Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold147
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: 880509
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.26
Warning! 187686 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:429609 original size:15 final size:15
Alignment explanation
Indices: 429568--429612 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
429558 ACTTAACATA
429568 TTTTAATATTTATA-
1 TTTTAATATTTATAT
*
429582 TTATAATATTTTATAT
1 TTTTAATA-TTTATAT
*
429598 TTTTATTATTTATAT
1 TTTTAATATTTATAT
429613 GATATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 13 0.50
16 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATATTTATAT
Found at i:429642 original size:21 final size:22
Alignment explanation
Indices: 429614--429667 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
429604 TATTTATATG
429614 ATAT-AAATAATATAATATA-A
1 ATATAAAATAATATAATATACA
* *
429634 ATATAAAATAATTTATTATACA
1 ATATAAAATAATATAATATACA
429656 ATA-AAAA-AATAT
1 ATATAAAATAATAT
429668 TAAATTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 8 0.28
21 17 0.59
22 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAAAATAATATAATATACA
Found at i:429702 original size:20 final size:20
Alignment explanation
Indices: 429662--429703 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
429652 TACAATAAAA
*
429662 AAATATTAAATTTAAGCTTC
1 AAATATTAAATTAAAGCTTC
429682 AAATATTAAAATTAAAG-TTC
1 AAATATT-AAATTAAAGCTTC
429702 AA
1 AA
429704 TTCATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (20 bp):
AAATATTAAATTAAAGCTTC
Found at i:430714 original size:2 final size:2
Alignment explanation
Indices: 430707--430734 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
430697 ATTGAATTTA
430707 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
430735 CTGGCACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435374 original size:10 final size:10
Alignment explanation
Indices: 435359--435399 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
435349 TACGAGCATA
435359 TTTAAATTTT
1 TTTAAATTTT
435369 TTTAAATTTT
1 TTTAAATTTT
* *
435379 TTT--ATGTA
1 TTTAAATTTT
435387 TTTAAATTTT
1 TTTAAATTTT
435397 TTT
1 TTT
435400 TCGAAATATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 6 0.24
10 19 0.76
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTAAATTTT
Found at i:438026 original size:15 final size:13
Alignment explanation
Indices: 437992--438022 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
437982 ATGTTTAGCC
437992 TATATTTATATTA
1 TATATTTATATTA
*
438005 TATATTTATATTT
1 TATATTTATATTA
438018 TATAT
1 TATAT
438023 ATTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATATTTATATTA
Found at i:438094 original size:18 final size:18
Alignment explanation
Indices: 438055--438102 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
438045 TATAATTTTT
*
438055 TTAAAT-TTTTT-AAATA
1 TTAAATATTTTTAAAAAA
438071 TATAAATATTTTTAAAAAA
1 T-TAAATATTTTTAAAAAA
*
438090 TTAAATATATTTA
1 TTAAATATTTTTA
438103 TATTTGACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 16 0.59
19 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAATATTTTTAAAAAA
Found at i:438504 original size:6 final size:6
Alignment explanation
Indices: 438453--438503 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
438443 AAAATCTAAA
* * *
438453 TATATT TATA-T TAAATA TATATT TATATT TATATT TATATT TATACT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
438500 TATA
1 TATA
438504 CCCAATTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:441435 original size:17 final size:16
Alignment explanation
Indices: 441386--441437 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
441376 TTACCCTTAC
441386 ATTATAAAATAATATTTT
1 ATTATAAAAT-ATA-TTT
*
441404 AATTTTAAAA-ATATTT
1 -ATTATAAAATATATTT
441420 ATTATAAAATATTATTT
1 ATTATAAAATA-TATTT
441437 A
1 A
441438 AAATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 8 0.28
16 4 0.14
17 9 0.31
19 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAAAATATATTT
Found at i:441441 original size:12 final size:13
Alignment explanation
Indices: 441411--441448 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
441401 TTTAATTTTA
441411 AAAATATTTATTAT
1 AAAATA-TTATTAT
441425 AAAATATTATT-T
1 AAAATATTATTAT
*
441437 AAAATAATATTA
1 AAAATATTATTA
441449 AATTCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 5 0.23
14 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATATTATTAT
Found at i:442802 original size:29 final size:28
Alignment explanation
Indices: 442761--442876 Score: 73
Period size: 29 Copynumber: 4.2 Consensus size: 28
442751 TATGATATAT
*
442761 TATAAAATAATTAATTATAATATAAATA
1 TATAAAATTATTAATTATAATATAAATA
** * *
442789 TATAAAATTTATTAAAAAT-TTATTAATA
1 TATAAAA-TTATTAATTATAATATAAATA
442817 TATTAAAATTTATATAAATTA-AATAT-AATA
1 TA-TAAAA-TTAT-T-AATTATAATATAAATA
* * *
442847 TTTTAAA-TA-TAATTATAATA-AAAAA
1 TATAAAATTATTAATTATAATATAAATA
442872 TATAA
1 TATAA
442877 TTATAAAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
24 5 0.07
25 11 0.16
27 2 0.03
28 16 0.24
29 22 0.32
30 6 0.09
31 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATAAAATTATTAATTATAATATAAATA
Found at i:442839 original size:16 final size:18
Alignment explanation
Indices: 442803--442839 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
442793 AAATTTATTA
*
442803 AAAATTTATTAATATATT
1 AAAATTTATTAATAAATT
442821 AAAATTTA-T-ATAAATT
1 AAAATTTATTAATAAATT
442837 AAA
1 AAA
442840 TATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTATTAATAAATT
Found at i:442847 original size:28 final size:29
Alignment explanation
Indices: 442773--442848 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
442763 TAAAATAATT
442773 AATTATAATATAAATATATAAAATTTATTAAA
1 AATTA-AATAT-AATAT-TAAAATTTATTAAA
* * *
442805 AATTTATTA-ATATATTAAAATTTA-TATA
1 AATTAAATATA-ATATTAAAATTTATTAAA
442833 AATTAAATATAATATT
1 AATTAAATATAATATT
442849 TTAAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
28 15 0.41
29 11 0.30
30 4 0.11
31 3 0.08
32 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTAAATATAATATTAAAATTTATTAAA
Found at i:442853 original size:30 final size:31
Alignment explanation
Indices: 442773--442853 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
442763 TAAAATAATT
*
442773 AATTATAATATAA-ATATATAAAATTTATTAAA
1 AATTA-AATATAATAT-TTTAAAATTTATTAAA
* * *
442805 AATT-TAT-TAATATATTAAAATTTA-TATA
1 AATTAAATATAATATTTTAAAATTTATTAAA
442833 AATTAAATATAATATTTTAAA
1 AATTAAATATAATATTTTAAA
442854 TATAATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.17
29 14 0.35
30 15 0.38
32 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AATTAAATATAATATTTTAAAATTTATTAAA
Found at i:443040 original size:15 final size:13
Alignment explanation
Indices: 443021--443054 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
443011 ATTTATTTAT
443021 TTTAAAATTATAAA
1 TTTAAAATT-TAAA
443035 TATTAAAATTTAAA
1 T-TTAAAATTTAAA
443049 TTTAAA
1 TTTAAA
443055 TACTTCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 6 0.32
15 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:445358 original size:23 final size:23
Alignment explanation
Indices: 445320--445363 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
445310 CTTGGTGATT
445320 AATTATTATAATAATAAATATAA
