292875--5292908 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5292865 TAAGTTTATA
5292875 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
5292892 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
5292909 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:5293027 original size:25 final size:24
Alignment explanation
Indices: 5292992--5293068 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
5292982 TAAAATGATT
5292992 ATATAAA-AATTTTAATAAATAAAA
1 ATATAAATAATTTTAA-AAATAAAA
* * *
5293016 ATATATATAATTATTAAACATTAAA
1 ATATAAATAATT-TTAAAAATAAAA
5293041 ATATAAAT-ATTTTAAAAAATTAAAA
1 ATATAAATAATTTT-AAAAA-TAAAA
5293066 ATA
1 ATA
5293069 ATTTGAGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 2 0.05
24 13 0.30
25 24 0.56
26 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAAATAATTTTAAAAATAAAA
Found at i:5309856 original size:16 final size:16
Alignment explanation
Indices: 5309835--5309894 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
5309825 CAAACAAATC
5309835 AAAATTATTTTAATTT
1 AAAATTATTTTAATTT
*
5309851 AAAATTTTTAATTAA-TT
1 AAAATTATT--TTAATTT
* *
5309868 AAATTTA-TTTAATTA
1 AAAATTATTTTAATTT
5309883 AAAATTTATTTT
1 AAAA-TTATTTT
5309895 TATTACAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 12 0.35
17 10 0.29
18 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAAATTATTTTAATTT
Found at i:5309867 original size:18 final size:18
Alignment explanation
Indices: 5309844--5309883 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5309834 CAAAATTATT
5309844 TTAATTTAAAATT-TTTAA
1 TTAA-TTAAAATTATTTAA
*
5309862 TTAATTAAATTTATTTAA
1 TTAATTAAAATTATTTAA
5309880 TTAA
1 TTAA
5309884 AAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAAAATTATTTAA
Found at i:5317053 original size:2 final size:2
Alignment explanation
Indices: 5317046--5317071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5317036 TAAATTGTGC
5317046 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
5317072 TGTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5319792 original size:21 final size:21
Alignment explanation
Indices: 5319760--5319817 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
5319750 TTGAATTTAG
5319760 GGTTCGAAGTTTAAGGTTTGA
1 GGTTCGAAGTTTAAGGTTTGA
*
5319781 GGTTC-AATGTTTATGGTTT-A
1 GGTTCGAA-GTTTAAGGTTTGA
* * *
5319801 AGTTCGAGGTTCAAGGT
1 GGTTCGAAGTTTAAGGT
5319818 AAAAAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.22, C:0.07, G:0.31, T:0.40
Consensus pattern (21 bp):
GGTTCGAAGTTTAAGGTTTGA
Found at i:5323407 original size:16 final size:16
Alignment explanation
Indices: 5323359--5323410 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5323349 AAAGAAATTT
* *
5323359 TTTTTCATCCTTCTAA
1 TTTTCCATCCTTCCAA
* *
5323375 TTTTCTA-CCTCTTCAA
1 TTTTCCATCCT-TCCAA
5323391 TTTTCCATCCTTCCAA
1 TTTTCCATCCTTCCAA
5323407 TTTT
1 TTTT
5323411 TTTCACTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTCCATCCTTCCAA
Found at i:5325247 original size:29 final size:28
Alignment explanation
Indices: 5325194--5325256 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
5325184 TTTAAGAAAA
5325194 TTGT-TAATATAACACCTGTACTTTTAAT
1 TTGTCTAATATAACACCTGTACTTTT-AT
*
5325222 TTGTCTAATATAACACTTG-ACATTTTAT
1 TTGTCTAATATAACACCTGTAC-TTTTAT
5325250 TTCGTCT
1 TT-GTCT
5325257 GTCAATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
TTGTCTAATATAACACCTGTACTTTTAT
