Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 151 of 163
Found at i:41521543 original size:426 final size:426
Alignment explanation
Indices: 41520750--41521604 Score: 1692
Period size: 426 Copynumber: 2.0 Consensus size: 426
41520740 GAATGACAAT
41520750 TGATTCAGAAAATTTTCCTCGGCTAGTGGTGTAATGACCTAAATTCACGGGCACCGAAAAAGTGA
1 TGATTCAGAAAATTTTCCTCGGCTAGTGGTGTAATGACCTAAATTCACGGGCACCGAAAAAGTGA
*
41520815 GTTATAGGGCCTCTGTCTTAGCAAAACAAGTTCGTAAATAATTATTAGGAGTAATTATGAGTTTA
66 GTTATAGGGCCTCCGTCTTAGCAAAACAAGTTCGTAAATAATTATTAGGAGTAATTATGAGTTTA
41520880 GTAGTGTGTTTAATTAAGCTTTGATTAGGTGAATTTAATTTAATTTAGAGTAATTAATAAAAAGG
131 GTAGTGTGTTTAATTAAGCTTTGATTAGGTGAATTTAATTTAATTTAGAGTAATTAATAAAAAGG
41520945 ACTAAATTGAATAAAGGGTGAAAGTCTAATTATAGATTAAAAAAAAGAAAGAGGGACTAAAATGG
196 ACTAAATTGAATAAAGGGTGAAAGTCTAATTATAGATTAAAAAAAAGAAAGAGGGACTAAAATGG
41521010 CAATTATGCCTATTGCATAAATTGAGGCCGCAAAACAGAGAAAAGTCTAAAGATTTTTCTTGATT
261 CAATTATGCCTATTGCATAAATTGAGGCCGCAAAACAGAGAAAAGTCTAAAGATTTTTCTTGATT
41521075 TTAATTTATAATTAATTAATATTATAATATAATAATATAAATTATTATTTAATTAGTATTATATT
326 TTAATTTATAATTAATTAATATTATAATATAATAATATAAATTATTATTTAATTAGTATTATATT
41521140 ATTATTATTATTAACTAATATATATATATATATATA
391 ATTATTATTATTAACTAATATATATATATATATATA
41521176 TGATTCAGAAAATTTTCCTCGGCTAGTGGTGTAATGACCTAAATTCACGGGCACCGAAAAAGTGA
1 TGATTCAGAAAATTTTCCTCGGCTAGTGGTGTAATGACCTAAATTCACGGGCACCGAAAAAGTGA
*
41521241 GTTATAGGGCCTCCGTCTTAGCAAAACGAGTTCGTAAATAATTATTAGGAGTAATTATGAGTTTA
66 GTTATAGGGCCTCCGTCTTAGCAAAACAAGTTCGTAAATAATTATTAGGAGTAATTATGAGTTTA
41521306 GTAGTGTGTTTAATTAAGCTTTGATTAGGTGAATTTAATTTAATTTAGAGTAATTAATAAAAAGG
131 GTAGTGTGTTTAATTAAGCTTTGATTAGGTGAATTTAATTTAATTTAGAGTAATTAATAAAAAGG
41521371 ACTAAATTGAATAAAGGGTGAAAGTCTAATTATAGATTAAAAAAAAGAAAGAGGGACTAAAATGG
196 ACTAAATTGAATAAAGGGTGAAAGTCTAATTATAGATTAAAAAAAAGAAAGAGGGACTAAAATGG
41521436 CAATTATGCCTATTGCATAAATTGAGGCCGCAAAACAGAGAAAAGTCTAAAGATTTTTCTTGATT
261 CAATTATGCCTATTGCATAAATTGAGGCCGCAAAACAGAGAAAAGTCTAAAGATTTTTCTTGATT
41521501 TTAATTTATAATTAATTAATATTATAATATAATAATATAAATTATTATTTAATTAGTATTATATT
326 TTAATTTATAATTAATTAATATTATAATATAATAATATAAATTATTATTTAATTAGTATTATATT
41521566 ATTATTATTATTAACTAATATATATATATATATATA
391 ATTATTATTATTAACTAATATATATATATATATATA
41521602 TGA
1 TGA
41521605 AATAAAAGAA
Statistics
Matches: 427, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
426 427 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (426 bp):
TGATTCAGAAAATTTTCCTCGGCTAGTGGTGTAATGACCTAAATTCACGGGCACCGAAAAAGTGA
GTTATAGGGCCTCCGTCTTAGCAAAACAAGTTCGTAAATAATTATTAGGAGTAATTATGAGTTTA
GTAGTGTGTTTAATTAAGCTTTGATTAGGTGAATTTAATTTAATTTAGAGTAATTAATAAAAAGG
ACTAAATTGAATAAAGGGTGAAAGTCTAATTATAGATTAAAAAAAAGAAAGAGGGACTAAAATGG
CAATTATGCCTATTGCATAAATTGAGGCCGCAAAACAGAGAAAAGTCTAAAGATTTTTCTTGATT
TTAATTTATAATTAATTAATATTATAATATAATAATATAAATTATTATTTAATTAGTATTATATT
ATTATTATTATTAACTAATATATATATATATATATA
Found at i:41528613 original size:16 final size:17
Alignment explanation
Indices: 41528589--41528626 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41528579 TTTCTTGATT
41528589 TTAAT-TTATAAT-TAA
1 TTAATATTATAATATAA
41528604 TTAATATTATAATATAA
1 TTAATATTATAATATAA
41528621 -TAATAT
1 TTAATAT
41528627 AAATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 13 0.62
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATTATAATATAA
Found at i:41534200 original size:45 final size:45
Alignment explanation
Indices: 41534150--41534241 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
41534140 AAATTCGATC
41534150 ATTAAGTGCTTATTTTGAGCTTTTGTATATAAAGCATAATAATAA
1 ATTAAGTGCTTATTTTGAGCTTTTGTATATAAAGCATAATAATAA
41534195 ATTAAGTGCTTATTTTGAGCTTTTGTATATAAAGCATAATAATAA
1 ATTAAGTGCTTATTTTGAGCTTTTGTATATAAAGCATAATAATAA
41534240 AT
1 AT
41534242 ATAAACTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (45 bp):
ATTAAGTGCTTATTTTGAGCTTTTGTATATAAAGCATAATAATAA
Found at i:41536691 original size:21 final size:22
Alignment explanation
Indices: 41536624--41536757 Score: 108
Period size: 23 Copynumber: 5.8 Consensus size: 22
41536614 ACACTAGCGC
* * *
41536624 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTTGT-GT
41536647 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
*
41536670 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
* * *
41536693 ACTCTCTGTTTAGCATTGTGTGT
1 GCTCTCTGATTAGCACT-TGTGT
* *
41536716 GCTCTCTGTTGCCTAGCACTTATGT
1 GCTCTCTGAT---TAGCACTTGTGT
*
41536741 GCTCTCTG-TTAGTACTT
1 GCTCTCTGATTAGCACTT
41536758 TGGTACTCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.07
22 1 0.01
23 65 0.69
24 3 0.03
25 12 0.13
26 6 0.06
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:41536764 original size:69 final size:69
Alignment explanation
Indices: 41536625--41536773 Score: 198
Period size: 69 Copynumber: 2.2 Consensus size: 69
41536615 CACTAGCGCG
*
41536625 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
41536690 TGTA
66 TGTA
* * *
41536694 CTCTCTGTTTAGCATTGTGT-GTGCTCTCTGTTGCCTAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCA-CGTCTCGTGCTCTCTGAT---TAGCACTTTATGTGCTCTCTGATTAGTAC
41536756 TTTG-GTA
62 TTTGTGTA
41536763 CTCTCTGTTTA
1 CTCTCTGTTTA
41536774 TTCCGTATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
69 39 0.54
70 14 0.19
71 13 0.18
72 6 0.08
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:41536771 original size:21 final size:23
Alignment explanation
Indices: 41536645--41536769 Score: 123
Period size: 23 Copynumber: 5.4 Consensus size: 23
41536635 AGCACGTCTC
41536645 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
41536668 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
41536691 GTACTCTCTGTTTAGCA-TTGTGT
1 GTGCTCTCTGATTAGCACTT-TGT
* *
41536714 GTGCTCTCTGTTGCCTAGCAC-TTAT
1 GTGCTCTCTGAT---TAGCACTTTGT
*
41536739 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
41536760 GTACTCTCTG
1 GTGCTCTCTG
41536770 TTTATTCCGT
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
21 14 0.16
22 4 0.05
23 50 0.57
24 1 0.01
25 12 0.14
26 6 0.07
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:41544440 original size:38 final size:37
Alignment explanation
Indices: 41544366--41544441 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
41544356 ATTATTGATA
*
41544366 ATTAATTTTAAATAATACATTTTAATATTTATCATAT
1 ATTAATTTTAAATAATACATTTTAATATATATCATAT
* **
41544403 ATTATTTTTAAATACATAGTTTTTACATATATA-CATAT
1 ATTAATTTTAAATA-ATACATTTTA-ATATATATCATAT
41544441 A
1 A
41544442 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 13 0.39
38 14 0.42
39 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (37 bp):
ATTAATTTTAAATAATACATTTTAATATATATCATAT
Found at i:41554612 original size:9 final size:9
Alignment explanation
Indices: 41554580--41554774 Score: 80
Period size: 9 Copynumber: 21.0 Consensus size: 9
41554570 TAAATTTTTT
*
41554580 TTATTAAAT
1 TTATTAAAA
*
41554589 TTGATATAAAC
1 TT-AT-TAAAA
41554600 TTATTAAAA
1 TTATTAAAA
*
41554609 TTATAAAAA
1 TTATTAAAA
*
41554618 ATA-TAAATA
1 TTATTAAA-A
41554627 TTA-TAAAA
1 TTATTAAAA
*
41554635 -TATAAAAA
1 TTATTAAAA
*
41554643 ATATATAAAA
1 TTAT-TAAAA
*
41554653 TTAATAAAA
1 TTATTAAAA
41554662 TATATTTAAAA
1 T-TA-TTAAAA
*
41554673 TAATTAAAA
1 TTATTAAAA
**
41554682 TTACAAAAA
1 TTATTAAAA
*
41554691 TGTATCAAAA
1 T-TATTAAAA
41554701 -TATTAAAAAA
1 TTATT--AAAA
* *
41554711 TAATAAAAA
1 TTATTAAAA
*
41554720 TT-GTAACAA
1 TTATTAA-AA
41554729 GTTA-TAAAA
1 -TTATTAAAA
*
41554738 ATATTAAAA
1 TTATTAAAA
*
41554747 ATATTAAAA
1 TTATTAAAA
41554756 TTGATATAAAA
1 TT-AT-TAAAA
41554767 TTA-TAAAA
1 TTATTAAAA
41554775 AAATCATAAA
Statistics
Matches: 143, Mismatches: 25, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
7 2 0.01
8 20 0.14
9 69 0.48
10 31 0.22
11 21 0.15
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATTAAAA
Found at i:41554643 original size:27 final size:27
Alignment explanation
Indices: 41554592--41554665 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
41554582 ATTAAATTTG
* * *
41554592 ATATAAACTTATTAAAAT-TATAAAAA
1 ATATAAAATTAATAAAATATAAAAAAA
*
41554618 ATATAAATATT-ATAAAATATAAAAAAT
1 ATATAAA-ATTAATAAAATATAAAAAAA
41554645 ATATAAAATTAATAAAATATA
1 ATATAAAATTAATAAAATATA
41554666 TTTAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 16 0.39
27 25 0.61
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATAAAATTAATAAAATATAAAAAAA
Found at i:41554661 original size:20 final size:19
Alignment explanation
Indices: 41554592--41554785 Score: 86
Period size: 19 Copynumber: 10.4 Consensus size: 19
41554582 ATTAAATTTG
* * *
