Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 1758877
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
File 4 of 12
Found at i:491834 original size:120 final size:120
Alignment explanation
Indices: 491705--491931 Score: 377
Period size: 120 Copynumber: 1.9 Consensus size: 120
491695 TTTATGTCGT
491705 ATTAATATTTTTTTC-ATATAATATTATATTTTGTATCTTATTTAGTTATTTTTTCATGTCA-TG
1 ATTAATATTTTTTTCTATATAATATTATATTTTGTATCTTATTTAGTTATTTTTT-ATGTCACT-
*
491768 CAATCATATTGTATTTAATATTATTGGTAACTCTATAAAATAAAGTTATTTTTTCCC
64 CAATCATATTGTATTTAATATTATTGATAACTCTATAAAATAAAGTTATTTTTTCCC
* * * *
491825 ATTAATATTTTTTTCTATATCATGTTATGTTTTGTATCTTATTTAGTTATTTTTTATGTCACTTA
1 ATTAATATTTTTTTCTATATAATATTATATTTTGTATCTTATTTAGTTATTTTTTATGTCACTCA
491890 ATCATATTGTATTTAATATTATTGATAACTCTATAAAATAAA
66 ATCATATTGTATTTAATATTATTGATAACTCTATAAAATAAA
491932 ATTTTTTAAT
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
120 63 0.63
121 37 0.37
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (120 bp):
ATTAATATTTTTTTCTATATAATATTATATTTTGTATCTTATTTAGTTATTTTTTATGTCACTCA
ATCATATTGTATTTAATATTATTGATAACTCTATAAAATAAAGTTATTTTTTCCC
Found at i:492010 original size:22 final size:23
Alignment explanation
Indices: 491985--492044 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
491975 AAGTTTTTAA
491985 TTATATTTA-ATTAATTT-TTGAT
1 TTAT-TTTATATTAATTTATTGAT
*
492007 TTATTTTATATTAATTTATTTAT
1 TTATTTTATATTAATTTATTGAT
*
492030 TTACTTTATAATTAA
1 TTATTTTAT-ATTAA
492045 ATTAGGTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.12
22 12 0.36
23 12 0.36
24 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTATTTTATATTAATTTATTGAT
Found at i:493725 original size:9 final size:9
Alignment explanation
Indices: 493694--493771 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
493684 TATAATAGAA
493694 TAATATATT
1 TAATATATT
* *
493703 TAATAGATA
1 TAATATATT
*
493712 CAATATATT
1 TAATATATT
*
493721 TAATATATA
1 TAATATATT
493730 T-ATCATATT
1 TAAT-ATATT
493739 T--T-TATT
1 TAATATATT
*
493745 TAA-ATTTT
1 TAATATATT
*
493753 TGATATATT
1 TAATATATT
493762 TAATA-ATT
1 TAATATATT
493770 TA
1 TA
493772 TATTATGTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
6 5 0.10
8 13 0.25
9 34 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (9 bp):
TAATATATT
Found at i:493739 original size:18 final size:18
Alignment explanation
Indices: 493686--493725 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
493676 GTAAAACATA
*
493686 TAATAGA-ATAATATATT
1 TAATAGATACAATATATT
493703 TAATAGATACAATATATT
1 TAATAGATACAATATATT
493721 TAATA
1 TAATA
493726 TATATATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (18 bp):
TAATAGATACAATATATT
Found at i:495713 original size:20 final size:20
Alignment explanation
Indices: 495685--495724 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
495675 CATCTTATAT
*
495685 TATTCATATATTTAATTTAA
1 TATTAATATATTTAATTTAA
495705 TATTAATATATTTAATTTAA
1 TATTAATATATTTAATTTAA
495725 GTAAATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAATATATTTAATTTAA
Found at i:497468 original size:4 final size:4
Alignment explanation
Indices: 497459--497485 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
497449 AACACAACTC
497459 AGAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGA
497486 CTAATGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:497515 original size:4 final size:4
Alignment explanation
Indices: 497508--497551 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
497498 AACTCGGAAG
* * *
497508 GAAA GAAA GAAA GAAA GAAA GGAA G-AC TAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
497552 GCCGTGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 1 0.03
4 33 0.97
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:504369 original size:2 final size:2
Alignment explanation
Indices: 504362--504386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
504352 CTACGCATTC
504362 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
504387 CACACACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:506100 original size:19 final size:20
Alignment explanation
Indices: 506050--506100 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
506040 ATAAATTAAA
506050 TTATTAAATATGTTAAAGTTT
1 TTATTAAA-ATGTTAAAGTTT
*
506071 TTAATATAAAT-TTAATA-TTT
1 TTATTA-AAATGTTAA-AGTTT
506091 TTATTAAAAT
1 TTATTAAAAT
506101 CATCGTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 8 0.31
22 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTATTAAAATGTTAAAGTTT
Found at i:506169 original size:20 final size:19
Alignment explanation
Indices: 506146--506201 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
506136 ATATTATATA
506146 TATTATATTATTTTTATGTT
1 TATTATA-TATTTTTATGTT
* * *
506166 TATTAAATATATTATATTTT
1 TATTATATAT-TTTTATGTT
*
506186 TATCATATATTTTTAT
1 TATTATATATTTTTAT
506202 ATCATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTATATATTTTTATGTT
Found at i:507014 original size:2 final size:2
Alignment explanation
Indices: 507007--507042 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
506997 GCGAACTCTT
507007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
507043 GATGGATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:507771 original size:20 final size:19
Alignment explanation
Indices: 507722--507772 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
507712 AGCTTATAAA
507722 TTTAATTAAT-TTTTTTAT
1 TTTAATTAATATTTTTTAT
507740 TTTAA-TATATATTTTTTATT
1 TTTAATTA-ATATTTTTTA-T
507760 TTTAATTAATATT
1 TTTAATTAATATT
507773 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.07
18 7 0.24
19 7 0.24
20 11 0.38
21 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTAATTAATATTTTTTAT
Found at i:508846 original size:23 final size:25
Alignment explanation
Indices: 508817--508869 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
508807 AATAAAAATT
*
508817 TTAAATTTTAT-TA-CTTTATT-TA
1 TTAAAATTTATATATCTTTATTATA
*
508839 TTAAAATTTATATATTTTTATTATA
1 TTAAAATTTATATATCTTTATTATA
508864 TTAAAA
1 TTAAAA
508870 AAATCATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 2 0.08
24 6 0.23
25 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAAAATTTATATATCTTTATTATA
Found at i:509621 original size:21 final size:22
Alignment explanation
Indices: 509596--509657 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
509586 AATGAAATTA
509596 TATTTATATAT-TTATATTATT
1 TATTTATATATATTATATTATT
* *
509617 TATTTAAATTATATTATATTTTT
1 TATTTATA-TATATTATATTATT
*
509640 TATTTTTA-ATATTATATT
1 TATTTATATATATTATATT
509658 CATGTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.49
22 3 0.09
23 15 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTATATATATTATATTATT
Found at i:509909 original size:11 final size:11
Alignment explanation
Indices: 509868--509909 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
509858 AATTATTTAA
*
509868 AAATTAAATTT
1 AAATTAAAATT
*
509879 AAATTATAA-T
1 AAATTAAAATT
509889 ATAATTAAAATT
1 A-AATTAAAATT
509901 AAATTAAAA
1 AAATTAAAA
509910 ATATTCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:510350 original size:18 final size:19
Alignment explanation
Indices: 510329--510370 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
510319 AGTTAATTTA
510329 AAATTTTAATTATA-AAAT
1 AAATTTTAATTATATAAAT
*
510347 AAA-TTTAATTATATTAAT
1 AAATTTTAATTATATAAAT
510365 AAATTT
1 AAATTT
510371 AATACTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 10 0.48
18 9 0.43
19 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTTTAATTATATAAAT
Found at i:510355 original size:17 final size:18
Alignment explanation
Indices: 510333--510373 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
510323 AATTTAAAAT
510333 TTTAATTATA-AAATAAA
1 TTTAATTATATAAATAAA
*
510350 TTTAATTATATTAATAAA
1 TTTAATTATATAAATAAA
510368 TTTAAT
1 TTTAAT
510374 ACTTAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATTATATAAATAAA
Found at i:511030 original size:17 final size:15
Alignment explanation
Indices: 511008--511056 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
510998 TAAATAATAA
511008 TATTTAAAATTTATATT
1 TATTTAAAA-TTA-ATT
*
511025 TATTTAATATTAATT
1 TATTTAAAATTAATT
511040 TATTTTATAAATTAATT
1 TA-TTTA-AAATTAATT
511057 AAATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 16 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTAAAATTAATT
Found at i:514055 original size:19 final size:20
Alignment explanation
Indices: 514031--514070 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
514021 GAGAGTTTTA
