Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 5 of 11
Found at i:361872 original size:13 final size:13
Alignment explanation
Indices: 361854--361878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361844 ATATTTTTTT
361854 ATTAATATTTATA
1 ATTAATATTTATA
361867 ATTAATATTTAT
1 ATTAATATTTAT
361879 TATAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:361897 original size:25 final size:25
Alignment explanation
Indices: 361864--361911 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
361854 ATTAATATTT
*
361864 ATAATTAATATTTATTATAATTTAAC
1 ATAATTAATATTAATTAT-ATTTAAC
361890 ATAA-TAATATTAATTATATTTA
1 ATAATTAATATTAATTATATTTA
361912 TAATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATTAATATTAATTATATTTAAC
Found at i:362254 original size:29 final size:30
Alignment explanation
Indices: 362220--362280 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
362210 ATTTAATTTA
* *
362220 ATTTAAATTATTATT-TAATAATA-AAAAAT
1 ATTTAAATT-TAATTATAAAAATATAAAAAT
362249 ATTTAAATTTAATTATAAAAATATAAAAAT
1 ATTTAAATTTAATTATAAAAATATAAAAAT
362279 AT
1 AT
362281 GAATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 16 0.57
30 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTTAAATTTAATTATAAAAATATAAAAAT
Found at i:362619 original size:28 final size:26
Alignment explanation
Indices: 362554--362616 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
362544 TTAAATTATT
* *
362554 ATTTAAATGATAAAAAATAATTTTAAA
1 ATTT-AATTATAAAAAATAAATTTAAA
*
362581 ATTTAATTATAAAATACATAAATTTAAT
1 ATTTAATTATAAAA-A-ATAAATTTAAA
362609 ATTATAAT
1 ATT-TAAT
362617 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 9 0.30
27 5 0.17
28 12 0.40
29 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAATTATAAAAAATAAATTTAAA
Found at i:362719 original size:26 final size:26
Alignment explanation
Indices: 362690--362754 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
362680 ACATTAATAT
*
362690 TTTTATATTATTTAAAATTTATTTA-A
1 TTTTATATTATTT-AAATATATTTATA
* *
362716 TTTTATATAAATTTTAATATATTTATA
1 TTTTATAT-TATTTAAATATATTTATA
362743 TATTTATATTAT
1 T-TTTATATTAT
362755 ATTTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 17 0.53
27 8 0.25
28 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATATTATTTAAATATATTTATA
Found at i:362748 original size:28 final size:29
Alignment explanation
Indices: 362709--362795 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 29
362699 ATTTAAAATT
362709 TATTTA-AT-TTTATA-TAAATTTTAATA
1 TATTTATATATTTATATTAAATTTTAATA
*
362735 TATTTATATATTTATATTATATTTATAATA
1 TATTTATATATTTATATTAAATTT-TAATA
* * *
362765 T-TTTTTA-AATTATATTACATTTTAAT-
1 TATTTATATATTTATATTAAATTTTAATA
362791 TATTT
1 TATTT
362796 TTTTTTTATG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 7 0.13
27 9 0.17
28 19 0.37
29 11 0.21
30 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTATATATTTATATTAAATTTTAATA
Found at i:362758 original size:56 final size:54
Alignment explanation
Indices: 362686--362795 Score: 127
Period size: 57 Copynumber: 2.0 Consensus size: 54
362676 TATTACATTA
* *
362686 ATATTTTTATATTATTTA-AA-ATTTATTT-AATTTTATATAAATTTTAATATATTT
1 ATATATTTATATTATTTATAATATTT-TTTAAATTATAT-TAAATTTTAAT-TATTT
*
362740 ATATATTTATATTATATTTATAATATTTTTTAAATTATATTACATTTTAATTATTT
1 ATATATTTATA-T-TATTTATAATATTTTTTAAATTATATTAAATTTTAATTATTT
362796 TTTTTTTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
54 10 0.21
55 1 0.02
56 11 0.23
57 15 0.31
58 11 0.23
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (54 bp):
ATATATTTATATTATTTATAATATTTTTTAAATTATATTAAATTTTAATTATTT
Found at i:362767 original size:20 final size:20
Alignment explanation
Indices: 362684--362767 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 20
362674 ACTATTACAT
*
362684 TAATATTTTTA-TATTATTTA
1 TAATATTTATATTA-TATTTA
362704 -AA-ATTTAT-TTA-ATTTTA
1 TAATATTTATATTATA-TTTA
* *
362721 TATAAATTT-TAATATATTTA
1 TA-ATATTTATATTATATTTA
362741 T-ATATTTATATTATATTTA
1 TAATATTTATATTATATTTA
362760 TAATATTT
1 TAATATTT
362768 TTTAAATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
16 1 0.02
17 4 0.08
18 13 0.25
19 15 0.29
20 17 0.33
21 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATATTTATATTATATTTA
Found at i:370509 original size:20 final size:22
Alignment explanation
Indices: 370469--370509 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
370459 GTATTATATT
*
370469 TATTTTATTATTTTATTTAAAA
1 TATTTTATTATTTTATATAAAA
370491 TATTTTA-TA-TTTATATAAA
1 TATTTTATTATTTTATATAAA
370510 TAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTATTATTTTATATAAAA
Found at i:370520 original size:29 final size:27
Alignment explanation
Indices: 370495--370549 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
370485 TTAAAATATT
370495 TTATATT-TATATAAATAATAATAAATAA
1 TTATATTATATATAAAT-ATAA-AAATAA
*
370523 TTATTTTATATATAAATATAAAAATAA
1 TTATATTATATATAAATATAAAAATAA
370550 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 10 0.40
29 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTATATTATATATAAATATAAAAATAA
Found at i:370557 original size:27 final size:29
Alignment explanation
Indices: 370502--370571 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 29
370492 ATTTTATATT
** *
370502 TATATAAATAATAATAAATAATTATTTTA
1 TATATAAATAATAATAAATAAAAAATTTA
370531 TATATAAAT-ATAA-AAATAAAAAATTTA
1 TATATAAATAATAATAAATAAAAAATTTA
*
370558 AATA-AAATTAATAA
1 TATATAAA-TAATAA
370572 AATTTTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 3 0.09
27 15 0.43
28 8 0.23
29 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TATATAAATAATAATAAATAAAAAATTTA
Found at i:370607 original size:13 final size:14
Alignment explanation
Indices: 370580--370609 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
370570 AAAATTTTAG
370580 ATATTTTATAAAAT
1 ATATTTTATAAAAT
370594 ATATTTTA-AAAAT
1 ATATTTTATAAAAT
370607 ATA
1 ATA
370610 AATAAGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTTTATAAAAT
Found at i:370705 original size:17 final size:17
Alignment explanation
Indices: 370683--370749 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
370673 GATAATTATT
*
370683 TAATTATAATATATTAA
1 TAATTAAAATATATTAA
*
370700 TAATTAAAATTATATAAA
1 TAATTAAAA-TATATTAA
* *
370718 T-TTTAAAATATTTTAA
1 TAATTAAAATATATTAA
* * *
370734 TATTTATATTATATTA
1 TAATTAAAATATATTA
370750 TATTTTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.17
17 25 0.62
18 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAAAATATATTAA
Found at i:370763 original size:33 final size:35
Alignment explanation
Indices: 370690--370790 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 35
370680 ATTTAATTAT
* * *
370690 AATATATTAATAATTA-AAATTATA-TAAATTTTAA
1 AATATTTTAAT-ATTATATATTATATTATATTTTAA
370724 AATATTTTAATATT-TATATTATATTATATTTT-A
1 AATATTTTAATATTATATATTATATTATATTTTAA
* * *
370757 ATTATTTTTATATTATATTTATATAATTATATTT
1 AATATTTTAATATTATATAT-TAT-ATTATATTT
370791 AATATTATCG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 23 0.41
34 21 0.38
35 3 0.05
36 9 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
AATATTTTAATATTATATATTATATTATATTTTAA
Found at i:370987 original size:3 final size:3
Alignment explanation
Indices: 370979--371010 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
370969 AAATATTCTC
370979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
371011 TTTTACCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:371314 original size:18 final size:18
Alignment explanation
Indices: 371246--371351 Score: 86
Period size: 20 Copynumber: 5.4 Consensus size: 18
371236 AGAAAGATTG
371246 ATTTTTTTCGAAAAAAATTA
1 ATTTTTTT--AAAAAAATTA
*
371266 ATTTTCTTGTAAATATGAATTA
1 ATTTT-TT-TAAA-A-AAATTA
*
371288 TTATTTTTTAAAAAAATTA
1 AT-TTTTTTAAAAAAATTA
**
371307 ATTTTTTTAATGAATGATTA
1 ATTTTTTTAA--AAAAATTA
*
371327 ATTTTTTAAAAAAAATTA
1 ATTTTTTTAAAAAAATTA
371345 ATTTTTT
1 ATTTTTT
371352 ATGTATAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
18 21 0.30
19 6 0.09
20 24 0.34
21 7 0.10