1 AATTATTATAATAATAAATATAA
445343 AATTAGTTATAA-AATAAATAT
1 AATTA-TTATAATAATAAATAT
445364 TGGGATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTATTATAATAATAAATATAA
Found at i:446573 original size:33 final size:32
Alignment explanation
Indices: 446535--446617 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
446525 AATAATAAAA
** * *
446535 ATATAATATCAATGTATAAACGTTTTAAAATTT
1 ATATAATAT-AAAATATAAACATATTAAAATTT
*
446568 ATATAATATAAAATATTAACATATTAAAATTT
1 ATATAATATAAAATATAAACATATTAAAATTT
*
446600 ATATAAATATAGAATATA
1 ATAT-AATATAAAATATA
446618 TTAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (32 bp):
ATATAATATAAAATATAAACATATTAAAATTT
Found at i:446642 original size:27 final size:28
Alignment explanation
Indices: 446588--446656 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
446578 AAATATTAAC
446588 ATATTAAAATTT-A-TATAAATATAGAAT
1 ATATT-AAATTTAATTATAAATATAGAAT
446615 ATATTAAATTTAATTATAACATA-A-AAT
1 ATATTAAATTTAATTATAA-ATATAGAAT
*
446642 ATAATTAAATATAAT
1 AT-ATTAAATTTAAT
446657 GAAAATTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 6 0.16
27 11 0.30
28 17 0.46
29 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATTAAATTTAATTATAAATATAGAAT
Found at i:448393 original size:2 final size:2
Alignment explanation
Indices: 448386--448428 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
448376 TTGTAAAATA
448386 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
448428 A
1 A
448429 ACTCTTTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:449550 original size:27 final size:27
Alignment explanation
Indices: 449482--449577 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 27
449472 AGGACAGAGG
* * * *
449482 TGGAGGTGGTGGTGACCTTCATGGCGA
1 TGGAGGTGGAGGTGGCCTCCTTGGCGA
* * *
449509 TCGAGGTGGTGGTGGCCTCCTTGGGGA
1 TGGAGGTGGAGGTGGCCTCCTTGGCGA
* * *
449536 TGGAGGTGGAGGTGGTCGCGTTGGCGA
1 TGGAGGTGGAGGTGGCCTCCTTGGCGA
449563 TGGAGGTGGAGGTGG
1 TGGAGGTGGAGGTGG
449578 AGGTGGGGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.11, C:0.12, G:0.52, T:0.24
Consensus pattern (27 bp):
TGGAGGTGGAGGTGGCCTCCTTGGCGA
Found at i:450860 original size:8 final size:8
Alignment explanation
Indices: 450849--450928 Score: 53
Period size: 8 Copynumber: 9.9 Consensus size: 8
450839 AAATTTAATA
450849 ATTTATAT
1 ATTTATAT
450857 ATTTATATCGT
1 ATTTATA---T
450868 ATTTATAT
1 ATTTATAT
450876 ATTTTTATAT
1 A--TTTATAT
450886 ATTT-T-T
1 ATTTATAT
*
450892 A-TTAGAT
1 ATTTATAT
450899 -TTTATA-
1 ATTTATAT
450905 ATTTATAT
1 ATTTATAT
*
450913 ATTTTTAT
1 ATTTATAT
450921 ACTTTATA
1 A-TTTATA
450929 ATTATATTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
7 12 0.21
8 20 0.35
9 5 0.09
10 8 0.14
11 8 0.14
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:450884 original size:10 final size:10
Alignment explanation
Indices: 450869--450921 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
450859 TTATATCGTA
450869 TTTATATATT
1 TTTATATATT
450879 TTTATATATT
1 TTTATATATT
*
450889 TTTAT-TAGAT
1 TTTATATA-TT
450899 TTTATA-A--
1 TTTATATATT
450906 TTTATATATT
1 TTTATATATT
450916 TTTATA
1 TTTATA
450922 CTTTATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 2 0.05
10 28 0.76
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTATATATT
Found at i:450900 original size:29 final size:28
Alignment explanation
Indices: 450841--450920 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 28
450831 ATTTAATTAA
* * *
450841 ATTTAATAATTTATATATTTATA-TCGT
1 ATTTTATAATTTATATATTTTTATTAGT
*
450868 ATTTATATATTTTTATATATTTTTATTAG-
1 ATTT-TATA-ATTTATATATTTTTATTAGT
450897 ATTTTATAATTTATATATTTTTAT
1 ATTTTATAATTTATATATTTTTAT
450921 ACTTTATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 19 0.42
28 7 0.16
29 17 0.38
30 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (28 bp):
ATTTTATAATTTATATATTTTTATTAGT
Found at i:451311 original size:14 final size:16
Alignment explanation
Indices: 451294--451325 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
451284 TCATTTTTTT
451294 AATTT-ATT-TTTAAA
1 AATTTAATTATTTAAA
451308 AATTTAATTATTTAAA
1 AATTTAATTATTTAAA
451324 AA
1 AA
451326 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTAATTATTTAAA
Found at i:451377 original size:21 final size:20
Alignment explanation
Indices: 451353--451422 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
451343 ATTATATAAT
451353 AAATAAATTTATATAATTATA
1 AAAT-AATTTATATAATTATA
*
451374 AAATAATTAAT-TAAATTATTA
1 AAATAATTTATAT-AATTA-TA
*
451395 AAAT-ATTTAAATAGATATATA
1 AAATAATTTATATA-AT-TATA
451416 AAATAAT
1 AAATAAT
451423 ATGTATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
19 1 0.03
20 16 0.40
21 19 0.47
22 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AAATAATTTATATAATTATA
Found at i:452101 original size:13 final size:13
Alignment explanation
Indices: 452085--452122 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
452075 TAAAATTTTG
452085 AATTTACTTTATC
1 AATTTACTTTATC
452098 AATTTACTTTATC
1 AATTTACTTTATC
452111 AATTTACTTTAT
1 AATTTACTTTAT
452123 TTTTTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTTACTTTATC
Found at i:452809 original size:4 final size:4
Alignment explanation
Indices: 452787--452822 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
452777 CTCTTTCGTA
*
452787 AAAT AAAGT AAAA AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAA
452823 CTTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:453813 original size:24 final size:24
Alignment explanation
Indices: 453782--453829 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
453772 TTTTATTTAT
453782 AAAAATTTATTAATA-TTAATATG
1 AAAAATTTATTAATAGTTAATATG
*
453805 AAAATATTTTTTAATAGTTTAATAT
1 AAAA-ATTTATTAATAG-TTAATAT
453830 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
26 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAAAATTTATTAATAGTTAATATG
Found at i:454149 original size:3 final size:3
Alignment explanation
Indices: 454141--454171 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
454131 TTTATATAAT
454141 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
454172 GATGTTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:454343 original size:39 final size:39
Alignment explanation
Indices: 454300--454400 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 39
454290 AGGTCGTAGC
* *
454300 GGCCTCCTTGGGGATGGAGGTGGAGGTGGAGGTGGTGGT
1 GGCCTCTTTGGCGATGGAGGTGGAGGTGGAGGTGGTGGT
454339 GGCCTCTTTGGCGATGGA---GGA---GGAGGTGGTGGT
1 GGCCTCTTTGGCGATGGAGGTGGAGGTGGAGGTGGTGGT
454372 GGCCTCTTTGGCGATGGAGGTGGAGGTGG
1 GGCCTCTTTGGCGATGGAGGTGGAGGTGG
454401 TGGCGGACTC
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
33 30 0.56
36 6 0.11
39 18 0.33
ACGTcount: A:0.11, C:0.12, G:0.53, T:0.24
Consensus pattern (39 bp):
GGCCTCTTTGGCGATGGAGGTGGAGGTGGAGGTGGTGGT
Found at i:454424 original size:60 final size:60
Alignment explanation
Indices: 454360--455165 Score: 1299
Period size: 60 Copynumber: 13.2 Consensus size: 60
454350 CGATGGAGGA
*
454360 GGAGGTGGTGGTGGCCTCTTTGGCGATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
**
454420 GGAGGTGGTGGTGGCCTCTTTGGGGATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
**
454480 GGAGGTGGTGGTGGCCTCTTTGGGGATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
* *
454540 GGAGGTGGTGGTGACGTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
* *
454600 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGATGGAGGTGGTGGCGGACTCCTTGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
454660 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
* *
454720 GGAGGTGGTGGTGGCCTCTTTGTCAATGGGGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
*
454780 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGATTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
454840 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
*
454900 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGATTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
*
454960 GGAGGTGGTGGTGGCCTCTTTGGGAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
1 GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
* * *
455020 GGAGGTGGTGGTGGCCTCTTTAGG-GATGGAGGTGGAGGTGGTGGTGGACTCCTTGGGGGTGGAG
1 GGAGGTGGTGGTGGCCTCTTT-GGCAATGGAGGTGGAGGTGGTGGCGGACTCC-T---CG-GG-G
455084 GT
59 GT
* * * *
455086 GGAGGTGGTGGTGGACTCCTTGGGGATGGAGGTGGAGGTGGAGGTGGTGGCCGACTCCTCGGGGG
1 GGAGGTGGTGGTGGCCT-CTTTGGCA---A--TGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGG
455151 T
60 T
455152 GGAGGTGGTGGTGG
1 GGAGGTGGTGGTGG
455166 AGGTCTACGG
Statistics
Matches: 703, Mismatches: 29, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
60 627 0.89
61 3 0.00
64 1 0.00
65 2 0.00
66 38 0.05
67 5 0.01
68 1 0.00
70 1 0.00
71 1 0.00
72 24 0.03
ACGTcount: A:0.10, C:0.13, G:0.53, T:0.24
Consensus pattern (60 bp):
GGAGGTGGTGGTGGCCTCTTTGGCAATGGAGGTGGAGGTGGTGGCGGACTCCTCGGGGGT
Found at i:455142 original size:39 final size:37
Alignment explanation
Indices: 455046--455169 Score: 157
Period size: 39 Copynumber: 3.4 Consensus size: 37
455036 TCTTTAGGGA
455046 TGGAGGTGGAGGTGGTGGTGGACTCCTTGGGGGTGGAGG
1 TGGAGGTGGAGGTGGT-G-GGACTCCTTGGGGGTGGAGG
*
455085 TGGAGGT---GGTGGT-GGACTCCTTGGGGATGGAGG
1 TGGAGGTGGAGGTGGTGGGACTCCTTGGGGGTGGAGG
*
455118 TGGAGGTGGAGGTGGTGGCCGACTCCTCGGGGGTGGAGG
1 TGGAGGTGGAGGTGGTGG--GACTCCTTGGGGGTGGAGG
*
455157 TGGTGGTGGAGGT
1 TGGAGGTGGAGGT
455170 CTACGGAGAC
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
33 26 0.35
36 12 0.16
37 1 0.01
39 36 0.48
ACGTcount: A:0.10, C:0.10, G:0.57, T:0.23
Consensus pattern (37 bp):
TGGAGGTGGAGGTGGTGGGACTCCTTGGGGGTGGAGG
Found at i:456400 original size:11 final size:10
Alignment explanation
Indices: 456379--456439 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
456369 TTTAATAATT
456379 TATAAATTTA
1 TATAAATTTA
456389 TATAATATTTA
1 TATAA-ATTTA
*
456400 TAT-ATTTTA
1 TATAAATTTA
**
456409 TATATTTTTA
1 TATAAATTTA
456419 T-TAAATTT-
1 TATAAATTTA
456427 TA-AAATTTA
1 TATAAATTTA
456436 TATA
1 TATA
456440 TTTATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.17
9 14 0.33
10 13 0.31
11 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATAAATTTA
Found at i:456408 original size:9 final size:9
Alignment explanation
Indices: 456385--456452 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
456375 AATTTATAAA
456385 TTTATATAAT
1 TTTATAT-AT
456395 ATTTATATAT
1 -TTTATATAT
456405 TTTATATATT
1 TTTATATA-T
*
456415 TTTATTAAAT
1 TTTA-TATAT
*
456425 TTTA-A-AA
1 TTTATATAT
456432 TTTATATA-
1 TTTATATAT
456440 TTTATATTAT
1 TTTATA-TAT
456450 TTT
1 TTT
456453 CATGTTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
7 5 0.10
8 8 0.16
9 11 0.22
10 15 0.31
11 10 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTATATAT
Found at i:456408 original size:20 final size:20
Alignment explanation
Indices: 456371--456412 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
456361 CGATTAAATT
456371 TAATAATTTATAAATTTATA
1 TAATAATTTATAAATTTATA
*
456391 TAAT-ATTTATATATTTTATA
1 TAATAATTTATA-AATTTATA
456411 TA
1 TA
456413 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATAATTTATAAATTTATA
Found at i:456437 original size:36 final size:38
Alignment explanation
Indices: 456377--456452 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 38
456367 AATTTAATAA
456377 TTTATAAATTTATATAATATTTATATATTT-TATATATT
1 TTTATAAATTTATATAATATTTATATATTTATAT-TATT
456415 TTTATTAAATTT-TA-AA-ATTTATATATTTATATTATT
1 TTTA-TAAATTTATATAATATTTATATATTTATATTATT
456451 TT
1 TT
456453 CATGTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
36 18 0.50
37 5 0.14
38 6 0.17
39 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTATAAATTTATATAATATTTATATATTTATATTATT
Found at i:456447 original size:27 final size:27
Alignment explanation
Indices: 456363--456448 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
456353 CAATAGTTCG
*
456363 ATTAAA-TTTAATAATTTATAAATTTAT
1 ATTAAATTTTAA-AATTTATATATTTAT
* * *
456390 A-TAATATTTATATATTTTATATATTTTT
1 ATTAA-ATTT-TAAAATTTATATATTTAT
456418 ATTAAATTTTAAAATTTATATATTTAT
1 ATTAAATTTTAAAATTTATATATTTAT
456445 ATTA
1 ATTA
456449 TTTTCATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 3 0.06
27 21 0.44
28 19 0.40
29 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTAAATTTTAAAATTTATATATTTAT
Found at i:456489 original size:22 final size:21
Alignment explanation
Indices: 456457--456517 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
456447 TATTTTCATG
* *
456457 TTTTATAATTATATTTAAAGTA
1 TTTTATTATTAAATTTAAA-TA
*
456479 TTTTATTATTAAATTTTAATA
1 TTTTATTATTAAATTTAAATA
*
456500 TTTGTATTACATAAATTT
1 TTT-TATTA-TTAAATTT
456518 TTTATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 5 0.15
22 21 0.64
23 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTATTATTAAATTTAAATA
Found at i:458458 original size:2 final size:2
Alignment explanation
Indices: 458451--458481 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
458441 ATACCTAACA
458451 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 A
458482 ACACAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:460276 original size:33 final size:33
Alignment explanation
Indices: 460239--460323 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
460229 CATGGCGATC
460239 GAGGTGGTGGCGACCTCCTTGGGGATGAAGGTG
1 GAGGTGGTGGCGACCTCCTTGGGGATGAAGGTG
* * *
460272 GAGGTGGTGGTGGCCTCCTTGGGGATGGAGGTG
1 GAGGTGGTGGCGACCTCCTTGGGGATGAAGGTG
460305 GAGGTGGTGGCAGA-CTCCT
1 GAGGTGGTGGC-GACCTCCT
460324 CAAGGGTGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.15, G:0.49, T:0.22
Consensus pattern (33 bp):
GAGGTGGTGGCGACCTCCTTGGGGATGAAGGTG
Found at i:460301 original size:27 final size:27
Alignment explanation
Indices: 460210--460310 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 27
460200 AGGGTAGAGG
* * *
460210 TGGAGGTGGTGGTGACCTTCATGGCGA
1 TGGAGGTGGTGGTGACCTCCTTGGGGA
* *
460237 TCGAGGTGGTGGCGACCTCCTTGGGGATGAA
1 TGGAGGTGGTGGTGACCTCCTT-GGG--G-A
*
460268 GGTGGAGGTGGTGGTGGCCTCCTTGGGGA
1 --TGGAGGTGGTGGTGACCTCCTTGGGGA
*
460297 TGGAGGTGGAGGTG
1 TGGAGGTGGTGGTG
460311 GTGGCAGACT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
27 31 0.53
28 2 0.03
29 1 0.02
30 2 0.03
31 1 0.02
32 3 0.05
33 19 0.32
ACGTcount: A:0.13, C:0.14, G:0.50, T:0.24
Consensus pattern (27 bp):
TGGAGGTGGTGGTGACCTCCTTGGGGA
Found at i:460403 original size:33 final size:32
Alignment explanation
Indices: 460239--460405 Score: 106
Period size: 33 Copynumber: 5.1 Consensus size: 32
460229 CATGGCGATC
* *
460239 GAGGTGGTGGC-GACCTCCTTGGGGATGAAGGTG
1 GAGGTGGTGGCAGA-CTCCTCGGGG-TGGAGGTG
