Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 141 of 175
Found at i:43480727 original size:16 final size:18
Alignment explanation
Indices: 43480686--43480720 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43480676 AATGGTACAA
43480686 AATAACTTTTATTATTTTG
1 AATAA-TTTTATTATTTTG
43480705 AATAATTTTATT-TTTT
1 AATAATTTTATTATTTT
43480721 ATTAATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
AATAATTTTATTATTTTG
Found at i:43480825 original size:24 final size:23
Alignment explanation
Indices: 43480781--43480825 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
43480771 CTTATTTATT
** *
43480781 ATTTGATTTTTTTATATTATAAC
1 ATTTGATTTTTAAATAATATAAC
43480804 ATTTGGATTTTTAAATAATATA
1 ATTT-GATTTTTAAATAATATA
43480826 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTTGATTTTTAAATAATATAAC
Found at i:43481189 original size:22 final size:23
Alignment explanation
Indices: 43481155--43481202 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
43481145 GTTTATTAAT
*
43481155 ATTTAATTTAAAATTTAAAATTA
1 ATTTAATTCAAAATTTAAAATTA
*
43481178 ATTTAA-TCAAAATTTATAATTA
1 ATTTAATTCAAAATTTAAAATTA
43481200 ATT
1 ATT
43481203 AACAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTCAAAATTTAAAATTA
Found at i:43487286 original size:25 final size:25
Alignment explanation
Indices: 43487240--43487292 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
43487230 TGATTAATGA
** * *
43487240 TTTAATTTTGTTTTAAATTTTTTAT
1 TTTAATTTCATTTTAAAGTTTTAAT
*
43487265 TTTAATTTCATTTTAACGTTTTAAT
1 TTTAATTTCATTTTAAAGTTTTAAT
43487290 TTT
1 TTT
43487293 CTCTAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTAATTTCATTTTAAAGTTTTAAT
Found at i:43494403 original size:51 final size:49
Alignment explanation
Indices: 43494367--43494816 Score: 357
Period size: 51 Copynumber: 8.9 Consensus size: 49
43494357 ATGAAAGTGA
43494367 AAGTGTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGAT
1 AAGT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAAT-GAT
* * * * * * ** *
43494418 AAATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAG
1 AAGT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AATGAT
* *
43494469 AAGCTTTGGTCACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGAT
1 AAG-TTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAAT-GAT
* * * * * ** *
43494520 AAATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGT-ACCGAG
1 AAGT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTAC--TACGTGAATGAT
*
43494571 AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGAT
1 AAG-TTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-TGAT
* * * * * * *
43494622 AAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGAA
1 AAGT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAAT-GAT
* * *
43494673 AAGCTTTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-T
1 AAG-TTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAAT-GAT
** * * * * *
43494723 AAAACTTGATCACGTGTATAGTACTATGTGAAGGTTATTACGTGAACCG-T
1 -AAGTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-TGAT
** *
43494773 AAAAATTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 -AAGTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
43494817 TATCGAATGA
Statistics
Matches: 315, Mismatches: 70, Indels: 29
0.76 0.17 0.07
Matches are distributed among these distances:
49 4 0.01
50 81 0.26
51 221 0.70
52 5 0.02
53 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (49 bp):
AAGTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATGAT
Found at i:43494523 original size:102 final size:102
Alignment explanation
Indices: 43494372--43494822 Score: 622
Period size: 102 Copynumber: 4.4 Consensus size: 102
43494362 AGTGAAAGTG
43494372 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
43494437 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* *
43494474 TTGGTCACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
*
43494539 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * *
43494576 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
43494641 AGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * * * * * *
43494678 TTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGATCACGTGTA
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* * ** * * **
43494741 TAGTACTATGTGAAGGTTATTACGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCT
* *
43494778 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
43494823 ATGATAATAG
Statistics
Matches: 313, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
100 39 0.12
101 40 0.13
102 234 0.75
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
Found at i:43494632 original size:153 final size:150
Alignment explanation
Indices: 43494383--43494823 Score: 397
Period size: 153 Copynumber: 2.9 Consensus size: 150
43494373 TGGTCACGTG
* * * * * * * * *
43494383 TGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTACTAAGT
1 TGTAGTACTAAGTGAAGGCTACAACATGAACCG-TAAA-ACTTGATCACGTGTATAGTACTATGT
* * * ** * *
43494447 GAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTATTGTGTGAAGGCTACTACG
64 GAAGGCTACTACGTGAACCGTA-AA-AATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACG
* * *
43494511 TGAATCGATAAA-TAATGGTCACATG
127 TGTATCGA-AAACT-ATAGTCACATA
* * * * * *
43494536 TGTAGTACTAAGTGAAGGCTACAATATGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTGTGT
1 TGTAGTACTAAGTGAAGGCTACAACATGAACCGTA-AAAC-TTGATCACGTGTATAGTACTATGT