*
514031 TTTGTTTTTC-ATTTTCTTT
1 TTTGTTTTTCTATTTACTTT
514050 TTTGTTTTTCTATTTACTTT
1 TTTGTTTTTCTATTTACTTT
514070 T
1 T
514071 CCAAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTGTTTTTCTATTTACTTT
Found at i:515475 original size:2 final size:2
Alignment explanation
Indices: 515468--515492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
515458 AAATCTATTA
515468 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
515493 CACATATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529168 original size:23 final size:22
Alignment explanation
Indices: 529113--529169 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
529103 TAAAATATAA
529113 ATTTAAATAAA-AATATTTAAAT
1 ATTT-AATAAATAATATTTAAAT
*
529135 -TTTATTTTAAATAATATTTAAAAT
1 ATTTA--ATAAATAATATTT-AAAT
529159 ATTTAATAAAT
1 ATTTAATAAAT
529170 TTTTTAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 4 0.14
23 12 0.43
24 4 0.14
25 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATAAATAATATTTAAAT
Found at i:529564 original size:29 final size:30
Alignment explanation
Indices: 529531--529587 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
529521 TTTACTTGTA
529531 AATTTATATATTTATAATTA-TATTTATAT
1 AATTTATATATTTATAATTATTATTTATAT
* * *
529560 AATTTTTATTTTTATCATTATTATTTAT
1 AATTTATATATTTATAATTATTATTTAT
529588 CAATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
AATTTATATATTTATAATTATTATTTATAT
Found at i:529583 original size:15 final size:15
Alignment explanation
Indices: 529541--529585 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
529531 AATTTATATA
529541 TTTATAATTA-TATT
1 TTTATAATTATTATT
* *
529555 TATATAATTTTTATT
1 TTTATAATTATTATT
*
529570 TTTATCATTATTATT
1 TTTATAATTATTATT
529585 T
1 T
529586 ATCAATAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATAATTATTATT
Found at i:530186 original size:20 final size:21
Alignment explanation
Indices: 530144--530186 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
530134 GTTTATATTT
* *
530144 ATATTATTTTTTGTATTTAAA
1 ATATTATATTTTGTATATAAA
530165 ATATTATATTTT-TATATAAA
1 ATATTATATTTTGTATATAAA
530185 AT
1 AT
530187 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTATATTTTGTATATAAA
Found at i:530745 original size:15 final size:17
Alignment explanation
Indices: 530714--530746 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
530704 TTAATTTTTA
530714 TTAAAAATAATTAAAAT
1 TTAAAAATAATTAAAAT
530731 TTAAAAA-AA-TAAAAT
1 TTAAAAATAATTAAAAT
530746 T
1 T
530747 GTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAATAATTAAAAT
Found at i:530851 original size:13 final size:13
Alignment explanation
Indices: 530835--530862 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
530825 ATTTTTAATT
530835 TTTAAATACATAA
1 TTTAAATACATAA
530848 TTTAAATACATAA
1 TTTAAATACATAA
530861 TT
1 TT
530863 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTAAATACATAA
Found at i:531169 original size:11 final size:12
Alignment explanation
Indices: 531102--531192 Score: 62
Period size: 12 Copynumber: 7.7 Consensus size: 12
531092 GTATTATAAA
*
531102 TTTATATAATAT
1 TTTATATTATAT
*
531114 TTTACATATATAT
1 TTTATAT-TATAT
*
531127 TTATATATT-CAT
1 TT-TATATTATAT
* * *
531139 GTCATATT-CAT
1 TTTATATTATAT
531150 TTTATATTATAT
1 TTTATATTATAT
*
531162 TTTA-ATTATTT
1 TTTATATTATAT
*
531173 TTTATATCATAT
1 TTTATATTATAT
*
531185 TTTTTATT
1 TTTATATT
531193 TGGTATATAT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
11 24 0.39
12 26 0.43
13 7 0.11
14 4 0.07
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:531191 original size:21 final size:22
Alignment explanation
Indices: 531149--531193 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
531139 GTCATATTCA
*
531149 TTTTATATTATATTTTAATTATT
1 TTTTATATCATATTTT-ATTATT
531172 TTTTATATCATATTTT-TTATT
1 TTTTATATCATATTTTATTATT
531193 T
1 T
531194 GGTATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
23 15 0.71
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATATCATATTTTATTATT
Found at i:531199 original size:21 final size:22
Alignment explanation
Indices: 531152--531200 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
531142 ATATTCATTT
* **
531152 TATATTATATTTTAATTATTTTT
1 TATATCATATTTT-ATTATTTGG
531175 TATATCATATTTT-TTATTTGG
1 TATATCATATTTTATTATTTGG
531196 TATAT
1 TATAT
531201 ATTTAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TATATCATATTTTATTATTTGG
Found at i:531585 original size:21 final size:20
Alignment explanation
Indices: 531544--531586 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
531534 AACTTATTTT
* *
531544 ATAATTAAATTTTTATTAATA
1 ATAATTAAA-ATTTATAAATA
531565 ATAATTAAAATTTATGAAATA
1 ATAATTAAAATTTAT-AAATA
531586 A
1 A
531587 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAATTAAAATTTATAAATA
Found at i:536775 original size:2 final size:2
Alignment explanation
Indices: 536768--536804 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
536758 GATACATGTT
*
536768 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
536805 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:537006 original size:16 final size:15
Alignment explanation
Indices: 536976--537014 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
536966 TACCGCCCAC
536976 ATATAGTATATTATAT
1 ATATA-TATATTATAT
536992 ATATATATATGTATAT
1 ATATATATAT-TATAT
*
537008 TTATATA
1 ATATATA
537015 ATAGAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATATATATTATAT
Found at i:543282 original size:24 final size:24
Alignment explanation
Indices: 543255--543323 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
543245 ATAAATATAA
543255 AATAAATATTTAATATATTA-TAT
1 AATAAATATTTAATATATTATTAT
*
543278 GAATATATATTTTAA-ATTATTATTAT
1 -AATAAATA-TTTAATA-TATTATTAT
*
543304 ATTAAA-ATTTATATATATTA
1 AATAAATATTTA-ATATATTA
543324 AATATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 4 0.11
24 15 0.41
25 15 0.41
26 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
AATAAATATTTAATATATTATTAT
Found at i:543320 original size:16 final size:17
Alignment explanation
Indices: 543281--543368 Score: 72
Period size: 16 Copynumber: 5.0 Consensus size: 17
543271 ATTATATGAA
* *
543281 TATATATTTTAAATTAT
1 TATATATATTAAAATAT
543298 TAT-TATATTAAAAT-T
1 TATATATATTAAAATAT
543313 TATATATATTAAATATAAT
1 TATATATATTAAA-AT-AT
*
543332 TATGATATAATAAAATAT
1 TAT-ATATATTAAAATAT
* *
543350 ATAAATATAATATAAATAT
1 -TATATATATTA-AAATAT
543369 AAATTATTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.07
16 18 0.30
17 5 0.08
18 10 0.17
19 14 0.23
20 9 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (17 bp):
TATATATATTAAAATAT
Found at i:543346 original size:36 final size:36
Alignment explanation
Indices: 543280--543377 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 36
543270 TATTATATGA
* *
543280 ATATATATTTTAAAT-T-ATTATTATATTAAAAT-T
1 ATATATATATTAAATATAATTATTATAATAAAATAT
543313 -TATATATATTAAATATAATTATGATATAATAAAATAT
1 ATATATATATTAAATATAATTAT--TATAATAAAATAT
*
543350 ATAAATATAATATAAATATAAATTATTA
1 ATATATAT-AT-TAAATAT-AATTATTA
543378 AATTTTTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
32 13 0.25
33 1 0.02
34 5 0.09
36 10 0.19
37 1 0.02
38 6 0.11
39 4 0.08
40 7 0.13
41 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
ATATATATATTAAATATAATTATTATAATAAAATAT
Found at i:543392 original size:14 final size:14
Alignment explanation
Indices: 543370--543404 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
543360 TATAAATATA
543370 AATTATTAAATTTTT
1 AATT-TTAAATTTTT
543385 AATTTTAAATTTTT
1 AATTTTAAATTTTT
543399 AATTTT
1 AATTTT
543405 TTATGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTAAATTTTT
Found at i:543588 original size:20 final size:18
Alignment explanation
Indices: 543565--543608 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
543555 TATATTTTGT
543565 TAATAATTTAACTTTTTTAA
1 TAATAATTT-A-TTTTTTAA
543585 TAATAAATTTATTTTTTAA
1 TAAT-AATTTATTTTTTAA
543604 -AATAA
1 TAATAA
543609 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.09
18 3 0.13
19 8 0.35
20 5 0.22
21 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATAATTTATTTTTTAA
Found at i:543969 original size:3 final size:3
Alignment explanation
Indices: 543961--543997 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
543951 TTCTGATGGG
543961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
543998 AAAAATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:544184 original size:18 final size:18
Alignment explanation