** * *
460272 GAGGTGGTGGTGGCCTCCTTGGGGATGGAGGTG
1 GAGGTGGTGGCAGACTCCTCGGGG-TGGAGGTG
*
460305 GAGGTGGTGGCAGACTCCTCAAGGGTGGAGGTG
1 GAGGTGGTGGCAGACTCCTC-GGGGTGGAGGTG
* ** ***** *
460338 GAGATGG-GGTTGGGGGGGTGGGGGT-GAGGGTG
1 GAGGTGGTGG-CAGACTCCTCGGGGTGGA-GGTG
460370 GAGGTGGTGGCAGACTCCTCGAGGGTGGAGGTG
1 GAGGTGGTGGCAGACTCCTCG-GGGTGGAGGTG
460403 GAG
1 GAG
460406 ATGGAGGTGG
Statistics
Matches: 100, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
31 2 0.02
32 19 0.19
33 73 0.73
34 6 0.06
ACGTcount: A:0.14, C:0.11, G:0.55, T:0.20
Consensus pattern (32 bp):
GAGGTGGTGGCAGACTCCTCGGGGTGGAGGTG
Found at i:460404 original size:6 final size:6
Alignment explanation
Indices: 460393--460463 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
460383 ACTCCTCGAG
* * * * * *
460393 GGTGGA GGTGGA GATGGA GGTGGG GGTGGA GGCGAA GATGGA GGTGGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
*
460441 GGTGGG GGT-GA GGGTGGA GGTGG
1 GGTGGA GGTGGA -GGTGGA GGTGG
460464 TGGCGGACTC
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 1 0.02
6 48 0.94
7 2 0.04
ACGTcount: A:0.15, C:0.01, G:0.68, T:0.15
Consensus pattern (6 bp):
GGTGGA
Found at i:460419 original size:24 final size:24
Alignment explanation
Indices: 460392--460463 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
460382 GACTCCTCGA
460392 GGGTGGAGGTGGAGATGGAGGTGG
1 GGGTGGAGGTGGAGATGGAGGTGG
* *
460416 GGGTGGAGGCGAAGATGGAGGTGG
1 GGGTGGAGGTGGAGATGGAGGTGG
* *
460440 GGGTGGGGGT-GAGGGTGGAGGTGG
1 GGGTGGAGGTGGA-GATGGAGGTGG
460464 TGGCGGACTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.15, C:0.01, G:0.68, T:0.15
Consensus pattern (24 bp):
GGGTGGAGGTGGAGATGGAGGTGG
Found at i:460450 original size:12 final size:12
Alignment explanation
Indices: 460392--460463 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
460382 GACTCCTCGA
460392 GGGTGGAGGTGG
1 GGGTGGAGGTGG
* *
460404 AGATGGAGGTGG
1 GGGTGGAGGTGG
* *
460416 GGGTGGAGGCGA
1 GGGTGGAGGTGG
* *
460428 AGATGGAGGTGG
1 GGGTGGAGGTGG
* *
460440 GGGTGGGGGTGA
1 GGGTGGAGGTGG
460452 GGGTGGAGGTGG
1 GGGTGGAGGTGG
460464 TGGCGGACTC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.15, C:0.01, G:0.68, T:0.15
Consensus pattern (12 bp):
GGGTGGAGGTGG
Found at i:460653 original size:15 final size:18
Alignment explanation
Indices: 460625--460661 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
460615 TTTTTATATT
460625 TAAATATATGTTAAAA-A
1 TAAATATATGTTAAAATA
460642 TAAATAT-T-TTAAAATA
1 TAAATATATGTTAAAATA
460658 TAAA
1 TAAA
460662 AAAATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATATATGTTAAAATA
Found at i:460730 original size:91 final size:93
Alignment explanation
Indices: 460623--460806 Score: 259
Period size: 92 Copynumber: 2.0 Consensus size: 93
460613 TATTTTTATA
* *
460623 TTTAAATATATGTTAAAAATAAAT-ATTTTAAAATATAA-AAAAAT-TGATAATTGTTAGTGAAA
1 TTTAAATATATGTTAAAAATAAATAATTTTAAAA-A-AATAAAAATACGATAATTATTAGTGAAA
* *
460685 TAAATTGTTTTC-GCTAGCTGGATATTGTC
64 TAAATTGTATGCAGCTAGCTGGATATTGTC
* *
460714 TTTAAATATATGTTAAAAATAAATAATTTTAAAAAAATAAAAATACGATAATTATTAGTGGAGTA
1 TTTAAATATATGTTAAAAATAAATAATTTTAAAAAAATAAAAATACGATAATTATTAGTGAAATA
*
460779 ATTTGTATGCAGCTAGCTGGATATTGTC
66 AATTGTATGCAGCTAGCTGGATATTGTC
460807 CTTATTGCTT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
90 2 0.02
91 31 0.38
92 32 0.39
93 17 0.21
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (93 bp):
TTTAAATATATGTTAAAAATAAATAATTTTAAAAAAATAAAAATACGATAATTATTAGTGAAATA
AATTGTATGCAGCTAGCTGGATATTGTC
Found at i:460747 original size:16 final size:17
Alignment explanation
Indices: 460716--460748 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
460706 ATATTGTCTT
460716 TAAATATATGTTAAAAA
1 TAAATATATGTTAAAAA
*
460733 TAAATA-ATTTTAAAAA
1 TAAATATATGTTAAAAA
460749 AATAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATATATGTTAAAAA
Found at i:461071 original size:19 final size:19
Alignment explanation
Indices: 461042--461101 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
461032 CGATTAAATT
461042 TAATAATTTATAAATTTATA
1 TAAT-ATTTATAAATTTATA
* *
461062 TAATATTTATATATTTTTA
1 TAATATTTATAAATTTATA
461081 TTAA-ATTT-TAAAATTTATA
1 -TAATATTTAT-AAATTTATA
461100 TA
1 TA
461102 TTTGTATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.09
19 24 0.71
20 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTTATAAATTTATA
Found at i:461087 original size:46 final size:46
Alignment explanation
Indices: 461034--461124 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
461024 CAATAGTTCG
461034 ATTAAA-TTTAATAATTTATAAATTTATATAATATTTATATATTTTT
1 ATTAAATTTTAA-AATTTATAAATTTATATAATATTTATATATTTTT
* * * *
461080 ATTAAATTTTAAAATTTATATATTTGTATTATATTTATTTATTTT
1 ATTAAATTTTAAAATTTATAAATTTATATAATATTTATATATTTT
461125 CATGTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 35 0.88
47 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (46 bp):
ATTAAATTTTAAAATTTATAAATTTATATAATATTTATATATTTTT
Found at i:461123 original size:27 final size:27
Alignment explanation
Indices: 461062--461115 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
461052 TAAATTTATA
*
461062 TAATATTTATATATTTTTATTAAATTT
1 TAATATTTATATATTTGTATTAAATTT
* *
461089 TAAAATTTATATATTTGTATTATATTT
1 TAATATTTATATATTTGTATTAAATTT
461116 ATTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TAATATTTATATATTTGTATTAAATTT
Found at i:461601 original size:14 final size:15
Alignment explanation
Indices: 461573--461610 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
461563 TGATCTTTTG
461573 ATTTAATTTTATCAA
1 ATTTAATTTTATCAA
*
461588 TTTTAATTTT-TCAA
1 ATTTAATTTTATCAA
461602 ATTTAATTT
1 ATTTAATTT
461611 AATTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTAATTTTATCAA
Found at i:464224 original size:2 final size:2
Alignment explanation
Indices: 464217--464243 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
464207 ACATAACAAC
464217 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
464244 ATACAAAAAC
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:465788 original size:3 final size:3
Alignment explanation
Indices: 465780--465808 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
465770 AACACAATAT
465780 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
465809 GTCGCGACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:466998 original size:28 final size:28
Alignment explanation
Indices: 466943--467013 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
466933 AATAAAGCCT
** *
466943 GGGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
466971 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
* *
466999 GAGGTTGGACTATCC
1 GGGGTTGGAGTATCC
467014 TCGACTGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:467065 original size:52 final size:51
Alignment explanation
Indices: 467002--467127 Score: 155
Period size: 53 Copynumber: 2.4 Consensus size: 51
466992 AAATAACGAG
* * * *
467002 GTTGGACTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCTCGATTGTGAAAAATTGGT-GTTTTGAAAATAAAATCGGA
* *
467054 GTTGGAGTATCCCCGATTAAAG-GAAAAATTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAATATCCTCGATT---GTGAAAAATTGGTGTTTTGAAAATAAAATCGGA
467107 GTTGGAATATCCTCGATTGTG
1 GTTGGAATATCCTCGATTGTG
467128 GAGAATTGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.02
51 1 0.02
52 15 0.24