** * * * *
43494600 GAAGGCTACTACGTGAATTG-ATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATG
64 GAAGGCTACTACGTGAACCGTAAAAAT--TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACG
*
43494664 TGTATCGAAAAGCTTTAGTCACATA
127 TGTATCGAAAA-CTATAGTCACATA
* * * *
43494689 TGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGATCACGTGTATAGTACTATGTGA
1 TGTAGTACTAAGTGAAGGCTACAACATGAACCGTAAAACTTGATCACGTGTATAGTACTATGTGA
* * *
43494754 AGGTTATTACGTGAACCGTAAAAATTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
66 AGGCTACTACGTGAACCGTAAAAATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
43494819 TCGAA
131 TCGAA
43494824 TGATAATAGT
Statistics
Matches: 232, Mismatches: 47, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
151 43 0.19
152 43 0.19
153 144 0.62
154 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (150 bp):
TGTAGTACTAAGTGAAGGCTACAACATGAACCGTAAAACTTGATCACGTGTATAGTACTATGTGA
AGGCTACTACGTGAACCGTAAAAATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
TCGAAAACTATAGTCACATA
Found at i:43497834 original size:27 final size:27
Alignment explanation
Indices: 43497792--43497870 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
43497782 TATACTAGGT
*
43497792 GTGCCACCTATTAGATAGGCACCAC-C
1 GTGCCACCTATCAGATAGGCACCACTC
***
43497818 AGTGCCACCTATCAGATAGGGGTCACTC
1 -GTGCCACCTATCAGATAGGCACCACTC
*
43497846 GTGCCGCCTATCAGATAGGCACCAC
1 GTGCCACCTATCAGATAGGCACCAC
43497871 ACTCCCTTCG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 42 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (27 bp):
GTGCCACCTATCAGATAGGCACCACTC
Found at i:43497954 original size:3 final size:3
Alignment explanation
Indices: 43497948--43497974 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43497938 CCACTACTAA
43497948 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43497975 TAAAGTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43502583 original size:7 final size:7
Alignment explanation
Indices: 43502571--43502599 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43502561 AGAGGTTTCC
43502571 CTTTTTT
1 CTTTTTT
43502578 CTTTTTT
1 CTTTTTT
43502585 -TTTTTT
1 CTTTTTT
43502591 CTTTTTT
1 CTTTTTT
43502598 CT
1 CT
43502600 CGTTTTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
CTTTTTT
Found at i:43502590 original size:13 final size:13
Alignment explanation
Indices: 43502572--43502597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43502562 GAGGTTTCCC
43502572 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
43502585 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
43502598 CTCGTTTTTG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:43509663 original size:24 final size:24
Alignment explanation
Indices: 43509631--43509679 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
43509621 ATGGGTAAGA
43509631 CTTTCATCCTACGACTACAAATGT
1 CTTTCATCCTACGACTACAAATGT
43509655 CTTTCATCCTACGACTACAAATGT
1 CTTTCATCCTACGACTACAAATGT
43509679 C
1 C
43509680 AATGTACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (24 bp):
CTTTCATCCTACGACTACAAATGT
Found at i:43509883 original size:16 final size:16
Alignment explanation
Indices: 43509862--43509892 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43509852 TTCACTATTA
*
43509862 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
43509878 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
43509893 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:43511013 original size:14 final size:15
Alignment explanation
Indices: 43510994--43511022 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43510984 GAATTTTCTT
43510994 GAAAAATT-ATTTTG
1 GAAAAATTAATTTTG
43511008 GAAAAATTAATTTTG
1 GAAAAATTAATTTTG
43511023 ATGAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
GAAAAATTAATTTTG
Found at i:43511547 original size:32 final size:33
Alignment explanation
Indices: 43511480--43511551 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
43511470 TTAATAGTTT
***
43511480 AATATTAAATTTAATTTAATATTTATCTTGATA
1 AATATTAAATTTAATTTAATATTTAAAGTGATA
*
43511513 AATATTATA-TTAATTTAATA-TTAAAGTGATTA
1 AATATTAAATTTAATTTAATATTTAAAGTGA-TA
43511545 AAT-TTAA
1 AATATTAA
43511552 TCATAGTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 9 0.27
32 16 0.48
33 8 0.24
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (33 bp):
AATATTAAATTTAATTTAATATTTAAAGTGATA
Found at i:43514305 original size:8 final size:8
Alignment explanation
Indices: 43514292--43514323 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
43514282 TGTTAAACAG
43514292 ATTGTTTT
1 ATTGTTTT
43514300 ATTGTTTT
1 ATTGTTTT
43514308 ATTGTTTT
1 ATTGTTTT
*
43514316 ATGGTTTT
1 ATTGTTTT
43514324 GGTGATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (8 bp):
ATTGTTTT
Found at i:43516376 original size:59 final size:59
Alignment explanation
Indices: 43516311--43516498 Score: 150
Period size: 59 Copynumber: 3.2 Consensus size: 59
43516301 ATTTTATTAA
43516311 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
* * ** * * * ** * * * *
43516370 ATCATATATTATGATTTTAGTA-AATTCATA-TAAGAATATTGATTATTAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCA-AATTA-TATTTTA-TAGT
* * * *
43516430 ATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTTTATAGT
43516489 ATCATATATT
1 ATCATATATT
43516499 ATGATTTGAG
Statistics
Matches: 91, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
57 5 0.05