22 9 0.13
23 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTTTTTTAAAAAAATTA
Found at i:371342 original size:38 final size:39
Alignment explanation
Indices: 371256--371351 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 39
371246 ATTTTTTTCG
*
371256 AAAAAAATTAATTTTCTTGTAAATATGAATTATTATTTTTT
1 AAAAAAATTAATTTT-TTGT-AATATGAATGATTATTTTTT
371297 AAAAAAATTAATTTTTT-T-A-ATGAATGATTAATTTTTT
1 AAAAAAATTAATTTTTTGTAATATGAATGATT-ATTTTTT
371334 AAAAAAAATTAATTTTTT
1 -AAAAAAATTAATTTTTT
371352 ATGTATAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
36 9 0.17
37 8 0.15
38 17 0.33
39 1 0.02
40 2 0.04
41 15 0.29
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (39 bp):
AAAAAAATTAATTTTTTGTAATATGAATGATTATTTTTT
Found at i:371352 original size:18 final size:18
Alignment explanation
Indices: 371290--371352 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
371280 ATGAATTATT
371290 ATTTTTT-AAAAAAATTA
1 ATTTTTTAAAAAAAATTA
* **
371307 ATTTTTTTAATGAATGATTA
1 A-TTTTTTAA-AAAAAATTA
371327 ATTTTTTAAAAAAAATTA
1 ATTTTTTAAAAAAAATTA
371345 ATTTTTTA
1 ATTTTTTA
371353 TGTATAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 1 0.03
18 20 0.54
19 9 0.24
20 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
ATTTTTTAAAAAAAATTA
Found at i:371621 original size:17 final size:18
Alignment explanation
Indices: 371607--371645 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
371597 ATTGAATTAT
371607 AATTTAAAAAAAATTTTAA
1 AATTTAAAAAAAA-TTTAA
*
371626 AATTTAAAAATAGATTTAA
1 AATTTAAAAA-AAATTTAA
371645 A
1 A
371646 TTTGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATTTAAAAAAAATTTAA
Found at i:372038 original size:27 final size:27
Alignment explanation
Indices: 372008--372059 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
371998 TATAAACATA
*
372008 TTTAAAATATT-TTATATTTATATTAAT
1 TTTAAAATATTAATA-ATTTATATTAAT
*
372035 TTTAATATATTAATAATTTATATTA
1 TTTAAAATATTAATAATTTATATTA
372060 TATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAAATATTAATAATTTATATTAAT
Found at i:372045 original size:14 final size:15
Alignment explanation
Indices: 372025--372071 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
372015 TATTTTATAT
372025 TTATATTAATTTTAA
1 TTATATTAATTTTAA
372040 -TATATTAATAATTTATA
1 TTATATTAAT--TTTA-A
*
372057 TTATATAAATTTTAA
1 TTATATTAATTTTAA
372072 ATTTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 8 0.30
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTAATTTTAA
Found at i:372146 original size:20 final size:16
Alignment explanation
Indices: 372099--372133 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
372089 GGTTATAATG
*
372099 TATTTTGATAATTTTA
1 TATTTTAATAATTTTA
372115 TATTTTAATAATTTTA
1 TATTTTAATAATTTTA
372131 TAT
1 TAT
372134 ATATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TATTTTAATAATTTTA
Found at i:372449 original size:11 final size:11
Alignment explanation
Indices: 372408--372452 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
372398 AGATATATTT
372408 ATATAAATATA
1 ATATAAATATA
*
372419 ATATTAAAAATA
1 ATA-TAAATATA
372431 AT-TAAAATATA
1 ATAT-AAATATA
372442 ATATAAATATA
1 ATATAAATATA
372453 TATTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 18 0.62
12 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAATATA
Found at i:372462 original size:16 final size:16
Alignment explanation
Indices: 372443--372490 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
372433 TAAAATATAA
372443 TATAAATATATATTTT
1 TATAAATATATATTTT
372459 TATAAA-A-ATATTTT
1 TATAAATATATATTTT
*
372473 T-TAAATATTATATATT
1 TATAAATA-TATATTTT
372489 TA
1 TA
372491 CTATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 4 0.15
14 9 0.33
15 1 0.04
16 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAAATATATATTTT
Found at i:373759 original size:32 final size:32
Alignment explanation
Indices: 373718--373807 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
373708 ATCCGAATCT
373718 GAAATGACCCGAACCCAAAATAACCTGAACCC
1 GAAATGACCCGAACCCAAAATAACCTGAACCC
*** *
373750 GAAATGACCCGAACTTGAAATAACTTGAACCC
1 GAAATGACCCGAACCCAAAATAACCTGAACCC
* *
373782 GAAATGACCTGAACTCGAAAATAACC
1 GAAATGACCCGAAC-CCAAAATAACC
373808 CGAAAATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
32 41 0.85
33 7 0.15
ACGTcount: A:0.43, C:0.28, G:0.14, T:0.14
Consensus pattern (32 bp):
GAAATGACCCGAACCCAAAATAACCTGAACCC
Found at i:373769 original size:16 final size:16
Alignment explanation
Indices: 373718--373811 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
373708 ATCCGAATCT
*
373718 GAAATGACCCGAACCC
1 GAAATAACCCGAACCC
* *
373734 AAAATAACCTGAACCC
1 GAAATAACCCGAACCC
* **
373750 GAAATGACCCGAACTT
1 GAAATAACCCGAACCC
**
373766 GAAATAACTTGAACCC
1 GAAATAACCCGAACCC
* * *
373782 GAAATGACCTGAACTC
1 GAAATAACCCGAACCC
373798 GAAAATAACCCGAA
1 G-AAATAACCCGAA
373812 AATTTTAAAA
Statistics
Matches: 59, Mismatches: 18, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
16 49 0.83
17 10 0.17
ACGTcount: A:0.44, C:0.28, G:0.15, T:0.14
Consensus pattern (16 bp):
GAAATAACCCGAACCC
Found at i:373770 original size:48 final size:49
Alignment explanation
Indices: 373717--373811 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 49
373707 GATCCGAATC
* *
373717 TGAAATGACCCGAACCCAAAATAACCTGAACCCG-AAATGACCCGAACT
1 TGAAATAACCCGAACCCAAAATAACCTGAACCCGAAAATAACCCGAACT
** * * *
373765 TGAAATAACTTGAACCCGAAATGACCTGAACTCGAAAATAACCCGAA
1 TGAAATAACCCGAACCCAAAATAACCTGAACCCGAAAATAACCCGAA
373812 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 28 0.72
49 11 0.28
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.15
Consensus pattern (49 bp):
TGAAATAACCCGAACCCAAAATAACCTGAACCCGAAAATAACCCGAACT
Found at i:376783 original size:23 final size:23
Alignment explanation
Indices: 376734--376784 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
376724 TATTTTTTTT
* * *
376734 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAAAAAACATA
376757 ATTTTTTAAAA-AAAAAAACATA
1 ATTTTTTAAAACAAAAAAACATA
*
376779 AATTTT
1 ATTTTT
376785 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTTTTAAAACAAAAAAACATA
Found at i:377330 original size:15 final size:17
Alignment explanation
Indices: 377310--377343 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
377300 CATTTCATAT
377310 TTTTTCTTT-TTT-TTC
1 TTTTTCTTTCTTTCTTC
377325 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
377342 TT
1 TT
377344 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:378375 original size:32 final size:32
Alignment explanation
Indices: 378326--378672 Score: 552
Period size: 32 Copynumber: 10.8 Consensus size: 32
378316 AAAATGGTGA
* * *
378326 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
378358 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
378390 TTTTAAATGGGTTGCCACCAACTTCTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
378422 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
378454 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
378486 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
378518 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
378550 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
378582 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
378614 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
378646 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
378673 AATTTAAAAG
Statistics
Matches: 294, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
31 1 0.00
32 292 0.99
33 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:378724 original size:27 final size:27
Alignment explanation
Indices: 378658--379449 Score: 1172
Period size: 27 Copynumber: 28.9 Consensus size: 27
378648 TGGAATGGGT
* * * *
378658 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
378685 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
378713 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
378740 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