41554592 ATATAAACTTATTAAAATT
1 ATATAAAATTATAAAAAAT
* *
41554611 ATA-AAAAATAT-AAATAT
1 ATATAAAATTATAAAAAAT
41554628 -TATAAAA-TATAAAAAAT
1 ATATAAAATTATAAAAAAT
*
41554645 ATATAAAATTAATAAAATAT
1 ATATAAAATT-ATAAAAAAT
* * * *
41554665 ATTTAAAATAATTAAAATT
1 ATATAAAATTATAAAAAAT
* *
41554684 ACA-AAAATGTAT-CAAAAT
1 ATATAAAAT-TATAAAAAAT
* *
41554702 ATTAAAAAATAAT-AAAAAT
1 A-TATAAAATTATAAAAAAT
*
41554721 -TGTAACAAGTTAT-AAAAAT
1 ATATAA-AA-TTATAAAAAAT
* * *
41554740 AT-TAAAAATATTAAAATT
1 ATATAAAATTATAAAAAAT
41554758 GATATAAAATTATAAAAAA-
1 -ATATAAAATTATAAAAAAT
41554777 ATCATAAAA
1 AT-ATAAAA
41554786 ACTTGAACTA
Statistics
Matches: 133, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.04
17 19 0.14
18 34 0.26
19 41 0.31
20 34 0.26
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATAAAATTATAAAAAAT
Found at i:41554690 original size:29 final size:27
Alignment explanation
Indices: 41554615--41554718 Score: 90
Period size: 29 Copynumber: 3.8 Consensus size: 27
41554605 AAAATTATAA
*
41554615 AAAATA-TAAATATT-ATAAAATATA-A
1 AAAATATTAAA-ATTAATAAAATATATC
*
41554640 AAAATATATAAAATTAATAAAATATATTT
1 AAAATAT-TAAAATTAATAAAATATA-TC
*
41554669 AAAATAATTAAAATTACA-AAAATGTATC
1 AAAAT-ATTAAAATTA-ATAAAATATATC
*
41554697 AAAATATTAAAAAATAATAAAA
1 AAAATATT-AAAATTAATAAAA
41554719 ATTGTAACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
25 6 0.09
26 3 0.05
27 18 0.27
28 16 0.24
29 20 0.30
30 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (27 bp):
AAAATATTAAAATTAATAAAATATATC
Found at i:41554756 original size:8 final size:9
Alignment explanation
Indices: 41554601--41554755 Score: 79
Period size: 10 Copynumber: 16.9 Consensus size: 9
41554591 GATATAAACT
*
41554601 TATTAAAAT
1 TATTAAAAA
41554610 TA-TAAAAA
1 TATTAAAAA
*
41554618 -A-TATAAA
1 TATTAAAAA
41554625 TATTATAAAA
1 TATTA-AAAA
*
41554635 TATAAAAAA
1 TATTAAAAA
*
41554644 TATATAAAAT
1 TAT-TAAAAA
*
41554654 TAATAAAATA
1 TATTAAAA-A
*
41554664 TATTTAAAA
1 TATTAAAAA
*
41554673 TAATTAAAAT
1 T-ATTAAAAA
*
41554683 TA-CAAAAA
1 TATTAAAAA
* *
41554691 TGTATCAAAA
1 TAT-TAAAAA
41554701 TATTAAAAAA
1 TATT-AAAAA
*
41554711 TAATAAAAA
1 TATTAAAAA
*
41554720 T-TGTAACAAG
1 TAT-TAA-AAA
41554730 T-TATAAAAA
1 TAT-TAAAAA
41554739 TATTAAAAA
1 TATTAAAAA
41554748 TATTAAAA
1 TATTAAAA
41554756 TTGATATAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.05
8 11 0.10
9 46 0.42
10 47 0.43
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
TATTAAAAA
Found at i:41555286 original size:22 final size:22
Alignment explanation
Indices: 41555237--41555305 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
41555227 AATACTTTTT
* *
41555237 ATAT-TTTTTTTATAATTTTAA
1 ATATGTTTTTATAAAATTTTAA
*
41555258 AGA--TTTTTATAGAAA-TTT-A
1 ATATGTTTTTATA-AAATTTTAA
41555277 ATATGTTTTTATAAAATTTTAA
1 ATATGTTTTTATAAAATTTTAA
41555299 ATATGTT
1 ATATGTT
41555306 GTATTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.08
20 13 0.33
21 15 0.38
22 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
ATATGTTTTTATAAAATTTTAA
Found at i:41555393 original size:14 final size:15
Alignment explanation
Indices: 41555368--41555401 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41555358 GTTCATATAA
41555368 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
41555383 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
41555397 -TTTTT
1 ATTTTT
41555402 GACTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:41559892 original size:17 final size:17
Alignment explanation
Indices: 41559862--41559894 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41559852 CAAATTCAAA
41559862 TTAAATAATATAATATT
1 TTAAATAATATAATATT
41559879 TTAAA-AATATTAATAT
1 TTAAATAATA-TAATAT
41559895 AAAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATAATATAATATT
Found at i:41574586 original size:23 final size:22
Alignment explanation
Indices: 41574540--41574587 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
41574530 TGATATTTGT
*
41574540 AATATTTTTATAAAGTATATTA
1 AATATTTTTATAAAGTATAATA
*
41574562 AATATTTTTTTAAAGTATCAATA
1 AATATTTTTATAAAGTAT-AATA
41574585 AAT
1 AAT
41574588 TTTAAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AATATTTTTATAAAGTATAATA
Found at i:41575976 original size:2 final size:2
Alignment explanation
Indices: 41575969--41575998 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41575959 TCATCAAAAT
*
41575969 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41575999 AAGTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:41585034 original size:18 final size:19
Alignment explanation
Indices: 41584993--41585036 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
41584983 GTGAAAGTTG
* *
41584993 AATCATTCTTTCATTTCTT
1 AATCTTTCTTTCATCTCTT
*
41585012 TATCTTTCTTTC-TCTCTT
1 AATCTTTCTTTCATCTCTT
41585030 AATCTTT
1 AATCTTT
41585037 GTATTCTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (19 bp):
AATCTTTCTTTCATCTCTT
Found at i:41589368 original size:18 final size:18
Alignment explanation
Indices: 41589354--41589388 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41589344 GTAATTAATT
41589354 TAAATTT-TTTAATTAAA
1 TAAATTTATTTAATTAAA
41589371 TAAATTTATTTAATTAAA
1 TAAATTTATTTAATTAAA
41589389 AACCTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATTTATTTAATTAAA
Found at i:41592318 original size:12 final size:12
Alignment explanation
Indices: 41592298--41592327 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41592288 GTTCAAGAGC
41592298 TAAAAAAATAAA
1 TAAAAAAATAAA
*
41592310 TAAATAAATAAA
1 TAAAAAAATAAA
41592322 TAAAAA
1 TAAAAA
41592328 GTTAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:41593548 original size:14 final size:14
Alignment explanation
Indices: 41593529--41593558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41593519 TTTTAATCCT
41593529 AAATTCAAAACTCA
1 AAATTCAAAACTCA
*
41593543 AAATTCAAACCTCA
1 AAATTCAAAACTCA
41593557 AA
1 AA
41593559 CCCTAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATTCAAAACTCA
Found at i:41593621 original size:28 final size:28
Alignment explanation
Indices: 41593577--41593645 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
41593567 CTAATTTTAG
* *
41593577 GGTTTAAAATTTGAGATAT-GAGGTTTGA
1 GGTTTAAGATTTTAGATATGGA-GTTTGA
*
41593605 GGTTTAAGATTTTAGATTTGGAGTTTGA
1 GGTTTAAGATTTTAGATATGGAGTTTGA
* *
41593633 AGCTTAAGATTTT
1 GGTTTAAGATTTT
41593646 GGATTTTGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (28 bp):
GGTTTAAGATTTTAGATATGGAGTTTGA
Found at i:41593650 original size:28 final size:28
Alignment explanation
Indices: 41593599--41593687 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
41593589 GAGATATGAG
*
41593599 GTTTGAGGTTTAAGATTTTAGA-TTTGGA
1 GTTTGAAG-TTAAGATTTTAGATTTTGGA
*
41593627 GTTTGAAGCTTAAGATTTTGGATTTTGGA
1 GTTTGAAG-TTAAGATTTTAGATTTTGGA
* *
41593656 -TTT-AAGTTAGAGATTTAATATTTTGGA
1 GTTTGAAGTTA-AGATTTTAGATTTTGGA
41593683 -TTTGA
1 GTTTGA
41593688 GGTTTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.06
27 20 0.38
28 23 0.44
29 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (28 bp):
GTTTGAAGTTAAGATTTTAGATTTTGGA
Found at i:41594529 original size:37 final size:37
Alignment explanation
Indices: 41594488--41594562 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
41594478 CTACAAACAC
41594488 TTACCACATGCCTTGAAGAAATTATTTTGTAAATCTT
1 TTACCACATGCCTTGAAGAAATTATTTTGTAAATCTT
41594525 TTACCACATGCCTTGAAGAAATTATTTTGTAAATCTT
1 TTACCACATGCCTTGAAGAAATTATTTTGTAAATCTT
41594562 T
1 T
41594563 CTCACCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (37 bp):
TTACCACATGCCTTGAAGAAATTATTTTGTAAATCTT
Found at i:41594697 original size:7 final size:7
Alignment explanation
Indices: 41594687--41594734 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
41594677 AATCCTAAAT
41594687 TCAAAAC
1 TCAAAAC
41594694 TCAAAAC
1 TCAAAAC
*
41594701 CCAAAAC
1 TCAAAAC
*
41594708 CCAAAAC
1 TCAAAAC
*
41594715 CCAAAACC
1 TCAAAA-C
*
41594723 TCAAATC
1 TCAAAAC
41594730 TCAAA
1 TCAAA
41594735 CCTTAAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.54, C:0.35, G:0.00, T:0.10
Consensus pattern (7 bp):
TCAAAAC
Found at i:41594707 original size:14 final size:14
Alignment explanation
Indices: 41594688--41594727 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
41594678 ATCCTAAATT
41594688 CAAAACTCAAAACC
1 CAAAACTCAAAACC
*
41594702 CAAAACCCAAAACC
1 CAAAACTCAAAACC
41594716 CAAAACCTCAAA
1 CAAAA-CTCAAA
41594728 TCTCAAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.57, C:0.38, G:0.00, T:0.05