53 34 0.54
54 11 0.17
55 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCTCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:467099 original size:53 final size:54
Alignment explanation
Indices: 467022--467124 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
467012 CCTCGACTGT
* * *
467022 GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAG
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
*
467076 GAAAAATTGGT-GTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATT
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
467125 GTGGAGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 34 0.76
54 11 0.24
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (54 bp):
GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
Found at i:469504 original size:13 final size:13
Alignment explanation
Indices: 469486--469511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
469476 ACAAAGATCC
469486 ATGTATCGATACA
1 ATGTATCGATACA
469499 ATGTATCGATACA
1 ATGTATCGATACA
469512 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:469507 original size:33 final size:33
Alignment explanation
Indices: 469465--469531 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
469455 AAACTTTTCA
***
469465 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
469498 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
469531 A
1 A
469532 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:469575 original size:19 final size:18
Alignment explanation
Indices: 469551--469618 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
469541 CAGTAGCTAA
469551 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
469570 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
469585 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
469602 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
469619 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:469591 original size:13 final size:13
Alignment explanation
Indices: 469573--469597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469563 ACAATACTTA
469573 TGTATCGATACAT
1 TGTATCGATACAT
469586 TGTATCGATACA
1 TGTATCGATACA
469598 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:469595 original size:32 final size:32
Alignment explanation
Indices: 469554--469616 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
469544 TAGCTAATTA
*
469554 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
469586 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
469617 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:469698 original size:21 final size:21
Alignment explanation
Indices: 469674--469730 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
469664 CATTTGTAGG
*
469674 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCAAAA
*
469695 ATGTATCGATACATTCTAAAA
1 ATGTATCGATACATTCCAAAA
469716 ATGTATCGATACATT
1 ATGTATCGATACATT
469731 TAGATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCAAAA
Found at i:470190 original size:12 final size:12
Alignment explanation
Indices: 470166--470204 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
470156 ATATGACATA
*
470166 AAAAAATAA-AT
1 AAAATATAATAT
470177 AAAATATAATAT
1 AAAATATAATAT
470189 AAAATATAATACT
1 AAAATATAATA-T
470202 AAA
1 AAA
470205 GAGAGAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
12 13 0.52
13 4 0.16
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:470686 original size:45 final size:45
Alignment explanation
Indices: 470635--470723 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
470625 TTTTGTATTC
*
470635 AAAGAAGTAATCTATCTATACCTAAGTTCATGTAAAAGTAGAAGA
1 AAAGAAGTAATATATCTATACCTAAGTTCATGTAAAAGTAGAAGA
* ** *
470680 AAAGAAGTTATATATCTATGGCTAAGTTCATTTAAAAGTAGAAG
1 AAAGAAGTAATATATCTATACCTAAGTTCATGTAAAAGTAGAAG
470724 TTTTCATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (45 bp):
AAAGAAGTAATATATCTATACCTAAGTTCATGTAAAAGTAGAAGA
Found at i:471258 original size:14 final size:14
Alignment explanation
Indices: 471235--471265 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
471225 ATTTAGTAAG
471235 TTTAAAATTTAAAT
1 TTTAAAATTTAAAT
*
471249 TTTAATATTTAAAT
1 TTTAAAATTTAAAT
471263 TTT
1 TTT
471266 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAAATTTAAAT
Found at i:472009 original size:7 final size:7
Alignment explanation
Indices: 471990--472035 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
471980 TATAAATTAT
471990 TTTTAAA
1 TTTTAAA
*
471997 TATTAAAA
1 T-TTTAAA
*
472005 TTTAATAA
1 TTTTA-AA
472013 TTTTAAA
1 TTTTAAA
472020 TTTTAAA
1 TTTTAAA
472027 TTTTAAA
1 TTTTAAA
472034 TT
1 TT
472036 ATGATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTTTAAA
Found at i:472028 original size:14 final size:14
Alignment explanation
Indices: 471990--472035 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
471980 TATAAATTAT
*
471990 TTTTAAATATTAAAA
1 TTTTAAAT-TTTAAA
*
472005 TTTAATAATTTTAAA
1 TTTTA-AATTTTAAA
472020 TTTTAAATTTTAAA
1 TTTTAAATTTTAAA
472034 TT
1 TT
472036 ATGATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.41
15 13 0.48
16 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAAATTTTAAA
Found at i:473144 original size:20 final size:20
Alignment explanation
Indices: 473119--473159 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
473109 CTTTTAAAAA
473119 ATATTTTTAT-ATTAATATTT
1 ATATTTTTATAATTAA-ATTT
473139 ATATTTTTATAATTAAATTT
1 ATATTTTTATAATTAAATTT
473159 A
1 A
473160 AATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTTTATAATTAAATTT
Found at i:475228 original size:14 final size:14
Alignment explanation
Indices: 475209--475265 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
475199 TAATATGATA
475209 TTATAATTATTATT
1 TTATAATTATTATT
475223 TTATAATT-TTATT
1 TTATAATTATTATT
* * *
475236 TTTTTATTAATATTT
1 TTATAATTATTA-TT
475251 ATTATAATTAATTAT
1 -TTATAATT-ATTAT
475266 AATAATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 11 0.33
14 10 0.30
15 2 0.06
16 7 0.21
17 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATAATTATTATT
Found at i:475240 original size:16 final size:18
Alignment explanation
Indices: 475215--475255 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
475205 GATATTATAA
475215 TTATTATTTTA-TAAT-T
1 TTATTATTTTATTAATAT
*
475231 TTATTTTTTTATTAATAT
1 TTATTATTTTATTAATAT
475249 TTATTAT
1 TTATTAT
475256 AATTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTTTATTAATAT
Found at i:475272 original size:25 final size:24
Alignment explanation
Indices: 475243--475296 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
475233 ATTTTTTTAT
*
475243 TAATATTTATTATAATTA-ATTATAA
1 TAATATTTA-T-TAATTATATAATAA
475268 TAATATTTATTAATTATATAATAA
1 TAATATTTATTAATTATATAATAA
475292 TAATA
1 TAATA
475297 AATGTGATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 12 0.44
25 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATATTTATTAATTATATAATAA
Found at i:475290 original size:43 final size:42
Alignment explanation
Indices: 475196--475290 Score: 95
Period size: 43 Copynumber: 2.2 Consensus size: 42
475186 TAAATAACGA
* *
475196 ATATAATATGATATTATAATTATTATTTTATAATTTTATTTTT
1 ATATAATATGATATTATAATTATTA-TTAATAATTTTATTATT
* *
475239 TTATTAATAT-TTATTATAATTAATTA-TAATAATATTTATTAATT
1 ATA-TAATATGATATTATAATT-ATTATTAATAAT-TTTATT-ATT