Indices: 544156--544212 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
544146 ATTGTAATTA
544156 AAAATTTATTTAATTCAAT
1 AAAA-TTATTTAATTCAAT
544175 AAAATTATTTGAATT-AAT
1 AAAATTATTT-AATTCAAT
*
544193 AAAA-T-TTTAAATCAAT
1 AAAATTATTTAATTCAAT
544209 AAAA
1 AAAA
544213 ATTTTATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 1 0.03
18 13 0.37
19 8 0.23
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTATTTAATTCAAT
Found at i:544211 original size:16 final size:16
Alignment explanation
Indices: 544164--544218 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
544154 TAAAAATTTA
*
544164 TTTAATTCAATAAAATT
1 TTTAAATCAATAAAA-T
* *
544181 ATTTGAATTAATAAAAT
1 -TTTAAATCAATAAAAT
544198 TTTAAATCAATAAAAAT
1 TTTAAATCAAT-AAAAT
544215 TTTA
1 TTTA
544219 TCAAACACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 9 0.29
17 10 0.32
18 12 0.39
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAAATCAATAAAAT
Found at i:544816 original size:21 final size:21
Alignment explanation
Indices: 544792--544845 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
544782 TAAATTTAAA
544792 AATT-TTATTTATGATAAAAAT
1 AATTCTTATTTATGA-AAAAAT
*
544813 AATTCTTATTTTTGAAAAAAT
1 AATTCTTATTTATGAAAAAAT
*
544834 ACTTCTT-TTTAT
1 AATTCTTATTTAT
544846 TGTTGTCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (21 bp):
AATTCTTATTTATGAAAAAAT
Found at i:546481 original size:3 final size:3
Alignment explanation
Indices: 546473--546504 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
546463 ATTGAGCCAA
546473 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
546505 AGGAAAATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:548469 original size:17 final size:17
Alignment explanation
Indices: 548447--548483 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
548437 TATCTCTACG
548447 AATTACTTGCTCTTGGT
1 AATTACTTGCTCTTGGT
548464 AATTACTTGCTCTTGGT
1 AATTACTTGCTCTTGGT
548481 AAT
1 AAT
548484 GTTTGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (17 bp):
AATTACTTGCTCTTGGT
Found at i:549762 original size:22 final size:23
Alignment explanation
Indices: 549732--549780 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
549722 TAATAATAAT
*
549732 AAAATACAAAAAA-A-AAGAGAAA
1 AAAAAACAAAAAATACAA-AGAAA
549754 AAAAAACAAAAAATACAAAGAAA
1 AAAAAACAAAAAATACAAAGAAA
549777 AAAA
1 AAAA
549781 TAAATGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 12 0.50
23 10 0.42
24 2 0.08
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.04
Consensus pattern (23 bp):
AAAAAACAAAAAATACAAAGAAA
Found at i:550066 original size:20 final size:20
Alignment explanation
Indices: 550038--550112 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
550028 TTTTACCTTG
550038 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
550058 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
550078 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
550098 ATGTATCGATACATT
1 ATGTATCGATACATT
550113 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:550105 original size:40 final size:39
Alignment explanation
Indices: 550038--550115 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
550028 TTTTACCTTG
* *
550038 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
550078 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
550116 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:556790 original size:27 final size:27
Alignment explanation
Indices: 556748--557354 Score: 597
Period size: 27 Copynumber: 22.6 Consensus size: 27
556738 TCTTGCATGG
* * *
556748 CTCCGTGACACCCTTTAAAGTCTACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* *
556775 CTCCGTGGCACTCTTTTAAGTCTACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* * * *
556802 CTCTGTGGTAGCCC-TTT-AGTTCACAT
1 CTCCGTGGCA-CCCTTTTAAGTCCACAA
* *
556828 CTCCGTGGCACCCTTTTAGGTCCACAG
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* * *
556855 CTCCATGGC-CCTCTTTAAAGTCCACGA
1 CTCCGTGGCACC-CTTTTAAGTCCACAA
*
556882 CTCCATGGCACCCTTTTAAAGTCCACAA
1 CTCCGTGGCACCCTTTT-AAGTCCACAA
* *
556910 CTCTGTGGCACCCTTTTAAGTCCATAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
*
556937 CTCCGTGGCA-CCTTTTAAAGTCCACGA
1 CTCCGTGGCACCCTTTT-AAGTCCACAA
*
556964 CTCTGTGGCACCCTTTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* *
556991 CTCCGTAGCACCCTTTTAAAGTCCACCA
1 CTCCGTGGCACCCTTTT-AAGTCCACAA
** * *
557019 CTCCGTGGCACTTTTTTAGGTCCACAC
1 CTCCGTGGCACCCTTTTAAGTCCACAA
*
557046 CTCCAT-G------TTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
*
557066 CTCCGTGGGACCCTTTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* *
557093 CTCCGTGGCAACCTTTCAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
** *
557120 CTCTATGGCACTCTTTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
** * * *
557147 CTCTATGGCACCTTTTTAAGTTCATAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* * *
557174 CTCTGTGGCAGCCTTTTTAAAGTCCACAG
1 CTCCGTGGCA-CCCTTTT-AAGTCCACAA
* * * *
557203 CTCTGTGGTACCCTTTCAAGTCCATAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* * *
557230 CTCCATGGCACCCTTTTAGGTCTACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
*
557257 CTCCGTGGTACCCTTTTTAAGTCCACAA
1 CTCCGTGGCACCC-TTTTAAGTCCACAA
557285 CTCCGTGGCACCCTTTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
*
557312 CTCCGTGGCATCCTTTTAAGTCCACAA
1 CTCCGTGGCACCCTTTTAAGTCCACAA
* * *
557339 GTCAGTGGCATCCTTT
1 CTCCGTGGCACCCTTT
557355 CAAAGCCCAC
Statistics
Matches: 483, Mismatches: 78, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.03
21 1 0.00
25 3 0.01
26 26 0.05
27 328 0.68
28 93 0.19
29 16 0.03
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.30
Consensus pattern (27 bp):
CTCCGTGGCACCCTTTTAAGTCCACAA
Found at i:556924 original size:82 final size:80
Alignment explanation
Indices: 556748--557365 Score: 576
Period size: 82 Copynumber: 7.7 Consensus size: 80
556738 TCTTGCATGG
* * * * ** *
556748 CTCCGTGACACCCTTTAAAGTCTACAACTCCGTGGCACTCTTTT-AAGTCTACAACTCTGTGGTA
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTAAAGTCCAC-ACTCCATGGCA
* *
556812 GCCC-TTT-AGTTCACAT
64 -CCCTTTTAAGTCCACAA
* * *
556828 CTCCGTGGCACCCTTTTAGGTCCACAGCTCCATGGC-CCTCTTTAAAGTCCACGACTCCATGGCA
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCT-TTTAAAGTCCAC-ACTCCATGGCA
556892 CCCTTTTAAAGTCCACAA
64 CCCTTTT-AAGTCCACAA
* * **
556910 CTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACCTTTTAAAGTCCACGACTCTGTGGCAC
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCAC-ACTCCATGGCAC
556975 CCTTTTAAGTCCACAA
65 CCTTTTAAGTCCACAA
* * * * *
556991 CTCCGTAGCACCCTTTTAAAGTCCACCACTCCGTGGCACTTTTTTAGGTCCACACCTCCAT-G--
1 CTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACA-CTCCATGGCA
557053 ----TTTAAGTCCACAA
64 CCCTTTTAAGTCCACAA
* * *
557066 CTCCGTGGGACCCTTTTAAGTCCACAACTCCGTGGCAACC-TTTCAAGTCCACAACTCTATGGCA
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC-ACCTTTTAAAGTCCAC-ACTCCATGGCA
*
557130 CTCTTTTAAGTCCACAA
64 CCCTTTTAAGTCCACAA
** * * * * ** *
557147 CTCTATGGCACCTTTTTAAGTTCATAACTCTGTGGCAGCCTTTTTAAAGTCCACAGCTCTGTGGT
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC-TTTTAAAGTCCACA-CTCCATGGC
* *
557212 ACCCTTTCAAGTCCATAA
63 ACCCTTTTAAGTCCACAA
* * * * * *
557230 CTCCATGGCACCCTTTTAGGTCTACAACTCCGTGGTACCCTTTTTAAGTCCACAACTCCGTGGCA
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCAC-ACTCCATGGCA
557295 CCCTTTTAAGTCCACAA
64 CCCTTTTAAGTCCACAA
* * * * *
557312 CTCCGTGGCATCCTTTTAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
1 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACA
557366 AGTCTGTGAC
Statistics
Matches: 442, Mismatches: 74, Indels: 43
0.79 0.13 0.08
Matches are distributed among these distances:
74 33 0.07
75 32 0.07
78 2 0.00
79 7 0.02
80 49 0.11
81 72 0.16
82 179 0.40
83 68 0.15
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (80 bp):
CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACACTCCATGGCACC
CTTTTAAGTCCACAA
Found at i:557378 original size:28 final size:28
Alignment explanation
Indices: 557279--557845 Score: 588
Period size: 28 Copynumber: 20.2 Consensus size: 28
557269 CTTTTTAAGT
* * * * *
557279 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
557306 CCACAACTCCGTGGCATCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
557333 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
557361 CCACAAGTCTGTGACATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
557389 CCGCGAGTCAGTGGCA-CCATTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* *
557417 CCACAAGTCAGTGGCATCTTTTCAGAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
557445 CCACAAGTCCGTAGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
557473 CCATAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
557501 CCACATAAGTTAGTGACACCCTTTTAAAGC
1 CCAC--AAGTCAGTGGCATCCTTTCAAAGC
* *
557531 CCACAAGTCCGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
** *
557559 CCACAAGTCAGTAACACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
557587 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
557615 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
557643 CCATAAGTTAGTGACATCCTTTCAATGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
557671 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
557699 TCACAAGTCCA-TGGCA-CCATTTCAAAGC
1 CCACAAGT-CAGTGGCATCC-TTTCAAAGC
* *
557727 CCATAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
557755 CTACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
557783 CCACAAGTCGGTGACATTCTTTGAAAAGC
1 CCACAAGTCAGTGGCATCCTTT-CAAAGC
* *
557812 CCATAAGTCAGTGAG-AACCTTTTCAAAGC
1 CCACAAGTCAGTG-GCATCC-TTTCAAAGC
557841 CCACA
1 CCACA
557846 CAAGTCGGTG
Statistics
Matches: 453, Mismatches: 75, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
27 50 0.11
28 344 0.76
29 31 0.07
30 28 0.06
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:558110 original size:54 final size:53
Alignment explanation
Indices: 558027--558184 Score: 176
Period size: 54 Copynumber: 3.0 Consensus size: 53
558017 CAACCTAATG
* *
558027 TCGCTGGCCTTGAATCAAGACATTAGCACTCATCCTCTTTCTTAAAGTCCAACA
1 TCGCTGGCCTTGAATC-AGACATTGGCACTCATCCTCTTTCTTTAAGTCCAACA
* * * * *
558081 TCGCTGGCCTTGAATCAGTACGTTGGCACT-TTCCTC-ATCTTTAAGTCTAATA
1 TCGCTGGCCTTGAATCAG-ACATTGGCACTCATCCTCTTTCTTTAAGTCCAACA
* * * *
558133 TGGTTGGCCTTGAATCAACACATTGGCACTCATCCCCTTTCTTTAAGTCCAA
1 TCGCTGGCCTTGAATC-AGACATTGGCACTCATCCTCTTTCTTTAAGTCCAA
558185 GCCTTGAATC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 36 0.42
53 12 0.14
54 37 0.44
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (53 bp):
TCGCTGGCCTTGAATCAGACATTGGCACTCATCCTCTTTCTTTAAGTCCAACA
Found at i:558460 original size:20 final size:20
Alignment explanation
Indices: 558412--558453 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
558402 AAAAATAATA
* *
558412 ATAATAAAATACAAAAAAGAG
1 ATAA-AAAATACAAAAAACAC
558433 ATAAAAAATACAAAAAACAC
1 ATAAAAAATACAAAAAACAC
558453 A
1 A
558454 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.12
Consensus pattern (20 bp):
ATAAAAAATACAAAAAACAC
Found at i:562118 original size:13 final size:13
Alignment explanation
Indices: 562100--562124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562090 CATTGCATAG
562100 TGTATCGATACAA
1 TGTATCGATACAA
562113 TGTATCGATACA
1 TGTATCGATACA
562125 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:562202 original size:33 final size:33
Alignment explanation
Indices: 562165--562231 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
562155 AGTAGCTTGA
562165 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
562198 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
562231 A
1 A
562232 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:562205 original size:13 final size:13
Alignment explanation
Indices: 562187--562211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562177 CAAAAAAATA
562187 TGTATCGATACAT
1 TGTATCGATACAT
562200 TGTATCGATACA
1 TGTATCGATACA
562212 ACATTTTATG
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:563276 original size:48 final size:46
Alignment explanation
Indices: 563122--563356 Score: 260
Period size: 48 Copynumber: 5.0 Consensus size: 46
563112 AAAGATGGAA
* *
563122 AAGGTGCTACTATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * * *
563168 -A--TGCCAATGTGCCGATTCAAGGTCAGCTACATTGGACTTAAATATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
* * * *
563214 AAAGTGCCAATATGCTGATTTAAGGCCAACGATATTGGACTTAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G
*
563261 CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAAG
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAG
* *
563309 CAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGGCTTCAAAG
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAG
563357 GAGACGCCAC
Statistics
Matches: 160, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
43 32 0.20
44 2 0.01
45 2 0.01
46 1 0.01
47 3 0.02
48 86 0.54
49 34 0.21
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (46 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Found at i:563431 original size:28 final size:28
Alignment explanation
Indices: 563374--563497 Score: 135
Period size: 28 Copynumber: 4.3 Consensus size: 28
563364 CACCAACTTG
*
563374 TGTGGGCTTTTGAGAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTGA-AGG-TTGCCACT-GACT
* *
563403 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
563431 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
563459 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
563489 TGTGGGCTT
1 TGTGGGCTT
563498 AAAAAGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.04
28 43 0.52
29 13 0.16
30 23 0.28
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:563482 original size:30 final size:30
Alignment explanation
Indices: 563400--563932 Score: 200
Period size: 30 Copynumber: 17.6 Consensus size: 30
563390 GTTTGCATCA
* * *
563400 ACTTGTGTGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
563428 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
563456 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
563486 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** * * *
563520 AGTTGTGAGC-TTACAAAAGAAAAAGTTCCACGG
1 ACTTGTGGGCTTTTGAAAAG----GGTGCCACTG
* * * * * *
563553 AGTTATGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * **
563582 ACTGGTGGGCGTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
563612 ATTTGTGGGC-TTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
563639 ACTTGTGGGCTTTTGAAAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG---AAAAGGGTGCCACTG
*
563672 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
563702 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** * * *
563736 AGTTGTGAGC-TTACAAAAGAAAAAGTTCCACGG
1 ACTTGTGGGCTTTTGAAAAG----GGTGCCACTG
* * * * * *
563769 AGTTATGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* **
563798 ACTTGTGGGCGTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
563828 ATTTGTGGGC-TTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
563855 ACTTGTGGGCTTTTGAAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG--AAAAGGGTGCCACTG
* *
563887 ACTTGTGGGC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
563916 ACTTGTGGACTTTTGAA
1 ACTTGTGGGCTTTTGAA
563933 GGGTGAGGAA
Statistics
Matches: 382, Mismatches: 84, Indels: 76
0.70 0.15 0.14
Matches are distributed among these distances:
27 42 0.11
28 47 0.12
29 76 0.20
30 88 0.23
31 4 0.01
32 20 0.05
33 57 0.15
34 48 0.13
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:563634 original size:27 final size:27
Alignment explanation
Indices: 563599--563713 Score: 95
Period size: 33 Copynumber: 3.9 Consensus size: 27
563589 GGCGTCGGAA
*
563599 AAGGGTGCCACTGATTTGTGGGCTTTG
1 AAGGGTGCCACTGACTTGTGGGCTTTG
*
563626 AAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAGGGTGCCACTGACTTGTGGGC-TTTG
***
563654 AAAAAAAAAATGCCACTGACTTGTGGGCTTTTG
1 -----AAGGGTGCCACTGACTTGTGGGC-TTTG
*
563687 AAAAGGGTGCCACTAACTTGTGGGCTT
1 --AAGGGTGCCACTGACTTGTGGGCTT
563714 AAAAAGAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
27 21 0.29
28 4 0.05
29 2 0.03
30 21 0.29
33 25 0.34
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (27 bp):
AAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:563780 original size:216 final size:215
Alignment explanation
Indices: 563402--563923 Score: 910
Period size: 216 Copynumber: 2.4 Consensus size: 215
563392 TTGCATCAAC
* * ***
563402 TTGTGTGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTT----AAAGGTTGCCACTGACTTGTG
1 TTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCCACTGACTTGTG
563463 GGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGA
65 GGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGA
563528 GCTTACAAAAGAAAAAGTTCCACGGAGTTATGGACTTTGGAAAAGATGCCACCGACTGGTGGGCG
130 GCTTACAAAAGAAAAAGTTCCACGGAGTTATGGACTTTGGAAAAGATGCCACCGACTGGTGGGCG
563593 TCGGAAAAGGGTGCCACTGAT
195 TCGGAAAAGGGTGCCACTGAT
563614 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAAATGCCACTGACTTGTG
1 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAAAAAATGCCACTGACTTGTG
563679 GGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGA
65 GGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGA
*
563744 GCTTACAAAAGAAAAAGTTCCACGGAGTTATGGACTTTGGAAAAGATGCCACCGACTTGTGGGCG
130 GCTTACAAAAGAAAAAGTTCCACGGAGTTATGGACTTTGGAAAAGATGCCACCGACTGGTGGGCG
563809 TCGGAAAAGGGTGCCACTGAT
195 TCGGAAAAGGGTGCCACTGAT
563830 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCCACTGACTTGTGG
1 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCCACTGACTTGTGG
* * *
563895 GC-TTTGAAAAAGATGCCACTGACTTGTGG
66 GCTTTTGAAAAGGGTGCCACTAACTTGTGG
563924 ACTTTTGAAG
Statistics
Matches: 296, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
211 30 0.10
212 7 0.02
214 24 0.08
215 27 0.09
216 208 0.70
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (215 bp):
TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCCACTGACTTGTGG
GCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGAG
CTTACAAAAGAAAAAGTTCCACGGAGTTATGGACTTTGGAAAAGATGCCACCGACTGGTGGGCGT
CGGAAAAGGGTGCCACTGAT
Found at i:563814 original size:29 final size:29
Alignment explanation
Indices: 563778--563928 Score: 153
Period size: 29 Copynumber: 5.1 Consensus size: 29
563768 GAGTTATGGA
*
563778 CTTTGGAAAAGATGCCACCGACTTGTGGG
1 CTTTGGAAAAGATGCCACTGACTTGTGGG
* * * *
563807 CGTCGGAAAAGGGTGCCACTGATTTGTGGG
1 CTTTGGAAAA-GATGCCACTGACTTGTGGG
* *
563837 CTTT-G-AAGGTTGCCACTGACTTGTGGG
1 CTTTGGAAAAGATGCCACTGACTTGTGGG
* *
563864 CTTTTGAAAAAAAAATGCCACTGACTTGTGGG
1 C-TTTG--GAAAAGATGCCACTGACTTGTGGG
* *
563896 CTTTGAAAAAGATGCCACTGACTTGTGGA
1 CTTTGGAAAAGATGCCACTGACTTGTGGG
563925 CTTT
1 CTTT
563929 TGAAGGGTGA
Statistics
Matches: 100, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
27 18 0.18
28 5 0.05
29 35 0.35
30 18 0.18
31 4 0.04
32 20 0.20
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (29 bp):
CTTTGGAAAAGATGCCACTGACTTGTGGG
Found at i:563931 original size:61 final size:59
Alignment explanation
Indices: 563820--563932 Score: 172
Period size: 61 Copynumber: 1.9 Consensus size: 59
563810 CGGAAAAGGG
* * * *
563820 TGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAA
1 TGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGACTTTTGAAAAAAAAA
563879 TGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGACTTTTGAA
1 TGCCACTGACTTGTGGGCTTTG--AAAGATGCCACTGACTTGTGGACTTTTGAA
563933 GGGTGAGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 21 0.44
61 27 0.56
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (59 bp):
TGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGACTTTTGAAAAAAAAA
Found at i:564162 original size:12 final size:12
Alignment explanation
Indices: 564147--564176 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
564137 GGCAAGTCGT
*
564147 TGATGAAGTTCC
1 TGATAAAGTTCC
564159 TGATAAAGTTCC
1 TGATAAAGTTCC
564171 TGATAA
1 TGATAA
564177 TAGGCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (12 bp):
TGATAAAGTTCC
Found at i:565309 original size:1 final size:1
Alignment explanation
Indices: 565303--565387 Score: 80
Period size: 1 Copynumber: 85.0 Consensus size: 1
565293 ATCCGGACCC
* * * * * * * *
565303 TTTTTTTTGTTTTTTTTTTGTTTTGTTTTGTTTTTTTGTTTTGTTTTTTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
565368 TTTTTGTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
565388 GTGGAGGACG
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:565326 original size:16 final size:16
Alignment explanation
Indices: 565303--565387 Score: 136
Period size: 16 Copynumber: 5.2 Consensus size: 16
565293 ATCCGGACCC
565303 TTTT-TTTTGTTTTTT
1 TTTTGTTTTGTTTTTT
565318 TTTTGTTTTGTTTTGTTT
1 TTTTGTTTTG-TTT-TTT
565336 TTTTGTTTTGTTTTTT
1 TTTTGTTTTGTTTTTT
565352 TTTTGTTTTTGTTTTTT
1 TTTTG-TTTTGTTTTTT
565369 TTTTGTTTTGTTTTTT
1 TTTTGTTTTGTTTTTT
565385 TTT
1 TTT
565388 GTGGAGGACG
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.06
16 27 0.41
17 22 0.33
18 13 0.20
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTGTTTTGTTTTTT
Found at i:577896 original size:21 final size:21
Alignment explanation
Indices: 577867--577909 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
577857 GCATTCTATT
577867 TTTGATTTTTTTATTA-TTATA
1 TTTGATTTTTTT-TTATTTATA
*
577888 TTTGCTTTTTTTTTATTTATA
1 TTTGATTTTTTTTTATTTATA
577909 T
1 T
577910 GTATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTGATTTTTTTTTATTTATA
Found at i:583902 original size:18 final size:18
Alignment explanation
Indices: 583881--583922 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
583871 ATTCTCTTAC
*
583881 TTATTATGCCTTCATTAA
1 TTATTATACCTTCATTAA
583899 TTATTATACCTTCATTAA
1 TTATTATACCTTCATTAA
583917 TTATTA
1 TTATTA
583923 GTAATATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTATACCTTCATTAA
Found at i:585696 original size:19 final size:19
Alignment explanation
Indices: 585665--585710 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
585655 AACTCTAGAT
*
585665 TAGATAT-TTGCTTTCATA
1 TAGATATATTGCTTTAATA
585683 TAGATATATTGCTTTAATA
1 TAGATATATTGCTTTAATA
*
585702 TATATATAT
1 TAGATATAT
585711 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TAGATATATTGCTTTAATA
Found at i:585739 original size:2 final size:2
Alignment explanation
Indices: 585699--585730 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
585689 TATTGCTTTA
585699 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
585731 GCATATATAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587030 original size:275 final size:281
Alignment explanation
Indices: 586730--587288 Score: 788
Period size: 280 Copynumber: 2.0 Consensus size: 281
586720 AAAAATTTCA
* *
586730 AAACTAAAAAAAAAAAAAATTCAACCTTCAACCATATAAAATATTTTATAATTATAATTTTTTTT
1 AAACTAAAAAAAAAAAAAATTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTG
*** * * **
586795 ATTAAAATCTACGTTTCTTATATTTGAGCAAATGATGCATA-A-ATTAAAGTACATATGGCATTG
66 ATTAAAATCTAAACTTCTTATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTG
* * *
586858 GCTAACTTATTTTGAATCTATCATAATAATTTAAACAC-TTTTTTTTTACG-A-TTTACAAAATC
131 GCTAACTTATTTTGAATCTATCATAACAATTAAAACACTTTTTTTTTTACGCAGTTTACAAAAAC
*
586920 ATATTTAATAAAAAATAAATCAACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAA
196 AAATTTAATAAAAAATAAATCAACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAA
*
586985 CTGTTTTAAGTTGAAAAAGTT
261 CTATTTTAAGTTGAAAAAGTT
* ** *
587006 AAACT-AAAAAAAAACATTTTCAACCTTTAACCATATAAAATATTTTATAAATATAATTTTTTTG
1 AAACTAAAAAAAAAAAAAATTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTG
* * * **
587070 ATTAGAATCTAAACTTCTTATATTTGAACATATGATATATATATATTAAAGTATGTATAACATTG
66 ATTAAAATCTAAACTTCTTATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTG
* * **
587135 GCTAACTTATTTTGAATCTATCATAGCGATTAAAACACTTTTTTTTTTTTGCAGTTTACAAAAAC
131 GCTAACTTATTTTGAATCTATCATAACAATTAAAACACTTTTTTTTTTACGCAGTTTACAAAAAC
* * * *
587200 AAATTTAATAAAAAATAAATTAACTTGAGCTTAAATAATTATAAGCTCTTGTTGGCACAATTCAA
196 AAATTTAATAAAAAATAAATCAACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAA
*
587265 CTATTTTAAGTTGAAAAGGTT
261 CTATTTTAAGTTGAAAAAGTT
587286 AAA
1 AAA
587289 TATTTATTTG
Statistics
Matches: 246, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
275 86 0.35
276 6 0.02
277 51 0.21
278 10 0.04
279 1 0.00
280 92 0.37
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (281 bp):
AAACTAAAAAAAAAAAAAATTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTG
ATTAAAATCTAAACTTCTTATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTG
GCTAACTTATTTTGAATCTATCATAACAATTAAAACACTTTTTTTTTTACGCAGTTTACAAAAAC
AAATTTAATAAAAAATAAATCAACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAA
CTATTTTAAGTTGAAAAAGTT
Found at i:587513 original size:8 final size:8
Alignment explanation
Indices: 587490--587523 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
587480 TATGTCAAAA
587490 TAAATTTT
1 TAAATTTT
* *
587498 TTATTTTT
1 TAAATTTT
587506 TAAATTTT
1 TAAATTTT
587514 TAAATTTT
1 TAAATTTT
587522 TA
1 TA
587524 TTATGATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TAAATTTT
Found at i:588484 original size:23 final size:23
Alignment explanation
Indices: 588455--588502 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
588445 TTTTTATTGA
*
588455 TTTATTTTTATTAAAAAT-ATTT
1 TTTAATTTTATTAAAAATAATTT
* *
588477 TTTAATTTTATTTAAATTAATTT
1 TTTAATTTTATTAAAAATAATTT
588500 TTT
1 TTT
588503 TCATATTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATTTTATTAAAAATAATTT
Found at i:588811 original size:32 final size:29
Alignment explanation
