Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold73
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: 1308442
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.31
Warning! 157727 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:590459 original size:25 final size:26
Alignment explanation
Indices: 590426--590515 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
590416 TAAAATTAAA
*
590426 TTATCTTTATAT-ATTTACATAAT-TT
1 TTATATTTATATAATTTA-ATAATATT
* *
590451 TTATATTTATTTAATTTAATTATATT
1 TTATATTTATATAATTTAATAATATT
*
590477 TTATATTAAATAATATATTTAAT--TA-T
1 TTATATT-TAT-ATA-ATTTAATAATATT
590503 TTAT-TTTATATAA
1 TTATATTTATATAA
590516 AAAATTAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 2 0.04
25 16 0.30
26 19 0.35
27 4 0.07
28 2 0.04
29 7 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTTATATAATTTAATAATATT
Found at i:590465 original size:17 final size:18
Alignment explanation
Indices: 590431--590477 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
590421 TTAAATTATC
590431 TTTA-TATATTTACATAA
1 TTTATTATATTTACATAA
**
590448 TTT-TTATATTTATTTAA
1 TTTATTATATTTACATAA
590465 TTTAATTATATTT
1 TTT-ATTATATTT
590478 TATATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 17 0.68
19 8 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATTATATTTACATAA
Found at i:590501 original size:17 final size:17
Alignment explanation
Indices: 590458--590501 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
590448 TTTTTATATT
* *
590458 TATTTAATTTAATTATA
1 TATTTAATTAAATAATA
590475 T-TTTATATTAAATAATA
1 TATTTA-ATTAAATAATA
590492 TATTTAATTA
1 TATTTAATTA
590502 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTAATTAAATAATA
Found at i:590537 original size:25 final size:25
Alignment explanation
Indices: 590495--590543 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
590485 AATAATATAT
* * *
590495 TTAATTATTTATTTTATATAAAAAA
1 TTAATTATTAAATATATATAAAAAA
*
590520 TTAATTATTAAATATATATTAAAA
1 TTAATTATTAAATATATATAAAAA
590544 TATAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATTATTAAATATATATAAAAAA
Found at i:590855 original size:34 final size:34
Alignment explanation
Indices: 590802--591016 Score: 256
Period size: 34 Copynumber: 6.4 Consensus size: 34
590792 GCATTTGTTA
*
590802 TTGATTAAAT-GGTGATTTGGTAGTTTACCATTG
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTG
* * *
590835 TTGATTAAATGGGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTG
* * *
590869 TTGACTAAATGGGAGATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTG
* ** *
590903 TTGATTAAATGAGAAATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTG
*
590937 TTGATTAAATGGGTAATTTGGT-GACTTACCATTG
1 TTGATTAAATGGGTGATTTGGTAG-CTTACCATTG
* * *
590971 TTGACTAAAT-GGTAGATTTGGTAGATTGCCATTG
1 TTGATTAAATGGGT-GATTTGGTAGCTTACCATTG
591005 TTGATTAAATGG
1 TTGATTAAATGG
591017 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
33 14 0.09
34 142 0.90
35 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
TTGATTAAATGGGTGATTTGGTAGCTTACCATTG
Found at i:590932 original size:102 final size:101
Alignment explanation
Indices: 590799--591016 Score: 319
Period size: 102 Copynumber: 2.1 Consensus size: 101
590789 CATGCATTTG
** * * * ** *
590799 TTATTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTATTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTAATTTGGTGACTTAC
*
590864 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGATTACCA
590900 TTATTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTAATTTGGTGACTTA
1 TTATTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTAATTTGGTGACTTA
* *
590965 CCATTGTTGACTAAATGGTAGATTTGGTAGATTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGATTACCA
*
591002 TTGTTGATTAAATGG
1 TTATTGATTAAATGG
591017 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 89 0.86
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (101 bp):
TTATTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTAATTTGGTGACTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGATTACCA
Found at i:595471 original size:34 final size:34
Alignment explanation
Indices: 595414--595629 Score: 256
Period size: 34 Copynumber: 6.4 Consensus size: 34
595404 AAGTGGGAGA
*
595414 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
595447 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
595481 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
**** *
595515 ATTGTTGATTAAATGAAAAATTTAGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
595549 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
595583 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
595617 ATTGTTGATTAAA
1 ATTGTTGATTAAA
595630 ATGTGGTTTA
Statistics
Matches: 156, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
33 17 0.11
34 139 0.89
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:595564 original size:102 final size:101
Alignment explanation
Indices: 595414--595629 Score: 317
Period size: 102 Copynumber: 2.1 Consensus size: 101
595404 AAGTGGGAGA
*** * * * * *
595414 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGAAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
595479 CCATTGTTGACTAAATGAG-AGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATG-GTAGATTTGGTAGCTTACC
595515 ATTGTTGATTAAATGAAAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-AAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* *
595580 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGTAGATTTGGTAGCTTACC
595617 ATTGTTGATTAAA
1 ATTGTTGATTAAA
595630 ATGTGGTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
101 16 0.16
102 87 0.84
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGAAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGTAGATTTGGTAGCTTACC
Found at i:596808 original size:13 final size:13
Alignment explanation
Indices: 596770--596800 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
596760 ATTAAATTTT
596770 AAAA-AAAATTAA
1 AAAATAAAATTAA
596782 AAAATAAAATTAA
1 AAAATAAAATTAA
596795 AAAATA
1 AAAATA
596801 TGAATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAATTAA
Found at i:597167 original size:12 final size:12
Alignment explanation
Indices: 597148--597190 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
597138 AATATTTATC
597148 TATT-TATTTTA
1 TATTATATTTTA
*
597159 TATCATATTTTA
1 TATTATATTTTA
*
597171 -ATTATTTTTTA
1 TATTATATTTTA
597182 TATTATATT
1 TATTATATT
597191 CGTATAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:597858 original size:27 final size:27
Alignment explanation
Indices: 597825--597884 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
597815 TCAAGATCCT
597825 TCTAATCTCTTTCAGTGGCTCTGATCA
1 TCTAATCTCTTTCAGTGGCTCTGATCA
597852 TCTAATCTCTTTCAGTGGCTCTGATCA
1 TCTAATCTCTTTCAGTGGCTCTGATCA
597879 TCTAAT
1 TCTAAT
597885 TGATCTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (27 bp):
TCTAATCTCTTTCAGTGGCTCTGATCA
Found at i:601757 original size:20 final size:20
Alignment explanation
Indices: 601718--601757 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
601708 TATATATTTT
**
601718 TAAAAAATAAATAATTATAA
1 TAAAAAATAAATAAAAATAA
*