58 10 0.11
59 36 0.40
60 25 0.27
61 10 0.11
62 4 0.04
63 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
Found at i:43516425 original size:119 final size:120
Alignment explanation
Indices: 43516300--43516588 Score: 492
Period size: 119 Copynumber: 2.4 Consensus size: 120
43516290 AATTATTTTA
*
43516300 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
* * *
43516365 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
43516419 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTT
43516483 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
43516539 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
43516589 GTTTAAATAT
Statistics
Matches: 160, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 109 0.68
120 51 0.32
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:43516446 original size:18 final size:18
Alignment explanation
Indices: 43516420--43516475 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
43516410 GATTATTAGA
43516420 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
43516437 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
43516453 A-TTTAA-T-AATTAT-T
1 ATTTTAATTAAATTATAT
43516467 ATTTTAATT
1 ATTTTAATT
43516476 TATATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.35
16 6 0.18
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:43516556 original size:59 final size:58
Alignment explanation
Indices: 43516374--43516556 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 58
43516364 TATAGTATCA
*
43516374 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
* * * * * *
43516432 TATA-TAT--TTTAATTAAAATAT-ATTTAATAATTATTATT-TTAATTTATATTTTA-CAGTAT
1 TATATTATGATTTAAGT-AAAT-TCATATAAGAA-TATTATTATTAA--GA-ATTTTATTA-AAT
*
43516491 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
43516552 TATAT
1 TATAT
43516557 ATTTTAATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
55 7 0.07
56 15 0.16
57 8 0.09
58 6 0.06
59 13 0.14
61 12 0.13
62 10 0.11
63 14 0.15
64 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:43516568 original size:18 final size:17
Alignment explanation
Indices: 43516540--43516574 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43516530 ATTATTAAGA
*
43516540 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43516557 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43516575 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43516682 original size:147 final size:149
Alignment explanation
Indices: 43516528--43516802 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
43516518 ATAAGAATAT
*
43516528 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
43516593 AAATATGAGTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
43516656 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
43516675 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
* *
43516740 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
43516803 CAATAATCAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 90 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:43516715 original size:18 final size:17
Alignment explanation
Indices: 43516687--43516721 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43516677 ATTATTAAGA
*
43516687 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43516704 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43516722 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43516932 original size:44 final size:45
Alignment explanation
Indices: 43516883--43516977 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
43516873 TTACACCTCT
* * *
43516883 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCTTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
43516927 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
43516972 ATTACA
1 ATTACA
43516978 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:43516977 original size:16 final size:16
Alignment explanation
Indices: 43516958--43517025 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
43516948 GATTTGCTAT
* *
43516958 TACACATCTATTCCAT
1 TACACATCTAATCCAA
*
43516974 TACACCTCTAATCCAA
1 TACACATCTAATCCAA
43516990 TACACATCTAATCCAA
1 TACACATCTAATCCAA
*
43517006 TACACCTCTAATCCAA
1 TACACATCTAATCCAA
43517022 TACA
1 TACA
43517026 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACATCTAATCCAA
Found at i:43516999 original size:32 final size:32
Alignment explanation
Indices: 43516958--43517025 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
43516948 GATTTGCTAT
* *
43516958 TACACATCTATTCCATTACACCTCTAATCCAA
1 TACACATCTAATCCAATACACCTCTAATCCAA
43516990 TACACATCTAATCCAATACACCTCTAATCCAA
1 TACACATCTAATCCAATACACCTCTAATCCAA
43517022 TACA
1 TACA
43517026 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (32 bp):
TACACATCTAATCCAATACACCTCTAATCCAA
Found at i:43517442 original size:29 final size:27
Alignment explanation
Indices: 43517397--43517463 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 27
43517387 TCAATTAAGT
*
43517397 AATCTTACATTTCATCAATAAAAT-AACAA
1 AATCTTA-ATTCCATC-ATAAAATCAA-AA
*
43517426 AATCTTAATTCCAATCATCAAATCAAAA
1 AATCTTAATTCC-ATCATAAAATCAAAA
43517454 AGATCTTAAT
1 A-ATCTTAAT
43517464 ACGGAACGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.31
Consensus pattern (27 bp):
AATCTTAATTCCATCATAAAATCAAAA
Found at i:43518017 original size:42 final size:42
Alignment explanation
Indices: 43517958--43518244 Score: 263