378768 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
378796 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
378823 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
378851 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
378879 TGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
378906 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
378933 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
378960 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
378987 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
379015 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
379042 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
379069 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
379097 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
379124 TGCCACGGAGTTGTGGACTTGAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
379151 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
**
379179 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
379206 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
379233 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
379260 TGCCACAGAGTTGTGGACTTAAAATGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
379287 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
379314 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
379342 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
379369 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
379397 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
379424 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
379450 AAAATGCCAC
Statistics
Matches: 699, Mismatches: 54, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
27 445 0.64
28 254 0.36
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:378727 original size:55 final size:54
Alignment explanation
Indices: 378658--379449 Score: 1172
Period size: 55 Copynumber: 14.5 Consensus size: 54
378648 TGGAATGGGT
* * * *
378658 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
378713 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
378768 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
378823 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGG
* *
378879 TGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
378933 TGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
378987 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
379042 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-G
* *
379097 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTGAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* **
379151 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
379206 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
379260 TGCCACAGAGTTGTGGACTTAAAATGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
379314 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
379369 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
379424 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
379450 AAAATGCCAC
Statistics
Matches: 676, Mismatches: 51, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
54 237 0.35
55 391 0.58
56 48 0.07
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:378869 original size:82 final size:81
Alignment explanation
Indices: 378658--379449 Score: 1190
Period size: 82 Copynumber: 9.6 Consensus size: 81
378648 TGGAATGGGT
* * * * *
378658 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
378723 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
378740 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
378805 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
378823 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGA
*
378888 GTTATGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
378906 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
378971 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
* * * *
378987 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
379052 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
379069 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
379133 GTTGTGGACTTGAAAGGG
64 GTTGTGGACTTAAAAGGG
* *
379151 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
379216 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
379233 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAATGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
379298 TGTGGACTAAAAAGGG
66 TGTGGACTTAAAAGGG
* * *
379314 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
379379 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* *
379397 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAG
379450 AAAATGCCAC
Statistics
Matches: 654, Mismatches: 46, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
81 118 0.18
82 373 0.57
83 163 0.25
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:380521 original size:15 final size:15
Alignment explanation
Indices: 380501--380530 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
380491 AGGGTGAAAA
380501 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
380516 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
380531 AGGATTAGGT
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:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:386750 original size:23 final size:23
Alignment explanation
Indices: 386701--386751 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
386691 TATTTTTTTT
* * *
386701 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAAAAAACATA
386724 ATTTTTTAAAA-AAAAAAACATA
1 ATTTTTTAAAACAAAAAAACATA
*
386746 AATTTT
1 ATTTTT
386752 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTTTTAAAACAAAAAAACATA
Found at i:387297 original size:15 final size:17
Alignment explanation
Indices: 387277--387310 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
387267 CATTTCATAT
387277 TTTTTCTTT-TTT-TTC
1 TTTTTCTTTCTTTCTTC
387292 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
387309 TT
1 TT
387311 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:388385 original size:17 final size:17
Alignment explanation
Indices: 388365--388407 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
388355 CCTTTCATAA
388365 AATATAAAAATAAAAAT
1 AATATAAAAATAAAAAT
* * *
388382 AATATAATAATATAATT
1 AATATAAAAATAAAAAT
388399 AAT-TAAAAA
1 AATATAAAAA
388408 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAAAAATAAAAAT
Found at i:389588 original size:32 final size:34
Alignment explanation
Indices: 389534--389598 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
389524 GTAAGGCTTA
* *
389534 TATTAATAATCTCATAATTTATAT-AATATAAAT
1 TATTAATAATATCAAAATTTATATAAATATAAAT
389567 TATTAAT-ATATCAAAATTTATATAAATATAAA
1 TATTAATAATATCAAAATTTATATAAATATAAA
389599 GTAGCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
TATTAATAATATCAAAATTTATATAAATATAAAT
Found at i:389595 original size:18 final size:16
Alignment explanation
Indices: 389549--389598 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
389539 ATAATCTCAT
389549 AATTTATAT-AATATA
1 AATTTATATAAATATA
389564 AA-TTAT-TAATATATCAA
1 AATTTATATAA-ATAT--A
389581 AATTTATATAAATATA
1 AATTTATATAAATATA
389597 AA
1 AA
389599 GTAGCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 6 0.21
16 3 0.10
17 3 0.10
18 8 0.28
19 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTATATAAATATA
Found at i:390505 original size:20 final size:20
Alignment explanation
Indices: 390477--390519 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
390467 TCTAAATTCG
390477 AAATGATTCAATTTGAACTT
1 AAATGATTCAATTTGAACTT
* *
390497 AAATTATTCAATTTGAATTT
1 AAATGATTCAATTTGAACTT
390517 AAA
1 AAA
390520 ATAATCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
AAATGATTCAATTTGAACTT
Found at i:390626 original size:28 final size:27
Alignment explanation
Indices: 390584--390636 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
390574 AAAATATGTT
* *
390584 AAAAAAATTTAAAAAGTAATTTAATTA