Consensus pattern (14 bp):
CAAAACTCAAAACC
Found at i:41596980 original size:16 final size:17
Alignment explanation
Indices: 41596959--41596997 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41596949 AATATAAATT
*
41596959 TATAAATTTATG-ACAA
1 TATAAAATTATGTACAA
41596975 TATAAAATTATGTACAA
1 TATAAAATTATGTACAA
41596992 T-TAAAA
1 TATAAAA
41596998 ATATACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (17 bp):
TATAAAATTATGTACAA
Found at i:41601110 original size:72 final size:72
Alignment explanation
Indices: 41600993--41601137 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
41600983 AGACATGCAT
*
41600993 TAACTTACTAGGTGTATCTTTTCTTTGAATCGTAATAATCAAATATTCCTTTTATTATATATATG
1 TAACTTACTAGGTGTATCTTTTCTTTGAATCGTAATAATCAAATATTCATTTTATTATATATATG
41601058 AAACACA
66 AAACACA
* *
41601065 TAACTTATTAGGTGTGTCTTTTCTTTGAATCGTAATAATCAAATATTCATTTTATTATATATATG
1 TAACTTACTAGGTGTATCTTTTCTTTGAATCGTAATAATCAAATATTCATTTTATTATATATATG
41601130 AAACACA
66 AAACACA
41601137 T
1 T
41601138 GGATTTTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (72 bp):
TAACTTACTAGGTGTATCTTTTCTTTGAATCGTAATAATCAAATATTCATTTTATTATATATATG
AAACACA
Found at i:41610403 original size:173 final size:173
Alignment explanation
Indices: 41610108--41610455 Score: 660
Period size: 173 Copynumber: 2.0 Consensus size: 173
41610098 ATATACGGAG
* *
41610108 ATTCAGTATTAGTAATCTACCAGCTCGAGGGAGAATGGGAGACAAGAGACTCCAAGTTAATTGAT
1 ATTCAGTATTAATAATCTACCAGCTCAAGGGAGAATGGGAGACAAGAGACTCCAAGTTAATTGAT
41610173 TATCGAAAGATGGTCCTCGAGATGATTAAGGAATTTGAAAAGGTTACATTCTAGTACCTTCCACG
66 TATCGAAAGATGGTCCTCGAGATGATTAAGGAATTTGAAAAGGTTACATTCTAGTACCTTCCACG
41610238 TGAGGAAAACCAAATGGCTGACGCTCTGGCTACTCTAGCCTCA
131 TGAGGAAAACCAAATGGCTGACGCTCTGGCTACTCTAGCCTCA
41610281 ATTCAGTATTAATAATCTACCAGCTCAAGGGAGAATGGGAGACAAGAGACTCCAAGTTAATTGAT
1 ATTCAGTATTAATAATCTACCAGCTCAAGGGAGAATGGGAGACAAGAGACTCCAAGTTAATTGAT
* *
41610346 TATCGAAAGATGGTCCTCGAGATGATTAAGGAATTTGAAAAGGTTACATTTTAGTACCTTCCATG
66 TATCGAAAGATGGTCCTCGAGATGATTAAGGAATTTGAAAAGGTTACATTCTAGTACCTTCCACG
41610411 TGAGGAAAACCAAATGGCTGACGCTCTGGCTACTCTAGCCTCA
131 TGAGGAAAACCAAATGGCTGACGCTCTGGCTACTCTAGCCTCA
41610454 AT
1 AT
41610456 GATGAAAGTA
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 171 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (173 bp):
ATTCAGTATTAATAATCTACCAGCTCAAGGGAGAATGGGAGACAAGAGACTCCAAGTTAATTGAT
TATCGAAAGATGGTCCTCGAGATGATTAAGGAATTTGAAAAGGTTACATTCTAGTACCTTCCACG
TGAGGAAAACCAAATGGCTGACGCTCTGGCTACTCTAGCCTCA
Found at i:41612033 original size:49 final size:49
Alignment explanation
Indices: 41611974--41612108 Score: 182
Period size: 49 Copynumber: 2.8 Consensus size: 49
41611964 TCTACAGGTT
* *
41611974 TACCATGAAGACATGAAGGGAAAGATTTAAGTCGCAACGACT-AATCCAG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACG-CTGAATCCAG
* * *
41612023 TACCACGAAGATATGAAGGGAAAGATTTAAGCCACAACGGTGAATCCAG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGCTGAATCCAG
* * *
41612072 TACCACGAAGATATAAAAGGAAAGGTTTAAGTCGCAA
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAA
41612109 TGGCGAACCT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
48 1 0.01
49 74 0.99
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (49 bp):
TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGCTGAATCCAG
Found at i:41612143 original size:98 final size:97
Alignment explanation
Indices: 41612035--41612341 Score: 371
Period size: 98 Copynumber: 3.2 Consensus size: 97
41612025 CCACGAAGAT
*
41612035 ATGAAGGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACGAAGATATAAAAGGAAAGGTTT
1 ATGAAAGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACGAAGATAT-AAAGGAAAGGTTT
41612100 AAGTCGCAATGGCGAACCTTATACCTTAGAAGC
65 AAGTCGCAATGGCGAACCTTATACCTTAGAAGC
* * *
41612133 ATGAAAGGAAAGATTTAAGCCACAACGGTGAATCTAGTACCGCGAAGATACAAAGAGAAA-G--T
1 ATGAAAGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACGAAGATATAAAG-GAAAGGTTT
* * * *
41612195 -CGT-G--ATGGCAAACCTTATACCTCATAAGC
65 AAGTCGCAATGGCGAACCTTATACCTTAGAAGC
* *
41612224 ATG-AAGGAAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGAAAAGGTT
1 ATGAAAGG-AAAGATTTAAGCCACAACGGTGAATCCAGTACCACGAAGATATAAAGG-AAAGGTT
* * *
41612288 TAAGTCGCAACGGTGAACCTTGTACCTTAG-AGAC
64 TAAGTCGCAATGGCGAACCTTATACCTTAGAAG-C
* *
41612322 ATGAAGGGAAAAATTTAAGC
1 ATGAAAGGAAAGATTTAAGC
41612342 GCAATGGCGA
Statistics
Matches: 175, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
90 5 0.03
91 70 0.40
92 1 0.01
93 1 0.01
94 3 0.02
95 3 0.02
96 1 0.01
97 7 0.04
98 81 0.46
99 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (97 bp):
ATGAAAGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACGAAGATATAAAGGAAAGGTTTA
AGTCGCAATGGCGAACCTTATACCTTAGAAGC
Found at i:41612471 original size:133 final size:133
Alignment explanation
Indices: 41612234--41612496 Score: 370
Period size: 133 Copynumber: 2.0 Consensus size: 133
41612224 ATGAAGGAAA
* * * * *
41612234 AGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGAAAAGGTTTAAGTCGCAAC
1 AGATTTAAGCAGCAACAGCGAACCCAGTACCACAAAGATATAAAGGAAAAGGTTTAAGCCGCAAC
* * *
41612299 GGTGAACCTTGTACCTTAGAGACATGAAGGGAAAAATTTAAG-CGCAATGGCGAATTTAGTACCA
66 GGTGAACCTTGTACCTAAAAGACATGAAGGGAAAAATTTAAGCCGCAATGGCGAATCTAGTACCA
41612363 TGC
131 TGC
* *
41612366 AGATTTAAGCAGCAACAGCGAACCCAGTACCACAAAGATAATGAAGGGAAAGGTTTAAGCCGCAA
1 AGATTTAAGCAGCAACAGCGAACCCAGTACCACAAAGAT-ATAAAGGAAAAGGTTTAAGCCGCAA
* *
41612431 CGGTGAACCTT-TCACCTCAAAAG-CATGGAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTA
65 CGGTGAACCTTGT-ACCT-AAAAGACATGAAGGGAAAAATTTAAGCCGCAATGGCGAATCTAGTA
41612494 CCA
128 CCA
41612497 CAAAGACATT
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
132 36 0.31
133 55 0.48
134 24 0.21
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (133 bp):
AGATTTAAGCAGCAACAGCGAACCCAGTACCACAAAGATATAAAGGAAAAGGTTTAAGCCGCAAC
GGTGAACCTTGTACCTAAAAGACATGAAGGGAAAAATTTAAGCCGCAATGGCGAATCTAGTACCA
TGC
Found at i:41621496 original size:28 final size:29
Alignment explanation
Indices: 41621451--41621505 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
41621441 TATGCTTTTT
* * *
41621451 TTAAAATTTAACTTATTT-TTATTTAATA
1 TTAAAATTTAAATAATTTATTAATTAATA
*
41621479 TTAAATTTTAAATAATTTATTAATTAA
1 TTAAAATTTAAATAATTTATTAATTAA
41621506 AATATCATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TTAAAATTTAAATAATTTATTAATTAATA
Found at i:41626100 original size:20 final size:21
Alignment explanation
Indices: 41626065--41626103 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41626055 ATTTTAAAAA
*
41626065 TAATTATTTTATCTTTTTATT
1 TAATTATTTCATCTTTTTATT
41626086 TAATT-TTTCATCTTTTTA
1 TAATTATTTCATCTTTTTA
41626104 GTTCTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
TAATTATTTCATCTTTTTATT
Found at i:41635087 original size:18 final size:18
Alignment explanation
Indices: 41635064--41635104 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
41635054 ATAGAATTTA
41635064 AATTAAATAAATTT-AATT
1 AATTAAA-AAATTTAAATT
41635082 AATTAAAAAATTTAAATT
1 AATTAAAAAATTTAAATT
41635100 AATTA
1 AATTA
41635105 CACTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAAAAATTTAAATT
Found at i:41635099 original size:14 final size:15
Alignment explanation
Indices: 41635053--41635101 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
41635043 TTGGGATGAG
41635053 AATAGAATTTAAATTA
1 AATA-AATTTAAATTA
41635069 AATAAATTTAATTAATTA
1 AATAAATTT-A--AATTA
41635087 AA-AAATTTAAATTA
1 AATAAATTTAAATTA
41635101 A
1 A
41635102 TTACACTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.20
15 5 0.17
16 6 0.20
17 6 0.20
18 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
AATAAATTTAAATTA
Found at i:41638971 original size:2 final size:2
Alignment explanation
Indices: 41638964--41638993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41638954 TCGGTAATGG
41638964 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
41638994 GATAGATAGA
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:41657995 original size:27 final size:27
Alignment explanation
Indices: 41657957--41658019 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
41657947 GTATAAATGG
41657957 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
41657984 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
41658011 ATGGTGCCT
1 GTGGTGCCT
41658020 TTCTATCAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:41658028 original size:27 final size:27
Alignment explanation
Indices: 41657958--41658038 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