Period size: 42 Copynumber: 6.8 Consensus size: 42
43517948 AGCTGAATCA
* * *
43517958 TAGGACCGGTCACGCCTTCTATAGTATCGATCATCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
*
43518000 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCGTCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
* * *
43518042 TAGGAACGATCCCACCTTCTGTAGTACCGATCATCAGGTGCA-
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTG-AG
* * *
43518084 TAAGAACGGTCCCGCCTTCTATAGTATCCATCATCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
* * * * * * * * *
43518126 TAGGAACGGTTCTGCCTGCGGTAGTAAC-AGTCCTCGGGAGTG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGA-TCATCAGGTGAG
* * ** * * * *
43518168 TAAGATCTATCACACCTTCTGTAGTATTGATCATCAGGAGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
** * *
43518210 TAGGAACGGTCCCATCTTCTATAGTAGCGATCATC
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATC
43518245 TGACGATCCG
Statistics
Matches: 192, Mismatches: 49, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
41 2 0.01
42 188 0.98
43 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (42 bp):
TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
Found at i:43518189 original size:126 final size:126
Alignment explanation
Indices: 43517964--43518244 Score: 332
Period size: 126 Copynumber: 2.2 Consensus size: 126
43517954 ATCATAGGAC
* * * *
43517964 CGGTCACGCCTTCTATAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTTCTGTAGTATCG
1 CGGTCCCGCCTTCTATAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACG
* * * * *
43518029 ATCGTCAGGTGAGTAGGAACGATCCCACCTTCTGTAGTACCGATCATCAGGTGCA-TAAGAA
66 ATCCTCAGGAGAGTAAGAACGATCACACCTTCTGTAGTACCGATCATCAGGAG-AGTAAGAA
* * *
43518090 CGGTCCCGCCTTCTATAGTATCCATCATCAGGTGAGTAGGAACGGTTCTGCCTGCGGTAGTAAC-
1 CGGTCCCGCCTTCTATAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACG
* * * * ** *
43518154 AGTCCTCGGGAGTGTAAGATCTATCACACCTTCTGTAGTATTGATCATCAGGAGAGTAGGAA
66 A-TCCTCAGGAGAGTAAGAACGATCACACCTTCTGTAGTACCGATCATCAGGAGAGTAAGAA
** *
43518216 CGGTCCCATCTTCTATAGTAGCGATCATC
1 CGGTCCCGCCTTCTATAGTATCGATCATC
43518245 TGACGATCCG
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
125 2 0.02
126 128 0.98
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (126 bp):
CGGTCCCGCCTTCTATAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACG
ATCCTCAGGAGAGTAAGAACGATCACACCTTCTGTAGTACCGATCATCAGGAGAGTAAGAA
Found at i:43527312 original size:20 final size:20
Alignment explanation
Indices: 43527283--43527356 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
43527273 TGTAGTGCTA
*
43527283 GCACCGAAGTGCAAATAGAG
1 GCACCGAAGTGCAAATAGGG
* * **
43527303 ACACCAAAGTATAAATAGGG
1 GCACCGAAGTGCAAATAGGG
*
43527323 GCACCGAAGTGCAAACAGGG
1 GCACCGAAGTGCAAATAGGG
43527343 GCACCGAAGTGCAA
1 GCACCGAAGTGCAA
43527357 TCTCCTACGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.28, T:0.09
Consensus pattern (20 bp):
GCACCGAAGTGCAAATAGGG
Found at i:43539842 original size:22 final size:22
Alignment explanation
Indices: 43539814--43539859 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
43539804 GTGTTGGGTC
43539814 CAAAGGATCTAATTTAACGTTG
1 CAAAGGATCTAATTTAACGTTG
43539836 CAAAGGATCTAATTTAACGTTG
1 CAAAGGATCTAATTTAACGTTG
43539858 CA
1 CA
43539860 TAGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (22 bp):
CAAAGGATCTAATTTAACGTTG
Found at i:43549157 original size:26 final size:26
Alignment explanation
Indices: 43549122--43549207 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 26
43549112 ACAGCTCTTA
* *
43549122 TGAGCGTCCCAA-TATATGGCTCTTCG
1 TGAGCTTCCCAATTA-AAGGCTCTTCG
* *
43549148 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCAATTAAAGGCTCTTCG
* *
43549174 TGAGCTTCCC-GTTAAAGGCTCTCCG
1 TGAGCTTCCCAATTAAAGGCTCTTCG
43549199 -GAGCTTCCC
1 TGAGCTTCCC
43549208 GATATGACTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.17
25 12 0.23
26 29 0.56
27 2 0.04
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.30
Consensus pattern (26 bp):
TGAGCTTCCCAATTAAAGGCTCTTCG
Found at i:43549207 original size:24 final size:26
Alignment explanation
Indices: 43549139--43549210 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
43549129 CCCAATATAT
43549139 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
43549165 GGCTCTTTGTGAGCTTCCCG-TTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
43549190 GGCTCTCCG-GAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
43549211 ATGACTCACT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 10 0.24
25 13 0.31
26 19 0.45
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:43555547 original size:41 final size:41
Alignment explanation
Indices: 43555502--43555623 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 41
43555492 TATGATTTTG
* *
43555502 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGAT-TCA
1 TGTAAGACCATGTCTGGGACA-TGGCATCGTATGTGATAACA
* *
43555543 TGTAAGACCCTGTCTGGGACAAAGGCATCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGAC-ATGGCATCG-TATGTGATAACA
* * *
43555586 TGTAAGACCATATCTGGGATATGGCATTGTATGTGATA
1 TGTAAGACCATGTCTGGGACATGGCATCGTATGTGATA
43555624 TATGTGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 35 0.51
42 15 0.22
43 19 0.28
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATGGCATCGTATGTGATAACA
Found at i:43561588 original size:22 final size:22
Alignment explanation
Indices: 43561560--43561607 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