1 AAAAAAATATAAAAAATAATTTAATTA
*
390611 AAAAAAATATACAAAAATATTTTAAT
1 AAAAAAATATA-AAAAATAATTTAAT
390637 AACACTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAAAATATAAAAAATAATTTAATTA
Found at i:390793 original size:24 final size:24
Alignment explanation
Indices: 390761--390808 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
390751 TGAATGACAC
390761 ATATCCAAATATATATAAGTATTA
1 ATATCCAAATATATATAAGTATTA
390785 ATATCCAAATATATATAAGTATTA
1 ATATCCAAATATATATAAGTATTA
390809 GTTGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATCCAAATATATATAAGTATTA
Found at i:391499 original size:19 final size:19
Alignment explanation
Indices: 391477--391526 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
391467 TAAAATGTTC
*
391477 TAATTTAATAAAAAATTAT
1 TAATTTAATAAAAAATAAT
* ** *
391496 TAATTGAGGATAAAATAAT
1 TAATTTAATAAAAAATAAT
391515 TAATTTAATAAA
1 TAATTTAATAAA
391527 TTGTTATGGG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
TAATTTAATAAAAAATAAT
Found at i:392974 original size:15 final size:15
Alignment explanation
Indices: 392954--392996 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
392944 AAAAAAATAT
*
392954 TATTTTTAGATATAA
1 TATTTTTAAATATAA
*
392969 TA-TTTTAAAAATAA
1 TATTTTTAAATATAA
*
392983 TATATTTAAATATA
1 TATTTTTAAATATA
392997 TTAACAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TATTTTTAAATATAA
Found at i:393202 original size:21 final size:22
Alignment explanation
Indices: 393167--393216 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
393157 TTACTCTTTT
393167 TTATTTAATTTTTAATA-AATAA
1 TTATTTAATTTTTAATATAA-AA
*
393189 TTATTTTA-TTTTAATATAAAA
1 TTATTTAATTTTTAATATAAAA
393210 TTATTTA
1 TTATTTA
393217 TGTAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTTAATTTTTAATATAAAA
Found at i:395755 original size:19 final size:18
Alignment explanation
Indices: 395723--395762 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
395713 TATTATCACG
*
395723 AATTTAAATGATAATCAT
1 AATTTAAATGATAATAAT
*
395741 AATTTAATATTATAATAAT
1 AATTTAA-ATGATAATAAT
395760 AAT
1 AAT
395763 ATTATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTTAAATGATAATAAT
Found at i:395764 original size:14 final size:14
Alignment explanation
Indices: 395745--395771 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
395735 AATCATAATT
395745 TAATATTATAATAA
1 TAATATTATAATAA
395759 TAATATTATAATA
1 TAATATTATAATA
395772 TTATTAATAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATTATAATAA
Found at i:395939 original size:22 final size:23
Alignment explanation
Indices: 395909--395978 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
395899 AAAAATAATT
* *
395909 ATAAAAATTTTAAATATTAATAA
1 ATAATAATTTTAAATAATAATAA
* *
395932 A-AATAATTTTTAATTAATATTAA
1 ATAATAA-TTTTAAATAATAATAA
395955 ATAATAA-TTTAAATTAA-AATAA
1 ATAATAATTTTAAA-TAATAATAA
395977 AT
1 AT
395979 TTATTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 15 0.39
23 18 0.47
24 5 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATAATTTTAAATAATAATAA
Found at i:396004 original size:22 final size:21
Alignment explanation
Indices: 395962--396004 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
395952 TAAATAATAA
*
395962 TTTAAATTAAAATAAATTTAT
1 TTTAAATTAAAATAAAATTAT
395983 TTTAAACTTAAAGA-AAAATTAT
1 TTTAAA-TTAAA-ATAAAATTAT
396005 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 12 0.63
23 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAATTAAAATAAAATTAT
Found at i:399544 original size:18 final size:17
Alignment explanation
Indices: 399523--399565 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
399513 GTAATAGTTA
*
399523 TTTATATTATTCAAATTT
1 TTTATATT-TTCAAAATT
*
399541 TTTAT-TTTTTAAAATT
1 TTTATATTTTCAAAATT
399557 TTTATATTT
1 TTTATATTT
399566 GATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 5 0.23
18 5 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTTCAAAATT
Found at i:399608 original size:13 final size:14
Alignment explanation
Indices: 399592--399626 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
399582 GTACATATTC
*
399592 AAATATAA-TATAA
1 AAATATAATTAAAA
399605 AAATATAATTAAAA
1 AAATATAATTAAAA
399619 AAATATAA
1 AAATATAA
399627 CTTTTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATATAATTAAAA
Found at i:401196 original size:55 final size:56
Alignment explanation
Indices: 401084--401188 Score: 128
Period size: 55 Copynumber: 1.9 Consensus size: 56
401074 ACTAATTTAA
* * *
401084 ATTAATAT-ATAATAATTATAATTTTTATTTAAATTTTATAATAAAATATAAAAAT
1 ATTAATATAAAAATAATTATAATTTTTATTTAAATTATATAATAAAAAATAAAAAT
*
401139 ATTAATATAAAAATAATTTTATATTTTT-TATT-AATTATA-AATAAAAAATA
1 ATTAATATAAAAATAATTATA-ATTTTTAT-TTAAATTATATAATAAAAAATA
401189 TGAATATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
55 18 0.42
56 17 0.40
57 8 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (56 bp):
ATTAATATAAAAATAATTATAATTTTTATTTAAATTATATAATAAAAAATAAAAAT
Found at i:401467 original size:14 final size:14
Alignment explanation
Indices: 401448--401509 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
401438 TGATATTTAT
401448 ATTAATATAATTAA
1 ATTAATATAATTAA
*
401462 ATTAATAAAATTTAA
1 ATTAATATAA-TTAA
401477 ATT--TA-AATTAA
1 ATTAATATAATTAA
*
401488 ATTATTATAA-TAA
1 ATTAATATAATTAA
401501 ATT-ATATAA
1 ATTAATATAA
401510 AATATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
11 7 0.17
12 7 0.17
13 10 0.24
14 11 0.26
15 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATATAATTAA
Found at i:402423 original size:16 final size:17
Alignment explanation
Indices: 402384--402425 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
402374 AATTTATTAT
*
402384 AAAATATTTTAAAATTTC
1 AAAATAATTTAAAA-TTC
402402 -AAATAATTTAAAA-TC
1 AAAATAATTTAAAATTC
402417 AAAATAATT
1 AAAATAATT
402426 AAATGTAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.09
16 8 0.36
17 12 0.55
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATAATTTAAAATTC
Found at i:402902 original size:17 final size:17
Alignment explanation
Indices: 402880--402918 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
402870 TGTAAAGTAA
402880 AAATAATAATAATAAAT
1 AAATAATAATAATAAAT
* *
402897 AAATAATATTAATTAAT
1 AAATAATAATAATAAAT
402914 AAATA
1 AAATA
402919 CCAATGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:407470 original size:27 final size:28
Alignment explanation
Indices: 407440--407492 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
407430 TAATATTTAT
407440 ATATT-TTTATAATTAAA-TAA-AATAAAA
1 ATATTATTT-TAA-TAAATTAATAATAAAA
407467 ATATTATTTTAATAAATTAATAATAA
1 ATATTATTTTAATAAATTAATAATAA
407493 TTTAAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 4 0.17
27 11 0.48
28 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATTATTTTAATAAATTAATAATAAAA
Found at i:407689 original size:21 final size:21
Alignment explanation
Indices: 407652--407710 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
407642 TTGAATAAGA
* *
407652 TTAAA-TTAATAAAAAATTAT
1 TTAAATTTAATTATAAATTAT
407672 TTAAATTTAATTATAAATTAT
1 TTAAATTTAATTATAAATTAT
* *
407693 ATAAATAGTAATTATAAA
1 TTAAAT-TTAATTATAAA
407711 AATATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.15
21 18 0.55
22 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAATTTAATTATAAATTAT
Found at i:407721 original size:46 final size:43
Alignment explanation
Indices: 407655--407747 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 43
407645 AATAAGATTA
407655 AATTAATAAAAAATTATTTAAATTTAATTATAAATTATATAAATAGT
1 AATTAATAAAAAATTATTT-AATTT--TTATAAATT-TATAAATAGT
* *
407702 AATT-ATAAAAATATT-TTTAATTTTTATTAATTTATAAATGGT
1 AATTAATAAAAA-ATTATTTAATTTTTATAAATTTATAAATAGT
407744 AATT
1 AATT
407748 CAAATTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
42 13 0.30
43 8 0.19
45 5 0.12
46 10 0.23
47 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (43 bp):
AATTAATAAAAAATTATTTAATTTTTATAAATTTATAAATAGT
Found at i:407894 original size:27 final size:26
Alignment explanation