41657948 TATAAATGGG
*
41657958 TGGTGCCTACCTGA-CAGGCGGCACCAG
1 TGGTGCCTACCT-ATCAGGCGGCACCAA
*
41657985 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
** *
41658012 TGGTGCCTTTCTATCAGGTGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
41658039 CTCGTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.21
Consensus pattern (27 bp):
TGGTGCCTACCTATCAGGCGGCACCAA
Found at i:41658184 original size:20 final size:23
Alignment explanation
Indices: 41658147--41658187 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
41658137 TTTTAATAAA
41658147 TATAAGAATTGTAGAAAAAATAT
1 TATAAGAATTGTAGAAAAAATAT
41658170 TATAA-AATT-TA-AAAAAAT
1 TATAAGAATTGTAGAAAAAAT
41658188 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TATAAGAATTGTAGAAAAAATAT
Found at i:41658306 original size:57 final size:55
Alignment explanation
Indices: 41658192--41658322 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
41658182 AAAAATTAAA
* * *
41658192 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
41658247 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
41658304 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
41658323 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:41658553 original size:26 final size:26
Alignment explanation
Indices: 41658496--41658553 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41658486 GTAAATTTTT
* * *
41658496 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
41658522 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
41658548 GCAGAA
1 GAAGAA
41658554 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:41658674 original size:26 final size:26
Alignment explanation
Indices: 41658644--41658702 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
41658634 ACAGATGGAA
* *
41658644 TTAATTCTATTTAAATTTGAATTTAT
1 TTAATTATATTTAAATTTGAATTAAT
* * **
41658670 TTAATAATTTTTATGTTTGAATTAAT
1 TTAATTATATTTAAATTTGAATTAAT
41658696 TTAATTA
1 TTAATTA
41658703 GGTTTAGCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (26 bp):
TTAATTATATTTAAATTTGAATTAAT
Found at i:41658708 original size:26 final size:26
Alignment explanation
Indices: 41658659--41658708 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
41658649 TCTATTTAAA
* **
41658659 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTAATTTAATAAGGTTTATG
*
41658685 TTTGAATTAATTTAATTAGGTTTA
1 TTTGAATTAATTTAATAAGGTTTA
41658709 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAAGGTTTATG
Found at i:41658785 original size:6 final size:6
Alignment explanation
Indices: 41658774--41658820 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
41658764 ATATTTGCAT
*
41658774 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATA
41658821 TTTAATGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:41659262 original size:6 final size:6
Alignment explanation
Indices: 41659253--41659277 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41659243 CTGCGACTGC
41659253 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
41659278 CCGGCTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:41661279 original size:17 final size:16
Alignment explanation
Indices: 41661247--41661278 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41661237 TTTTTTTTAA
41661247 AAAATATTTAATATAT
1 AAAATATTTAATATAT
41661263 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
41661278 A
1 A
41661279 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:41663010 original size:12 final size:12
Alignment explanation
Indices: 41662993--41663018 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41662983 TTGATATTTG
41662993 AAAATTATAATA
1 AAAATTATAATA
41663005 AAAATTATAATA
1 AAAATTATAATA
41663017 AA
1 AA
41663019 TATCATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTATAATA
Found at i:41663026 original size:21 final size:21
Alignment explanation
Indices: 41663002--41663050 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41662992 GAAAATTATA
* *
41663002 ATAAAAATTATAATAAATATC
1 ATAAAAAATAAAATAAATATC
*
41663023 ATAAAAAATAAAATGAATATC
1 ATAAAAAATAAAATAAATATC
*
41663044 ACAAAAA
1 ATAAAAA
41663051 CAATTGGGGT
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:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAAAAATAAAATAAATATC
Found at i:41663367 original size:18 final size:18
Alignment explanation
Indices: 41663344--41663396 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 18
41663334 TTGAAAGCTC
41663344 ACCGAATAAATCAATTAA
1 ACCGAATAAATCAATTAA
*
41663362 ACCGAACATGAAAATGAATTAA
1 ACCG-A-AT--AAATCAATTAA
*
41663384 ATCGAATAAATCA
1 ACCGAATAAATCA
41663397 TAAAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
20 4 0.14
21 1 0.04
22 13 0.46
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (18 bp):
ACCGAATAAATCAATTAA
Found at i:41665372 original size:19 final size:21
Alignment explanation
Indices: 41665343--41665385 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
41665333 TCACATCAAT
*
41665343 AAATAATTT-AAAAATTAAAA
1 AAATAATTTAAAAAAATAAAA
41665363 AAAT-ATTTAAAAAAATAAAA
1 AAATAATTTAAAAAAATAAAA
41665383 AAA
1 AAA
41665386 AGTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAATTTAAAAAAATAAAA
Found at i:41665395 original size:20 final size:21
Alignment explanation
Indices: 41665343--41665395 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
41665333 TCACATCAAT
* *
41665343 AAATAATT-TAAAAATTAAAA
1 AAATAGTTATAAAAAATAAAA
*
41665363 AAATATTTA-AAAAAATAAAA
1 AAATAGTTATAAAAAATAAAA
41665383 AAA-AGTTATAAAA
1 AAATAGTTATAAAA
41665396 GTTATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATAGTTATAAAAAATAAAA
Found at i:41666880 original size:29 final size:30
Alignment explanation
Indices: 41666838--41666938 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
41666828 TTTTAGGGGT
*
41666838 AAAATGTAATTTTTAGAAGTTTT-GAGGTCA
1 AAAATGTAATTTTAAGAAGTTTTAG-GGTCA
*
41666868 AAAATGGAATTTTAAGAAGTTTTAGGGTCA
1 AAAATGTAATTTTAAGAAGTTTTAGGGTCA
** * *
41666898 AAAATGTAATTTTGGGAAG-TTCAGAGT-A
1 AAAATGTAATTTTAAGAAGTTTTAGGGTCA
41666926 AAAATGTAATTTT
1 AAAATGTAATTTT
41666939 TGAAAGTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
28 14 0.22
29 6 0.10
30 42 0.67
31 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTAAGAAGTTTTAGGGTCA
Found at i:41669692 original size:17 final size:17
Alignment explanation
Indices: 41669620--41669698 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
41669610 AACAATTTTT
*
41669620 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
41669637 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
*** * *
41669654 AACCCAAAATGAATTTA
1 AATTTAAAATAAATTCA
41669671 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
41669688 AATTTTAAAAT
1 AA-TTTAAAAT
41669699 TAAAAGTTAG
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
17 42 0.84
18 8 0.16
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:41674572 original size:21 final size:20
Alignment explanation
Indices: 41674531--41674573 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41674521 TTTTATTAAT
*
41674531 TTAATATTAAAGTGATTATC
1 TTAATATTAAAGTAATTATC
*
41674551 TTAATATTAAATTAATTTATC
1 TTAATATTAAAGTAA-TTATC
41674572 TT
1 TT
41674574 GTAGATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TTAATATTAAAGTAATTATC
Found at i:41674671 original size:58 final size:63
Alignment explanation
Indices: 41674518--41674678 Score: 167
Period size: 58 Copynumber: 2.6 Consensus size: 63
41674508 TAGATTAATT
* * *
41674518 GTATTTTATTAATTTAATATTAAAGTGATTATC-TTAATATTAAATTAATTTATCTTGTAGATAA
1 GTATTATATTAATTTAATATTAAAGTGATTAACTTTAATAGTAAATTAATTTATC-T-TAGATAA
* *
41674582 GTATTCTATTAATTTAATAGATTTAA-T-ATTAACTTTAAT-GT-AA-T-ATTTATC-TAGATAA
1 GTATTATATTAATTTAAT--ATTAAAGTGATTAACTTTAATAGTAAATTAATTTATCTTAGATAA
* *
41674640 GTATTATATTAATTTAATATTGAAGTGATTAAGTTTAAT
1 GTATTATATTAATTTAATATTAAAGTGATTAACTTTAAT
41674679 TATGGTAGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
56 5 0.06
57 1 0.01
58 35 0.41
61 7 0.08
62 1 0.01
63 2 0.02
64 23 0.27
65 6 0.07
66 5 0.06
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (63 bp):
GTATTATATTAATTTAATATTAAAGTGATTAACTTTAATAGTAAATTAATTTATCTTAGATAA
Found at i:41682192 original size:17 final size:19
Alignment explanation
Indices: 41682170--41682204 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
41682160 ATAAATATTC
41682170 AGTTCATT-TT-TAATTTA
1 AGTTCATTATTATAATTTA
41682187 AGTTCATTATTATAATTT
1 AGTTCATTATTATAATTT