475283 ATATAATA
1 ATATAATA
475291 ATAATAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
42 6 0.14
43 23 0.53
44 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (42 bp):
ATATAATATGATATTATAATTATTATTAATAATTTTATTATT
Found at i:476163 original size:14 final size:14
Alignment explanation
Indices: 476144--476170 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
476134 AAATTGAAAG
476144 TAAATTTCAAATCT
1 TAAATTTCAAATCT
476158 TAAATTTCAAATC
1 TAAATTTCAAATC
476171 AAACTTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTTCAAATCT
Found at i:479166 original size:2 final size:2
Alignment explanation
Indices: 479159--479196 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
479149 GGAGTAGCTG
*
479159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
479197 GATAATCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:479313 original size:2 final size:2
Alignment explanation
Indices: 479306--479331 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
479296 AGAGAATTAA
479306 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
479332 CACCGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482515 original size:18 final size:19
Alignment explanation
Indices: 482477--482515 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
482467 AAAAATAATT
* *
482477 ATTTGATTCATAATATTAA
1 ATTTGATGCAAAATATTAA
482496 ATTTGATGCAAAAT-TTAA
1 ATTTGATGCAAAATATTAA
482514 AT
1 AT
482516 AATATTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTTGATGCAAAATATTAA
Found at i:483118 original size:15 final size:15
Alignment explanation
Indices: 483098--483126 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
483088 AACACATAAT
483098 ATATTTAGAATTTAA
1 ATATTTAGAATTTAA
483113 ATATTTAGAATTTA
1 ATATTTAGAATTTA
483127 TTTTTTTTAT
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:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
ATATTTAGAATTTAA
Found at i:483941 original size:22 final size:22
Alignment explanation
Indices: 483916--483961 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
483906 TAATGTGGAT
483916 GGATCTACATGAGGGAAAGCAA
1 GGATCTACATGAGGGAAAGCAA
483938 GGATCTACATGAGGGAAAGCAA
1 GGATCTACATGAGGGAAAGCAA
483960 GG
1 GG
483962 CTTATGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.35, T:0.13
Consensus pattern (22 bp):
GGATCTACATGAGGGAAAGCAA
Found at i:485349 original size:158 final size:158
Alignment explanation
Indices: 485053--485372 Score: 543
Period size: 159 Copynumber: 2.0 Consensus size: 158
485043 CATGCTAAAT
*
485053 AAGGTTTCACGAATGAAATAAGATTAGATCAGAATTAGAGTTTTATAAAAGAATTTAGTTATCTA
1 AAGGTTTCACGAATGAAATAAGATTAGATCAGAATTAGAGTTTTATAAAAGAATTTACTTATCTA
**
485118 AACTTGAACCAAATTTGAAATTTTATTTTATTATTTAAATTTTATTTTAAAATATTATATTAATA
66 AACTTGAACCAAATCCGAAATTTTATTTTATTATTTAAATTTTATTTTAAAATATTATATTAATA
485183 TTTATATATTTTTATAATATTATATGTG
131 TTTATATATTTTTATAATATTATATGTG
* *
485211 AAGGTTTCATGAATGAAATGAGATTAGATC-GAAATTAGAGTTTTATAAAAGAATTTTACTTATC
1 AAGGTTTCACGAATGAAATAAGATTAGATCAG-AATTAGAGTTTTATAAAAGAA-TTTACTTATC
* *
485275 TAAACTTGAACTAGATCCGAAATTTTATTTTATTATTTAAATTTTATTTTAAAAGTATTATATTA
64 TAAACTTGAACCAAATCCGAAATTTTATTTTATTATTTAAATTTTATTTTAAAA-TATTATATTA
485340 ATATTTATATATTTTTATAATATTATATGTG
128 ATATTTATATATTTTTATAATATTATATGTG
485371 AA
1 AA
485373 CTTTAAATTT
Statistics
Matches: 152, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
157 1 0.01
158 49 0.32
159 59 0.39
160 43 0.28
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (158 bp):
AAGGTTTCACGAATGAAATAAGATTAGATCAGAATTAGAGTTTTATAAAAGAATTTACTTATCTA
AACTTGAACCAAATCCGAAATTTTATTTTATTATTTAAATTTTATTTTAAAATATTATATTAATA
TTTATATATTTTTATAATATTATATGTG
Found at i:486979 original size:2 final size:2
Alignment explanation
Indices: 486972--486999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
486962 GGGTCATAAA
486972 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
487000 GGCTCTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:487492 original size:12 final size:11
Alignment explanation
Indices: 487453--487484 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
487443 TCATATCATT
487453 ATATTAACAAAA
1 ATATTAA-AAAA
487465 ATATTAAAAAA
1 ATATTAAAAAA
487476 ATATTAAAA
1 ATATTAAAA
487485 TACATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATTAAAAAA
Found at i:489074 original size:2 final size:2
Alignment explanation
Indices: 489067--489093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
489057 AATTTTAATT
489067 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
489094 CTTATGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492978 original size:21 final size:21
Alignment explanation
Indices: 492953--492994 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
492943 TATATGATTA
492953 ATTAAATATGTAAACATGATG
1 ATTAAATATGTAAACATGATG
492974 ATTAAATATGTAAACATGATG
1 ATTAAATATGTAAACATGATG
492995 TGATCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTAAATATGTAAACATGATG
Found at i:688164 original size:2 final size:2
Alignment explanation
Indices: 688157--688190 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
688147 TTATTTTCAC
* *
688157 AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
688191 TTAAATCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:688175 original size:10 final size:10
Alignment explanation
Indices: 688157--688190 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
688147 TTATTTTCAC
*
688157 ATATATATAT
1 ATATGTATAT
688167 ATATGTATAT
1 ATATGTATAT
688177 ATATGTATAT
1 ATATGTATAT
688187 ATAT
1 ATAT
688191 TTAAATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATGTATAT
Found at i:688357 original size:13 final size:13
Alignment explanation
Indices: 688339--688368 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
688329 AATTCATGTT
688339 TTTATATTATATC
1 TTTATATTATATC
*
688352 TTTATATTATATT
1 TTTATATTATATC
688365 TTTA
1 TTTA
688369 AAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATATTATATC
Found at i:692372 original size:22 final size:21
Alignment explanation
Indices: 692314--692381 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
692304 AATATCAACA
*
692314 AAATTAAAAATAAAA-AATTT
1 AAATTAAATATAAAATAATTT
692334 AAATTAAAGTCAT-AAATAATTT
1 AAATTAAA-T-ATAAAATAATTT
*
692356 AAATTAAATATTAAAAT-ACTT
1 AAATTAAATA-TAAAATAATTT
692377 AAATT
1 AAATT
692382 TAACTCAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 9 0.22
21 13 0.32
22 19 0.46
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (21 bp):
AAATTAAATATAAAATAATTT
Found at i:692838 original size:15 final size:15
Alignment explanation
Indices: 692814--692852 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
692804 ACCAAAAGCT
*
692814 GAGAAAAAGCCAGCG
1 GAGAAGAAGCCAGCG
*
692829 GAGAAGAAGCCCGCG
1 GAGAAGAAGCCAGCG
*
692844 GAGGAGAAG
1 GAGAAGAAG
692853 AAGACGGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.41, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCAGCG
Found at i:695883 original size:17 final size:16
Alignment explanation
Indices: 695851--695881 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
695841 AATGAGGATC
695851 GAGTTTGAATTTTTTA
1 GAGTTTGAATTTTTTA
695867 GAGTTTGAATTTTTT
1 GAGTTTGAATTTTTT
695882 TATTAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (16 bp):