601738 TAAATAATAAATAAAAATAA
1 TAAAAAATAAATAAAAATAA
601758 AAGCAGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAATAAATAAAAATAA
Found at i:602193 original size:18 final size:18
Alignment explanation
Indices: 602162--602196 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
602152 TTAAAAGTTA
*
602162 AATTATTTAAATTTATTC
1 AATTAATTAAATTTATTC
*
602180 AATTAATTATATTTATT
1 AATTAATTAAATTTATT
602197 TATAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTAATTAAATTTATTC
Found at i:602302 original size:19 final size:19
Alignment explanation
Indices: 602275--602324 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
602265 TAATTTTTTT
602275 AAAAT-TAATTAAAAATAA
1 AAAATATAATTAAAAATAA
602293 AAAATATAATTTAAAAATAA
1 AAAATATAA-TTAAAAATAA
602313 AAAA-ATAATTAA
1 AAAATATAATTAA
602325 TTTTATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.30
19 7 0.23
20 14 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATATAATTAAAAATAA
Found at i:602361 original size:20 final size:22
Alignment explanation
Indices: 602319--602364 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
602309 ATAAAAAAAT
*
602319 AATTAATTTTATAAATTACTTG
1 AATTAATATTATAAATTACTTG
*
602341 AATTAATATTA-AAA-TATTTG
1 AATTAATATTATAAATTACTTG
602361 AATT
1 AATT
602365 GATAGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTAATATTATAAATTACTTG
Found at i:604493 original size:32 final size:32
Alignment explanation
Indices: 604426--604521 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 32
604416 ATAATCATAT
* * *
604426 TTAA-AATATTATATTTAATATAAATATTAATAAA
1 TTAATAAT-TTATA-TT-ATATATATTTTAAAAAA
604460 TTAATAATTTATATTATATATATTTTAAAAAA
1 TTAATAATTTATATTATATATATTTTAAAAAA
* *
604492 TTTATATATTTATAATATTATATATTTTAA
1 TTAATA-ATTTATATTA-TATATATTTTAA
604522 TTATTTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
32 19 0.35
33 11 0.20
34 21 0.39
35 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAATAATTTATATTATATATATTTTAAAAAA
Found at i:604497 original size:16 final size:17
Alignment explanation
Indices: 604476--604521 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
604466 ATTTATATTA
604476 TATATATTTTAAAAAAT
1 TATATATTTTAAAAAAT
* *
604493 T-TATATATTTATAATAT
1 TATATAT-TTTAAAAAAT
604510 TATATATTTTAA
1 TATATATTTTAA
604522 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATTTTAAAAAAT
Found at i:604526 original size:16 final size:16
Alignment explanation
Indices: 604422--604522 Score: 58
Period size: 16 Copynumber: 6.7 Consensus size: 16
604412 TATTATAATC
*
604422 ATATTTAAAATA-T-T
1 ATATTTATAATATTAT
*
604436 ATA-TT-TAATA-TAA
1 ATATTTATAATATTAT
*
604449 ATATTAATAA-ATTA-
1 ATATTTATAATATTAT
*
604463 ATAATTTATATTA-TAT
1 AT-ATTTATAATATTAT
* *
604479 ATATTTTAAAAAATTTAT
1 ATA-TTTATAATA-TTAT
604497 ATATTTATAATATTAT
1 ATATTTATAATATTAT
604513 ATATTT-TAAT
1 ATATTTATAAT
604523 TATTTTTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
14 7 0.10
15 18 0.27
16 19 0.28
17 7 0.10
18 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTATAATATTAT
Found at i:604533 original size:33 final size:33
Alignment explanation
Indices: 604443--604521 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
604433 ATTATATTTA
* * * * *
604443 ATATAAATATTAATAAATTAATA-ATTTATATT
1 ATATATATTTTAAAAAATTTATATATTTATAAT
604475 ATATATATTTTAAAAAATTTATATATTTATAAT
1 ATATATATTTTAAAAAATTTATATATTTATAAT
604508 ATTATATATTTTAA
1 A-TATATATTTTAA
604522 TTATTTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 19 0.47
33 9 0.22
34 12 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
ATATATATTTTAAAAAATTTATATATTTATAAT
Found at i:605615 original size:55 final size:55
Alignment explanation
Indices: 605554--605663 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
605544 ATTAATGTAA
*
605554 AATGAAAAGATATTAATGTAGTATGATCTTGATTTATTATAATCTTATAGATATT
1 AATGAAAAGATATTAATGTAGTATGATCTTGATTGATTATAATCTTATAGATATT
* * *
605609 AATGAAAAGATATTAATGTAGTATGATCTTGATTGATTATATTTTTATGGATATT
1 AATGAAAAGATATTAATGTAGTATGATCTTGATTGATTATAATCTTATAGATATT
605664 CATTTACAAT
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:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (55 bp):
AATGAAAAGATATTAATGTAGTATGATCTTGATTGATTATAATCTTATAGATATT
Found at i:606985 original size:21 final size:22
Alignment explanation
Indices: 606939--606985 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
606929 GGTTATAATT
*
606939 ATAAAAATATTTTTTATTTATTA
1 ATAAAAATATTTTTTATTCA-TA
*
606962 ATAAAAATATTTTTTGTTCA-A
1 ATAAAAATATTTTTTATTCATA
606983 ATA
1 ATA
606986 TATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
23 18 0.82
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAAAAATATTTTTTATTCATA
Found at i:608408 original size:21 final size:21
Alignment explanation
Indices: 608365--608410 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
608355 TATCTCTCTA
* * *
608365 CTCTCTAAAATTTTCTTACTT
1 CTCTCTAAAATTTTATCAATT
608386 CTCTCTAAAATTTTATCAATT
1 CTCTCTAAAATTTTATCAATT
608407 CTCT
1 CTCT
608411 TATTTCTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (21 bp):
CTCTCTAAAATTTTATCAATT
Found at i:608624 original size:14 final size:15
Alignment explanation
Indices: 608607--608679 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 15
608597 TTATATTGTT
*
608607 GTAATTAGTTGATA-
1 GTAATTAGTTTATAG
608621 GTAATTA-TTTATTATG
1 GTAATTAGTTTA-TA-G
* *
608637 TGGAATTAGGTTTA-AA
1 -GTAATTA-GTTTATAG
608653 GTAATTAGTTTATAG
1 GTAATTAGTTTATAG
608668 GTAATTAGTTTA
1 GTAATTAGTTTA
608680 AAGCCTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.06
14 14 0.30
15 19 0.40
17 7 0.15
19 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (15 bp):
GTAATTAGTTTATAG
Found at i:613069 original size:15 final size:15
Alignment explanation
Indices: 613049--613089 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
613039 TGATCCTGTT
613049 CATCCACCACCCATG
1 CATCCACCACCCATG
* *
613064 CATCCACAACCCGTG
1 CATCCACCACCCATG
613079 CATCCACCACC
1 CATCCACCACC
613090 TGTTTACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.27, C:0.54, G:0.07, T:0.12
Consensus pattern (15 bp):
CATCCACCACCCATG
Found at i:613604 original size:36 final size:36
Alignment explanation
Indices: 613559--613755 Score: 173
Period size: 36 Copynumber: 5.3 Consensus size: 36
613549 TATCTCGGAT
613559 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
1 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
* * * * * *
613595 TAGTTGTTGATTGTAGTTATCGTGCAGAT-TATCTCGGAT
1 TAGTTGTTGATAGTAGTAAT-GTG-AAATATA-C-AGAAA
613634 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
1 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
* * * * * * *
613670 TATTTGTTGATTGTAGTTATCGTG-CATATTATCTCGGAT
1 TAGTTGTTGATAGTAGTAAT-GTGAAATA-TA-C-AGAAA
*
613709 TAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAA
1 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
*
613745 TATTTGTTGAT
1 TAGTTGTTGAT
613756 TGTAATTATC
Statistics
Matches: 123, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
36 52 0.42
37 15 0.12
38 14 0.11
39 42 0.34
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (36 bp):
TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAA
Found at i:613623 original size:75 final size:75
Alignment explanation
Indices: 613500--613785 Score: 509
Period size: 75 Copynumber: 3.8 Consensus size: 75
613490 ACAAAATTGT
* * *
613500 TAATGTGAAATATGCAGAAATATTTATTGATTGTAGTTATCGTACAGATTATCTCGGATTAGTTG
1 TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTG
613565 TTGATAGTAG
66 TTGATAGTAG
*
613575 TAATGTGAAATATACAGAAATAGTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTG
1 TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTG
613640 TTGATAGTAG
66 TTGATAGTAG
*
613650 TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCATATTATCTCGGATTAGTTG
1 TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTG
613715 TTGATAGTAG
66 TTGATAGTAG
* *
613725 TAATGTGAAATATGCAGAAATATTTGTTGATTGTAATTATCGTGCAGATTATCTCGGATTA
1 TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTA
613786 TCATTTCATC
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 202 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (75 bp):
TAATGTGAAATATACAGAAATATTTGTTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTG
TTGATAGTAG
Found at i:614280 original size:9 final size:8
Alignment explanation
Indices: 614259--614325 Score: 73
Period size: 9 Copynumber: 7.9 Consensus size: 8
614249 GATTCAAGAT
614259 ATTAAAAA
1 ATTAAAAA
614267 ATTAAAATA
1 ATTAAAA-A
614276 ATTAAAAA
1 ATTAAAAA
*
614284 TTTTAAAAA
1 -ATTAAAAA
614293 ATTATAAAA
1 ATTA-AAAA
614302 ATTTAAAAAA
1 A-TT-AAAAA
614312 ATT-AAAA
1 ATTAAAAA
614319 ATTAAAA
1 ATTAAAA
614326 TATGTAGCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
7 7 0.14
8 14 0.27
9 22 0.43
10 7 0.14
11 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATTAAAAA
Found at i:614281 original size:17 final size:17
Alignment explanation
Indices: 614259--614327 Score: 79
Period size: 17 Copynumber: 4.0 Consensus size: 17
614249 GATTCAAGAT
614259 ATTAAAAAATTAAAATA
1 ATTAAAAAATTAAAATA
*
614276 ATTAAAAATTTTAAAA-A
1 ATTAAAAA-ATTAAAATA
*
614293 ATTATAAAAATTTAAAAAA
1 ATTA-AAAAA-TTAAAATA
614312 ATT-AAAAATTAAAATA
1 ATTAAAAAATTAAAATA
614328 TGTAGCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 7 0.16
17 18 0.40
18 16 0.36
19 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAAAAATTAAAATA
Found at i:614290 original size:26 final size:27
Alignment explanation
Indices: 614259--614327 Score: 90
Period size: 26 Copynumber: 2.6 Consensus size: 27
614249 GATTCAAGAT
*
614259 ATTAAAAAATTAAAATAA-TTAAAAAT
1 ATTAAAAAATTAAAATAATTTAAAAAA
*
614285 TTTAAAAAATTATAAA-AATTTAAAAAA
1 ATTAAAAAATTA-AAATAATTTAAAAAA
614312 ATT-AAAAATTAAAATA
1 ATTAAAAAATTAAAATA
614328 TGTAGCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.08
26 22 0.59
27 12 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTAAAAAATTAAAATAATTTAAAAAA
Found at i:614300 original size:19 final size:19
Alignment explanation
Indices: 614261--614319 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
614251 TTCAAGATAT
* *
614261 TAAAAAATTAAAATAA-T-
1 TAAAAATTTAAAAAAATTA
*
614278 TAAAAATTTTAAAAAATTA
1 TAAAAATTTAAAAAAATTA
614297 TAAAAATTTAAAAAAATTA
1 TAAAAATTTAAAAAAATTA
614316 -AAAA
1 TAAAA
614320 TTAAAATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 13 0.36
18 5 0.14
19 18 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATTTAAAAAAATTA
Found at i:614965 original size:5 final size:5
Alignment explanation
Indices: 614955--615038 Score: 55
Period size: 5 Copynumber: 16.4 Consensus size: 5
614945 GATCTATTGG
* * * ** *
614955 TTTAA TTTAA -TAAA TTTAA TTTGA TTTAA TTTAAA TTTTAA -ATAA AATAT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT-AA -TTTAA TTTAA TTTAA
*
615005 TTTAA TTTAA TTTAA TTTAAA TTATTA TTTAA TT
1 TTTAA TTTAA TTTAA TTT-AA TT-TAA TTTAA TT
615039 AAAAATTTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 6 0.10
5 41 0.66
6 11 0.18
7 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:615036 original size:41 final size:40
Alignment explanation
Indices: 614967--615046 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
614957 TAATTTAATA
* *
614967 AATTTAATTTGATTTAATTTAAATTTTAAATAAAATATTTT
1 AATTTAATTTAATTTAAATTAAATTTTAAATAAAA-ATTTT
* *
615008 AATTTAATTTAATTTAAATT-ATTATTTAATTAAAAATTT
1 AATTTAATTTAATTTAAATTAAAT-TTTAAATAAAAATTT
615047 ATATTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (40 bp):
AATTTAATTTAATTTAAATTAAATTTTAAATAAAAATTTT
Found at i:615193 original size:21 final size:21
Alignment explanation
Indices: 615147--615197 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
615137 TTACTTATAA
615147 AAAAATTTTGATAGAGACAAT
1 AAAAATTTTGATAGAGACAAT
* **
615168 TAAAATTTTTTTA-AGACTAAT
1 AAAAATTTTGATAGAGAC-AAT
615189 AAAAATTTT
1 AAAAATTTT
615198 ATATTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (21 bp):
AAAAATTTTGATAGAGACAAT
Found at i:618087 original size:12 final size:12
Alignment explanation
Indices: 618070--618107 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
618060 GGTAAATATA
618070 TATATTTAATTT
1 TATATTTAATTT
618082 TATATTTATAATTT
1 TATA-TT-TAATTT
618096 T-TATTTAATTT
1 TATATTTAATTT
618107 T
1 T
618108 TTTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 4 0.17
14 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:619028 original size:15 final size:15
Alignment explanation
Indices: 619008--619037 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
618998 TAATTTAAAT
619008 AAATTAAATATTTAA
1 AAATTAAATATTTAA
619023 AAATTAAATATTTAA
1 AAATTAAATATTTAA
619038 TTTATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTAAATATTTAA
Found at i:619751 original size:18 final size:16
Alignment explanation
Indices: 619711--619751 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
619701 CACAAAGATA
*
619711 TATATATATATTTATT
1 TATATTTATATTTATT
619727 TATATTTATATTTATAT
1 TATATTTATATTTAT-T
619744 TATCATTT
1 TAT-ATTT
619752 TCAACCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
17 4 0.18
18 4 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTATATTTATT
Found at i:621065 original size:15 final size:15
Alignment explanation
Indices: 621047--621092 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
621037 CTATATTAAA
621047 ATTGATAATATATTT
1 ATTGATAATATATTT
*
621062 ATTGATAATTTATTT
1 ATTGATAATATATTT
* *
621077 ATATAATTATATATTT
1 AT-TGATAATATATTT
621093 TAAATTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
ATTGATAATATATTT
Found at i:621552 original size:24 final size:25
Alignment explanation
Indices: 621501--621549 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
621491 TCATGAATAA
* *
621501 AAAAATATTTATAAAAGGCTAAGGG
1 AAAAACATGTATAAAAGGCTAAGGG
*
621526 AAAAACATGTATAAAAGGTTAAGG
1 AAAAACATGTATAAAAGGCTAAGG
621550 AAATTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (25 bp):
AAAAACATGTATAAAAGGCTAAGGG
Found at i:621714 original size:2 final size:2
Alignment explanation
Indices: 621701--621758 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
621691 AACCAAATTC
* *
621701 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
621743 TA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
621759 AGCCGTCTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:622807 original size:13 final size:16