Indices: 407840--407895 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
407830 ATTTTTATCC
* * *
407840 TATTTTAATTTTTTATTTTATAATTT
1 TATTTGAATTTTATATTTTATAACTT
*
407866 TATTTGAATTTTCATATTTTATTACTT
1 TATTTGAATTTT-ATATTTTATAACTT
407893 TAT
1 TAT
407896 ACTTCCTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (26 bp):
TATTTGAATTTTATATTTTATAACTT
Found at i:408908 original size:20 final size:21
Alignment explanation
Indices: 408863--408919 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
408853 TTTTTAATTT
408863 TTTTATATATTTAAAATATTA
1 TTTTATATATTTAAAATATTA
*
408884 TTTTATAT-TTTAATAT-TTA
1 TTTTATATATTTAAAATATTA
408903 TATTTATATATATTAAA
1 T-TTTATATAT-TTAAA
408920 TATAAATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.13
20 14 0.45
21 9 0.29
22 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATATTTAAAATATTA
Found at i:409710 original size:3 final size:3
Alignment explanation
Indices: 409702--409736 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
409692 TGTCCTCATT
*
409702 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
409737 TGAGGCTGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:410373 original size:23 final size:22
Alignment explanation
Indices: 410330--410412 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
410320 TAATAAAATA
* * *
410330 TAAATTTAAACTTAAATCTATT
1 TAAATCTAAACTAAAATCTATC
410352 TAAATCTAAACTAAAAATCTATC
1 TAAATCTAAACT-AAAATCTATC
* * * *
410375 TAAACCTAAACTCAAGTTTATC
1 TAAATCTAAACTAAAATCTATC
410397 TAAA-CTTAAACTAAAA
1 TAAATC-TAAACTAAAA
410413 GTTCAATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
21 1 0.02
22 30 0.60
23 19 0.38
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (22 bp):
TAAATCTAAACTAAAATCTATC
Found at i:411682 original size:17 final size:17
Alignment explanation
Indices: 411652--411690 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
411642 TTTTTCTTAT
* *
411652 AAATATTTAAAAAATAA
1 AAATAATTAAAAAAAAA
*
411669 AAATAATTATAAAAAAA
1 AAATAATTAAAAAAAAA
411686 AAATA
1 AAATA
411691 TAAATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATTAAAAAAAAA
Found at i:411683 original size:19 final size:19
Alignment explanation
Indices: 411649--411701 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
411639 GAATTTTTCT
411649 TATAAATATTTAAAAAATAAAA
1 TATAAATA--TAAAAAA-AAAA
*
411671 -ATAATTATAAAAAAAAAA
1 TATAAATATAAAAAAAAAA
411689 TATAAATATAAAA
1 TATAAATATAAAA
411702 GACATGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
21 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TATAAATATAAAAAAAAAA
Found at i:412146 original size:15 final size:15
Alignment explanation
Indices: 412126--412164 Score: 71
Period size: 14 Copynumber: 2.7 Consensus size: 15
412116 ATATTTTACT
412126 AATTAATTTCACTTA
1 AATTAATTTCACTTA
412141 AATTAA-TTCACTTA
1 AATTAATTTCACTTA
412155 AATTAATTTC
1 AATTAATTTC
412165 TTCATCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAATTTCACTTA
Found at i:412421 original size:19 final size:21
Alignment explanation
Indices: 412392--412430 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
412382 ATTTTAAATC
412392 AATTAAAAATAATA-ATTTTA
1 AATTAAAAATAATATATTTTA
412412 AATT-AAAATAATATATTTT
1 AATTAAAAATAATATATTTT
412431 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAAAAATAATATATTTTA
Found at i:412538 original size:7 final size:7
Alignment explanation
Indices: 412526--412551 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
412516 ATTTAAACTT
412526 AATTTAA
1 AATTTAA
412533 AATTTAA
1 AATTTAA
412540 AATTTAA
1 AATTTAA
412547 AATTT
1 AATTT
412552 TTCTAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:412671 original size:2 final size:2
Alignment explanation
Indices: 412666--412692 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
412656 CCCCACCCCT
412666 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
412693 TCACCACACC
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:414662 original size:17 final size:17
Alignment explanation
Indices: 414640--414674 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
414630 TCATGTTTGA
414640 CATATTCAGATATGGAT
1 CATATTCAGATATGGAT
414657 CATATTCAGATATGGAT
1 CATATTCAGATATGGAT
414674 C
1 C
414675 TGGGTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (17 bp):
CATATTCAGATATGGAT
Found at i:418550 original size:23 final size:22
Alignment explanation
Indices: 418514--418556 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
418504 ATTTTTATTT
* *
418514 ATATTATATTAAAATTATATAA
1 ATATTATATAAAAATAATATAA
418536 ATATTAATATAAAAATAATAT
1 ATATT-ATATAAAAATAATAT
418557 TTTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATTATATAAAAATAATATAA
Found at i:420663 original size:35 final size:35
Alignment explanation
Indices: 420605--420679 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 35
420595 TTAATTATTT
*
420605 AATAATATTAAAAAAAATTAATTAATTTTTAA-AA
1 AATAATATTAAAAAAAATAAATTAATTTTTAATAA
420639 AATAATATTAAAAAATTAA-AAATTAATTTTTAATAA
1 AATAATATTAAAAAA--AATAAATTAATTTTTAATAA
420675 AATAA
1 AATAA
420680 AAAATTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 15 0.41
35 13 0.35
36 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (35 bp):
AATAATATTAAAAAAAATAAATTAATTTTTAATAA
Found at i:420683 original size:31 final size:32
Alignment explanation
Indices: 420594--420688 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 32
420584 TTATATTAAT
*
420594 ATTAATTATTTAATAATATTAAAAAAAATT---A
1 ATTAATT-TTTAATAATAAT-AAAAAAATTAAAA
*
420625 ATTAATTTTTAAAAAATAATATTAAAAAATTAAAA
1 ATTAATTTTT-AATAATAATA--AAAAAATTAAAA
420660 ATTAATTTTTAATAA-AAT-AAAAAATTAAA
1 ATTAATTTTTAATAATAATAAAAAAATTAAA
420689 TTTAAAATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
30 15 0.27
31 14 0.25
32 8 0.15
33 3 0.05
34 4 0.07
35 11 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
ATTAATTTTTAATAATAATAAAAAAATTAAAA
Found at i:420684 original size:23 final size:21
Alignment explanation
Indices: 420634--420701 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 21
420624 AATTAATTTT
420634 TAAAAAA-TAATATTAAAAAA
1 TAAAAAATTAATATTAAAAAA
* *
420654 TTAAAAATTAATTTTTAATAAAA
1 TAAAAAATTAA-TATTAA-AAAA
* *
420677 TAAAAAATTAA-ATTTAAAAT
1 TAAAAAATTAATATTAAAAAA
420697 TAAAA
1 TAAAA
420702 TTTAAAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 14 0.36
21 6 0.15
22 5 0.13
23 14 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAATTAATATTAAAAAA
Found at i:420695 original size:12 final size:12
Alignment explanation
Indices: 420680--420713 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
420670 AATAAAATAA
420680 AAAATTAAATTT
1 AAAATTAAATTT
420692 AAAATTAAAATTT
1 AAAATT-AAATTT
*
420705 AAAAGTAAA
1 AAAATTAAA
420714 AGTGATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:420713 original size:19 final size:19
Alignment explanation
Indices: 420672--420714 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
420662 TAATTTTTAA
**
420672 TAAAATAAAAAATTAAATT
1 TAAAATAAAAAATTAAAAG
* *
420691 TAAAATTAAAATTTAAAAG
1 TAAAATAAAAAATTAAAAG
420710 TAAAA
1 TAAAA
420715 GTGATCGGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAATAAAAAATTAAAAG
Found at i:420946 original size:18 final size:18
Alignment explanation
Indices: 420900--420946 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
420890 ATTTTTTACG
420900 ATATAATT-TATTTTTAA
1 ATATAATTATATTTTTAA
* *
420917 TTATTAA-AATATTTTTAA
1 ATA-TAATTATATTTTTAA
420935 ATATAATTATAT
1 ATATAATTATAT
420947 AAGTTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATAATTATATTTTTAA
Found at i:421007 original size:48 final size:48
Alignment explanation
Indices: 420893--421039 Score: 160
Period size: 47 Copynumber: 3.1 Consensus size: 48
420883 TTAAATAATT
* * * *
420893 TTTTACGATATAATTTATTTTTAATTATTAAAATATTTTTAAATATA-ATTA
1 TTTTAAGATATAATTTATTTTT-ATTTTTAAAA-A--TTTAAATTTATTTTA
* *
420944 -TATAAG-TTTAA-TTATTTTTATTTTTAAAAATTTAAATTTATTTTA
1 TTTTAAGATATAATTTATTTTTATTTTTAAAAATTTAAATTTATTTTA
420989 TTTTAAGATATAATTTA-TTTTATTTTTAAAAATTTAAATTTATTTTTA