41682205 GCACTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (19 bp):
AGTTCATTATTATAATTTA
Found at i:41685137 original size:39 final size:40
Alignment explanation
Indices: 41685078--41685157 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
41685068 AAGAGGCATG
*
41685078 TCCAATATGAAAAGGGTTGTGACTTTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
*
41685118 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
41685157 T
1 T
41685158 TGAGTGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:41692036 original size:14 final size:14
Alignment explanation
Indices: 41692017--41692050 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41692007 ATTAAAATAT
*
41692017 AAATAAATTTTATG
1 AAATAAATTTAATG
*
41692031 AAATAAATTTAATT
1 AAATAAATTTAATG
41692045 AAATAA
1 AAATAA
41692051 TAAAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATAAATTTAATG
Found at i:41693070 original size:8 final size:8
Alignment explanation
Indices: 41693053--41693094 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
41693043 ACGTAGCCTT
41693053 TAAAATTA
1 TAAAATTA
*
41693061 TAAAAATA
1 TAAAATTA
41693069 T-AAATTA
1 TAAAATTA
*
41693076 TTAAAATGA
1 -TAAAATTA
41693085 TAAAATTA
1 TAAAATTA
41693093 TA
1 TA
41693095 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:41693075 original size:15 final size:17
Alignment explanation
Indices: 41693053--41693094 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
41693043 ACGTAGCCTT
41693053 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATGA
*
41693069 T-AAATTATTAAAATGA
1 TAAAATTATAAAAATGA
41693085 TAAAATTATA
1 TAAAATTATA
41693095 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATGA
Found at i:41694730 original size:29 final size:30
Alignment explanation
Indices: 41694674--41694731 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
41694664 AGTTAATGAT
* * * *
41694674 TAAATTTGTTAAAATTTTTAGATTTAGGAC
1 TAAATTTGATAAAATTTATAAATATAGGAC
41694704 TAAA-TTGATAAAATTTATAAATATAGGA
1 TAAATTTGATAAAATTTATAAATATAGGA
41694732 GAGCTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (30 bp):
TAAATTTGATAAAATTTATAAATATAGGAC
Found at i:41698764 original size:15 final size:15
Alignment explanation
Indices: 41698744--41698782 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41698734 GGGTAAAGTA
*
41698744 TAATTTTACTTTTAT
1 TAATTTTAATTTTAT
*
41698759 TAATTTAAATTTTAT
1 TAATTTTAATTTTAT
*
41698774 AAATTTTAA
1 TAATTTTAA
41698783 AAAATCTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTTAATTTTAT
Found at i:41701492 original size:6 final size:6
Alignment explanation
Indices: 41701481--41701508 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41701471 TCCTTTTCAA
41701481 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
41701509 GGAGATTGTT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:41701617 original size:21 final size:21
Alignment explanation
Indices: 41701588--41701628 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41701578 ACAACAATGA
*
41701588 TGATAAGATTAATTATTATAG
1 TGATAAGATTAAGTATTATAG
*
41701609 TGATGAGATTAAGTATTATA
1 TGATAAGATTAAGTATTATA
41701629 ACAGTGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
TGATAAGATTAAGTATTATAG
Found at i:41701932 original size:24 final size:23
Alignment explanation
Indices: 41701883--41701937 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
41701873 AAGAAACACT
**
41701883 TAAAAAATATATTTCATATTGTA
1 TAAAAAATATATTTCATATTAAA
41701906 TAAAAAATTATATTTCATATTAAA
1 TAAAAAA-TATATTTCATATTAAA
41701930 TAATAAAA
1 TAA-AAAA
41701938 AAGACAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 17 0.61
25 4 0.14
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAAATATATTTCATATTAAA
Found at i:41711859 original size:41 final size:40
Alignment explanation
Indices: 41711811--41711911 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
41711801 TCGACCTCGA
** *
41711811 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
41711851 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
41711889 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
41711912 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:41713266 original size:23 final size:23
Alignment explanation
Indices: 41713224--41713292 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
41713214 ACGCTAGCGC
* * *
41713224 GCTTACTATTCAGCACTGTGTGT
1 GCTTACTGTTCTGCATTGTGTGT
41713247 GCTTACTGTTCTGCATTGTGTGT
1 GCTTACTGTTCTGCATTGTGTGT
*
41713270 GCCCT-CTGTT-TAGCATTGTGTGT
1 G-CTTACTGTTCT-GCATTGTGTGT
41713293 ACTTCTGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTCTGCATTGTGTGT
Found at i:41713304 original size:22 final size:23
Alignment explanation
Indices: 41713259--41713322 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
41713249 TTACTGTTCT
* *
41713259 GCATTGTGTGTGCCCTCTGTTTA
1 GCATTGTGTGTGACCTCTGATTA
*
41713282 GCATTGTGTGT-ACTTCTGATTA
1 GCATTGTGTGTGACCTCTGATTA
*
41713304 GCACTT-TGTGTGCCCTCTG
1 GCA-TTGTGTGTGACCTCTG
41713323 TTGCCCAGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42
Consensus pattern (23 bp):
GCATTGTGTGTGACCTCTGATTA
Found at i:41724270 original size:30 final size:29
Alignment explanation
Indices: 41724209--41724276 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
41724199 TATATTTTTA
*
41724209 TAATTTTTAAAGAATCAAAATAAAAGTTTT
1 TAATTTTTAAAAAATCAAAATAAAAG-TTT
*
41724239 TAATTTTTAGGAAAAATCAAAATATAA-TTT
1 TAATTTTTA--AAAAATCAAAATAAAAGTTT
41724269 T-ATTTTTA
1 TAATTTTTA
41724277 TTAATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 13 0.38
32 14 0.41
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (29 bp):
TAATTTTTAAAAAATCAAAATAAAAGTTT
Found at i:41736838 original size:8 final size:8
Alignment explanation
Indices: 41736827--41736852 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
41736817 ATTATATTAA
41736827 ATAAATTT
1 ATAAATTT
41736835 ATAAATTT
1 ATAAATTT
41736843 ATAAATTT
1 ATAAATTT
41736851 AT
1 AT
41736853 TAGTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATAAATTT
Found at i:41737849 original size:3 final size:3
Alignment explanation
Indices: 41737841--41737869 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41737831 CCAAACAGCC
41737841 GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
41737870 ACTGCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:41744597 original size:16 final size:15
Alignment explanation
Indices: 41744579--41744608 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41744569 AATTTAAATT
41744579 TTTTAAAAAAAATCA
1 TTTTAAAAAAAATCA
*
41744594 TTTTAAAGAAAATCA
1 TTTTAAAAAAAATCA
41744609 AGCCCTTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TTTTAAAAAAAATCA
Found at i:41757449 original size:20 final size:20
Alignment explanation
Indices: 41757420--41757460 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41757410 TTTTATATAC
41757420 TAACAAAAGATAAAACTCTA
1 TAACAAAAGATAAAACTCTA
*
41757440 TAACAGAAGATAAAACTCTA
1 TAACAAAAGATAAAACTCTA
41757460 T
1 T
41757461 GTTATATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (20 bp):
TAACAAAAGATAAAACTCTA
Found at i:41760076 original size:11 final size:10
Alignment explanation
Indices: 41760060--41760089 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
41760050 TATTAAGTAT
41760060 AAAAAAATAA
1 AAAAAAATAA
41760070 AAAAAAATAA
1 AAAAAAATAA
41760080 AAAAAAATAA
1 AAAAAAATAA
41760090 GTGTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:41764203 original size:21 final size:21
Alignment explanation
Indices: 41764179--41764219 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41764169 ATAAGAACTG
* *
41764179 TAAAAATTATTATATATTTTT
1 TAAAAATTATAATAAATTTTT
41764200 TAAAAATTATAATAAATTTT
1 TAAAAATTATAATAAATTTT
41764220 ACAATTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAAATTATAATAAATTTTT
Found at i:41770235 original size:3 final size:3
Alignment explanation
Indices: 41770221--41770279 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
41770211 ATGGGTAACT
* *
41770221 ATG ATG AAG ATG ATG ATG ATG ATG ATG ACTTG CTTG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A--TG -ATG ATG ATG ATG ATG
*
41770269 ATG AGG ATG AT
1 ATG ATG ATG AT
41770280 TATAATGAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 43 0.91
4 2 0.04
5 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41773456 original size:17 final size:17
Alignment explanation
Indices: 41773425--41773458 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41773415 CACATCTCAG