Found at i:5327062 original size:18 final size:18
Alignment explanation
Indices: 5327039--5327081 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5327029 TTTTCAGTTA
5327039 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
5327057 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
5327075 TAATTAA
1 TAATTAA
5327082 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:5332663 original size:60 final size:60
Alignment explanation
Indices: 5332590--5332713 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 60
5332580 AAAAATTGTG
* * * * *
5332590 TTTTTTGGTGTTGGCCATGCAATGGTCGACACCTCT-TTTTTCAGATAAAAAATTTCAAAT
1 TTTTTTGGTGTTGGCAATGCAATGGCCGACACCCCTATTTATCAGATAAAAAA-ATCAAAT
* *
5332650 TTTTTTGGTGTTGGCAATGCAATGGCCGATACCCCTATTTATCTGATAAAAAAATCAAAT
1 TTTTTTGGTGTTGGCAATGCAATGGCCGACACCCCTATTTATCAGATAAAAAAATCAAAT
5332710 TTTT
1 TTTT
5332714 GAGTATCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 42 0.75
61 14 0.25
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (60 bp):
TTTTTTGGTGTTGGCAATGCAATGGCCGACACCCCTATTTATCAGATAAAAAAATCAAAT
Found at i:5334320 original size:62 final size:61
Alignment explanation
Indices: 5334183--5334501 Score: 301
Period size: 62 Copynumber: 5.2 Consensus size: 61
5334173 AGATAAATTA
* * * * *
5334183 TTGGCCATGCAATGGTCGACACCCCTATTTATATGATAAAAAAA--TCAAATTTTTGGGTG
1 TTGGCCATGCAATGGTCGACACCCCTTTTTTTAAGATAAAAAAATTTCAATTTTTTTGGTG
* * *
5334242 TTGGCCATGTAATGGTCGACACCCATTTTTTTAAGATAAAAAAATTTTAATTTTTTTTGGTG
1 TTGGCCATGCAATGGTCGACACCCCTTTTTTTAAGATAAAAAAATTTCAA-TTTTTTTGGTG
** ** * *
5334304 TTGGCCATTTAATGGTCGACA-CCCTCTTTTTGCATATAAAAAAATTTCAATTTTTTTTTGTG
1 TTGGCCATGCAATGGTCGACACCCCT-TTTTTTAAGATAAAAAAATTTCAA-TTTTTTTGGTG
* * * * *
5334366 TTGGCCATTCCATGGCCGACACCCCTTTTTTGTCAGAT-AAAAAATTTGAATTTTTTTGGTG
1 TTGGCCATGCAATGGTCGACACCCCTTTTTT-TAAGATAAAAAAATTTCAATTTTTTTGGTG
* * * * * *
5334427 TTGACCATGCCATAGTCGACACTCCCTTTTTATT-TGGT-AAAAAA-TTAAATTTTTTTGGTG
1 TTGGCCATGCAATGGTCGACAC-CCCTTTTT-TTAAGATAAAAAAATTTCAATTTTTTTGGTG
*
5334487 TTGGCCATGTAATGG
1 TTGGCCATGCAATGG
5334502 CCCACACAAA
Statistics
Matches: 219, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
59 39 0.18
60 26 0.12
61 42 0.19
62 103 0.47
63 9 0.04
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (61 bp):
TTGGCCATGCAATGGTCGACACCCCTTTTTTTAAGATAAAAAAATTTCAATTTTTTTGGTG
Found at i:5334469 original size:123 final size:120
Alignment explanation
Indices: 5334187--5334508 Score: 355
Period size: 124 Copynumber: 2.6 Consensus size: 120
5334177 AAATTATTGG
* * * *
5334187 CCATGCAATGGTCGACACCCCTATTTATATGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGT
1 CCATGCAATGGTCGACACCCCTTTTTATATG-TAAAAAATTCAATTTTTTTGGTGTTGGCCATGT
* * *
5334252 AATGGTCGACACCCATTTTTTTAAGATAAAAAAATTTTAATTTTTTTTGGTGTTGG
65 AATGGCCGACACCCATTTTTTTAAGATAAAAAAATTTGAATTTTTTTTGGTGTTGA
** * *
5334308 CCATTTAATGGTCGACACCCTCTTTTTGCATAT-AAAAAAATTTCAATTTTTTTTTGTGTTGGCC
1 CCATGCAATGGTCGACACCC-CTTTTT--ATATGTAAAAAA-TTCAA-TTTTTTTGGTGTTGGCC
* * *
5334372 AT-TCCATGGCCGACACCCCTTTTTTGTCAGAT-AAAAAATTTGAA-TTTTTTTGGTGTTGA
61 ATGT-AATGGCCGACACCCATTTTTT-TAAGATAAAAAAATTTGAATTTTTTTTGGTGTTGA
* * * *
5334431 CCATGCCATAGTCGACACTCCCTTTTTATTTGGTAAAAAATTAAATTTTTTTGGTGTTGGCCATG
1 CCATGCAATGGTCGACAC-CCCTTTTTATAT-GTAAAAAATTCAATTTTTTTGGTGTTGGCCATG
*
5334496 TAATGGCCCACAC
64 TAATGGCCGACAC
5334509 AAACTTCTCC
Statistics