43561550 AAAATTCTAA
43561560 TGGTTTTGATTTAATCTCGATT
1 TGGTTTTGATTTAATCTCGATT
43561582 TGGTTTTGATTTAATCTCGATT
1 TGGTTTTGATTTAATCTCGATT
43561604 TGGT
1 TGGT
43561608 CCCGATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.08, G:0.21, T:0.54
Consensus pattern (22 bp):
TGGTTTTGATTTAATCTCGATT
Found at i:43562353 original size:26 final size:25
Alignment explanation
Indices: 43562323--43562407 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 25
43562313 CTTATGAGTG
*
43562323 TCCCGATATATGGCTCTTCGCGAGCT
1 TCCCGATATAAGGCTCTTCG-GAGCT
*
43562349 TCCCGAT-TAAAGGCTCTTTGTGAGCT
1 TCCCGATAT-AAGGCTCTTCG-GAGCT
* * *
43562375 TCTCGTTA-AAGGCTCTTCGAAGCT
1 TCCCGATATAAGGCTCTTCGGAGCT
*
43562399 TCCTGATAT
1 TCCCGATAT
43562408 GGCTCGCTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
24 9 0.20
25 11 0.24
26 26 0.57
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
TCCCGATATAAGGCTCTTCGGAGCT
Found at i:43562389 original size:25 final size:26
Alignment explanation
Indices: 43562334--43562401 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
43562324 CCCGATATAT
43562334 GGCTCTTCGCGAGCTTCCCGATTAAA
1 GGCTCTTCGCGAGCTTCCCGATTAAA
* * *
43562360 GGCTCTTTGTGAGCTTCTCG-TTAAA
1 GGCTCTTCGCGAGCTTCCCGATTAAA
*
43562385 GGCTCTTCG-AAGCTTCC
1 GGCTCTTCGCGAGCTTCC
43562402 TGATATGGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 6 0.17
25 13 0.36
26 17 0.47
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (26 bp):
GGCTCTTCGCGAGCTTCCCGATTAAA
Found at i:43562470 original size:24 final size:24
Alignment explanation
Indices: 43562323--43562483 Score: 89
Period size: 24 Copynumber: 6.6 Consensus size: 24
43562313 CTTATGAGTG
*
43562323 TCCCGATATATGGCTCTTCGCGAGCT
1 TCCCGTTA-ATGGCTCTTCG-GAGCT
* *
43562349 TCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCCG-TTAATGGCTCTTCG-GAGCT
* * *
43562375 TCTCGTTAAAGGCTCTTCGAAGCT
1 TCCCGTTAATGGCTCTTCGGAGCT
* * *
43562399 TCCTGAT-ATGGCTCGCTT--GAACT
1 TCCCGTTAATGGCT--CTTCGGAGCT
* * *
43562422 TCCCGAT-A-GAGCTATTCAGAGCT
1 TCCCGTTAATG-GCTCTTCGGAGCT
*
43562445 TCCCGTTAATGGCTCTTTGGAGCT
1 TCCCGTTAATGGCTCTTCGGAGCT
* *
43562469 TCTCGTTATTGGCTC
1 TCCCGTTAATGGCTC
43562484 GCATGAGCTT
Statistics
Matches: 105, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
21 2 0.02
22 1 0.01
23 28 0.27
24 32 0.30
25 17 0.16
26 23 0.22
27 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
TCCCGTTAATGGCTCTTCGGAGCT
Found at i:43566298 original size:30 final size:31
Alignment explanation
Indices: 43566264--43566324 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
43566254 CTTTATAATA
*
43566264 TAATAATAGTTATATA-TGTATTAATATTTT
1 TAATAATAGTTATATATTATATTAATATTTT
*
43566294 TAATAATAGTTATATATTATATTATTATTTT
1 TAATAATAGTTATATATTATATTAATATTTT
43566325 ATGTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (31 bp):
TAATAATAGTTATATATTATATTAATATTTT
Found at i:43566348 original size:29 final size:29
Alignment explanation
Indices: 43566291--43566398 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
43566281 GTATTAATAT
* * *
43566291 TTTTAATAATAGTTATATATTATATTATTA
1 TTTTATTATTAGTAATATATTAT-TTATTA
43566321 TTTTATGTATTAGTAATAT-TTATTTATTA
1 TTTTAT-TATTAGTAATATATTATTTATTA
* * * **
43566350 TATTATTACTAG-CATATATTACACTATTA
1 TTTTATTATTAGTAATATATTA-TTTATTA
43566379 TTTTATTTATTAGTAATATA
1 TTTTA-TTATTAGTAATATA
43566399 CAAATTTAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
27 4 0.06
28 8 0.13
29 20 0.32
30 15 0.24
31 15 0.24
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTTATTATTAGTAATATATTATTTATTA
Found at i:43571639 original size:14 final size:13
Alignment explanation
Indices: 43571620--43571688 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 13
43571610 CACAAACTAA
43571620 TCCTCTCTCAAATT
1 TCCTCTCT-AAATT
43571634 T-C-CTCTAAATT
1 TCCTCTCTAAATT
43571645 TCCTCTC--AATT
1 TCCTCTCTAAATT
*
43571656 TGCTCTC--AATT
1 TCCTCTCTAAATT
43571667 TCCTCT-TAAATT
1 TCCTCTCTAAATT
43571679 T-CTCT-TAAAT
1 TCCTCTCTAAAT
43571689 CCCTATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
11 34 0.69
12 10 0.20
13 4 0.08
14 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.01, T:0.46
Consensus pattern (13 bp):
TCCTCTCTAAATT
Found at i:43571645 original size:11 final size:11
Alignment explanation
Indices: 43571624--43571680 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
43571614 AACTAATCCT
43571624 CTCTCAAATTTC
1 CTCT-AAATTTC
43571636 CTCTAAATTTC
1 CTCTAAATTTC
* *
43571647 CTCTCAATTTG
1 CTCTAAATTTC
*
43571658 CTCTCAATTTC
1 CTCTAAATTTC
43571669 CTCTTAAATTTC
1 CTC-TAAATTTC
43571681 TCTTAAATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 29 0.73
12 11 0.28
ACGTcount: A:0.23, C:0.30, G:0.02, T:0.46
Consensus pattern (11 bp):
CTCTAAATTTC
Found at i:43571655 original size:22 final size:23
Alignment explanation
Indices: 43571624--43571688 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
43571614 AACTAATCCT
43571624 CTCTCAAATTTCCTCTAAATTTC
1 CTCTCAAATTTCCTCTAAATTTC
* *
43571647 CTCTC-AATTTGCTCTCAATTTC
1 CTCTCAAATTTCCTCTAAATTTC
*
43571669 CTCTTAAATTT-CTCTTAAAT
1 CTCTCAAATTTCCTC-TAAAT
43571689 CCCTATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 22 0.61
23 14 0.39
ACGTcount: A:0.25, C:0.28, G:0.02, T:0.46
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTAAATTTC
Found at i:43572854 original size:7 final size:7
Alignment explanation
Indices: 43572842--43572881 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