**
41773425 CACCTAATATGGATATT
1 CACCTAATACAGATATT
41773442 CACCTAATACAGATATT
1 CACCTAATACAGATATT
41773459 AACATATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (17 bp):
CACCTAATACAGATATT
Found at i:41777284 original size:19 final size:18
Alignment explanation
Indices: 41777256--41777294 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41777246 CTTATTACAT
* *
41777256 TAAAAAAAATCTTTAATA
1 TAAAAAAAATATCTAATA
41777274 TAAATAAAAATATCTAATA
1 TAAA-AAAAATATCTAATA
41777293 TA
1 TA
41777295 CATCCCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAAAATATCTAATA
Found at i:41778474 original size:18 final size:17
Alignment explanation
Indices: 41778431--41778483 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
41778421 TCGTTTCACT
*
41778431 AAAAA-TAATTTTTATA
1 AAAAATTAATTTTTTTA
*
41778447 AATAATTTAATTTTTTTGA
1 AA-AAATTAATTTTTTT-A
41778466 AAAAATTAATATTTTTTA
1 AAAAATTAAT-TTTTTTA
41778484 GTGTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 17 0.57
19 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAAAATTAATTTTTTTA
Found at i:41779155 original size:15 final size:15
Alignment explanation
Indices: 41779135--41779184 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
41779125 ACTACGAAAC
41779135 ATTTATTATTAATAT
1 ATTTATTATTAATAT
* *
41779150 ATTTATAAGTAATAAAT
1 ATTTATTATTAAT--AT
*
41779167 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
41779182 ATT
1 ATT
41779185 AATATTGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 16 0.57
17 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:41779226 original size:16 final size:15
Alignment explanation
Indices: 41779207--41779246 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
41779197 TTGCAAAAAA
41779207 TATTATTTAAAAATAT
1 TATTATTTAAAAAT-T
41779223 TATT-TTT-AAAATT
1 TATTATTTAAAAATT
41779236 TATTA-TTAAAA
1 TATTATTTAAAA
41779247 TAAAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTTAAAAATT
Found at i:41779238 original size:13 final size:14
Alignment explanation
Indices: 41779203--41779248 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
41779193 ATATTTGCAA
*
41779203 AAAATATTA-TTTA
1 AAAATATTATTTTT
41779216 AAAATATTATTTTT
1 AAAATATTATTTTT
*
41779230 AAAAT-TTATTATT
1 AAAATATTATTTTT
41779243 AAAATA
1 AAAATA
41779249 AAATTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTATTTTT
Found at i:41779381 original size:13 final size:14
Alignment explanation
Indices: 41779361--41779392 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
41779351 AATATTGAAA
41779361 AATA-TAATATTTT
1 AATATTAATATTTT
41779374 -ATATTAATATTTT
1 AATATTAATATTTT
41779387 AATATT
1 AATATT
41779393 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:41781217 original size:22 final size:23
Alignment explanation
Indices: 41781192--41781235 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
41781182 TTTTAAAAGT
*
41781192 ACTTCTCAAAATCACT-TTCAAC
1 ACTTCTCAAAAGCACTATTCAAC
* *
41781214 ACTTTTTAAAAGCACTATTCAA
1 ACTTCTCAAAAGCACTATTCAA
41781236 AAACAATGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (23 bp):
ACTTCTCAAAAGCACTATTCAAC
Found at i:41781385 original size:55 final size:55
Alignment explanation
Indices: 41781320--41781429 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
41781310 TGGATTTATA
* *
41781320 CACTTAATAATCTTAAATCGAATTTGATTTAAAAAAAAGTACTTCTATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAAGTACTTCAATCTTAAAT
* *
41781375 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAATGTATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAAGTACTTCAATCTTAAAT
41781430 TAGTGACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.39
Consensus pattern (55 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAAGTACTTCAATCTTAAAT
Found at i:41788669 original size:53 final size:54
Alignment explanation
Indices: 41788589--41788695 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 54
41788579 TGGATTTATA
**
41788589 CACTTAATAATCTTAAATTGAATTTGA-TTAAAAAAAGTATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAGTATTTCAATCTTAAAT
*
41788642 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGTATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAGTATTTCAATCTTAAAT
41788696 TAGTGACAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
53 25 0.50
54 25 0.50
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAGTATTTCAATCTTAAAT
Found at i:41789445 original size:18 final size:18
Alignment explanation
Indices: 41789424--41789461 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41789414 TGAATTTTCG
*
41789424 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
41789442 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
41789460 AA
1 AA
41789462 GATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:41792561 original size:18 final size:18
Alignment explanation
Indices: 41792535--41792572 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41792525 TGAATTTTCG
*
41792535 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
41792553 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
41792571 AA
1 AA
41792573 GATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:41801954 original size:17 final size:17
Alignment explanation
Indices: 41801922--41801954 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41801912 TGTGGTTGAA
41801922 TAAAAATATTTGATAAT
1 TAAAAATATTTGATAAT
41801939 TAAAACATATTT-ATAA
1 TAAAA-ATATTTGATAA
41801955 AAAATTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAAATATTTGATAAT
Found at i:41804655 original size:43 final size:43
Alignment explanation
Indices: 41804594--41804724 Score: 181
Period size: 43 Copynumber: 3.0 Consensus size: 43
41804584 AAAAATAGTG
* *
41804594 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGTC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAATGCC
* * *
41804637 GCTAAAGAACGTGGTCTTTAGCAGCGCTTTTCATACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAATGCC
* * *
41804680 GCTAAAAGAACATGGTCTTTAGCGACGCTTTTCTCACAAAAGCC
1 GCT-AAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAATGCC
41804724 G
1 G
41804725 TTAACATTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 41 0.54
44 35 0.46
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAATGCC
Found at i:41806036 original size:118 final size:119
Alignment explanation
Indices: 41805828--41806060 Score: 398
Period size: 118 Copynumber: 2.0 Consensus size: 119
41805818 TTTGCTTTTA
*
41805828 TTTCCTGCTGAAATAGATAAGACAACTGTCATTAAGAAATTTCCACTTGATGAAAAACAACTTAT
1 TTTCCTGCTGAAAAAGATAAGACAACTGTCATTAAGAAATTTCCACTTGATGAAAAACAACTTAT
*
41805893 ACACAGGTAAACATGAAGGCTATACTTG-AATATAACAGAAAAATGCTTCTGTT
66 ACACAGGTAAACATGAAAGCTATACTTGAAATATAACAGAAAAATGCTTCTGTT
**
41805946 TTTCCTGCTGAAAAAGATAAGACAA-TGGTCATTAAGAAATTTCCACTTGATGAAAAACAGTTTA
1 TTTCCTGCTGAAAAAGATAAGACAACT-GTCATTAAGAAATTTCCACTTGATGAAAAACAACTTA
*
41806010 TACACAGGTAAACGTGAAAGCTATACTTGAAATATAACAGAAAAATGCTTC
65 TACACAGGTAAACATGAAAGCTATACTTGAAATATAACAGAAAAATGCTTC
41806061 AAGTTGCTTA
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
117 1 0.01
118 86 0.80
119 21 0.19
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (119 bp):
TTTCCTGCTGAAAAAGATAAGACAACTGTCATTAAGAAATTTCCACTTGATGAAAAACAACTTAT
ACACAGGTAAACATGAAAGCTATACTTGAAATATAACAGAAAAATGCTTCTGTT
Found at i:41807433 original size:12 final size:12
Alignment explanation
Indices: 41807416--41807440 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41807406 TCCATAAAAG
41807416 AAGATTAAGAAA
1 AAGATTAAGAAA
41807428 AAGATTAAGAAA
1 AAGATTAAGAAA
41807440 A
1 A
41807441 CCATCTAATG
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAGATTAAGAAA
Found at i:41807542 original size:17 final size:17
Alignment explanation
Indices: 41807516--41807561 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
41807506 CCAACGGGAT
41807516 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* **
41807533 TTAGATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
41807550 TTAAATTTATTT
1 TTAAATTTATTT
41807562 AAATTAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:41808335 original size:30 final size:29
Alignment explanation
Indices: 41808299--41808361 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
41808289 GTTATAACCT
*
41808299 AATAAAT-ATTATTAATAATAAATAAAAATA
1 AATAAATGATTAATAATAA-AAATAAAAA-A
* *
41808329 AATAAATGTTTAATATTAAAAATAAAAAA
1 AATAAATGATTAATAATAAAAATAAAAAA
41808358 AATA
1 AATA
41808362 GAAAACGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.17