Alignment explanation
Indices: 622787--622824 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
622777 TTATATCAAT
622787 ATATAATATT-TTA-A
1 ATATAATATTATTATA
622801 ATA-AATATTATTATA
1 ATATAATATTATTATA
622816 ATATAATAT
1 ATATAATAT
622825 AATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 4 0.19
16 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAATATTATTATA
Found at i:622834 original size:16 final size:16
Alignment explanation
Indices: 622798--622849 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
622788 TATAATATTT
*
622798 TAAATA-AATATTAT-
1 TAAATATAATATAATA
622812 TATAATATAATATAATA
1 TA-AATATAATATAATA
*
622829 TAAATATGATATAA-A
1 TAAATATAATATAATA
622844 TAAATA
1 TAAATA
622850 AATTATCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 18 0.55
17 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATATAATATAATA
Found at i:623913 original size:3 final size:3
Alignment explanation
Indices: 623905--623948 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
623895 GAAAGTGTAA
623905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
623949 AGAAAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:625413 original size:12 final size:12
Alignment explanation
Indices: 625392--625426 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
625382 TTTAGAAAAC
*
625392 TATATATATATA
1 TATATGTATATA
625404 TATATGTATATA
1 TATATGTATATA
*
625416 TGTATGTATAT
1 TATATGTATAT
625427 GTCCAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
TATATGTATATA
Found at i:626138 original size:21 final size:20
Alignment explanation
Indices: 626104--626143 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
626094 TAAGTGAATT
*
626104 AAAATTTTATTTTATTATTA
1 AAAATTTAATTTTATTATTA
626124 AAAATATTAATTTTATTATT
1 AAAAT-TTAATTTTATTATT
626144 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTTAATTTTATTATTA
Found at i:626140 original size:26 final size:23
Alignment explanation
Indices: 626112--626156 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
626102 TTAAAATTTT
*
626112 ATTTTATTA-TTA-AAAATATTA
1 ATTTTATTATTTATAAAAAATTA
626133 ATTTTATTATTTATAAAAAATTA
1 ATTTTATTATTTATAAAAAATTA
626156 A
1 A
626157 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTATTATTTATAAAAAATTA
Found at i:627086 original size:2 final size:2
Alignment explanation
Indices: 627079--627113 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
627069 ACCCACACTA
627079 AT AT AT AT AT 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 AT AT AT AT AT A
627114 CATACGGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:629536 original size:16 final size:16
Alignment explanation
Indices: 629510--629552 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
629500 TATTAAAAAT
629510 TATAGTATTTTATCAAA
1 TATA-TATTTTATCAAA
*
629527 TATATATTTTTATTAAA
1 TATATA-TTTTATCAAA
*
629544 TATTTATTT
1 TATATATTT
629553 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TATATATTTTATCAAA
Found at i:629537 original size:17 final size:17
Alignment explanation
Indices: 629517--629552 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
629507 AATTATAGTA
629517 TTTTATCAAATATATAT
1 TTTTATCAAATATATAT
* *
629534 TTTTATTAAATATTTAT
1 TTTTATCAAATATATAT
629551 TT
1 TT
629553 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATCAAATATATAT
Found at i:631240 original size:29 final size:28
Alignment explanation
Indices: 631170--631245 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
631160 TTTAATTTAA
* * *
631170 TTTAATATAATTAAAAAAAGTCTTTAAAT
1 TTTAATTTATTTAAATAAA-TCTTTAAAT
* * *
631199 TTTAATTTTTTTAGATAAATCTTTATAT
1 TTTAATTTATTTAAATAAATCTTTAAAT
*
631227 TTTTATTATATTTAAATAA
1 TTTAATT-TATTTAAATAA
631246 GTTACTAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTAATTTATTTAAATAAATCTTTAAAT
Found at i:640110 original size:13 final size:12
Alignment explanation
Indices: 640087--640115 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
640077 AGTTATAAGT
640087 AAAAATTAAAAA
1 AAAAATTAAAAA
640099 AAAAATTAAAAA
1 AAAAATTAAAAA
640111 AAAAA
1 AAAAA
640116 GAAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:640677 original size:27 final size:25
Alignment explanation
Indices: 640644--640700 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
640634 TAATTTATGT
640644 AATATAA-ATTATTAAAATATATATAA
1 AATATAATATT-TT-AAATATATATAA
*
640670 ATATATAATATTTTAAATATATTTAA
1 A-ATATAATATTTTAAATATATATAA
640696 AATAT
1 AATAT
640701 GATAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.14
26 13 0.46
27 8 0.29
28 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATAATATTTTAAATATATATAA
Found at i:640873 original size:35 final size:32
Alignment explanation
Indices: 640834--640897 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 32
640824 TTTTTTTAAT
640834 TTTTTATTTGTATATATT-TATTATATTTAAATAAA
1 TTTTTATTT-T-TATATTATATT-T-TTTAAATAAA
640869 TTTTTATTTTTATATTATATTTTTTAAAT
1 TTTTTATTTTTATATTATATTTTTTAAAT
640898 TTTTAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 7 0.25
33 7 0.25
34 5 0.18
35 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (32 bp):
TTTTTATTTTTATATTATATTTTTTAAATAAA
Found at i:640884 original size:29 final size:30
Alignment explanation
Indices: 640852--640926 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
640842 TGTATATATT
*
640852 TATTATATTTAAATAAATTTTT-ATTTTTA
1 TATTATATTTAAATAAATTTTTAATCTTTA
**
640881 TATTATATTT-TTTAAATTTTTAATCTTTA
1 TATTATATTTAAATAAATTTTTAATCTTTA
*
640910 -ATTTAAATTTAAATAAA
1 TA-TTATATTTAAATAAA
640927 CTATTTAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
28 10 0.27
29 23 0.62
30 4 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTATATTTAAATAAATTTTTAATCTTTA
Found at i:640890 original size:19 final size:18
Alignment explanation
Indices: 640817--640892 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 18
640807 AAAAATTAAA
* *
640817 ATTTTAATTTTTTTA-AT
1 ATTTTTATTTTTATATAT
*
640834 -TTTTTATTTGTATATAT
1 ATTTTTATTTTTATATAT
* * * *
640851 -TTATTATATTTAAATAA
1 ATTTTTATTTTTATATAT
640868 ATTTTTATTTTTATATTAT
1 ATTTTTATTTTTATA-TAT
640887 ATTTTT
1 ATTTTT
640893 TAAATTTTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
16 11 0.25
17 14 0.32
18 11 0.25
19 8 0.18
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (18 bp):
ATTTTTATTTTTATATAT
Found at i:642933 original size:2 final size:2
Alignment explanation
Indices: 642926--642957 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
642916 GAGGAAAAGT
642926 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
642958 CGAGGAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:648756 original size:2 final size:2
Alignment explanation
Indices: 648749--648788 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
648739 TCTCGTTGTT
648749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
648789 CACTATTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:649106 original size:24 final size:24
Alignment explanation
Indices: 649079--649131 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
649069 CTTTAAAATA
* *
649079 ATTATTTATTTGTATTATA-TTTAT
1 ATTATTT-TTTATATTATACTTAAT