Indices: 588728--588813 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 29
588718 AGTATTTATC
* *
588728 ATATTTTTAT-TAATTATAATTATATTTA
1 ATATTTTTATATATTTATAATTATATTAA
* *
588756 ATA-TATTATATATTAATAAATTATATTAA
1 ATATTTTTATATATTTAT-AATTATATTAA
588785 ATAAATTTTTATATATTTATATATTATAT
1 AT--ATTTTTATATATTTATA-ATTATAT
588814 ATTTATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 5 0.11
28 8 0.17
29 12 0.26
31 2 0.04
32 19 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTTTATATATTTATAATTATATTAA
Found at i:588832 original size:15 final size:15
Alignment explanation
Indices: 588741--588821 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
588731 TTTTTATTAA
588741 TTATA-ATTATAT-T
1 TTATATATTATATAT
*
588754 TAATATATTATATAT
1 TTATATATTATATAT
* * *
588769 TAATAAATTATATTAA
1 TTATATATTATA-TAT
* * *
588785 ATAAATTTTTATATAT
1 TTATA-TATTATATAT
588801 TTATATATTATATAT
1 TTATATATTATATAT
588816 TTATAT
1 TTATAT
588822 TTTAATTATT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
13 4 0.08
14 7 0.13
15 27 0.52
16 9 0.17
17 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATATTATATAT
Found at i:588833 original size:40 final size:38
Alignment explanation
Indices: 588720--588833 Score: 99
Period size: 40 Copynumber: 2.9 Consensus size: 38
588710 GTTTATAAAG
* * *
588720 TATTTATCATATT-TTTATTA-ATTATAATTATATTTAA
1 TATTTAT-ATATTATATATTATATTTTAATTATTTTTAA
* * *
588757 TATATTATATATTAATAAATTATA-TTAAATAAATTTTTATA
1 TAT-TTATATATT-ATATATTATATTTTAAT-TATTTTTA-A
588798 TATTTATATATTATATATTTATATTTTAATTATTTT
1 TATTTATATATTATATA-TTATATTTTAATTATTTT
588834 ACAATATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
37 8 0.13
38 4 0.07
39 13 0.22
40 26 0.43
41 9 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (38 bp):
TATTTATATATTATATATTATATTTTAATTATTTTTAA
Found at i:589284 original size:32 final size:34
Alignment explanation
Indices: 589210--589300 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 34
589200 ATTTTAAATA
*
589210 TAATATTATAAAATAATAAATATAAGGATAAATATAT
1 TAATATTTTAAAA-AAT--ATATAAGGATAAATATAT
* *
589247 AAATATTTTAAAAAATATATAA-TATAAAT-TAT
1 TAATATTTTAAAAAATATATAAGGATAAATATAT
* **
589279 TAATATATTAAAATTTATATAA
1 TAATATTTTAAAAAATATATAA
589301 AAATAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.45
33 6 0.13
34 6 0.13
36 3 0.06
37 11 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (34 bp):
TAATATTTTAAAAAATATATAAGGATAAATATAT
Found at i:589350 original size:16 final size:16
Alignment explanation
Indices: 589268--589351 Score: 52
Period size: 16 Copynumber: 5.2 Consensus size: 16
589258 AAAATATATA
589268 ATATAAATTATT-AAT
1 ATATAAATTATTAAAT
*
589283 ATATTAAAATTTATATAAAA
1 ATA-T-AAA-TTAT-TAAAT
* *
589303 ATA-AAATTTTTTAA-
1 ATATAAATTATTAAAT
*
589317 ATAT-AATTA-TAATTT
1 ATATAAATTATTAA-AT
589332 ATATAAATTATTAAAT
1 ATATAAATTATTAAAT
589348 ATAT
1 ATAT
589352 TTTTAATTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 19
0.67 0.09 0.24
Matches are distributed among these distances:
13 2 0.04
14 7 0.13
15 10 0.19
16 14 0.27
17 9 0.17
18 4 0.08
19 1 0.02
20 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATAAATTATTAAAT
Found at i:589358 original size:29 final size:27
Alignment explanation
Indices: 589313--589380 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 27
589303 ATAAAATTTT
* *
589313 TTAAATATAATTATAATTTATATAAATTA
1 TTAAATATATTTTTAA-TTA-ATAAATTA
*
589342 TTAAATATATTTTTAATTAATAAATTT
1 TTAAATATATTTTTAATTAATAAATTA
*
589369 TTATATA-ATTTT
1 TTAAATATATTTT
589381 ATATTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.14
27 13 0.37
28 3 0.09
29 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAATATATTTTTAATTAATAAATTA
Found at i:589377 original size:19 final size:19
Alignment explanation
Indices: 589317--589378 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
589307 AATTTTTTAA
*
589317 ATATAATT-AT-AATTTAT
1 ATATAATTAATAAATTTTT
*
589334 ATA-AATTATTAAATATATTT
1 ATATAATTAATAAAT-T-TTT
589354 -T-TAATTAATAAATTTTT
1 ATATAATTAATAAATTTTT
589371 ATATAATT
1 ATATAATT
589379 TTATATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
16 4 0.11
17 7 0.20
18 5 0.14
19 17 0.49
20 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATAATTAATAAATTTTT
Found at i:589567 original size:31 final size:31
Alignment explanation
Indices: 589532--589590 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
589522 TACTAAAAAG
*
589532 AAAATAACCCTTT-TAAAAATTTCATCCAAAC
1 AAAATAACCCTTTAAAAAAATTT-ATCCAAAC
*
589563 AAAATAATCCTTTAAAAAAATTTATCCA
1 AAAATAACCCTTTAAAAAAATTTATCCA
589591 TTTGCTGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAATAACCCTTTAAAAAAATTTATCCAAAC
Found at i:597555 original size:16 final size:16
Alignment explanation
Indices: 597534--597584 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
597524 TTCAGATTTT
*
597534 TTTTGGATTTGGATCA
1 TTTTGGATTCGGATCA
* * *
597550 TTTTGGGTTCGGGTTA
1 TTTTGGATTCGGATCA
*
597566 TTTTGGATTCAGATCA
1 TTTTGGATTCGGATCA
597582 TTT
1 TTT
597585 CGAGTTCATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.08, G:0.25, T:0.51
Consensus pattern (16 bp):
TTTTGGATTCGGATCA
Found at i:598031 original size:8 final size:8
Alignment explanation
Indices: 598018--598050 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
598008 GTAATTTCAT
598018 ATTAAAAA
1 ATTAAAAA
598026 ATTAAAAA
1 ATTAAAAA
598034 ATT-AAAA
1 ATTAAAAA
*
598041 ATAAAAAA
1 ATTAAAAA
598049 AT
1 AT
598051 AATAGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTAAAAA
Found at i:599753 original size:25 final size:25
Alignment explanation
Indices: 599700--599772 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 25
599690 ATTTATATTA
* *
599700 TATC-AATTAAAT-ATT-ATTTTTA
1 TATCAAATTTAATAATTAATTTTTT
599722 TAT-AAATTTAATAATTAATTTTTT
1 TATCAAATTTAATAATTAATTTTTT
*
599746 TATCAAA-TTAATAATTAGATATTTT
1 TATCAAATTTAATAATTA-ATTTTTT
599771 TA
1 TA
599773 ATTTGTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 10 0.23
23 3 0.07
24 19 0.44
25 11 0.26
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (25 bp):
TATCAAATTTAATAATTAATTTTTT
Found at i:600428 original size:15 final size:15
Alignment explanation
Indices: 600405--600434 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
600395 ATATATTTTA
*
600405 TAAATAATTAATAAT
1 TAAACAATTAATAAT
600420 TAAACAATTAATAAT
1 TAAACAATTAATAAT
600435 ATAGTTGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAACAATTAATAAT
Found at i:600863 original size:18 final size:18
Alignment explanation
Indices: 600836--600882 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
600826 TTTAAAATTT
* *
600836 TTAATCATTAAATAAATA
1 TTAATAATTAAATAAAAA
*
600854 TTAATAATTAATTAAAAA
1 TTAATAATTAAATAAAAA
600872 TATAA-AATTAA
1 T-TAATAATTAA
600883 TTTTAAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAATAATTAAATAAAAA
Found at i:609850 original size:19 final size:19
Alignment explanation
Indices: 609828--609867 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
609818 AATTTTTAAA
609828 ATATTTAAATATT-TATATT
1 ATATTT-AATATTATATATT
*
609847 ATATTTTATATTATATATT
1 ATATTTAATATTATATATT
609866 AT
1 AT
609868 TTTTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTAATATTATATATT
Found at i:609882 original size:19 final size:19
Alignment explanation
Indices: 609836--609894 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
609826 AAATATTTAA
609836 ATATT-TATATTATATTTT
1 ATATTATATATTATATTTT
*
609854 ATATTATATATTATTTTTT
1 ATATTATATATTATATTTT
* *
609873 GTA-TAGTATATAATATTATT
1 ATATTA-TATATTATATT-TT
609893 AT
1 AT
609895 GTCCTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 7 0.21
19 23 0.70
20 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATATTATATATTATATTTT
Found at i:611222 original size:2 final size:2
Alignment explanation
Indices: 611215--611247 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
611205 GCAAACAGAA
611215 AG AG 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 AG AG A
611248 TGAGGCACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:612297 original size:13 final size:15
Alignment explanation
Indices: 612261--612334 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
612251 GGTTTAACAA
*
612261 TTTATGTATAT-ATAT
1 TTTATTTATATAAT-T
612276 TTTATTTAT-TAATT
1 TTTATTTATATAATT
612290 TTTATTATATAATAATT
1 TTTATT-TAT-ATAATT
* * *
612307 ATT-TTTAAATTATT
1 TTTATTTATATAATT
612321 TTATATTTATATAA
1 TT-TATTTATATAA
612335 AATTTGATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 14 0.30
15 16 0.35
16 9 0.20