1 TTTTAAGATATAATTTATTTTTATTTTTAAAAATTTAAATTTA-TTTTA
421037 TTT
1 TTT
421040 GATTATATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
44 9 0.11
45 3 0.04
46 6 0.07
47 38 0.46
48 19 0.23
49 4 0.05
50 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTTAAGATATAATTTATTTTTATTTTTAAAAATTTAAATTTATTTTA
Found at i:421048 original size:48 final size:48
Alignment explanation
Indices: 420959--421054 Score: 149
Period size: 47 Copynumber: 2.0 Consensus size: 48
420949 GTTTAATTAT
*
420959 TTTTATTTTTAAAAATTTAAATTTATTTTATTTTAAGATATAA-TTTA
1 TTTTATTTTTAAAAATTTAAATTTATTTTATTTGAAGATATAAGTTTA
**
421006 TTTTATTTTTAAAAATTTAAATTTATTTTTATTTGATTATATAAGTTTA
1 TTTTATTTTTAAAAATTTAAATTTA-TTTTATTTGAAGATATAAGTTTA
421055 AATTTTTACA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 25 0.57
48 15 0.34
49 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (48 bp):
TTTTATTTTTAAAAATTTAAATTTATTTTATTTGAAGATATAAGTTTA
Found at i:421203 original size:144 final size:141
Alignment explanation
Indices: 420997--421392 Score: 383
Period size: 144 Copynumber: 2.8 Consensus size: 141
420987 TATTTTAAGA
* * * *
420997 TATAATTTA-TTTTATTTTTAAAAATTTAAATTTA-TTTTTATTTGATTATATAAGTTTAAATTT
1 TATAATTAATTTTTATTTATAAAAATTTAAATTTATTTTTTGTTTGATTATATGAGTTTAAATTT
* * *
421060 TTACAGATGAAATTTATTTTTATTAGTAAAAATTTAAATTTACTTTTTGATTTTGATTT-TACCA
66 TTA-AGAT-AAATTTATTTTTATTAGTAAAAATTTAAATTTA-TTTTTGAGTATG-TTTATAACA
** *
421124 GTTTATCTTTTTTA-
127 GTTTAAATTTTTAAC
* * * * *
421138 TATTATTAATTTTTATTTGTGAAAGTTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATT
1 TATAATTAATTTTTATTTATAAAAATTTAAATTTA-TTTTTTGTTTGATTATATGAGTTTAAATT
* * * * * *
421203 TTT-TGAGTAATATTTATATTTATTTGTAAAAGTTTAAATGTGT-TTTTTTAGTATGTTTATAAG
65 TTTAAGA-TAA-ATTTATTTTTATTAGTAAAAATTTAAAT-T-TATTTTTGAGTATGTTTATAAC
421266 AGTTTAAATTTTTAAC
126 AGTTTAAATTTTTAAC
* * * ** *
421282 TTATAATTTATTTTTATTTATAAAAATTTAAATGTGTTTTTTGAGTGATTATATGAGTTTATATT
1 -TATAATTAATTTTTATTTATAAAAATTTAAATTTATTTTTTGTTTGATTATATGAGTTTAAATT
*
421347 TTTATGATATAATTTATTTTTATTTA-TAAAAATTTAAATTTATTTT
65 TTTAAGATA-AATTTATTTTTA-TTAGTAAAAATTTAAATTTATTTT
421393 GTGTATTGAT
Statistics
Matches: 207, Mismatches: 34, Indels: 26
0.78 0.13 0.10
Matches are distributed among these distances:
141 7 0.03
142 30 0.14
143 54 0.26
144 81 0.39
145 35 0.17
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (141 bp):
TATAATTAATTTTTATTTATAAAAATTTAAATTTATTTTTTGTTTGATTATATGAGTTTAAATTT
TTAAGATAAATTTATTTTTATTAGTAAAAATTTAAATTTATTTTTGAGTATGTTTATAACAGTTT
AAATTTTTAAC
Found at i:421235 original size:72 final size:71
Alignment explanation
Indices: 421001--421392 Score: 318
Period size: 71 Copynumber: 5.5 Consensus size: 71
420991 TTAAGATATA
* * * *
421001 ATTTA-TTTTATTTTTAAAAATTTAAATTTA--TTTTTATTTGATTATATAAGTTTAAATTTTTA
1 ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATTTTT-
*
421063 CAGATGAA-
65 -TGAT-AAT
* * * ** **
421071 ATTTATTTTTATTAGTAAAAATTTAAATTTA-CTTTTTGATTTTGATTTTACCAGTTTATCTTTT
1 ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTTG-TTTT-ATTATATGAGTTTAAATTTT
*
421135 TT-ATATT
64 TTGATAAT
* * *
421142 ATTAATTTTTATTTGTGAAAGTTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATTTTTT
1 ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATTTTTT
421207 GAGTAAT
66 GA-TAAT
* * * * * *
421214 ATTTATATTTATTTGTAAAAGTTTAAATGTGTTTTTTTAGTATGT-TTATAAGAGTTTAAA-TTT
1 ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTT-GT-TTTATTATATGAGTTTAAATTTT
* *
421277 TTAACTTAT
64 TTGA-TAAT
* * * ** * *
421286 AATTTATTTTTATTTATAAAAATTTAAATGT-GTTTTTTGAGTGATTATATGAGTTTATATTTTT
1 -ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATTTTT
421350 ATGAT-AT
65 -TGATAAT
*
421357 AATTTATTTTTATTTATAAAAATTTAAATTTATTTT
1 -ATTTATTTTTATTTGTAAAAATTTAAATTTATTTT
421393 GTGTATTGAT
Statistics
Matches: 262, Mismatches: 45, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
70 23 0.09
71 103 0.39
72 70 0.27
73 48 0.18
74 18 0.07
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (71 bp):
ATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTTGTTTTATTATATGAGTTTAAATTTTTT
GATAAT
Found at i:421700 original size:36 final size:35
Alignment explanation
Indices: 421651--421740 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 35
421641 TTTATTAAAA
*
421651 ATTAAAAAATTAATT-TTTTAATTTTTTAATATATTTT
1 ATTAAAAAATTAATTAATTTAATTTTTT--TA-ATTTT
*
421688 -TTAAAAATTTAATTAAATTTAATTTTTTTAATTTT
1 ATTAAAAAATTAATT-AATTTAATTTTTTTAATTTT
421723 ATTAAAAAATTAA-TAATT
1 ATTAAAAAATTAATTAATT
421741 AATATGTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
34 4 0.09
35 6 0.13
36 26 0.55
38 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
ATTAAAAAATTAATTAATTTAATTTTTTTAATTTT
Found at i:421740 original size:39 final size:38
Alignment explanation
Indices: 421658--421754 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 38
421648 AAAATTAAAA
*
421658 AATTAATTTTTTAATTTTTTAATATATTTTTTAAAAATTT
1 AATTAA-TATTTAATTTTTT-ATATATTTTTTAAAAATTT
421698 AATTAA-ATTTAATTTTTT-TA-ATTTTATTAAAAAATTAAT
1 AATTAATATTTAATTTTTTATATATTTT-TT-AAAAATT--T
421737 AATTAATATGTTAATTTT
1 AATTAATAT-TTAATTTT
421755 AAAAAATATT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
35 5 0.10
36 4 0.08
37 7 0.14
38 11 0.22
39 7 0.14
40 8 0.16
41 8 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
AATTAATATTTAATTTTTTATATATTTTTTAAAAATTT
Found at i:422199 original size:50 final size:50
Alignment explanation
Indices: 422145--422245 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
422135 TTCAAAGTTT
422145 AATCTGTCATTTATACCACTTTCAGAATTTTAAAAAAAATGTATTATTTA
1 AATCTGTCATTTATACCACTTTCAGAATTTTAAAAAAAATGTATTATTTA
422195 AATCTGTCATTTATACCACTTTCAGAATTTTAAAAAAAATGTATTATTTA
1 AATCTGTCATTTATACCACTTTCAGAATTTTAAAAAAAATGTATTATTTA
422245 A
1 A
422246 TTTAAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.42
Consensus pattern (50 bp):
AATCTGTCATTTATACCACTTTCAGAATTTTAAAAAAAATGTATTATTTA
Found at i:424115 original size:16 final size:16
Alignment explanation
Indices: 424082--424138 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
424072 ACCCAAAATA
*
424082 CGAAATGATTCGAAACT
1 CGAAATGA-TCCAAACT
424099 CGAAATGATCCAAACT
1 CGAAATGATCCAAACT
** *
424115 CGAAATGATCTGAATT
1 CGAAATGATCCAAACT
424131 CGAAATGA
1 CGAAATGA
424139 CTCAACAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 28 0.78
17 8 0.22
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (16 bp):
CGAAATGATCCAAACT
Found at i:424952 original size:26 final size:26
Alignment explanation
Indices: 424923--424976 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
424913 TAATTTAAAT
*
424923 TTAAAATAA-TTTAAACTTAAAAATAA
1 TTAAAA-AATTTTAAAATTAAAAATAA
*
424949 TTAAAAAATTTTAAAATTTAAAATAA
1 TTAAAAAATTTTAAAATTAAAAATAA
424975 TT
1 TT
424977 TAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAAAAAATTTTAAAATTAAAAATAA
Found at i:424953 original size:16 final size:16
Alignment explanation
Indices: 424904--424950 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
424894 AAATGATTCG
*
424904 AATTCAAAATAATTTA
1 AATTAAAAATAATTTA
*
424920 AATTTAAAATAATTTA
1 AATTAAAAATAATTTA
424936 AACTTAAAAATAATT
1 AA-TTAAAAATAATT
424951 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAAAATAATTTA
Found at i:425729 original size:229 final size:233
Alignment explanation
Indices: 425295--425753 Score: 730
Period size: 229 Copynumber: 2.0 Consensus size: 233
425285 ATATCAGAAA
* * * *
425295 ATTAATTTTATGAATTGAATATCTAGTAAAATTTTTTTAAATAGGTATAATATAAGTGATAAAAT
1 ATTAATTTTATGAATTGAATATCCAGTAAAAATTTTTAAAATAGATATAATATAAGTGATAAAAT
* *
425360 ATATTTATATTTATAAAAAAATTAAAATTAAAATTTATATAAACACCTTTTTAAAGAATTAAATA
66 ATATTTATATTTATAAAAAAATTAAAATTAAAATTTATATAAACACCTTTTAAAAAAATTAAATA
* **
425425 TATATTCTCAATTCAAATCATAAAATAAATGAGTAAAGATGAAAAAAACTAACATTAAGTCATTT
131 TATATTCTCAATTCAAACCATAAAATAAATGAGTAAAGATGAAAAAAACTAACAGGAAGTCATTT
*
425490 AATTAAACAAACCTATAAATTACATAATGAAAAAGGATT
196 AATTAAACAAACCTATAAATGACATAAT-AAAAAGGATT
* *