Matches: 166, Mismatches: 24, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
121 49 0.30
122 16 0.10
123 45 0.27
124 51 0.31
125 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (120 bp):
CCATGCAATGGTCGACACCCCTTTTTATATGTAAAAAATTCAATTTTTTTGGTGTTGGCCATGTA
ATGGCCGACACCCATTTTTTTAAGATAAAAAAATTTGAATTTTTTTTGGTGTTGA
Found at i:5337543 original size:61 final size:61
Alignment explanation
Indices: 5337429--5337978 Score: 531
Period size: 60 Copynumber: 9.1 Consensus size: 61
5337419 ACAAATTTAA
* * * * *
5337429 TTTTTTATC-AAATAAAATGGGAGTGTCGACCATGGCATGGCCAACACAAAAAAAAATTTGAACT
1 TTTTTTATCTGAA-AAAA-GGG-GTGTCGGCCATTGCATGGCCAACAC-CAAAAAAATTTGAAAT
* *** *
5337493 TTTTTTATCTGAAAAAAGGGGTGTAGGCCATTGCATGATAAATACCAAAAAAATTTGAAAT
1 TTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * *
5337554 TTTTTTATCTGTAAAAAAGGGGTGTCGACCATTGCATGGCCAATA-CAAAAAAAATTGAAA-
1 TTTTTTATCTG-AAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * *
5337614 TTTTTTATCTGAAAAAAGGAGGTGTCAGCCATTGCATGGTCAACACC-TAAAAATTTG-AAT
1 TTTTTTATCTGAAAAAAGG-GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * *
5337674 TTTTTTATCAGATAAATAA-GAGTGTCGGCCATTGCATGGCCAACACC-AAAAAATTTG-ATT
1 TTTTTTATCTGA-AAA-AAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * *
5337734 TTTTTTATCAGATAAATAA-GGGTGTCGGCCATTGAATGGCCCACACCAAAAAAATTTGAAAT
1 TTTTTTATCTGA-AAA-AAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * *
5337796 TTTTTTATTTGAAAAAAGGGATGTCGGTCATTGCATGGCCAACACCAAAAAAATTTGAAAT
1 TTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * * * * *
5337857 TTTTTTATCTAAAAAAATGGAGTGTCGGTCATTGTATGGCTAACACCCAAAAAA-TT--AA-
1 TTTTTTATCTGAAAAAA-GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
* * * * * *
5337915 TTTTTTAT-TCGATAAATAGGAGTATCGGCTATTGCATGACCAACATC-AAAAAA-TT-AAAT
1 TTTTTTATCT-GA-AAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
5337974 TTTTT
1 TTTTT
5337979 ATTTGACAAA
Statistics
Matches: 417, Mismatches: 54, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
57 9 0.02
58 33 0.08
59 21 0.05
60 132 0.32
61 113 0.27
62 91 0.22
63 3 0.01
64 13 0.03
65 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (61 bp):
TTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAT
Found at i:5338623 original size:10 final size:8
Alignment explanation
Indices: 5338598--5338654 Score: 62
Period size: 8 Copynumber: 6.6 Consensus size: 8
5338588 AACTTTCAAC
5338598 TTTTTATA
1 TTTTTATA
5338606 TTTTTATA
1 TTTTTATA
5338614 TTAATTTATA
1 TT--TTTATA
5338624 TTTTTAT-
1 TTTTTATA
5338631 TTTTTAATTA
1 TTTTT-A-TA
5338641 TTTTTATA
1 TTTTTATA
5338649 TATTTT
1 T-TTTT
5338655 TCTATCATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
7 5 0.12
8 19 0.44
9 6 0.14
10 13 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTATA
Found at i:5338754 original size:18 final size:18
Alignment explanation
Indices: 5338722--5338760 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5338712 TTAATAACAT
*
5338722 TTTATAATATTTAAATATA
1 TTTATAATATATAAA-ATA
5338741 TTTA-AATATATAAAATA
1 TTTATAATATATAAAATA
5338758 TTT
1 TTT
5338761 TTCAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATAATATATAAAATA
Found at i:5341144 original size:12 final size:12
Alignment explanation
Indices: 5341127--5341157 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5341117 GAACAAGCTT
*
5341127 GTTTATTGGCTC
1 GTTTATTGACTC
5341139 GTTTATTGACTC