649103 ATTATTTTTTATATTATACTTAAT
1 ATTATTTTTTATATTATACTTAAT
649127 ATTAT
1 ATTAT
649132 CAGATCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTATTTTTTATATTATACTTAAT
Found at i:649128 original size:12 final size:11
Alignment explanation
Indices: 649081--649131 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
649071 TTAAAATAAT
*
649081 TATT-TATTTG
1 TATTATATTTA
649091 TATTATATTTA
1 TATTATATTTA
*
649102 TATTATTTTTTA
1 TATTA-TATTTA
*
649114 TATTATACTTAA
1 TATTATA-TTTA
649126 TATTAT
1 TATTAT
649132 CAGATCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 4 0.12
11 11 0.32
12 19 0.56
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTATATTTA
Found at i:654789 original size:3 final size:3
Alignment explanation
Indices: 654781--654819 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
654771 GAAAGTGTAA
654781 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
654820 AGAAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:654827 original size:22 final size:22
Alignment explanation
Indices: 654779--654827 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
654769 AAGAAAGTGT
654779 AAAA-TAATAATAATAATAATA
1 AAAATTAATAATAATAATAATA
*
654800 ATAATTAATAATAATAATAA-A
1 AAAATTAATAATAATAATAATA
654821 GAAAATT
1 -AAAATT
654828 TTGTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATTAATAATAATAATAATA
Found at i:657008 original size:21 final size:20
Alignment explanation
Indices: 656974--657013 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
656964 TAAGTGATTT
*
656974 AAAATTTTATTTTATTATTA
1 AAAATTTAATTTTATTATTA
656994 AAAATATTAATTTTATTATT
1 AAAAT-TTAATTTTATTATT
657014 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTTAATTTTATTATTA
Found at i:657009 original size:26 final size:23
Alignment explanation
Indices: 656982--657026 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
656972 TTAAAATTTT
*
656982 ATTTTATTA-TTA-AAAATATTA
1 ATTTTATTATTTATAAAAAATTA
657003 ATTTTATTATTTATAAAAAATTA
1 ATTTTATTATTTATAAAAAATTA
657026 A
1 A
657027 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTATTATTTATAAAAAATTA
Found at i:657957 original size:2 final size:2
Alignment explanation
Indices: 657950--658002 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
657940 ACCCACACTA
657950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
657992 AT AT AT AT AT A
1 AT AT AT AT AT A
658003 CATACATACG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:660096 original size:10 final size:10
Alignment explanation
Indices: 660082--660116 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
660072 TCCCGCCCGC
*
660082 CCCCCCCCCC
1 CCCCCCCCCA
660092 CCCCCCCCCA
1 CCCCCCCCCA
*
660102 CCCCACCCCA
1 CCCCCCCCCA
660112 CCCCC
1 CCCCC
660117 TTTTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.91, G:0.00, T:0.00
Consensus pattern (10 bp):
CCCCCCCCCA
Found at i:660441 original size:16 final size:16
Alignment explanation
Indices: 660415--660457 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
660405 TATTAAAAAT
660415 TATAGTATTTTATCAAA
1 TATA-TATTTTATCAAA
*
660432 TATATATTTTTATTAAA
1 TATATA-TTTTATCAAA
*
660449 TATTTATTT
1 TATATATTT
660458 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TATATATTTTATCAAA
Found at i:660442 original size:17 final size:17
Alignment explanation
Indices: 660422--660457 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
660412 AATTATAGTA
660422 TTTTATCAAATATATAT
1 TTTTATCAAATATATAT
* *
660439 TTTTATTAAATATTTAT
1 TTTTATCAAATATATAT
660456 TT
1 TT
660458 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATCAAATATATAT
Found at i:670992 original size:13 final size:12
Alignment explanation
Indices: 670969--670997 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
670959 AGTTATAAGT
670969 AAAAATTAAAAA
1 AAAAATTAAAAA
670981 AAAAATTAAAAA
1 AAAAATTAAAAA
670993 AAAAA
1 AAAAA
670998 GAAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:671563 original size:27 final size:25
Alignment explanation
Indices: 671530--671586 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
671520 TAATTTATGT
671530 AATATAA-ATTATTAAAATATATATAA
1 AATATAATATT-TT-AAATATATATAA
*
671556 ATATATAATATTTTAAATATATTTAA
1 A-ATATAATATTTTAAATATATATAA
671582 AATAT
1 AATAT
671587 GATAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.14
26 13 0.46
27 8 0.29
28 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATAATATTTTAAATATATATAA
Found at i:671768 original size:29 final size:29
Alignment explanation
Indices: 671736--671817 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
671726 TGTATATATT
*
671736 TATTATATTTAAATAAATTTTTATTTTTA
1 TATTATATTTAAATAAATTTTTATCTTTA
**
671765 TATTATATTTTTA-AAATTTTTAATCTTTA
1 TATTATATTTAAATAAATTTTT-ATCTTTA
*
671794 -ATTTAAATTTAAATAAATTATTTA
1 TA-TTATATTTAAATAAATT-TTTA
671818 ACATACATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 9 0.21
29 25 0.58
30 6 0.14
31 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTATATTTAAATAAATTTTTATCTTTA
Found at i:671774 original size:19 final size:18
Alignment explanation
Indices: 671701--671777 Score: 61
Period size: 17 Copynumber: 4.4 Consensus size: 18
671691 AAAAATTTTA
* *
671701 ATTTTAATTTTTTTA-AT
1 ATTTTTATTTTTATATAT
*
671718 -TTTTTATTTGTATATAT
1 ATTTTTATTTTTATATAT
* * * *
671735 -TTATTATATTTAAATAA
1 ATTTTTATTTTTATATAT
671752 ATTTTTATTTTTATATTAT
1 ATTTTTATTTTTATA-TAT
671771 ATTTTTA
1 ATTTTTA
671778 AAATTTTTAA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
16 11 0.24
17 14 0.31
18 11 0.24
19 9 0.20
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (18 bp):
ATTTTTATTTTTATATAT
Found at i:673816 original size:2 final size:2
Alignment explanation
Indices: 673809--673838 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
673799 GAGGAAAAGT
673809 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
673839 CGAGGAATGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:678767 original size:32 final size:32
Alignment explanation
Indices: 678731--678796 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
678721 GAGCAGTTTG
*
678731 TTTTAGATCGGATTTAGTAAGAATTTTGTAAT
1 TTTTAGATCAGATTTAGTAAGAATTTTGTAAT
678763 TTTTAGATCAGATTTAGTAAGAATTTTGTAAT
1 TTTTAGATCAGATTTAGTAAGAATTTTGTAAT
678795 TT
1 TT
678797 AGATTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (32 bp):
TTTTAGATCAGATTTAGTAAGAATTTTGTAAT
Found at i:678824 original size:3 final size:3
Alignment explanation
Indices: 678816--678856 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
678806 TGATTTAAAA
678816 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
678857 AATAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:679694 original size:2 final size:2
Alignment explanation
Indices: 679687--679711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
679677 TCTCGTTGTT
679687 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
679712 CTTATTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:679887 original size:24 final size:24
Alignment explanation
Indices: 679855--679904 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
679845 CACTTTCATA
679855 AATAGTTCCCGATATGAAAATGAC