GAGTTTGAATTTTTTA
Found at i:696383 original size:19 final size:20
Alignment explanation
Indices: 696353--696390 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
696343 AATATTTTTA
*
696353 TATTTAATTTTAAATTTAAT
1 TATTTAATTTTAAAATTAAT
696373 TATTT-ATTTTAAAATTAA
1 TATTTAATTTTAAAATTAA
696391 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTAATTTTAAAATTAAT
Found at i:696393 original size:20 final size:20
Alignment explanation
Indices: 696353--696394 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
696343 AATATTTTTA
*
696353 TATTTAATTTTAAATTTAAT
1 TATTTAATTTTAAATTAAAT
696373 TATTT-ATTTTAAAATTAAAT
1 TATTTAATTTT-AAATTAAAT
696393 TA
1 TA
696395 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTAATTTTAAATTAAAT
Found at i:696403 original size:25 final size:25
Alignment explanation
Indices: 696346--696403 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
696336 TGTGAAAAAT
** *
696346 ATTTTTATATTTAATTTTAAATTTA
1 ATTTTTATATTTAAAATTAAATTAA
696371 ATTATTTAT-TTTAAAATTAAATTAAA
1 ATT-TTTATATTTAAAATTAAATT-AA
696397 ATTTTTA
1 ATTTTTA
696404 ATAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATATTTAAAATTAAATTAA
Found at i:700007 original size:15 final size:14
Alignment explanation
Indices: 699987--700051 Score: 53
Period size: 17 Copynumber: 4.5 Consensus size: 14
699977 GTGTAATTAT
699987 ATTATATAAAATAA
1 ATTATATAAAATAA
*
700001 ATATATATAATATTATA
1 AT-TATATAA-AATA-A
*
700018 ATATATATTAAA-AA
1 AT-TATATAAAATAA
*
700032 ATTA-ATAAAAAAA
1 ATTATATAAAATAA
700045 ATTATAT
1 ATTATAT
700052 CACTAAAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.12
13 8 0.19
14 7 0.17
15 8 0.19
16 4 0.10
17 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTATATAAAATAA
Found at i:710400 original size:2 final size:2
Alignment explanation
Indices: 710395--710423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
710385 GGAGAGATAA
710395 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
710424 AGGGGGGATA
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:710853 original size:8 final size:9
Alignment explanation
Indices: 710768--710860 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
710758 TAAAATAAAC
710768 ATATAATAA
1 ATATAATAA
*
710777 ATATATTAA
1 ATATAATAA
* *
710786 A-ATTATTA
1 ATATAATAA
*
710794 ATATATTAA
1 ATATAATAA
*
710803 GATTTATATAA
1 -ATATA-ATAA
710814 ATAT-AT-A
1 ATATAATAA
**
710821 ATATTTTAA
1 ATATAATAA
710830 ATATAATTATA
1 ATATAA-TA-A
710841 ATATAA-AA
1 ATATAATAA
710849 ATATAATAA
1 ATATAATAA
710858 ATA
1 ATA
710861 ATTAGTTACC
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
7 5 0.08
8 15 0.24
9 24 0.38
10 9 0.14
11 10 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATATAATAA
Found at i:711103 original size:34 final size:32
Alignment explanation
Indices: 711035--711131 Score: 88
Period size: 34 Copynumber: 2.9 Consensus size: 32
711025 GTGATTTAAC
* *
711035 TTAAA-AATTTATGTATTTTTTAATATTTATATAT
1 TTAAATAATTTA--TATTTTATAAAATTTA-ATAT
* * *
711069 TTAAAATATTTTTTATTTATATAAATTTTAATAT
1 TT-AAATAATTTATATTT-TATAAAATTTAATAT
*
711103 TTTAATAATTTATATTTTATAAAATTTAA
1 TTAAATAATTTATATTTTATAAAATTTAA
711132 AAAATATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
32 11 0.22
33 12 0.24
34 13 0.25
35 11 0.22
36 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
TTAAATAATTTATATTTTATAAAATTTAATAT
Found at i:711113 original size:27 final size:25
Alignment explanation
Indices: 711052--711127 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
711042 TTTATGTATT
711052 TTTTAATATTTATATATTTAAAATA
1 TTTTAATATTTATATATTTAAAATA
* *
711077 TTTT-TTATTTATATAAATTT-TAATA
1 TTTTAATATTTATAT--ATTTAAAATA
*
711102 TTTTAATAATTTATATTTTATAAAAT
1 TTTTAAT-ATTTATATATT-TAAAAT
711128 TTAAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 9 0.22
25 14 0.35
26 6 0.15
27 11 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAATATTTATATATTTAAAATA
Found at i:711114 original size:16 final size:17
Alignment explanation
Indices: 711038--711131 Score: 61
Period size: 18 Copynumber: 5.5 Consensus size: 17
711028 ATTTAACTTA
* *
711038 AAAATTTATGTATTTTTT
1 AAAATTTA-ATATTTTAT
*
711056 AATATTT-ATATATTTA-
1 AAAATTTAATAT-TTTAT
**
711072 AAATATTTTTTATTTATAT
1 AAA-ATTTAATATTT-TAT
*
711091 AAATTTTAATATTTTA-
1 AAAATTTAATATTTTAT
*
711107 ATAATTT-ATATTTTAT
1 AAAATTTAATATTTTAT
711123 AAAATTTAA
1 AAAATTTAA
711132 AAAATATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
15 8 0.14
16 16 0.28
17 12 0.21
18 19 0.33
19 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
AAAATTTAATATTTTAT
Found at i:711129 original size:25 final size:25
Alignment explanation
Indices: 711052--711153 Score: 65
Period size: 24 Copynumber: 4.2 Consensus size: 25
711042 TTTATGTATT
711052 TTTTAAT-ATTTATATA-TTTAAAA
1 TTTTAATAATTTATATATTTTAAAA
* * *
711075 TATTT-TTTATTTATATAAATTTTAATA
1 T-TTTAATAATTTATAT--ATTTTAAAA
711102 TTTTAATAATTTATAT-TTTATAAAA
1 TTTTAATAATTTATATATTT-TAAAA
** *
711127 -TTTAA-AAAATATAT-TTTTAATA
1 TTTTAATAATTTATATATTTTAAAA
711149 TTTTA
1 TTTTA
711154 TATATTATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
22 4 0.06
23 16 0.25
24 19 0.30
25 4 0.06
26 4 0.06
27 16 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTAATAATTTATATATTTTAAAA
Found at i:711186 original size:21 final size:20
Alignment explanation
Indices: 711143--711186 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
711133 AAATATATTT
*
711143 TTAATATTTTATATATTATA
1 TTAATATTTTATATATTAAA
711163 TTAATATATTTATAT-TTACAA
1 TTAATAT-TTTATATATTA-AA
711184 TTA
1 TTA
711187 TCAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATTTTATATATTAAA
Found at i:713222 original size:20 final size:23
Alignment explanation
Indices: 713169--713223 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
713159 TAAATTTATA
*
713169 TTTATTATTTTAATATATATTAAT
1 TTTA-TATTTTAATATATATAAAT
713193 TTTATATTTTAA-ATATA-AAAT
1 TTTATATTTTAATATATATAAAT
*
713214 TTTATTTTTT
1 TTTATATTTT
713224 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 5 0.17
23 8 0.28
24 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATATTTTAATATATATAAAT
Found at i:713224 original size:22 final size:24
Alignment explanation
Indices: 713169--713227 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 24
713159 TAAATTTATA
*
713169 TTTATTATTTTAATATATATTAAT
1 TTTATTATTTTAATATATATAAAT
713193 TTTA-TATTTTAA-ATATA-AAAT
1 TTTATTATTTTAATATATATAAAT
*
713214 TTTATTTTTTTAAT
1 TTTATTATTTTAAT
713228 TTTTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 7 0.23
22 12 0.39
23 8 0.26
24 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATTATTTTAATATATATAAAT
Found at i:713228 original size:35 final size:33
Alignment explanation
Indices: 713188--713281 Score: 89
Period size: 35 Copynumber: 2.7 Consensus size: 33
713178 TTAATATATA
713188 TTAATTTTATATTTTAAATATAAAATTTTATTTTT
1 TTAATTTT-TA-TTTAAATATAAAATTTTATTTTT
* * **
713223 TTAATTTTTTAATTAAATTATTATTTTTTATTTTT
1 TTAA-TTTTTATTTAAA-TATAAAATTTTATTTTT
* *
713258 TTATAATTTTATTTAAAAATAAAA
1 TTA-ATTTTTATTTAAATATAAAA
713282 AATTATTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
34 8 0.17
35 33 0.72
36 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTAATTTTTATTTAAATATAAAATTTTATTTTT
Found at i:713269 original size:26 final size:26