1 GTTTATTGACTC
5341151 GTTTATT
1 GTTTATT
5341158 TATTAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (12 bp):
GTTTATTGACTC
Found at i:5341299 original size:23 final size:23
Alignment explanation
Indices: 5341243--5341330 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
5341233 TCATTAACAT
*
5341243 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* * *
5341267 TGTTCATGAACATGCTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
5341290 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
5341313 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
5341331 TGAACATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 33 0.61
24 18 0.33
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:5341340 original size:23 final size:23
Alignment explanation
Indices: 5341296--5341341 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5341286 TTAATGTTCG
* *
5341296 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
5341319 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
5341342 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:5346613 original size:14 final size:14
Alignment explanation
Indices: 5346596--5346623 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5346586 TATGGGGCTA
5346596 TCTGACTGGGAATC
1 TCTGACTGGGAATC
5346610 TCTGACTGGGAATC
1 TCTGACTGGGAATC
5346624 GGTATGGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
TCTGACTGGGAATC
Found at i:5348583 original size:10 final size:10
Alignment explanation
Indices: 5348568--5348595 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5348558 ATTCACTTTC
5348568 AAAATTAATA
1 AAAATTAATA
5348578 AAAATTAATA
1 AAAATTAATA
5348588 AAAATTAA
1 AAAATTAA
5348596 ATTACTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATTAATA
Found at i:5349807 original size:13 final size:14
Alignment explanation
Indices: 5349789--5349817 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5349779 TTTAAAATGG
5349789 TAAATTTT-TAATT
1 TAAATTTTATAATT
5349802 TAAATTTTATAATT
1 TAAATTTTATAATT
5349816 TA
1 TA
5349818 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATTTTATAATT
Found at i:5349831 original size:16 final size:17
Alignment explanation
Indices: 5349803--5349836 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5349793 TTTTTAATTT
*
5349803 AAATTTTATAATTTATA
1 AAATTTTATAATTAATA
5349820 AAATTTTA-AATTAATA
1 AAATTTTATAATTAATA
5349836 A
1 A
5349837 TAATATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTTATAATTAATA
Found at i:5350860 original size:16 final size:17
Alignment explanation
Indices: 5350835--5350876 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5350825 TTTTAAGTAA
5350835 GTAATCTTTTA-TATTAT
1 GTAAT-TTTTAGTATTAT
*
5350852 GTTATTTTTATGTATTAT
1 GTAATTTTTA-GTATTAT
5350870 GTAATTT
1 GTAATTT
5350877 ATAACACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 12 0.57
ACGTcount: A:0.26, C:0.02, G:0.10, T:0.62
Consensus pattern (17 bp):
GTAATTTTTAGTATTAT
Found at i:5351267 original size:29 final size:30
Alignment explanation
Indices: 5351215--5351272 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
5351205 TTTCAAAATT
*
5351215 ATATATGAACTTTGATTTGATGTGTAATTTG
1 ATATATGAACTTTGATTT-ATGTGCAATTTG
*
5351246 ATATATGAATTTTGATTT-TGTGCAATT
1 ATATATGAACTTTGATTTATGTGCAATT
5351273 ATACACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.50
Consensus pattern (30 bp):