1 AATAGTTCCCGATATGAAAATGAC
679879 AATAGTTCCCGATATGAAAATGAC
1 AATAGTTCCCGATATGAAAATGAC
679903 AA
1 AA
679905 GATAACTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
AATAGTTCCCGATATGAAAATGAC
Found at i:680061 original size:12 final size:11
Alignment explanation
Indices: 680024--680074 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
680014 TTAAAATAAT
*
680024 TATT-TATTTG
1 TATTATATTTA
680034 TATTATATTTA
1 TATTATATTTA
*
680045 TATTATTTTTCA
1 TATTATATTT-A
*
680057 TATTATACTTAA
1 TATTATA-TTTA
680069 TATTAT
1 TATTAT
680075 CAGATCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 4 0.12
11 14 0.41
12 14 0.41
13 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTATATTTA
Found at i:684908 original size:14 final size:14
Alignment explanation
Indices: 684889--684920 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
684879 ATTTTAAAAT
684889 ATATAAAAATATTA
1 ATATAAAAATATTA
684903 ATATAAAAATATTA
1 ATATAAAAATATTA
684917 ATAT
1 ATAT
684921 TATAGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAAAAATATTA
Found at i:685540 original size:20 final size:20
Alignment explanation
Indices: 685474--685544 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
685464 TTTTTATTTA
* *
685474 AATTTAATTATAAAATATAAA
1 AATTTAATAATAAAATA-AAT
*
685495 AATATTAATATTAAAAT-AAT
1 AAT-TTAATAATAAAATAAAT
* *
685515 ATTTTAATAATATAATAAAT
1 AATTTAATAATAAAATAAAT
685535 AATTTAATAA
1 AATTTAATAA
685545 GCTTTTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 11 0.27
20 16 0.39
21 3 0.07
22 11 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAATAATAAAATAAAT
Found at i:686501 original size:15 final size:17
Alignment explanation
Indices: 686472--686517 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
686462 AAAATTATAC
686472 ATAAATATATATTTAAT
1 ATAAATATATATTTAAT
686489 ATAAATAT-T-TTTAAT
1 ATAAATATATATTTAAT
* *
686504 -TTATTATATATTTA
1 ATAAATATATATTTA
686518 TAAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 5 0.20
17 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAAATATATATTTAAT
Found at i:689255 original size:21 final size:21
Alignment explanation
Indices: 689229--689273 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
689219 AAAAACACTT
689229 AAAATAAGT-GAAAGGATGAGG
1 AAAATAAGTAG-AAGGATGAGG
689250 AAAATAAGTAGAAGGATGAGG
1 AAAATAAGTAGAAGGATGAGG
689271 AAA
1 AAA
689274 GACCTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.13
Consensus pattern (21 bp):
AAAATAAGTAGAAGGATGAGG
Found at i:690815 original size:19 final size:18
Alignment explanation
Indices: 690791--690826 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
690781 ATTTAATAAC
690791 TCATATATCTATATTATAT
1 TCATATATCT-TATTATAT
*
690810 TCATATATGTTATTATA
1 TCATATATCTTATTATA
690827 ATTATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (18 bp):
TCATATATCTTATTATAT
Found at i:690934 original size:22 final size:21
Alignment explanation
Indices: 690909--690960 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
690899 AAATTATGTA
690909 TTTATTTTATATCATATTATAT-
1 TTTATTTT-T-TCATATTATATG
*
690931 TTTAATTATTTTTATATTATATG
1 TTT-ATT-TTTTCATATTATATG
690954 TTTATTT
1 TTTATTT
690961 ATCTTATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 7 0.27
24 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTCATATTATATG
Found at i:690949 original size:11 final size:12
Alignment explanation
Indices: 690922--690962 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
690912 ATTTTATATC
690922 ATATTATATTTT
1 ATATTATATTTT
690934 A-ATTAT-TTTT
1 ATATTATATTTT
690944 ATATTATATGTTT
1 ATATTATAT-TTT
690957 AT-TTAT
1 ATATTAT
690963 CTTATAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.19
11 10 0.38
12 6 0.23
13 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:690967 original size:22 final size:22
Alignment explanation
Indices: 690922--690968 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
690912 ATTTTATATC
*
690922 ATATTATATTTTAATTATTTTT
1 ATATTATATTTTAATTATTCTT
*
690944 ATATTATATGTTTATTTA-TCTT
1 ATATTATAT-TTTAATTATTCTT
690966 ATA
1 ATA
690969 GAGTCACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATATTATATTTTAATTATTCTT
Found at i:691496 original size:19 final size:19
Alignment explanation
Indices: 691470--691511 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
691460 GTATATGTAG
691470 TATAAATAA-AT--ATAAT
1 TATAAATAATATAAATAAT
691486 TATAAATAATATAAATAAT
1 TATAAATAATATAAATAAT
691505 TATAAAT
1 TATAAAT
691512 TTTATTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
19 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAAATAATATAAATAAT
Found at i:693238 original size:19 final size:19
Alignment explanation
Indices: 693214--693267 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
693204 CATCAAATTT
* *
693214 TATTTTTATTTTTTTAATA
1 TATTTTTATTTATTTAACA
* *
693233 TATTTTAATATATTTAACA
1 TATTTTTATTTATTTAACA
693252 TATCTTTTATTATATT
1 TAT-TTTTATT-TATT
693268 AAAATCATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 18 0.67
20 5 0.19
21 4 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTTATTTAACA
Found at i:693240 original size:10 final size:10
Alignment explanation
Indices: 693225--693267 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
693215 ATTTTTATTT
693225 TTTTAATATA
1 TTTTAATATA
693235 TTTTAATATA
1 TTTTAATATA
* *
693245 TTTAACATATC
1 TTTTA-ATATA
*
693256 TTTTATTATA
1 TTTTAATATA
693266 TT
1 TT
693268 AAAATCATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATATA
Found at i:693494 original size:28 final size:27
Alignment explanation
Indices: 693435--693524 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
693425 CACCCATTTG
* *
693435 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
693462 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
693490 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
693515 TTTGTCAAAA
1 TTTGTCAAAA
693525 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:698068 original size:28 final size:27
Alignment explanation
Indices: 698009--698098 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
697999 CACCCATTTG
* *
698009 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
698036 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
698064 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
698089 TTTGTCAAAA
1 TTTGTCAAAA
698099 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:699352 original size:23 final size:24
Alignment explanation
Indices: 699306--699357 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
699296 TGAATATATT
* *
699306 ATTATTATTATTTTAAATATAATA
1 ATTATTATTATTTAAAATAAAATA
699330 ATTATTATT-TTTAAAATAAAATA
1 ATTATTATTATTTAAAATAAAATA
699353 ATTAT
1 ATTAT
699358 ATAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATTATTATTTAAAATAAAATA
Found at i:702535 original size:16 final size:16
Alignment explanation
Indices: 702516--702546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
702506 TCTGTCCTTT
702516 TTTTTTTAATTTTTTC
1 TTTTTTTAATTTTTTC
*
702532 TTTTTTTCATTTTTT
1 TTTTTTTAATTTTTT
702547 TCTTCATTCT
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:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTAATTTTTTC
Found at i:702535 original size:17 final size:17
Alignment explanation
Indices: 702515--702550 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
702505 TTCTGTCCTT
*
702515 TTTTTTTTAATTTTTTC
1 TTTTTTTCAATTTTTTC
*
702532 TTTTTTTCATTTTTTTC
1 TTTTTTTCAATTTTTTC
702549 TT
1 TT
702551 CATTCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTCAATTTTTTC
Found at i:708328 original size:18 final size:18
Alignment explanation
Indices: 708307--708361 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
708297 TATATATTTA
708307 TATAAATTTTAATATAAT
1 TATAAATTTTAATATAAT
708325 TAT-AA-TTT-AT-T-A-
1 TATAAATTTTAATATAAT
* *
708337 TATAAATTTTAAAATATT
1 TATAAATTTTAATATAAT
708355 TATAAAT
1 TATAAAT
708362 GAACTTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
12 3 0.10
13 3 0.10
14 4 0.14
15 3 0.10
16 4 0.14
17 2 0.07
18 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAAATTTTAATATAAT
Found at i:709339 original size:36 final size:35
Alignment explanation
Indices: 709273--709340 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
709263 ATTATTTTTT
709273 ATATAATAAAAAATTTAATTTAATTATAAATATTA
1 ATATAATAAAAAATTTAATTTAATTATAAATATTA
*
709308 ATATAA-AATAAAATTTTAATATT-ATTTTAAATA
1 ATATAATAA-AAAA-TTTAAT-TTAATTATAAATA
709341 ATATATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 2 0.07
35 10 0.34
36 15 0.52
37 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATAATAAAAAATTTAATTTAATTATAAATATTA
Found at i:709344 original size:15 final size:16
Alignment explanation
Indices: 709324--709354 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
709314 AATAAAATTT
709324 TAATAT-TATTTTAAA
1 TAATATATATTTTAAA
709339 TAATATATATTTTAAA
1 TAATATATATTTTAAA
709355 ATGAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATATATTTTAAA
Found at i:709499 original size:185 final size:178
Alignment explanation
Indices: 709188--709543 Score: 482
Period size: 177 Copynumber: 2.0 Consensus size: 178
709178 TAAATAGTTT
* * * * *
709188 ATAAAACATAAAATTTCTCAATTATAAGAGAGGCTTGGCTTGGAGTAAAGTTTTTTTCAGTTCAA
1 ATAAAACATAAAATCTCTCAATTATAAGAGAGGCTTGACTTGAAATAAAGTTTTTTTCAATTCAA
* *
709253 TTTAATTTAAATTATTTTTTATATAATAAAAAATTTAATTTAATTATAAATATTAATATAAAATA
66 TTTAATTTAAATTATTATTTAAATAATAAAAAATTTAATTTAATTATAAATATTAATATAAAAT-
709318 AAATTTTAATATTATTTT-A-AATAATATATATTTTAAAATGAATTCAA
130 AAATTTTAATATTATTTTAATAATAATATATATTTTAAAATGAATTCAA
* * * *
709365 ATAAAATATAAAATCTCTTAATTATAAGAGATGCTTGACTTGAAATAAAATTTTTTAACTTCAAA
1 ATAAAACATAAAATCTCTCAATTATAAGAGAGGCTTGACTTGAAAT-AAAGTTTTT---TTC-AA
*
709430 TTTAATTTAATTTAAATTATTATTTAAATAATAGATAATAATTTAATTTAATTATAAATATTAAT
61 TTCAATTTAATTTAAATTATTATTTAAATAATA-A-AA-AATTTAATTTAATTATAAATATTAAT
**
709495 ATAAAATATTTTTTAATATTATTTTAAATAATAATATATATTTTAAAAT
123 ATAAAATAAATTTTAATATTATTTT-AATAATAATATATATTTTAAAAT
709544 CTACTCGACT
Statistics
Matches: 154, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
177 39 0.25
178 8 0.05
181 3 0.02
182 31 0.20
183 1 0.01
184 18 0.12
185 33 0.21
186 1 0.01
187 20 0.13
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (178 bp):
ATAAAACATAAAATCTCTCAATTATAAGAGAGGCTTGACTTGAAATAAAGTTTTTTTCAATTCAA
TTTAATTTAAATTATTATTTAAATAATAAAAAATTTAATTTAATTATAAATATTAATATAAAATA
AATTTTAATATTATTTTAATAATAATATATATTTTAAAATGAATTCAA
Found at i:709539 original size:30 final size:30
Alignment explanation
Indices: 709447--709540 Score: 77
Period size: 35 Copynumber: 3.0 Consensus size: 30
709437 TAATTTAAAT
*
709447 TATTA-TTTAAATAATAGATA-ATAATTTAA
1 TATTATTTTAAATAATA-ATATATATTTTAA
* *
709476 T-TTAATTATAAATATTAATATAAAATATTTTTTAA
1 TATT-ATTTTAAATAATAATAT---ATA--TTTTAA
709511 TATTATTTTAAATAATAATATATATTTTAA
1 TATTATTTTAAATAATAATATATATTTTAA
709541 AATCTACTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
28 2 0.04
29 5 0.10
30 15 0.29
32 3 0.06
33 3 0.06
35 21 0.41
36 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TATTATTTTAAATAATAATATATATTTTAA
Found at i:717967 original size:59 final size:58
Alignment explanation
Indices: 717876--717987 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 58
717866 CTCACCTTTT
* *
717876 ATTTTATTTTTAATGAGTTAGACCTCACACTTTGACTTTCAAATATAGAATCAATTTC
1 ATTTTATTTTCAATGAGTTAGACCTCACACTTTCACTTTCAAATATAGAATCAATTTC
*
717934 ATTTTATTTTCAATGGGGTTAGACCTCACACTTTCACTTTCAAATATAGAATCA
1 ATTTTATTTTCAAT-GAGTTAGACCTCACACTTTCACTTTCAAATATAGAATCA
717988 TCAATAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
58 13 0.26
59 37 0.74
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (58 bp):
ATTTTATTTTCAATGAGTTAGACCTCACACTTTCACTTTCAAATATAGAATCAATTTC
Found at i:718776 original size:10 final size:10
Alignment explanation
Indices: 718739--718777 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
718729 TAGTAGATAT
718739 AATATAAAAA
1 AATATAAAAA
*
718749 AATAAAAAAA
1 AATATAAAAA
718759 AATAATAAAAA
1 AAT-ATAAAAA
*
718770 TATATAAA
1 AATATAAA
718778 TATAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AATATAAAAA
Found at i:719773 original size:20 final size:20
Alignment explanation
Indices: 719748--719806 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
719738 TTTACCTATT
719748 AAAATTTTATATAAATATAA
1 AAAATTTTATATAAATATAA
*
719768 AAAATTTTAAATAAA-ATAA
1 AAAATTTTATATAAATATAA
*
719787 TAAA--TTATATAAATATAA
1 AAAATTTTATATAAATATAA
719805 AA
1 AA
719807 TAAATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 7 0.21
20 14 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTTTATATAAATATAA
Found at i:719800 original size:28 final size:27
Alignment explanation
Indices: 719755--719831 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
719745 ATTAAAATTT
**
719755 TATATAAATATAAAAAATTTTAAATAAA
1 TATATAAAT-TATTAAATTTTAAATAAA
* *
719783 -ATAATAAATTATATAAATATAAAATAAA
1 TAT-ATAAATTAT-TAAATTTTAAATAAA
719811 TATATAAATTATTAATATTTT
1 TATATAAATTATTAA-ATTTT
719832 TTTTTGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.18
28 30 0.77
29 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TATATAAATTATTAAATTTTAAATAAA
Found at i:719827 original size:19 final size:20
Alignment explanation
Indices: 719754--719819 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
719744 TATTAAAATT
719754 TTATATAAATATA-AA-AAA
1 TTATATAAATATATAATAAA
*
719772 TT-T-TAAATAAAATAATAAA
1 TTATATAAAT-ATATAATAAA
*
719791 TTATATAAATATAAAATAAA
1 TTATATAAATATATAATAAA
719811 -TATATAAAT
1 TTATATAAAT
719820 TATTAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 5 0.12
17 3 0.08
18 4 0.10
19 14 0.35
20 9 0.22
21 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTATATAAATATATAATAAA
Found at i:720375 original size:17 final size:17
Alignment explanation
Indices: 720349--720381 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
720339 CATTTCAATT
720349 TAAAAAATT-ATTTAAG
1 TAAAAAATTAATTTAAG
720365 TAAAAATATTAATTTAA
1 TAAAAA-ATTAATTTAA
720382 AAAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAAAATTAATTTAAG
Found at i:720383 original size:13 final size:13
Alignment explanation
Indices: 720345--720392 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
720335 TATTCATTTC
720345 AATTTAAAAAATT
1 AATTTAAAAAATT
*