17 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (15 bp):
TTTATTTATATAATT
Found at i:614019 original size:20 final size:20
Alignment explanation
Indices: 613987--614043 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
613977 TATATAATTT
613987 ATAATTATAATTAAATAAA-A
1 ATAATT-TAATTAAATAAATA
*
614007 TATTATTTAATTAAATAAATA
1 -ATAATTTAATTAAATAAATA
614028 ATAATTTAATTTAAAT
1 ATAATTTAA-TTAAAT
614044 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTTAATTAAATAAATA
Found at i:614200 original size:21 final size:21
Alignment explanation
Indices: 614167--614207 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
614157 ATCAAGGTGG
*
614167 ATTAAAAATAAAAGAAAAATC
1 ATTAAAAATAAAAAAAAAATC
*
614188 ATTAGAAAAAAAAAAAAAAA
1 ATTA-AAAATAAAAAAAAAA
614208 ACCTTGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (21 bp):
ATTAAAAATAAAAAAAAAATC
Found at i:614949 original size:19 final size:16
Alignment explanation
Indices: 614902--614952 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 16
614892 TTTAATTATT
614902 ATTAAAT-TATATTTA
1 ATTAAATCTATATTTA
614917 ATTAAATC-ATATTTA
1 ATTAAATCTATATTTA
614932 ATTCAAATACATATATTTA
1 ATT-AAAT-C-TATATTTA
614951 AT
1 AT
614953 ATTTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 1 0.03
19 9 0.29
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATCTATATTTA
Found at i:615327 original size:21 final size:20
Alignment explanation
Indices: 615302--615341 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
615292 TATCACTAAT
615302 TTTTAAATAAAAATAAATTTA
1 TTTTAAA-AAAAATAAATTTA
*
615323 TTTTAAACAAAATAAATTT
1 TTTTAAAAAAAATAAATTT
615342 GATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTAAAAAAAATAAATTTA
Found at i:615670 original size:30 final size:30
Alignment explanation
Indices: 615634--615694 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
615624 TGATCCAATA
*
615634 ATTTAAATTTTAAATTTTATGTATATTTAT
1 ATTTAAATTTTAAATTTTATGTAAATTTAT
615664 ATTTAAATTTTAAATTTTATGTAAATTTAT
1 ATTTAAATTTTAAATTTTATGTAAATTTAT
615694 A
1 A
615695 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
ATTTAAATTTTAAATTTTATGTAAATTTAT
Found at i:615895 original size:20 final size:20
Alignment explanation
Indices: 615866--615913 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
615856 ATAAAAATTT
615866 AATT-AAAAATATCATAATA
1 AATTAAAAAATATCATAATA
*
615885 AATTAAAAAATATTATAATA
1 AATTAAAAAATATCATAATA
615905 AATATAAAA
1 AAT-TAAAA
615914 TTAAAGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTAAAAAATATCATAATA
Found at i:617937 original size:25 final size:26
Alignment explanation
Indices: 617909--617961 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
617899 CTTATTTTAA
* *
617909 TTAATTAAGATCAAATTTTTA-ATAT
1 TTAATAAAGATAAAATTTTTATATAT
**
617934 TTAATAAATTTAAAATTTTTATATAT
1 TTAATAAAGATAAAATTTTTATATAT
617960 TT
1 TT
617962 TTAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAATAAAGATAAAATTTTTATATAT
Found at i:617942 original size:18 final size:18
Alignment explanation
Indices: 617921--617967 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
617911 AATTAAGATC
617921 AAATTTTTAATATTTAAT
1 AAATTTTTAATATTTAAT
** *
617939 AAATTTAAAAT-TTTTAT
1 AAATTTTTAATATTTAAT
*
617956 ATATTTTTAATA
1 AAATTTTTAATA
617968 AAATTTATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATTTTTAATATTTAAT
Found at i:617979 original size:28 final size:28
Alignment explanation
Indices: 617933--618005 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
617923 ATTTTTAATA
* *
617933 TTTAAT-AAATTTAAAATTTTTATATATT
1 TTTAATAAAATTT-ATATTTTAATATATT
617961 TTTAATAAAATTTATA-TTTAATATATT
1 TTTAATAAAATTTATATTTTAATATATT
**
617988 GATATATAAAATTTATAT
1 TTTA-ATAAAATTTATAT
618006 ATTATAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 12 0.32
28 20 0.53
29 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTAATAAAATTTATATTTTAATATATT
Found at i:618007 original size:13 final size:13
Alignment explanation
Indices: 617965--618007 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
617955 TATATTTTTA
617965 ATAAAATTTATAT
1 ATAAAATTTATAT
* *
617978 TTAATATATTGATAT
1 ATAA-A-ATTTATAT
617993 ATAAAATTTATAT
1 ATAAAATTTATAT
618006 AT
1 AT
618008 TATAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 12 0.50
14 2 0.08
15 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
ATAAAATTTATAT
Found at i:618007 original size:21 final size:20
Alignment explanation
Indices: 617976--618031 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
617966 TAAAATTTAT
*
617976 ATTTAATATATTGATATATAAA
1 ATTT-ATATATT-ATAAATAAA
617998 ATTTATATATTATAAATAAA
1 ATTTATATATTATAAATAAA
*
618018 ATATATTATATTAT
1 ATTTA-TATATTAT
618032 TTCATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 12 0.39
21 15 0.48
22 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTATATATTATAAATAAA
Found at i:620903 original size:8 final size:8
Alignment explanation
Indices: 620892--620993 Score: 57
Period size: 8 Copynumber: 12.8 Consensus size: 8
620882 TATATTTAAA
*
620892 TTATATTT
1 TTATATAT
620900 TTATAT-T
1 TTATATAT
620907 TTAATATAT
1 TT-ATATAT
* **
620916 TTAAATGG
1 TTATATAT
620924 TTATATAT
1 TTATATAT
* *
620932 ATAAAT-T
1 TTATATAT
620939 TTAATATAT
1 TT-ATATAT
*
620948 TAATA-AT
1 TTATATAT
620955 TTATATTAT
1 TTATA-TAT
* * *
620964 ATAAATTT
1 TTATATAT
*
620972 TTAAATAT
1 TTATATAT
620980 TTATATAT
1 TTATATAT
620988 TTATAT
1 TTATAT
620994 TATAATTATT
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
7 11 0.16
8 49 0.70
9 10 0.14
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
TTATATAT
Found at i:620904 original size:19 final size:18
Alignment explanation
Indices: 620877--620917 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
620867 GTTACTTCTA
620877 ATTTGTATATTTAAATTAT
1 ATTTGTATATTTAAA-TAT
* *
620896 ATTTTTATATTTTAATAT
1 ATTTGTATATTTAAATAT
620914 ATTT
1 ATTT
620918 AAATGGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTGTATATTTAAATAT
Found at i:620918 original size:16 final size:16
Alignment explanation
Indices: 620882--620982 Score: 63
Period size: 16 Copynumber: 6.5 Consensus size: 16
620872 TTCTAATTTG
620882 TATATTTAAA--TT-A
1 TATATTTAAATTTTAA
* *
620895 TATTTTTATATTTTAA
1 TATATTTAAATTTTAA
*
620911 TATATTTAAATGGTT-A
1 TATATTTAAAT-TTTAA
*
620927 TATATATAAATTTTAA
1 TATATTTAAATTTTAA
*
620943 TATA-TTAATAATTT-A
1 TATATTTAA-ATTTTAA
*
620958 TATTATATAAATTTTTAA
1 TA-TATTTAAA-TTTTAA
620976 -ATATTTA
1 TATATTTA
620983 TATATTTATA
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
13 8 0.12
15 10 0.15
16 38 0.58
17 9 0.14
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATTTAAATTTTAA
Found at i:620940 original size:32 final size:32
Alignment explanation
Indices: 620882--620997 Score: 127
Period size: 32 Copynumber: 3.7 Consensus size: 32
620872 TTCTAATTTG
* *
620882 TATATTTA-AA-TTATATT-TTTATATTTTAA
1 TATATTTATAATTTATATTATATAAATTTTAA
620911 TATATTTA-AATGGTTATA-TATATAAATTTTAA
1 TATATTTATAAT--TTATATTATATAAATTTTAA
*
620943 TATATTAATAATTTATATTATATAAATTTTTAA
1 TATATTTATAATTTATATTATATAAA-TTTTAA
620976 -ATATTTATATATTTATATTATA
1 TATATTTATA-ATTTATATTATA
620998 ATTATTTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
29 10 0.13
31 6 0.08
32 38 0.51
33 21 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TATATTTATAATTTATATTATATAAATTTTAA
Found at i:620946 original size:18 final size:18
Alignment explanation
Indices: 620925--620986 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 18
620915 TTTAAATGGT
620925 TATATATATAAATTTTAA
1 TATATATATAAATTTTAA
620943 TATAT-TA-ATAA-TTT-A
1 TATATATATA-AATTTTAA
620958 TAT-TATATAAATTTTTAAA
1 TATATATATAAA-TTTT-AA
*
620977 TATTTATATA
1 TATATATATA
620987 TTTATATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
14 1 0.03
15 8 0.22
16 5 0.14
17 7 0.19
18 5 0.14
19 4 0.11
20 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATATATAAATTTTAA
Found at i:621719 original size:13 final size:13
Alignment explanation
Indices: 621701--621725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
621691 TGGAAAGGGG
621701 GAAAGAAAAAAAA
1 GAAAGAAAAAAAA
621714 GAAAGAAAAAAA
1 GAAAGAAAAAAA
621726 CAACGTTACT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAAAA
Found at i:621852 original size:2 final size:2
Alignment explanation
Indices: 621845--621872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
621835 GGCTCATGCA
621845 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
621873 TGTCAGTTTG
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:621995 original size:13 final size:13