43572832 TAGTCGATTG
43572842 GTATTTA
1 GTATTTA
43572849 GTATTTA
1 GTATTTA
43572856 GTATTTA
1 GTATTTA
43572863 GTATTTA
1 GTATTTA
43572870 GTATTTA
1 GTATTTA
43572877 GTATT
1 GTATT
43572882 ATGTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:43576576 original size:125 final size:125
Alignment explanation
Indices: 43576146--43576587 Score: 665
Period size: 126 Copynumber: 3.5 Consensus size: 125
43576136 CCCAAACATG
* * *
43576146 CTACTATAGCAAAAGCGCGTCCACGAGGGTGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
43576211 TAGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCTAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * *
43576270 CTACTGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCATAAATTATTCTCAAATAGCATCCTCC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
43576335 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTA-TTTTTCCAGGAC
* *
43576396 CTACTGTAGCAAAAGCGCATCCATGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
43576460 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
65 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * *
43576521 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATCCTTCTGATAA-AGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
43576585 CTT
65 CTT
43576588 TGATTTTATC
Statistics
Matches: 289, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
124 65 0.22
125 108 0.37
126 114 0.39
127 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:43582026 original size:4 final size:4
Alignment explanation
Indices: 43582017--43582041 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
43582007 GCAAAAGAAA
43582017 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
43582042 TTAATCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:43583886 original size:12 final size:13
Alignment explanation
Indices: 43583848--43583886 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
43583838 GGCCCGACTG
43583848 TATTAATTTTTTA
1 TATTAATTTTTTA
*
43583861 TATTATTATTTTTA
1 TATTAAT-TTTTTA
43583875 TA-TAATTTTTTA
1 TATTAATTTTTTA
43583887 AAAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 9 0.39
14 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:43584050 original size:17 final size:19
Alignment explanation
Indices: 43584030--43584064 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
43584020 TTAAAATAGT
43584030 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
43584047 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
43584065 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:43592195 original size:13 final size:13
Alignment explanation
Indices: 43592169--43592207 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
43592159 ACCTAAGTTC
*
43592169 ATAACAGAAGCAG
1 ATAACAGAATCAG
*
43592182 ATATCAGAATCAG
1 ATAACAGAATCAG
43592195 ATAACAG-ATCAG
1 ATAACAGAATCAG
43592207 A
1 A
43592208 CGTACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (13 bp):
ATAACAGAATCAG
Found at i:43597638 original size:85 final size:84
Alignment explanation
Indices: 43597539--43597745 Score: 270
Period size: 85 Copynumber: 2.4 Consensus size: 84
43597529 CGCTTACAGA
*
43597539 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATAAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAA-AAACGCCACTAAAGATAAT
*
43597604 ATTCTTTAGCGACGCTTAGG
65 ATTCTTTAGCGACACTTAGG
* ** * * *** * *
43597624 AAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTGGGAGAAAACGCTGTTAAAGATCATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATAATA
* *
43597689 TTCTTTAGTGGCACTTAGG
66 TTCTTTAGCGACACTTAGG
43597708 AAGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 AA-AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
43597746 GTGGTCAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 33 0.31
85 73 0.69
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATAATA
TTCTTTAGCGACACTTAGG
Found at i:43597642 original size:42 final size:42
Alignment explanation
Indices: 43597520--43597790 Score: 287
Period size: 42 Copynumber: 6.4 Consensus size: 42
43597510 ACGTCGCTAA
* * *
43597520 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
* * * * *
43597564 CTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATAATATT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
*
43597607 CTTTAGCGACGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * * * *
43597649 CTTTAGTGGCGCTTGGGAGAAAACGCTGTTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* *
43597691 CTTTAGTGGCACTTAGGAAGAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGATCATGTT
* *
43597734 CTTTAGCGGCGCGT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGA-TCA-TGTT
*
43597776 CTTTAGCTGCGCTTA
1 CTTTAGCGGCGCTTA
43597791 TTTCACAATC
Statistics
Matches: 192, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.01
42 110 0.57
43 68 0.35
44 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:43597776 original size:85 final size:81
Alignment explanation
Indices: 43597539--43597782 Score: 265
Period size: 85 Copynumber: 2.9 Consensus size: 81
43597529 CGCTTACAGA
* * *
43597539 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATAAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCT--GGAAA-AAACGCCGCTAAAGAT-AT
* *
43597604 ATTCTTTAGCGACGCTTAGG
62 GTTCTTTAGCGACACTTAGG
* * * *
43597624 AAAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTGGGAGAAAACGCTGTTAAAGATCATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-T-GGAAAAAACGCCGCTAAAGAT-ATG