425529 ATTAATTTTATGAATTGAATATCCAGTAAAAATTTTTAAAATTGATATAATATGAGTGATAAAAT
1 ATTAATTTTATGAATTGAATATCCAGTAAAAATTTTTAAAATAGATATAATATAAGTGATAAAAT
* *
425594 ATTTTTATATTTAT-AAAAAATTAAAATTAAAATTTATATAAATA-CTTTTAAAAAAATT-AA-A
66 ATATTTATATTTATAAAAAAATTAAAATTAAAATTTATATAAACACCTTTTAAAAAAATTAAATA
* *
425655 TA-CTTCTCAATTCAAACCATAAAATAAATGAGTAAAGATTAAAAAAACTAACAGGAAGTCATTT
131 TATATTCTCAATTCAAACCATAAAATAAATGAGTAAAGATGAAAAAAACTAACAGGAAGTCATTT
425719 AATTAAACAAACCTATAAATGACATAATAAAAAGG
196 AATTAAACAAACCTATAAATGACATAATAAAAAGG
425754 GCTTACTAAG
Statistics
Matches: 209, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
228 7 0.03
229 84 0.40
230 3 0.01
231 2 0.01
232 12 0.06
233 29 0.14
234 72 0.34
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (233 bp):
ATTAATTTTATGAATTGAATATCCAGTAAAAATTTTTAAAATAGATATAATATAAGTGATAAAAT
ATATTTATATTTATAAAAAAATTAAAATTAAAATTTATATAAACACCTTTTAAAAAAATTAAATA
TATATTCTCAATTCAAACCATAAAATAAATGAGTAAAGATGAAAAAAACTAACAGGAAGTCATTT
AATTAAACAAACCTATAAATGACATAATAAAAAGGATT
Found at i:426997 original size:23 final size:23
Alignment explanation
Indices: 426971--427023 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
426961 TTTATATTTT
426971 TTAATTAA-ATT-AATATTATCTAA
1 TTAATTAACATTAAAT-TTAT-TAA
*
426994 TTAAATAACATTAAATTTATTAA
1 TTAATTAACATTAAATTTATTAA
*
427017 ATAATTA
1 TTAATTA
427024 TATATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 15 0.60
24 7 0.28
25 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATTAACATTAAATTTATTAA
Found at i:427265 original size:20 final size:20
Alignment explanation
Indices: 427213--427269 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
427203 ATCGGACAAA
*
427213 TAAATTTAAATAAATTATTATT
1 TAAATTTAAAT--ATTTTTATT
* **
427235 TATATAAAAATATTTTTATT
1 TAAATTTAAATATTTTTATT
427255 TAAATTTAAATATTT
1 TAAATTTAAATATTT
427270 ATTAATATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 20 0.71
22 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTTAAATATTTTTATT
Found at i:427824 original size:32 final size:33
Alignment explanation
Indices: 427767--427856 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 33
427757 AATTTTTAAA
427767 AAAT-TTAAATAGATATTGATTATAAACTTGAT
1 AAATATTAAATAGATATTGATTATAAACTTGAT
* * * * *
427799 GATTATTAAATATA-ATTGTTTATAAATTTGAT
1 AAATATTAAATAGATATTGATTATAAACTTGAT
*
427831 AAATATTAAA-AAATATT-ATTCATAAA
1 AAATATTAAATAGATATTGATT-ATAAA
427857 TTTATCATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 4 0.09
32 34 0.74
33 8 0.17
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (33 bp):
AAATATTAAATAGATATTGATTATAAACTTGAT
Found at i:430101 original size:2 final size:2
Alignment explanation
Indices: 430094--430134 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
430084 GAGATTTTCA
*
430094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
430135 AATAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:430716 original size:17 final size:17
Alignment explanation
Indices: 430694--430751 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 17
430684 TAAGTTTGAA
430694 TTATTATTTAATTTAAT
1 TTATTATTTAATTTAAT
430711 TTATTATTTAATTAATAAT
1 TTATTATTTAATT--TAAT
430730 TATAATTTATTTAAATTTAAT
1 T-T-A-TTATTT-AATTTAAT
430751 T
1 T
430752 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 13 0.37
19 5 0.14
20 1 0.03
21 6 0.17
22 6 0.17
23 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATTTAATTTAAT
Found at i:430752 original size:21 final size:23
Alignment explanation
Indices: 430699--430755 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
430689 TTGAATTATT
*
430699 ATTTAATT-TAATTTATTATTTA
1 ATTTAATTATAATTTATTATTAA
430721 ATTAATAATTATAATTTA-T-TTAA
1 ATT--TAATTATAATTTATTATTAA
430744 ATTTAATTATAA
1 ATTTAATTATAA
430756 AAATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 6 0.19
24 6 0.19
25 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATTATAATTTATTATTAA
Found at i:430807 original size:10 final size:10
Alignment explanation
Indices: 430792--430827 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
430782 ATAAAATAAC
430792 TTTTAAAATA
1 TTTTAAAATA
*
430802 TTTTAATATA
1 TTTTAAAATA
430812 TTTT-AAATA
1 TTTTAAAATA
430821 TTTTAAA
1 TTTTAAA
430828 TCAACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:430823 original size:9 final size:9
Alignment explanation
Indices: 430792--430828 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
430782 ATAAAATAAC
430792 TTTTAAAATA
1 TTTT-AAATA
430802 TTTTAATATA
1 TTTTAA-ATA
430812 TTTTAAATA
1 TTTTAAATA
430821 TTTTAAAT
1 TTTTAAAT
430829 CAACTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTAAATA
Found at i:431110 original size:19 final size:18
Alignment explanation
Indices: 431073--431109 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
431063 AAATAATGAA
* *
431073 TAAAAAATTGATAGTTTT
1 TAAAAAATAGAAAGTTTT
431091 TAAAAAATAGAAAGTTTT
1 TAAAAAATAGAAAGTTTT
431109 T
1 T
431110 TTCCTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
TAAAAAATAGAAAGTTTT
Found at i:433046 original size:21 final size:21
Alignment explanation
Indices: 433021--433077 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
433011 ATTTAAAATA
*
433021 ATATTAAAATATTAATTTTTT
1 ATATTAAAATATTAATATTTT
*
433042 ATATTAATAT-TTATATATTTT
1 ATATTAAAATATTA-ATATTTT
433063 ATAATT-AAATATTAA
1 AT-ATTAAAATATTAA
433078 AATAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTAAAATATTAATATTTT
Found at i:433047 original size:13 final size:14
Alignment explanation
Indices: 433002--433060 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
432992 TCTAAAAATT
*
433002 TATATTAGTATTTA
1 TATATTAATATTTA
* *
433016 -A-AATAATATTAA
1 TATATTAATATTTA
* *
433028 AATATTAAT-TTTT
1 TATATTAATATTTA
433041 TATATTAATATTTA
1 TATATTAATATTTA
433055 TATATT
1 TATATT
433061 TTATAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
12 8 0.24
13 12 0.35
14 14 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TATATTAATATTTA
Found at i:434586 original size:15 final size:14
Alignment explanation
Indices: 434556--434591 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
434546 GAGTGTAGGA
*
434556 TTTTGAGTTTGGGG
1 TTTTGATTTTGGGG
434570 TTTTGATTTTGGGGG
1 TTTTGATTTT-GGGG
434585 TTTTGAT
1 TTTTGAT
434592 AGTCTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.08, C:0.00, G:0.36, T:0.56
Consensus pattern (14 bp):
TTTTGATTTTGGGG
Found at i:437475 original size:17 final size:18
Alignment explanation
Indices: 437439--437486 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
437429 GTTACCCTCG
437439 ATAATATATAAATTATAT
1 ATAATATATAAATTATAT
437457 ATAAT-TATAAATTTAATAT
1 ATAATATATAAA-TT-ATAT
437476 ATATATATATA
1 ATA-ATATATA
437487 TGTAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 7 0.27
20 2 0.08
21 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATATATAAATTATAT
Found at i:437779 original size:24 final size:24
Alignment explanation
Indices: 437752--437802 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
437742 TTATTTAAAA
**
437752 TAATATTAAAAATTATTTTTATAT
1 TAATATTAAAAATTAAATTTATAT
* *
437776 TAATATTTATAATTAAATTTATAT
1 TAATATTAAAAATTAAATTTATAT
437800 TAA
1 TAA
437803 AAACTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATATTAAAAATTAAATTTATAT
Found at i:437786 original size:12 final size:11
Alignment explanation
Indices: 437769--437803 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
437759 AAAAATTATT
437769 TTTATATTAATA
1 TTTATATTAA-A
437781 TTTATAATTAAA
1 TTTAT-ATTAAA
437793 TTTATATTAAA
1 TTTATATTAAA
437804 AACTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 11 0.50
13 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:438522 original size:53 final size:55
Alignment explanation
Indices: 438459--438564 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 55
438449 TGAGTTTTTT
438459 TTTTTAATTATCA-TAGTGTTG-CT-TTTATAGTTGCCCATACTAGCAAAAGTTTG
1 TTTTTAATTATCAGT-GTGTTGCCTCTTTATAGTTGCCCATACTAGCAAAAGTTTG
* * * *
438512 TTTTTAATTATGAGTTTGTTGCTCTCTTTGTAGTTGCCCATGCTAGCAAAAGT