30 16 0.55
31 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AATAAATGATTAATAATAAAAATAAAAAA
Found at i:41812563 original size:41 final size:41
Alignment explanation
Indices: 41812506--41812711 Score: 174
Period size: 41 Copynumber: 5.1 Consensus size: 41
41812496 AAAAACTCAG
* * * *
41812506 CCTTTAGTGGCGCTTTCACATAAGTGTCGCTATTGCTCTGA
1 CCTTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGA
* * * *
41812547 CCTTTAGCGACGCTTTCTCATAA-CTGTCACTATTG---TAA
1 CCTTTAGCGGCGCTTTCTCATAAGC-GCCGCTATTGCTCTGA
** *
41812585 TTTTTAGCGGCG-TTTTTCCATTAA-CGCCGCTATTGCTCTGA
1 CCTTTAGCGGCGCTTTCT-CA-TAAGCGCCGCTATTGCTCTGA
** * *
41812626 CCTTTAGCGATGCTTGCTCATAAGCGCCGCTATTTCTCTGA
1 CCTTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGA
* * *
41812667 CCTTTAGTGGCGCTTTCTCATAAGCGCCTCTATTGCTAT-A
1 CCTTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGA
41812707 CCTTT
1 CCTTT
41812712 TACGGCGTTT
Statistics
Matches: 130, Mismatches: 27, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
37 4 0.03
38 21 0.16
39 4 0.03
40 9 0.07
41 89 0.68
42 3 0.02
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (41 bp):
CCTTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGA
Found at i:41817140 original size:29 final size:29
Alignment explanation
Indices: 41817108--41817164 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
41817098 AAAATGAGAC
41817108 TTTTTGGA-TACTCGAGGG-AAAAATGGTA
1 TTTTTGGACT-CTCGAGGGCAAAAATGGTA
41817136 TTTTTGGACTCTCGAGGGCAAAAATGGTA
1 TTTTTGGACTCTCGAGGGCAAAAATGGTA
41817165 ATTTAGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (29 bp):
TTTTTGGACTCTCGAGGGCAAAAATGGTA
Found at i:41817276 original size:29 final size:28
Alignment explanation
Indices: 41817244--41817616 Score: 232
Period size: 29 Copynumber: 12.8 Consensus size: 28
41817234 AATCGAGATC
41817244 AAAAATGGAATTTTTGGACACG-TGGGGGT
1 AAAAATGGAATTTTTGGA-A-GTTGGGGGT
* *
41817273 -AAAATGGTAATTTTTGAAAGTTTTGGGGT
1 AAAAATGG-AATTTTTGGAAG-TTGGGGGT
* *
41817302 CAAAATGGAATTTTTGGAAATTTGGGGGT
1 AAAAATGGAATTTTTGG-AAGTTGGGGGT
* * *
41817331 AAAAATGTAATTTTTAGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTGGGGGT
* *
41817360 CAAAAATGGAATTTTTGGAAGTTTTGAGGT
1 -AAAAATGGAATTTTTGGAAG-TTGGGGGT
* * * *
41817390 CAAAATGGAATTTTTAGATGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTT-GGGGGT
* * *
41817419 AAAAATGAAATTTTTGAAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTGGGGGT
* * **
41817448 CAAAAATAGAATTTTTGGAAATTTAAGGGT
1 -AAAAATGGAATTTTTGG-AAGTTGGGGGT
* **
41817478 -AAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAG-TTGGGGGT
* * **
41817506 CAAAAATGGAATTTTTTGATGTTTAAGGGT
1 -AAAAATGGAATTTTTGGAAG-TTGGGGGT
* * *
41817536 AAAAATGTAATTTTTGAAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTGGGGGT
* * **
41817565 CAAAAATAGAATTTTTGGAAATTCAAGGGT
1 -AAAAATGGAATTTTTGGAAGTT-GGGGGT
*
41817595 -AAAATGTAATTTTTGGATAGTT
1 AAAAATGGAATTTTTGGA-AGTT
41817617 TAGGGACTTT
Statistics
Matches: 274, Mismatches: 53, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.01
28 48 0.18
29 120 0.44
30 101 0.37
31 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTGGGGGT
Found at i:41817282 original size:59 final size:58
Alignment explanation
Indices: 41817210--41817379 Score: 202
Period size: 59 Copynumber: 2.9 Consensus size: 58
41817200 AGACATCCGA
* * * * *
41817210 GGGTAAAATGGTAATTTTTAGGAAAATCGAGATCAAAAATGGAATTTTTGGACACGTGG
1 GGGTAAAATGGTAATTTTTA-GAAATTTGGGGTCAAAAATGGAATTTTTGGAAACGTGG
**
41817269 GGGTAAAATGGTAATTTTT-GAAAGTTTTGGGGTC-AAAATGGAATTTTTGGAAATTTGG
1 GGGTAAAATGGTAATTTTTAGAAA--TTTGGGGTCAAAAATGGAATTTTTGGAAACGTGG
*
41817327 GGGTAAAAAT-GTAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAA
1 GGGT-AAAATGGTAATTTTTAGAA-ATTTGGGGTCAAAAATGGAATTTTTGGAA
41817380 GTTTTGAGGT
Statistics
Matches: 97, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
57 4 0.04
58 43 0.44
59 50 0.52
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTAGAAATTTGGGGTCAAAAATGGAATTTTTGGAAACGTGG
Found at i:41817395 original size:59 final size:58
Alignment explanation
Indices: 41817244--41817617 Score: 355
Period size: 58 Copynumber: 6.4 Consensus size: 58
41817234 AATCGAGATC
* *
41817244 AAAAATGGAATTTTTGGACACG--TGGGGGT-AAAATGGTAATTTTT-GAAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGA-A-GTTTTGGGGTCAAAATGG-AATTTTTAG-AAGTTTAGGGGT
* * * * * *
41817302 CAAAATGGAATTTTTGGAAATTTGGGGGTAAAAATGTAATTTTTAGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTAGAAGTTTAGGGGT
* * *
41817360 CAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTAGATGTTCAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTAGAAGTTTAGGGGT
* * * * * *
41817419 AAAAATGAAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTTAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGAATTTTTAGAAGTTTAGGGGT
* * * * *
41817478 -AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTTGATGTTTAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGAATTTTTAGAAGTTTAGGGGT
* * * * * * *
41817536 AAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGAATTTTTAGAAGTTTAGGGGT
*
41817595 -AAAATGTAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
41817618 AGGGACTTTT
Statistics
Matches: 272, Mismatches: 36, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.00
58 137 0.50
59 134 0.49
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTAGAAGTTTAGGGGT
Found at i:41817402 original size:117 final size:118
Alignment explanation
Indices: 41817242--41817617 Score: 409
Period size: 117 Copynumber: 3.2 Consensus size: 118
41817232 AAAATCGAGA
* * * * *
41817242 TCAAAAATGGAATTTTTGGACACG--TGGGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 TCAAAAATGGAATTTTTGGA-A-GTTTTGAGGTCAAAATGG-AATTTTTGAATGTTTAGGGGTAA
* * * **
41817304 AAATGGAATTTTTGGAAA-TTTGGGGGT-AAAAAT-GTAATTTTTAGAAGTTTTGGGG
63 AAATGAAATTTTT-GAAAGTTTTGGGGTCAAAAATAG-AATTTTTAGAAATTTAAGGG
*
41817359 TCAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTT-AGATGTTCAGGGGTAAAA
1 TCAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGA-ATGTTTAGGGGTAAAA
*
41817423 ATGAAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTTAAGGG
65 ATGAAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTAGAAATTTAAGGG
* *
41817477 T--AAAATGTAATTTTTGGAAGTTTT-AGGGTCAAAAATGGAATTTTTTG-ATGTTTAAGGGTAA
1 TCAAAAATGGAATTTTTGGAAGTTTTGA-GGTC-AAAATGGAA-TTTTTGAATGTTTAGGGGTAA
* * *
41817538 AAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGG
63 AAATGAAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTAGAAATTTAAGGG
*
41817594 T--AAAATGTAATTTTTGGATAGTTT
1 TCAAAAATGGAATTTTTGGA-AGTTT
41817618 AGGGACTTTT
Statistics
Matches: 230, Mismatches: 17, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
115 2 0.01
116 32 0.14
117 155 0.67
118 40 0.17
119 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (118 bp):
TCAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGAATGTTTAGGGGTAAAAA
TGAAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTAGAAATTTAAGGG
Found at i:41817619 original size:117 final size:115
Alignment explanation
Indices: 41817362--41817621 Score: 421
Period size: 117 Copynumber: 2.2 Consensus size: 115
41817352 TTTGGGGTCA
* * *
41817362 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTAGATGTTCAGGGGTAAAAATGA
1 AAAATGTAATTTTTGGAAGTTTAG-GGTCAAAATGGAATTTTTAGATGTTCAAGGGTAAAAATGA
*
41817427 AATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTTAAGGGT
65 AATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGGT
* *
41817478 AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTTGATGTTTAAGGGTAAAAATG
1 AAAATGTAATTTTTGGAAG-TTTAGGGTC-AAAATGGAATTTTTAGATGTTCAAGGGTAAAAATG
*
41817543 TAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGGT
64 AAATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGGT
41817595 AAAATGTAATTTTTGGATAGTTTAGGG
1 AAAATGTAATTTTTGGA-AGTTTAGGG
41817622 ACTTTTAGGG
Statistics
Matches: 134, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
116 22 0.16
117 110 0.82
118 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (115 bp):
AAAATGTAATTTTTGGAAGTTTAGGGTCAAAATGGAATTTTTAGATGTTCAAGGGTAAAAATGAA
ATTTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAATTCAAGGGT
Found at i:41819327 original size:10 final size:11
Alignment explanation
Indices: 41819309--41819350 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
41819299 TCTTTTTAAA
41819309 TTTATAATAAT
1 TTTATAATAAT
* *
41819320 TTTAAATATAAA
1 TTTATA-ATAAT
41819332 TTTATAATAAT
1 TTTATAATAAT
41819343 TTTA-AATA