ATATATGAACTTTGATTTATGTGCAATTTG
Found at i:5363295 original size:23 final size:23
Alignment explanation
Indices: 5363269--5363312 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5363259 ATATAAGATA
*
5363269 TATTTAATTAAATGCAGACATAC
1 TATTCAATTAAATGCAGACATAC
* *
5363292 TATTCATTTAAATGTAGACAT
1 TATTCAATTAAATGCAGACAT
5363313 GTCATCCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (23 bp):
TATTCAATTAAATGCAGACATAC
Found at i:5389772 original size:19 final size:21
Alignment explanation
Indices: 5389726--5389773 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5389716 CGATGCTAGA
5389726 TAAGGTATCAATACTTTTGTG
1 TAAGGTATCAATACTTTTGTG
* *
5389747 AAAGGTATCGATAC-TTTGT-
1 TAAGGTATCAATACTTTTGTG
5389766 TAAGGTAT
1 TAAGGTAT
5389774 ATGGACCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 5 0.21
21 12 0.50
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (21 bp):
TAAGGTATCAATACTTTTGTG
Found at i:5392554 original size:6 final size:6
Alignment explanation
Indices: 5392527--5392620 Score: 61
Period size: 6 Copynumber: 16.0 Consensus size: 6
5392517 GGCTTTCATT
* * * *
5392527 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA ATATAA ATCTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* ** **
5392574 A-TTCA ATTTAA ATTTTAA A-ACAA ATTTAA ATTTAA AAATAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
5392621 TCTTAAAATA
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
4 1 0.02
5 9 0.14
6 48 0.73
7 8 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:5392568 original size:18 final size:17
Alignment explanation
Indices: 5392530--5392640 Score: 80
Period size: 18 Copynumber: 6.3 Consensus size: 17
5392520 TTTCATTATT
* * *
5392530 TAAATTTAGAATAATTT
1 TAAATTTAAAATAAATC
5392547 TAAATTTAAATATAAATC
1 TAAATTTAAA-ATAAATC
* * * *
5392565 TAAACTTAAATTCAATT
1 TAAATTTAAAATAAATC
* *
5392582 TAAATTTTAAAACAAATT
1 TAAA-TTTAAAATAAATC
5392600 TAAATTTAAAAATAAAT-
1 TAAATTT-AAAATAAATC
*
5392617 TTAATCTTAAAATAAATC
1 TAAAT-TTAAAATAAATC
5392635 TGAAAT
1 T-AAAT
5392641 GGGTTTAGTT
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
17 33 0.45
18 38 0.51
19 3 0.04
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:5392607 original size:53 final size:52
Alignment explanation
Indices: 5392527--5392627 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
5392517 GGCTTTCATT
* * * *
5392527 ATTTAAATTTAGAATAATTTTAAATTTAAATATAAATCTAAACTTAAATTCA
1 ATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATCTAAACTTAAATTCA
* *
5392579 ATTTAAATTTTAAAACAAATTTAAATTTAAAAATAAATTTAATCTTAAA
1 ATTTAAA-TTTAAAACAAATTTAAATTTAAAAATAAATCTAAACTTAAA
5392628 ATAAATCTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 7 0.17
53 35 0.83
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (52 bp):
ATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATCTAAACTTAAATTCA
Found at i:5393122 original size:39 final size:39
Alignment explanation
Indices: 5393079--5393222 Score: 157
Period size: 39 Copynumber: 3.7 Consensus size: 39
5393069 ACTGATGATG
5393079 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCA
* * * **
5393118 ATCTGCCTCAAGCTCGAGGTAAGAGATTGGTTGATGGTG--
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATG--GGTGCA
* * * * *
5393157 ATCTGCCCTAGGCTCAGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCA
*
5393196 ATCTGCCCCAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