Alignment explanation
Indices: 621979--622004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
621969 AATGGTTAAA
621979 TTAATAAAATTAT
1 TTAATAAAATTAT
621992 TTAATAAAATTAT
1 TTAATAAAATTAT
622005 GATATACAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATAAAATTAT
Found at i:622321 original size:15 final size:16
Alignment explanation
Indices: 622292--622322 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
622282 ATTTTTAATC
622292 AAAATTTTGTATTTTT
1 AAAATTTTGTATTTTT
622308 AAAATTTT-TATTTTT
1 AAAATTTTGTATTTTT
622323 GAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
AAAATTTTGTATTTTT
Found at i:623722 original size:6 final size:5
Alignment explanation
Indices: 623709--623753 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
623699 TTAAATATAA
*
623709 ATATT ATATGT ATATT A-A-T ATAAT ATATT ATATT -TATT ATATT AT
1 ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
623754 TTTTAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 22 0.63
6 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:624658 original size:18 final size:17
Alignment explanation
Indices: 624613--624666 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 17
624603 TTATTTATTT
*
624613 ATTATTTATAAGATTAAA
1 ATTATTT-TAATATTAAA
624631 ATTATATTTTAATATTTAAA
1 A-T-TATTTTAATA-TTAAA
624651 ATTATTTTAAT-TTAAA
1 ATTATTTTAATATTAAA
624667 TTAATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.16
18 10 0.31
19 6 0.19
20 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTATTTTAATATTAAA
Found at i:624680 original size:13 final size:14
Alignment explanation
Indices: 624657--624687 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
624647 TAAAATTATT
624657 TTAATTTAAATTAA
1 TTAATTTAAATTAA
624671 TTAA-TTAAATTAA
1 TTAATTTAAATTAA
624684 TTAA
1 TTAA
624688 ATTACTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTTAAATTAA
Found at i:629778 original size:41 final size:41
Alignment explanation
Indices: 629732--629945 Score: 236
Period size: 41 Copynumber: 5.2 Consensus size: 41
629722 TTTAGCAACA
* *
629732 TTTTGCTATGAAACATCACTAACTAATTAAAATTAGTGGAG
1 TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGGAG
** * *
629773 TTTTGCTATGAAACACCGCTAAATAATTAAAATTAGCGGCA-
1 TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGG-AG
* * *
629814 TTTTGCTATGAAATGTCACAAAATAATTAAAATTAGTGGTG
1 TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGGAG
* *
629855 TTTTGCTATGAAACGTCGCTAAATAATTAAAATTAAT-GACG
1 TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGGA-G
* * * * *
629896 ATTTACTATTAAATGCCACTAAATAATTAAAATTAGT-GACG
1 TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGGA-G
629937 TTTTGCTAT
1 TTTTGCTAT
629946 TTACAATTGC
Statistics
Matches: 145, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
40 1 0.01
41 143 0.99
42 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (41 bp):
TTTTGCTATGAAACGTCACTAAATAATTAAAATTAGTGGAG
Found at i:629860 original size:82 final size:82
Alignment explanation
Indices: 629729--629945 Score: 285
Period size: 82 Copynumber: 2.6 Consensus size: 82
629719 GATTTTAGCA
** *
629729 ACATTTTGCTATGAAACATCACTAACTAATTAAAATTAGTGGAGTTTTGCTATGAAACACCGCTA
1 ACATTTTGCTATGAAATGTCACTAAATAATTAAAATTAGTGGAGTTTTGCTATGAAACACCGCTA
*
629794 AATAATTAAAATTAGCG
66 AATAATTAAAATTAACG
* * * **
629811 GCATTTTGCTATGAAATGTCACAAAATAATTAAAATTAGTGGTGTTTTGCTATGAAACGTCGCTA
1 ACATTTTGCTATGAAATGTCACTAAATAATTAAAATTAGTGGAGTTTTGCTATGAAACACCGCTA
*
629876 AATAATTAAAATTAATG
66 AATAATTAAAATTAACG
* * *
629893 ACGA-TTTACTATTAAATGCCACTAAATAATTAAAATTAGT-GACGTTTTGCTAT
1 AC-ATTTTGCTATGAAATGTCACTAAATAATTAAAATTAGTGGA-GTTTTGCTAT
629946 TTACAATTGC
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 115 0.98
83 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (82 bp):
ACATTTTGCTATGAAATGTCACTAAATAATTAAAATTAGTGGAGTTTTGCTATGAAACACCGCTA
AATAATTAAAATTAACG
Found at i:630095 original size:42 final size:42
Alignment explanation
Indices: 630049--630128 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
630039 TTTCACCTTG
* * * * *
630049 AAAAAGCGACTATATTTTTTCAATTAGCGGCATTTTTATTTA
1 AAAAAGCCACTATAGTTTTTAAATTAACAGCATTTTTATTTA
630091 AAAAAGCCACTATAGTTTTTAAATTAACAGCATTTTTA
1 AAAAAGCCACTATAGTTTTTAAATTAACAGCATTTTTA
630129 AATAAAAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (42 bp):
AAAAAGCCACTATAGTTTTTAAATTAACAGCATTTTTATTTA
Found at i:630901 original size:2 final size:2
Alignment explanation
Indices: 630890--630928 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
630880 GTCTTCGTTT
630890 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
630929 AATAAAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:637653 original size:20 final size:20
Alignment explanation
Indices: 637630--637670 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
637620 ACATTTCAAA
637630 TATGTATTGACACATTCACT
1 TATGTATTGACACATTCACT
**
637650 TATGTATTGATGCATTCACT
1 TATGTATTGACACATTCACT
637670 T
1 T
637671 GTTGTATCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (20 bp):
TATGTATTGACACATTCACT
Found at i:639494 original size:81 final size:79
Alignment explanation
Indices: 639359--639539 Score: 206
Period size: 81 Copynumber: 2.3 Consensus size: 79
639349 TTTTAGAGAT
* *
639359 AATAACGGGGTTGGAGTATCCTCGATTATGGAAAATCGATGTTCTAGAAATAAAAAATCAGGG-T
1 AATAACGGGGTTGGAGTATCCTCAATTATAGAAAATCGATGTTCTAGAAAT--AAAATC-GGGAT
* **
639423 TGGAGTATCCCTTCGAA
63 TGAAGTATCCCCGCGAA
* * *
639440 AATAACAGGGTTGGAGTATCCAT-AATTATAGAAAATCGGTGTT-TTGAAAATAAAATCGGGATT
1 AATAACGGGGTTGGAGTATCC-TCAATTATAGAAAATCGATGTTCTAG-AAATAAAATCGGGATT
639503 GAAGTATCCCCGCGAA
64 GAAGTATCCCCGCGAA
* *
639519 AATAATGGGGTTAGAGTATCC
1 AATAACGGGGTTGGAGTATCC
639540 CCGATTGTGA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 39 0.45
80 2 0.02
81 41 0.48
82 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (79 bp):
AATAACGGGGTTGGAGTATCCTCAATTATAGAAAATCGATGTTCTAGAAATAAAATCGGGATTGA
AGTATCCCCGCGAA
Found at i:639555 original size:79 final size:79
Alignment explanation
Indices: 639359--639620 Score: 239
Period size: 79 Copynumber: 3.3 Consensus size: 79
639349 TTTTAGAGAT
* * * *
639359 AATAACGGGGTTGGAGTATCCTCGATTATG-GAAAATCGATGTTCTAGAAATAAAAAATCAGGGT
1 AATAACGGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTGTT-TTGAAA-ATAAAATC-GGGT
*
639423 TGGAGTATCCCTTCGAA
63 TGAAGTATCCCTTCGAA
* ***
639440 AATAACAGGGTTGGAGTATCCATAATTAT-AGAAAATCGGTGTTTTGAAAATAAAATCGGGATTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTGTTTTGAAAATAAAATCGGG-TTG
**
639504 AAGTATCCCCGCGAA
65 AAGTATCCCTTCGAA
* * * * * *
639519 AATAATGGGGTTAGAGTATCCCCGATTGTGAG-AAATCAGTATTTT-AGAAATAAAGTCGGGGTT
1 AATAACGGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTGTTTTGA-AAATAAAATC-GGGTT
639582 -AGAGTATCCCTTC-AGA
64 GA-AGTATCCCTTCGA-A
* *
639598 AATAATGGGATTGGAGTATCCCC
1 AATAACGGGGTTGGAGTATCCCC
639621 AATGAAATAA
Statistics
Matches: 150, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
78 6 0.04
79 97 0.65
80 10 0.07
81 37 0.25
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (79 bp):
AATAACGGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTGTTTTGAAAATAAAATCGGGTTGA
AGTATCCCTTCGAA
Found at i:639700 original size:50 final size:51
Alignment explanation
Indices: 639634--639749 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
639624 GAAATAACGG
639634 GGTTGGAGTATCCCCGATTGT-AAAAATTGATGTTGGAGAAATAAAATCAGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTGGAGAAATAAAA-CAGA
* ** *
639685 -GTTGGAGTATTCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTGGAGAAATAAAACAGA
639735 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
639750 TTGGAAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 22 0.38
51 36 0.62
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTGGAGAAATAAAACAGA
Found at i:639806 original size:48 final size:49
Alignment explanation
Indices: 639750--639858 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 49
639740 GAGTATCCCC
* *
639750 TTGGAAATAACGA-GGTTAGAGTATCCTCGATGGTGAAAAATTGATGTT
1 TTGGAAATAACGAGGGTTAGAGTATCCCCGATGATGAAAAATTGATGTT
* * * *
639798 TTGGAAATAAAACTAGGGTTGGAGTATCCCCGATTATGGAAAATTGATGTT
1 TTGGAAAT--AACGAGGGTTAGAGTATCCCCGATGATGAAAAATTGATGTT
*
639849 TTAGAAATAA
1 TTGGAAATAA
639859 AGCCAAGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
48 8 0.16
49 2 0.04
50 4 0.08
51 37 0.73
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (49 bp):
TTGGAAATAACGAGGGTTAGAGTATCCCCGATGATGAAAAATTGATGTT
Done.