* *
43597689 TTCTTTAGTGGCACTTAGG
63 TTCTTTAGCGACACTTAGG
*
43597708 AAGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCGTGGTCAAAAACGCCGCTAAA-AGTAG
1 AA-AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TGG-AAAAAACGCCGCTAAAGA-TA-
43597772 TGTTCTTTAGC
61 TGTTCTTTAGC
43597783 TGCGCTTATT
Statistics
Matches: 134, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
84 37 0.28
85 96 0.72
86 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (81 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTGGAAAAAACGCCGCTAAAGATATGTTC
TTTAGCGACACTTAGG
Found at i:43597776 original size:127 final size:127
Alignment explanation
Indices: 43597541--43597789 Score: 301
Period size: 127 Copynumber: 2.0 Consensus size: 127
43597531 CTTACAGAAA
*
43597541 AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATAATAT
1 AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTAAGAAAATAAACGCCACTAAAGATAATAT
*
43597606 TCTTTAGCGACGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAG-TGGCGCTTGGGAG
66 TCTTTAGCGACGCGTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCT-GCGCTTGGGAG
* * * * * * * * *
43597668 AAAACGCTGTTAAAGATCATGTTCTTTAGTGGCACTTAGGAAGA-AAACGCCGCTAAAGATCATG
1 AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCAC-TAAGAAAATAAACGCCACTAAAGATAATA
* *
43597732 TTCTTTAGCGGCGCGT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCTGCGCTT
65 TTCTTTAGCGACGCGTAGG-AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCTGCGCTT
43597790 ATTTCACAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
126 4 0.04
127 93 0.89
128 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (127 bp):
AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTAAGAAAATAAACGCCACTAAAGATAATAT
TCTTTAGCGACGCGTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTGGGAG
Found at i:43598289 original size:21 final size:21
Alignment explanation
Indices: 43598243--43598311 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
43598233 ACTTCTATCG
* *
43598243 CTGCTTCTCTTGCTGC-GACCT
1 CTGCTTCCCTCGCTGCAG-CCT
* * * *
43598264 TTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
*
43598285 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCAGCCT
43598306 CTGCTT
1 CTGCTT
43598312 TAAGTTGTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.03, C:0.39, G:0.19, T:0.39
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:43603107 original size:9 final size:9
Alignment explanation
Indices: 43603090--43603910 Score: 196
Period size: 9 Copynumber: 94.2 Consensus size: 9
43603080 TAAGTATAAT
*
43603090 TAAGCTATG
1 TAAGTTATG
43603099 TAAGTTATG
1 TAAGTTATG
43603108 T-A-TTATG
1 TAAGTTATG
43603115 TAAGTTAT-
1 TAAGTTATG
*
43603123 TTA-TTATG
1 TAAGTTATG
* *
43603131 AAAATTATG
1 TAAGTTATG
*
43603140 TAAGTTGTG
1 TAAGTTATG
43603149 T-A-TTATG
1 TAAGTTATG
*
43603156 -AA--AAT-
1 TAAGTTATG
* *
43603161 TATGCTATG
1 TAAGTTATG
43603170 TAAGTTATG
1 TAAGTTATG
* *
43603179 TAAGTCATA
1 TAAGTTATG
43603188 TAAGTTATG
1 TAAGTTATG
43603197 T-A-TTATG
1 TAAGTTATG
43603204 TAAGTTATG
1 TAAGTTATG
43603213 TAAGTTAT-
1 TAAGTTATG
*
43603221 TTA-TTATG
1 TAAGTTATG
* * *
43603229 AAAATTAAG
1 TAAGTTATG
43603238 TAAGTTATG
1 TAAGTTATG
*
43603247 TAATTTATG
1 TAAGTTATG
*
43603256 -AA-TAAT-
1 TAAGTTATG
***
43603262 TAAAAAAATG
1 T-AAGTTATG
43603272 TAAGTTATG
1 TAAGTTATG
43603281 TAAG-T-TG
1 TAAGTTATG
43603288 TAAGTTATG
1 TAAGTTATG
43603297 TAAGTTATG
1 TAAGTTATG
*
43603306 TATA-ATAT-
1 TA-AGTTATG
**
43603314 TAA-TTAAC
1 TAAGTTATG
43603322 TAAGTTATG
1 TAAGTTATG
*
43603331 TAATTTATG
1 TAAGTTATG
*
43603340 TATAATATTAATG
1 --TAA-GTT-ATG
43603353 TAAGTTATG
1 TAAGTTATG
*
43603362 TAATTTATG
1 TAAGTTATG
43603371 T-A--TAT-
1 TAAGTTATG
43603376 TAA-TTAAT-
1 TAAGTT-ATG
43603384 TAAGTTATG
1 TAAGTTATG
*
43603393 TAATTTATG
1 TAAGTTATG
* *
43603402 TATAATATTAAAG
1 --TAA-GTT-ATG
43603415 TAAGTTATG
1 TAAGTTATG
*
43603424 TAATTTATG
1 TAAGTTATG
*
43603433 -AA-TAAT-
1 TAAGTTATG
***
43603439 TAAAAAAATG
1 T-AAGTTATG
43603449 TAAGTTATG
1 TAAGTTATG
43603458 TAAG-T-TG
1 TAAGTTATG
43603465 TAAGTTATG
1 TAAGTTATG
*
43603474 TATA-ATAT-
1 TA-AGTTATG
**
43603482 TAA-TTAAC
1 TAAGTTATG
43603490 TAAGTTATG
1 TAAGTTATG
*
43603499 TAATTTATG
1 TAAGTTATG
*
43603508 TATAATATTAATG
1 --TAA-GTT-ATG
43603521 TAAGTTATG
1 TAAGTTATG
*
43603530 TAATTTATG
1 TAAGTTATG
43603539 T-A--TAT-
1 TAAGTTATG
43603544 TAA-TTAAT-
1 TAAGTT-ATG
43603552 TAAGTTATG
1 TAAGTTATG
*
43603561 TAATTTATG
1 TAAGTTATG
* *
43603570 TATAATATTAAAG
1 --TAA-GTT-ATG
43603583 TAAGTTATG
1 TAAGTTATG
*
43603592 TAATTTATG
1 TAAGTTATG
*
43603601 -AA-TAAT-
1 TAAGTTATG
***
43603607 TAAAAAAATG
1 T-AAGTTATG
43603617 TAAGTTATG
1 TAAGTTATG
*
43603626 T-AGGT-TG
1 TAAGTTATG
43603633 TAAGTTATG
1 TAAGTTATG
43603642 TAAGTTATG
1 TAAGTTATG
**
43603651 TATA-ACAT-
1 TA-AGTTATG
43603659 TAA-TTAAT-
1 TAAGTT-ATG
43603667 TAAGTTATG
1 TAAGTTATG
*
43603676 TAATTTATG
1 TAAGTTATG
*
43603685 TATAATATTAATG
1 --TAA-GTT-ATG
43603698 TAAGTTATG
1 TAAGTTATG
*
43603707 TAATTTATG
1 TAAGTTATG
* *
43603716 TATAATATTAAAG
1 --TAA-GTT-ATG
43603729 TAAGTTATG
1 TAAGTTATG
*
43603738 TATA-ATATG
1 TA-AGTTATG
*
43603747 -AA-TAAT-
1 TAAGTTATG
***
43603753 TAAAAAAATG
1 T-AAGTTATG
43603763 TAAGTTATG
1 TAAGTTATG
43603772 TAAG-T-TG
1 TAAGTTATG
43603779 TAAGTTATG
1 TAAGTTATG
43603788 TAAG-T-TG
1 TAAGTTATG
43603795 TAAGTTATG