5393223 TGGCTTATAA
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
37 3 0.04
39 76 0.92
41 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCA
Found at i:5393160 original size:78 final size:79
Alignment explanation
Indices: 5393071--5393264 Score: 266
Period size: 78 Copynumber: 2.5 Consensus size: 79
5393061 TGAGATTTAC
*
5393071 TGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCAATCTGCCTCAAGCTCGAG
1 TGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCAATCTGCCCCAAGCTCGAG
5393136 GTAAGAGATTGG-T
66 GTAAGAGATTGGCT
* * * * * * * *
5393149 TGATGGTGATCTGCCCTAGGCTCAGGGTAAAAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGG
1 TGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCAATCTGCCCCAAGCTCGAG
5393214 GTAAGAGATTGGCT
66 GTAAGAGATTGGCT
* *
5393228 T-ATAATGATCTGCCCCAAGCTTGAGGGTAAGAGATCG
1 TGATGATGATCTGCCCCAAGCTCG-GGGTAAGAGATCG
5393265 GGGTTTTCCA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
78 84 0.86
79 14 0.14
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (79 bp):
TGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGGTGCAATCTGCCCCAAGCTCGAG
GTAAGAGATTGGCT
Found at i:5393769 original size:49 final size:48
Alignment explanation
Indices: 5393499--5393774 Score: 190
Period size: 49 Copynumber: 5.6 Consensus size: 48
5393489 TGGTACTAAA
* * * * * *
5393499 TTCGCCGTTACGGCTTAAATTTTTCCTTTCATGCTTCGGAGGTATAAGG
1 TTCGCCATTACGACTTAAATCTTTCCCTTCATGCTTC-TAGGTACAAGG
* *
5393548 TTCGCCATTACGACTTAAATCTTTCCCTTTATGTCTTCGT-GGTAC-TGG
1 TTCGCCATTACGACTTAAATCTTTCCCTTCATG-CTTC-TAGGTACAAGG
* * * * *
5393596 ATTCGTCATTGCGGCTTAAATCTTTCTCTTCATG-TCTCTAAGGTATAAGG
1 -TTCGCCATTACGACTTAAATCTTTCCCTTCATGCT-TCT-AGGTACAAGG
* * * *
5393646 TTTGCCATTGCGAGTTAAA-CATTTCCCTTCAAAT-CTTCGT-GGTAC-TGG
1 TTCGCCATTACGACTTAAATC-TTTCCCTTC--ATGCTTC-TAGGTACAAGG
* ** *
5393694 ATTCGCCGTCGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGG
1 -TTCGCCATTACGACTTAAATCTTTCCCTTCATGCTTCT-AGGTACAAGG
5393744 TTCGCCATTACGACTTAAA-CATTTCCCTTCA
1 TTCGCCATTACGACTTAAATC-TTTCCCTTCA
5393775 AATCTTTGTG
Statistics
Matches: 177, Mismatches: 32, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
47 5 0.03
48 12 0.07
49 144 0.81
50 12 0.07
51 4 0.02
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (48 bp):
TTCGCCATTACGACTTAAATCTTTCCCTTCATGCTTCTAGGTACAAGG
Found at i:5393818 original size:49 final size:49
Alignment explanation
Indices: 5393765--5393984 Score: 131
Period size: 49 Copynumber: 4.5 Consensus size: 49
5393755 GACTTAAACA
*
5393765 TTTCCCTTCAAATCTTTGTGGTACCGGGTTTGCCGTTGCGGCCTCAACC
1 TTTCCCTTCAAATCTTTATGGTACCGGGTTTGCCGTTGCGGCCTCAACC
* * * * * * * *
5393814 TTTCCCATTTC--TTCCTTATGGAACTGGATTTGTCGTTGCAGCCTCAATC
1 TTTCCC--TTCAAATCTTTATGGTACCGGGTTTGCCGTTGCGGCCTCAACC
* * * * ** *
5393863 TTTCCCAT-AATATCTGCTAAGGTATCGGGTTCACCGTTGCGGCCTTAACC
1 TTTCCCTTCAA-ATCT-TTATGGTACCGGGTTTGCCGTTGCGGCCTCAACC
* * ** ** ** *
5393913 TTTCCCTTCAAATATTCATGGTACTAGGTTCACCGTTATGGCCTTAACC
1 TTTCCCTTCAAATCTTTATGGTACCGGGTTTGCCGTTGCGGCCTCAACC
* **
5393962 TTTCCCATCTCATCTTTATGGTA
1 TTTCCCTTCAAATCTTTATGGTA
5393985 TTAGATTCGC
Statistics
Matches: 125, Mismatches: 39, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
47 1 0.01
49 87 0.70
50 32 0.26
51 5 0.04
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (49 bp):
TTTCCCTTCAAATCTTTATGGTACCGGGTTTGCCGTTGCGGCCTCAACC
Done.