1 TTTTTAATTATCAGTGTGTTGC-CTCTTTATAGTTGCCCATACTAGCAAAAGT
438565 ACCAATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
53 17 0.38
54 1 0.02
55 2 0.04
56 25 0.56
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (55 bp):
TTTTTAATTATCAGTGTGTTGCCTCTTTATAGTTGCCCATACTAGCAAAAGTTTG
Found at i:439941 original size:14 final size:14
Alignment explanation
Indices: 439922--439952 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
439912 GTAGAAATTC
439922 TTTATTTTATTTAT
1 TTTATTTTATTTAT
*
439936 TTTATTTTCTTTAT
1 TTTATTTTATTTAT
439950 TTT
1 TTT
439953 CTAATTTTTA
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:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:440084 original size:29 final size:29
Alignment explanation
Indices: 440009--440084 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
439999 TTTTTTTAAT
440009 AATTTAAA-TTAATTTTTTATTAAAAATTA
1 AATTTAAATTTAATTTTTTA-TAAAAATTA
* *
440038 AATATAAAATTTTTATTTTTTA-AAAAATTTA
1 AAT-TTAAA-TTTAATTTTTTATAAAAA-TTA
*
440069 AATTTAAATTTGATTT
1 AATTTAAATTTAATTT
440085 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 10 0.26
30 13 0.33
31 6 0.15
32 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
AATTTAAATTTAATTTTTTATAAAAATTA
Found at i:440259 original size:20 final size:19
Alignment explanation
Indices: 440236--440276 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
440226 TTTATATTTG
*
440236 AATTAATCTTAATATAAAAT
1 AATTAAACTTAATA-AAAAT
*
440256 AATTAAACTTGATAAAAAT
1 AATTAAACTTAATAAAAAT
440275 AA
1 AA
440277 AATATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTAAACTTAATAAAAAT
Found at i:440742 original size:15 final size:15
Alignment explanation
Indices: 440714--440755 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
440704 GGAAATAAAA
* *
440714 ATTAAATTTGATAAT
1 ATTAAATATAATAAT
440729 ATTAAATATAATAAT
1 ATTAAATATAATAAT
*
440744 -TAAAATATAATA
1 ATTAAATATAATA
440756 TGATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAAATATAATAAT
Found at i:440856 original size:8 final size:8
Alignment explanation
Indices: 440843--440876 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
440833 TTTTAAATAT
440843 AATTATAA
1 AATTATAA
440851 AATTATAA
1 AATTATAA
440859 AATTATAA
1 AATTATAA
440867 AATATATAA
1 AAT-TATAA
440876 A
1 A
440877 TATAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTATAA
Found at i:440864 original size:16 final size:17
Alignment explanation
Indices: 440843--440898 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
440833 TTTTAAATAT
440843 AATTATAAAAT-TATAA
1 AATTATAAAATATATAA
440859 AATTATAAAATATATAA
1 AATTATAAAATATATAA
* *
440876 ATATAATATAAATATATGA
1 A-ATTATA-AAATATATAA
440895 AATT
1 AATT
440899 TTAACTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.32
17 6 0.18
18 7 0.21
19 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTATAAAATATATAA
Found at i:440910 original size:21 final size:18
Alignment explanation
Indices: 440847--440897 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
440837 AAATATAATT
*
440847 ATAAAAT-TATAAA-ATT
1 ATAAAATATATAAATATA
440863 ATAAAATATATAAATATA
1 ATAAAATATATAAATATA
440881 ATATAAATATATGAAAT
1 ATA-AAATATAT-AAAT
440898 TTTAACTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 5 0.17
19 8 0.27
20 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATATATAAATATA
Found at i:441572 original size:2 final size:2
Alignment explanation
Indices: 441565--441602 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
441555 AAAAGGGTAA
441565 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
441603 TATCCTTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442667 original size:22 final size:21
Alignment explanation
Indices: 442642--442716 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
442632 TAAATTATTA
*
442642 TTTAATAAAAGAATATTTATAT
1 TTTAATAATA-AATATTTATAT
* * *
442664 TTTAATTATAAATATATAAAT
1 TTTAATAATAAATATTTATAT
442685 TTTAATATATAAAT-TTTAATAT
1 TTTAATA-ATAAATATTT-ATAT
442707 TTTAATAATA
1 TTTAATAATA
442717 TTTAAATAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 20 0.45
22 24 0.55
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTTAATAATAAATATTTATAT
Found at i:442677 original size:21 final size:22
Alignment explanation
Indices: 442653--442713 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
442643 TTAATAAAAG
442653 AATATTTATATTTTAAT-TATA
1 AATATTTATATTTTAATATATA
* *
442674 AATATATAAATTTTAATATATA
1 AATATTTATATTTTAATATATA
442696 AAT-TTTAATATTTTAATA
1 AATATTT-ATATTTTAATA
442714 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTATATTTTAATATATA
Found at i:442706 original size:12 final size:14
Alignment explanation
Indices: 442674--442706 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
442664 TTTAATTATA
442674 AATATATAAATTTT
1 AATATATAAATTTT
442688 AATATATAAATTTT
1 AATATATAAATTTT
442702 AATAT
1 AATAT
442707 TTTAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATATAAATTTT
Found at i:443993 original size:21 final size:21
Alignment explanation
Indices: 443967--444006 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
443957 TGTAAAAAAC
443967 TTTTTACTTAT-AGAAAATTTA
1 TTTTTA-TTATAAGAAAATTTA
*
443988 TTTTTATTTTAAGAAAATT
1 TTTTTATTATAAGAAAATT
444007 GACCTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTTATTATAAGAAAATTTA
Found at i:444568 original size:5 final size:5
Alignment explanation
Indices: 444553--444675 Score: 60
Period size: 5 Copynumber: 24.2 Consensus size: 5
444543 TGATAATTTA
* * *
444553 TATAT TTTAT TATAT TATAAT TATATT TAAAAT T-T-T TATAT TATAA
1 TATAT TATAT TATAT TAT-AT TATA-T T-ATAT TATAT TATAT TATAT
* * *
444599 TA-ATT TATAT TATA- TAAAT TATAA AATAT T-TA- TATATT TATATT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATA-T TATA-T
* *
444643 TATAT TTTAT TTTAAT TATTAT TATAT TATAT T
1 TATAT TATAT TAT-AT TA-TAT TATAT TATAT T
444676 CATACAATCA
Statistics
Matches: 91, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
3 3 0.03
4 9 0.10
5 49 0.54
6 27 0.30
7 3 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:444641 original size:14 final size:14
Alignment explanation
Indices: 444538--444656 Score: 66
Period size: 14 Copynumber: 7.9 Consensus size: 14
444528 ATCAATCATG
444538 ATATTTGATAATTTAT
1 ATATTT-AT-ATTTAT
444554 ATATTT-TATTATATT
1 ATATTTATATT-TA-T
*
444569 ATAATTATATTTA-
1 ATATTTATATTTAT
* *
444582 AAATTTTTATATTAT
1 ATATTTATAT-TTAT
444597 AATAATTTATATTATAT
1 -AT-ATTTATATT-TAT
*
444614 AAATTATAAAATATTTAT
1 ATATT-T---ATATTTAT
444632 ATATTTATATTTAT
1 ATATTTATATTTAT
444646 AT-TTTAT-TTTA
1 ATATTTATATTTA
444657 ATTATTATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 28
0.70 0.07 0.24
Matches are distributed among these distances:
12 4 0.05
13 15 0.18
14 16 0.19
15 11 0.13
16 14 0.17
17 11 0.13
18 7 0.08
19 5 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
ATATTTATATTTAT
Found at i:445064 original size:18 final size:19
Alignment explanation
Indices: 445041--445078 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
445031 TAGTTGAATT
445041 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
445059 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
445078 A
1 A
445079 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:445347 original size:8 final size:8
Alignment explanation
Indices: 445336--445369 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
445326 ATTTAACAAA
445336 AAATTATT
1 AAATTATT
445344 AAATTATT
1 AAATTATT
445352 -AATTATT
1 AAATTATT
*
445359 AAATTTTT
1 AAATTATT
445367 AAA
1 AAA
445370 ATATGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTATT
Found at i:445357 original size:15 final size:15
Alignment explanation
Indices: 445337--445368 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
445327 TTTAACAAAA
445337 AATTATTAAATTATT
1 AATTATTAAATTATT
*
445352 AATTATTAAATTTTT
1 AATTATTAAATTATT
445367 AA
1 AA
445369 AATATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATTAAATTATT
Done.