1 TTTATAATA
41819351 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.15
11 13 0.50
12 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTATAATAAT
Found at i:41819331 original size:23 final size:23
Alignment explanation
Indices: 41819305--41819358 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
41819295 ACTTTCTTTT
41819305 TAAATTTATAATAATTTTAAATA
1 TAAATTTATAATAATTTTAAATA
41819328 TAAATTTATAATAATTTTAAATA
1 TAAATTTATAATAATTTTAAATA
41819351 TAAATTTA
1 TAAATTTA
41819359 AACTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATTTATAATAATTTTAAATA
Found at i:41819367 original size:18 final size:19
Alignment explanation
Indices: 41819321--41819395 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 19
41819311 TATAATAATT
*
41819321 TTAAATATAAATTTATAATAATT
1 TTAAATATAAA-TT-T-A-AATC
41819344 TTAAATATAAATTTAAA-C
1 TTAAATATAAATTTAAATC
*
41819362 TTAAAT-TAAATTTAAATT
1 TTAAATATAAATTTAAATC
*
41819380 TTAGA-ATAAATTTAAA
1 TTAAATATAAATTTAAA
41819396 ATGAGTTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 10 0.21
18 20 0.43
19 2 0.04
20 1 0.02
21 1 0.02
22 2 0.04
23 11 0.23
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (19 bp):
TTAAATATAAATTTAAATC
Found at i:41819391 original size:23 final size:23
Alignment explanation
Indices: 41819305--41819380 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
41819295 ACTTTCTTTT
*
41819305 TAAATTTATAATAATTTTAAATA
1 TAAATTTATAATAATATTAAATA
*
41819328 TAAATTTATAATAATTTTAAATA
1 TAAATTTATAATAATATTAAATA
*
41819351 TAAATTTA-AACTTAA-ATTAAATT
1 TAAATTTATAA--TAATATTAAATA
41819374 TAAATTT
1 TAAATTT
41819381 TAGAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.04
23 44 0.90
24 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTATAATAATATTAAATA
Found at i:41819395 original size:6 final size:6
Alignment explanation
Indices: 41819303--41819380 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
41819293 GGACTTTCTT
* * *
41819303 TTTAAA TTTATAA --TAAT TTTAAA TATAAA TTTATAA --TAAT TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
* *
41819349 TATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
41819381 TAGAATAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 9 0.16
6 41 0.73
7 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:41820379 original size:20 final size:20
Alignment explanation
Indices: 41820336--41820379 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41820326 TACATATTAT
* *
41820336 CACTGTTCATGACATGATCT
1 CACTGTTCATGACATGACCC
*
41820356 CACTGTTCATGACTTGACCC
1 CACTGTTCATGACATGACCC
41820376 CACT
1 CACT
41820380 ATTCTTAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (20 bp):
CACTGTTCATGACATGACCC
Found at i:41822214 original size:23 final size:23
Alignment explanation
Indices: 41822163--41822216 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
41822153 CTTATAAATT
41822163 ATATAAAAATTCATTTTTTAATA
1 ATATAAAAATTCATTTTTTAATA
* * *
41822186 GT-TAAAATTTTATTCTTTT-ATA
1 ATATAAAAATTCATT-TTTTAATA
41822208 ATATAAAAA
1 ATATAAAAA
41822217 CTGTATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATAAAAATTCATTTTTTAATA
Found at i:41835447 original size:23 final size:23
Alignment explanation
Indices: 41835421--41835490 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
41835411 TTCATTTAAT
*
41835421 TTAATCGAATATATTCACGAATA
1 TTAATCGAATATATTCACGAACA
* ** *
41835444 TTAAACGACCATATTCATGAACA
1 TTAATCGAATATATTCACGAACA
* *
41835467 TATAATTGAATATATTCACAAACA
1 T-TAATCGAATATATTCACGAACA
41835491 ATATTAATGG
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAATCGAATATATTCACGAACA
Found at i:41835613 original size:12 final size:12
Alignment explanation
Indices: 41835596--41835639 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
41835586 TAAATGAGTC
41835596 ATAAACGAATCA
1 ATAAACGAATCA
* *
41835608 ATAAACG-AGCTT
1 ATAAACGAATC-A
41835620 ATAAACGAATCA
1 ATAAACGAATCA
41835632 ATAAACGA
1 ATAAACGA
41835640 GCTTTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (12 bp):
ATAAACGAATCA
Found at i:41835625 original size:24 final size:24
Alignment explanation
Indices: 41835596--41835648 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
41835586 TAAATGAGTC
41835596 ATAAACGAATCAATAAACGAGCTT
1 ATAAACGAATCAATAAACGAGCTT
41835620 ATAAACGAATCAATAAACGAGCTT
1 ATAAACGAATCAATAAACGAGCTT
*
41835644 TTAAA
1 ATAAA
41835649 TGAGTTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (24 bp):
ATAAACGAATCAATAAACGAGCTT
Found at i:41836130 original size:21 final size:20
Alignment explanation
Indices: 41836095--41836135 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
41836085 TTTAATTTTG
* *
41836095 CATTTATGTTTTATTTGAAGA
1 CATTTATGATGTATTT-AAGA
41836116 CATTTATGATGTATTTAAGA
1 CATTTATGATGTATTTAAGA
41836136 TATTGTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
CATTTATGATGTATTTAAGA
Found at i:41836471 original size:29 final size:30
Alignment explanation
Indices: 41836428--41836486 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
41836418 GAATTGGATC
41836428 AAATCAAAATTTCATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
* *
41836458 AAATCAAAA-TTCATGTATACAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
41836487 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:41841762 original size:2 final size:2
Alignment explanation
Indices: 41841757--41841785 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41841747 ACTTAAAAAA
41841757 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41841786 ATAGCGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41848445 original size:17 final size:17
Alignment explanation
Indices: 41848423--41848456 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41848413 TTCAAAACAG
41848423 ATTATTTTAATAAATAA
1 ATTATTTTAATAAATAA
*
41848440 ATTATTTTTATAAATAA
1 ATTATTTTAATAAATAA
41848457 TAAAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTTTAATAAATAA
Found at i:41848692 original size:30 final size:30
Alignment explanation
Indices: 41848652--41848722 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
41848642 TTCTTTGTAA
41848652 ATTT-AAAATTTAATCTATATA-TTTTTAT
1 ATTTAAAAATTTAATCTATATATTTTTTAT
* *
41848680 ATTTAAAAAATTT-ATTTATTTATTTTTTAT
1 ATTT-AAAAATTTAATCTATATATTTTTTAT
*
41848710 ATTTCAAAATTTA
1 ATTTAAAAATTTA
41848723 TATTCAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 14 0.39
30 18 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTAAAAATTTAATCTATATATTTTTTAT
Found at i:41849102 original size:44 final size:44
Alignment explanation
Indices: 41849038--41849122 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
41849028 GCTTTTTTTT
* * *
41849038 TCACTCAATTGGATAATTGAATTTTCAAAATGTATCAAAAAAGC
1 TCACTCAATTGGATAATTGAACTTGCAAAATGCATCAAAAAAGC
* * *
41849082 TCACTCAATTGGGTACTTGAACTTGCAAAATGCATTAAAAA
1 TCACTCAATTGGATAATTGAACTTGCAAAATGCATCAAAAA
41849123 GTCCTCAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (44 bp):
TCACTCAATTGGATAATTGAACTTGCAAAATGCATCAAAAAAGC
Found at i:41851322 original size:30 final size:29
Alignment explanation
Indices: 41851279--41851380 Score: 115
Period size: 29 Copynumber: 3.5 Consensus size: 29
41851269 AATTCGAGGA
41851279 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAATGGTAATTTTT-GTGAAATCGGGGT
*
41851309 TAAAAATGG-AA-TTTTG-GAAAGTTCGGGGG
1 T-AAAATGGTAATTTTTGTGAAA--TCGGGGT
41851338 T-AAATGGTAATTTTTTGTGAAATCGGGGT
1 TAAAATGGTAA-TTTTTGTGAAATCGGGGT
41851367 TAAAATGG-AATTTT
1 TAAAATGGTAATTTT
41851381 GGAAAGTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
27 10 0.16
28 7 0.11
29 20 0.32
30 14 0.23
31 11 0.18
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGTGAAATCGGGGT
Found at i:41851334 original size:29 final size:27
Alignment explanation
Indices: 41851252--41851399 Score: 113
Period size: 30 Copynumber: 5.1 Consensus size: 27
41851242 CCCAGGGGCA
* * *
41851252 AAAATGGAATTTTAGAAAATTCGAGGAT
1 AAAATGGAATTTT-GGAAATTCGGGGGT
*
41851280 AAAATGGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAATTCGGGGGT
41851310 AAAAATGGAATTTTGGAAAGTTCGGGGGT
1 -AAAATGGAATTTTGGAAA-TTCGGGGGT
*
41851339 -AAATGGTAATTTTTTGTGAAA-TCGGGGTT
1 AAAATGG-AA--TTTTG-GAAATTCGGGGGT
*
41851368 AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAA-TTCGGGGGT
41851396 AAAA
1 AAAA
41851400 ACATAATTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
26 4 0.04
27 15 0.15
28 20 0.20
29 22 0.22
30 24 0.24
31 14 0.14
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAATTCGGGGGT
Done.