720358 ATTTAAGTAAAAATATT
1 AATT---TAAAAA-ATT
720375 AATTTAAAAAATT
1 AATTTAAAAAATT
720388 AATTT
1 AATTT
720393 GAATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
16 6 0.21
17 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AATTTAAAAAATT
Found at i:720410 original size:31 final size:30
Alignment explanation
Indices: 720345--720406 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
720335 TATTCATTTC
*
720345 AATTTAAAAAATTATTTAAGTAAAAATATT
1 AATTTAAAAAATTATTTAAGTAAAAATATA
720375 AATTTAAAAAATTAATTTGAA-TAAAAA-ATA
1 AATTTAAAAAATT-ATTT-AAGTAAAAATATA
720405 AA
1 AA
720407 ATTTCTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 17 0.59
31 10 0.34
32 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AATTTAAAAAATTATTTAAGTAAAAATATA
Found at i:721115 original size:28 final size:26
Alignment explanation
Indices: 721068--721121 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
721058 ATATTTGATC
*
721068 TATTAATAATATAAAAATTTATTATTT
1 TATTAATAAAATAAAAATTTA-TATTT
721095 TATTAA-AAAATAAAATTATTTATATTT
1 TATTAATAAAATAAAA--ATTTATATTT
721122 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.33
27 11 0.46
28 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTAATAAAATAAAAATTTATATTT
Found at i:721366 original size:16 final size:15
Alignment explanation
Indices: 721319--721366 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
721309 TAAATATTAA
721319 AATTATT-ATTTTAT
1 AATTATTAATTTTAT
721333 AATT-TTAATTTT-T
1 AATTATTAATTTTAT
*
721346 TATTATTAATATTTAT
1 AATTATTAAT-TTTAT
721362 AATTA
1 AATTA
721367 ATTATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 6 0.21
14 14 0.50
15 3 0.11
16 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTATTAATTTTAT
Found at i:722003 original size:3 final size:3
Alignment explanation
Indices: 721995--722029 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
721985 GGCCAAACAC
* *
721995 AAG AAG AAG AAG AAG AAG AAC AAT AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
722030 CAAAAGGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:722022 original size:15 final size:15
Alignment explanation
Indices: 722004--722032 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
721994 CAAGAAGAAG
722004 AAGAAGAAGAACAAT
1 AAGAAGAAGAACAAT
722019 AAGAAGAAGAACAA
1 AAGAAGAAGAACAA
722033 AAGGATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.21, T:0.03
Consensus pattern (15 bp):
AAGAAGAAGAACAAT
Found at i:722691 original size:2 final size:2
Alignment explanation
Indices: 722684--722710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
722674 ATTGGAAAGC
722684 AT 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 AT A
722711 CATGTTAGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:724707 original size:24 final size:24
Alignment explanation
Indices: 724649--724711 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
724639 TTAAAAAATT
*
724649 TAAATATTAAATTTATAATTTTAA
1 TAAATATTAAATTTATAATTCTAA
*
724673 T-AATAAATAAATTT-TAATTCTAA
1 TAAAT-ATTAAATTTATAATTCTAA
724696 TAAATATGTAAATTTA
1 TAAATAT-TAAATTTA
724712 AAGAATGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAATATTAAATTTATAATTCTAA
Found at i:724773 original size:20 final size:20
Alignment explanation
Indices: 724732--724773 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
724722 GATTTAAATC
*
724732 TTATCAAATATAATAACTTT
1 TTATCAAATATAATAACATT
*
724752 TTAT-AAATATATATAAGATT
1 TTATCAAATATA-ATAACATT
724772 TT
1 TT
724774 TTTTGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATCAAATATAATAACATT
Found at i:725299 original size:11 final size:11
Alignment explanation
Indices: 725281--725310 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
725271 TAAATTAAAA
725281 TTTT-ATTTAT
1 TTTTAATTTAT
725291 TTTTAATTTAT
1 TTTTAATTTAT
725302 TTTTAATTT
1 TTTTAATTT
725311 TTTATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTAATTTAT
Found at i:726515 original size:16 final size:16
Alignment explanation
Indices: 726504--726537 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
726494 TAATTTTATT
726504 ATTTTTA-TATTTCTAA
1 ATTTTTATTATTT-TAA
726520 ATTTTTATTATTTTAA
1 ATTTTTATTATTTTAA
726536 AT
1 AT
726538 ATATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTATTATTTTAA
Found at i:727364 original size:29 final size:32
Alignment explanation
Indices: 727309--727370 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
727299 ATTATTTAAA
727309 AAATAAAATATTTGAATATTATATAATTAAATTT
1 AAATAAAATATTT--ATATTATATAATTAAATTT
727343 AAATAAAATATTT-T-TTAT-TAATTAAATT
1 AAATAAAATATTTATATTATATAATTAAATT
727371 ATCATCTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.36
30 4 0.14
31 1 0.04
34 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
AAATAAAATATTTATATTATATAATTAAATTT
Found at i:727847 original size:26 final size:25
Alignment explanation
Indices: 727791--727846 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
727781 ATAAAATGTC
*
727791 AAAATTTGTATAATATAAATATTAAT
1 AAAATTTATATAATATAAATATT-AT
*
727817 AAAATTTATATAAATATATAATATTTT
1 AAAATTTATAT-AATATA-AATATTAT
727844 AAA
1 AAA
727847 TGTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 10 0.38
28 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATTTATATAATATAAATATTAT
Found at i:729084 original size:2 final size:2
Alignment explanation
Indices: 729073--729110 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
729063 AATGAAAAGT
729073 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
729111 CGTGGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:730069 original size:3 final size:3
Alignment explanation
Indices: 730063--730100 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
730053 GAAGAAAAGT
730063 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
730101 TGTTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:730579 original size:14 final size:14
Alignment explanation
Indices: 730552--730584 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
730542 AAACGCATGT
730552 AATTTTTATATTTC
1 AATTTTTATATTTC
730566 AATTTCTTAT-TTTC
1 AATTT-TTATATTTC
730580 AATTT
1 AATTT
730585 GTAATGCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTTATATTTC
Found at i:731675 original size:34 final size:34
Alignment explanation
Indices: 731637--731821 Score: 141
Period size: 34 Copynumber: 5.6 Consensus size: 34
731627 TAAATCACCT
*
731637 ATTTAATCAACAATGACAAACTATCAAATTTCTC
1 ATTTAATCAACAATGACAAACTATCAAATCTCTC
* * *
731671 ATTTAGT---CAA-G-CAAACCATCAAATCAC-C
1 ATTTAATCAACAATGACAAACTATCAAATCTCTC
* * *
731699 TTTTAATTAATAAT-AGCAAACTATCAAATCTCTC
1 ATTTAATCAACAATGA-CAAACTATCAAATCTCTC
* * * * * * *
731733 ATTTAGTCAACAATAATAAACCACCAAATCACCC
1 ATTTAATCAACAATGACAAACTATCAAATCTCTC
* *
731767 ATTAAATCAACAATGACAAACTATTAAATCTCTC
1 ATTTAATCAACAATGACAAACTATCAAATCTCTC
* * *
731801 GTTTAATCAATAATAACAAAC
1 ATTTAATCAACAATGACAAAC
731822 CACCAAACCA
Statistics
Matches: 112, Mismatches: 31, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
28 6 0.05
29 13 0.12
30 1 0.01
31 5 0.04
33 14 0.12
34 72 0.64
35 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (34 bp):
ATTTAATCAACAATGACAAACTATCAAATCTCTC
Done.