Alignment explanation
Indices: 713211--713271 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
713201 TTAAATATAA
713211 AATTTTATTTTTTTAATTTTTTAATT
1 AATTTTATTTTTTTAATTTTTTAATT
*
713237 AAATTATTA-TTTTTT-ATTTTTTTA-T
1 -AATT-TTATTTTTTTAATTTTTTAATT
713262 AATTTTATTT
1 AATTTTATTT
713272 AAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.10
24 6 0.19
25 1 0.03
26 8 0.26
27 10 0.32
28 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
AATTTTATTTTTTTAATTTTTTAATT
Found at i:713481 original size:15 final size:14
Alignment explanation
Indices: 713428--713481 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
713418 TTTATTTATG
713428 TATAAATAAATATA
1 TATAAATAAATATA
*
713442 T-TTAATAAA-A-A
1 TATAAATAAATATA
*
713453 TATAAATCATATATA
1 TATAAAT-AAATATA
713468 TATAAATATAATAT
1 TATAAATA-AATAT
713482 TTTATTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
11 2 0.06
12 5 0.16
13 9 0.29
14 3 0.10
15 12 0.39
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAAATAAATATA
Found at i:715261 original size:29 final size:29
Alignment explanation
Indices: 715200--715257 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
715190 AATAATAACA
*
715200 TATTTATTACTATACTTAGTAATTTGAAT
1 TATTTATTACTATACTTAGTAATTTCAAT
*
715229 TATTTATTACTATACTTGGTAA-TTCAAT
1 TATTTATTACTATACTTAGTAATTTCAAT
715257 T
1 T
715258 TATTAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.52
Consensus pattern (29 bp):
TATTTATTACTATACTTAGTAATTTCAAT
Found at i:720239 original size:19 final size:20
Alignment explanation
Indices: 720190--720239 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
720180 AATTTTAAAT
*
720190 TTTAAGTAAAT-TCGTATAA
1 TTTAATTAAATATCGTATAA
*
720209 TTTAATT-CATATCGT-TAA
1 TTTAATTAAATATCGTATAA
720227 TTTAATTAAATAT
1 TTTAATTAAATAT
720240 TTTACATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTAATTAAATATCGTATAA
Found at i:720380 original size:49 final size:49
Alignment explanation
Indices: 720269--720382 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 49
720259 TAAATTTTTT
*
720269 TAAAAATTA-ATAA-TTTTTAATAAAAAATTATTTTTAAATTAAAAATA
1 TAAAAAGTATATAATTTTTTAATAAAAAATTATTTTTAAATTAAAAATA
* * * *
720316 TAAAAAGTATGTAATTTTTTAATGAATAATT-TTTTTAAAATTTAAAAT-
1 TAAAAAGTATATAATTTTTTAATAAAAAATTATTTTT-AAATTAAAAATA
720364 TAAAAA-TATCTATAATTTT
1 TAAAAAGTA--TATAATTTT
720383 ATTTTATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
47 10 0.18
48 14 0.25
49 32 0.57
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (49 bp):
TAAAAAGTATATAATTTTTTAATAAAAAATTATTTTTAAATTAAAAATA
Found at i:720442 original size:21 final size:21
Alignment explanation
Indices: 720397--720442 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
720387 TATTATTAAA
*
720397 ATTATAATTTAATTTTTATAT
1 ATTATAATTTAATTTTGATAT
720418 ATTATTAA-TTAA-TTTGATAT
1 ATTA-TAATTTAATTTTGATAT
720438 GATTA
1 -ATTA
720443 CACTTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 12 0.55
22 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTATAATTTAATTTTGATAT
Found at i:720734 original size:47 final size:50
Alignment explanation
Indices: 720665--720760 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 50
720655 ATAAAAACTA
* *
720665 AAATAATAATATCATTAATTATT-TTTATATTAAT-ATTTACAATTAATTTT
1 AAATAATAATATCATTAATTATTATATA-AATAATAATTTA-AATTAATTTT
*
720715 AAATAA-AATAT-ATT-TTTATTATATAAATAATAATTTAAATTAATTT
1 AAATAATAATATCATTAATTATTATATAAATAATAATTTAAATTAATTT
720761 AATTTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
47 19 0.46
48 11 0.27
49 5 0.12
50 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATAATAATATCATTAATTATTATATAAATAATAATTTAAATTAATTTT
Found at i:725437 original size:41 final size:41
Alignment explanation
Indices: 725380--725464 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
725370 GAAAATAATA
*
725380 ATACTAGCTTGTAGTCATGTTCTTAATATATATATATATAT
1 ATACTAGCTTGTAGTCATGTACTTAATATATATATATATAT
725421 ATACTAGCTTGTAGTCATGTACTTAATATATATATATATAT
1 ATACTAGCTTGTAGTCATGTACTTAATATATATATATATAT
725462 ATA
1 ATA
725465 TATCATGGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (41 bp):
ATACTAGCTTGTAGTCATGTACTTAATATATATATATATAT
Found at i:726035 original size:17 final size:18
Alignment explanation
Indices: 726016--726053 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
726006 TAATTAATAT
726016 AAATATATTTATTT-TTTA
1 AAAT-TATTTATTTATTTA
*
726034 AAATTTTTTATTTATTTA
1 AAATTATTTATTTATTTA
726052 AA
1 AA
726054 GTGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAATTATTTATTTATTTA
Found at i:726724 original size:20 final size:23
Alignment explanation
Indices: 726699--726739 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
726689 TTAATTTTAT
726699 ATAATT-TA-TTATAA-AATATA
1 ATAATTATAGTTATAATAATATA
726719 ATAATTATAGTTATAATAATA
1 ATAATTATAGTTATAATAATA
726740 AAAACTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 6 0.33
23 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAATTATAGTTATAATAATATA
Found at i:726792 original size:19 final size:20
Alignment explanation
Indices: 726770--726814 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
726760 TTTTAAAATA
* *
726770 TTTTATTAT-AAATTTATTT
1 TTTTATGATGAAATTGATTT
*
726789 TTTTATGATGAAGTTGATTT
1 TTTTATGATGAAATTGATTT
726809 TTTTAT
1 TTTTAT
726815 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTTATGATGAAATTGATTT
Found at i:727711 original size:31 final size:31
Alignment explanation
Indices: 727673--727739 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
727663 TAATTTAAAT
* *
727673 TATTATTAAATAGAAAAT-AATAAAATACAAA
1 TATTATTAAATA-AAAATCAATAAAACAAAAA
*
727704 TATTATTAAATATAAATCAATAAAACAAAAA
1 TATTATTAAATAAAAATCAATAAAACAAAAA
727735 TATTA
1 TATTA
727740 CCAATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (31 bp):
TATTATTAAATAAAAATCAATAAAACAAAAA
Found at i:727720 original size:16 final size:16
Alignment explanation
Indices: 727668--727720 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
727658 AAATCTAATT
727668 TAAATTATTATTAAATA
1 TAAA-TATTATTAAATA
* * *
727685 GAAA-ATAATAAAATA
1 TAAATATTATTAAATA
*
727700 CAAATATTATTAAATA
1 TAAATATTATTAAATA
727716 TAAAT
1 TAAAT
727721 CAATAAAACA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 12 0.43
16 13 0.46
17 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAATATTATTAAATA
Found at i:734960 original size:17 final size:19
Alignment explanation
Indices: 734928--734966 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
734918 TTATAACATA
734928 TTTATTAATCATAAATT-T
1 TTTATTAATCATAAATTAT
734946 TTTATTAAT-ATAAATTAT
1 TTTATTAATCATAAATTAT
734964 TTT
1 TTT
734967 TAACTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTAATCATAAATTAT
Found at i:735085 original size:2 final size:2
Alignment explanation
Indices: 735080--735108 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
735070 GATCTAGCGC
735080 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 A
735109 CACACACATG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:737774 original size:2 final size:2
Alignment explanation
Indices: 737767--737798 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
737757 AGACTCTGAT
737767 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
737799 GTTGAGATTA
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
Done.