1 TAAGTTATG
43603804 TAAGTTATG
1 TAAGTTATG
*
43603813 TATA-ATAT-
1 TA-AGTTATG
43603821 TAA-TTAAT-
1 TAAGTT-ATG
43603829 TAAGTTATG
1 TAAGTTATG
*
43603838 TAATTTATG
1 TAAGTTATG
*
43603847 TATAATATTAATG
1 --TAA-GTT-ATG
43603860 TAAGTTATG
1 TAAGTTATG
*
43603869 TAATTTATG
1 TAAGTTATG
43603878 T-A--TAT-
1 TAAGTTATG
43603883 TAA-TTAAT-
1 TAAGTT-ATG
43603891 TAAGTTATG
1 TAAGTTATG
*
43603900 TAATTTATG
1 TAAGTTATG
43603909 TA
1 TA
43603911 TAATATTAAT
Statistics
Matches: 617, Mismatches: 98, Indels: 194
0.68 0.11 0.21
Matches are distributed among these distances:
5 3 0.00
6 15 0.02
7 76 0.12
8 94 0.15
9 332 0.54
10 23 0.04
11 42 0.07
12 14 0.02
13 18 0.03
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:43603116 original size:16 final size:16
Alignment explanation
Indices: 43603095--43603214 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
43603085 ATAATTAAGC
43603095 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
43603111 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
43603127 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
43603136 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
43603152 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
43603166 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
43603184 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
43603200 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
43603215 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:43603137 original size:25 final size:25
Alignment explanation
Indices: 43603109--43603263 Score: 129
Period size: 25 Copynumber: 6.2 Consensus size: 25
43603099 TAAGTTATGT
43603109 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43603134 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43603159 ATTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
43603182 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
43603207 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43603232 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
43603260 ATTA
1 ATTA
43603264 AAAAAATGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 71 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:43603241 original size:34 final size:35
Alignment explanation
Indices: 43603135--43603940 Score: 185
Period size: 34 Copynumber: 23.2 Consensus size: 35
43603125 ATTATGAAAA
* *
43603135 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTA----ATGTAAG
*
43603174 TTATGTAAGTCATAT-AAGTTATG--TATT-ATGTAAG
1 TTATGTAAGT--TATGAA-TTATGAAAATTAATGTAAG
**
43603208 TTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
43603242 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
43603276 TTATGTAAGTTGT-AAGTTATGTAAGTT-ATGTATA-
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTA-AG
* * * *
43603310 ATAT-TAA-TTAACT-AAGTTATG-TAATTTATGTATAATA
1 TTATGTAAGTT-A-TGAA-TTATGAAAATTAATG--TAA-G
43603347 TTAATGTAAGTTATGTAATTTATGTATATTAATTAAT-TAAG
1 TT-ATGTAAGTTATG-AA-TTATG-A-A--AATTAATGTAAG
* * *
43603388 TTATGTAATTTATG---TAT-AATATTAAAGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
43603419 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* *
43603453 TTATGTAAGTTGT-AAGTTATGTATAATATTAATTAACTAAG
1 TTATGTAAGTTATGAA-TTATG-A-AA-ATTAA-T--GTAAG
* *
43603494 TTATGTAATTTATG---TAT-AATATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
43603525 TTATGTAATTTATGTA-TAT--TAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
43603556 TTATGTAATTTATG---TAT-AATATTAAAGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
43603587 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
43603621 TTATGTAGGTTGT-AAGTTATGTAAGTT-ATGTATA-
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTA-AG
** * * * *
43603655 ACAT-TAA-TTAATTAAGTTATG-TAATTTATGTATAATA
1 TTATGTAAGTT-ATGAA-TTATGAAAATTAATG--TAA-G
*
43603692 TTAATGTAAGTTATGTAATTTATGTATAATATTAAAGTAAG
1 TT-ATGTAAGTTATG-AA-TTATG-A-AA-ATTAATGTAAG
* * * *
43603733 TTATGTATA-ATATGAATAATTAAAA-AAATGTAAG
1 TTATGTA-AGTTATGAATTATGAAAATTAATGTAAG
* * *
43603767 TTATGTAAGTTGT-AAGTTATG-TAAGT--TGTAAG
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTAAG
* * *
43603799 TTATGTAAGTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* *
43603833 TTATGTAATTTATG---TAT-AATATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
43603864 TTATGTAATTTATGTA-TAT--TAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
43603895 TTATGTAATTTATGTATAATATTAATTAATTAAT-TAAG
1 TTATGTAAGTTATG-A-ATTATGAA--AATTAATGTAAG
43603933 TTATGTAA
1 TTATGTAA
43603941 TCGAGGATGT
Statistics
Matches: 582, Mismatches: 98, Indels: 175
0.68 0.11 0.20
Matches are distributed among these distances:
29 3 0.01
30 16 0.03
31 111 0.19
32 46 0.08
33 40 0.07
34 195 0.34
35 18 0.03
36 9 0.02
37 3 0.01
38 32 0.05
39 25 0.04
40 39 0.07
41 27 0.05
42 6 0.01
43 1 0.00
44 5 0.01
45 6 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.45
Consensus pattern (35 bp):
TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
Found at i:43603291 original size:16 final size:16
Alignment explanation
Indices: 43603270--43603302 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43603260 ATTAAAAAAA
43603270 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43603286 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43603302 T
1 T
43603303 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:43603297 original size:25 final size:25
Alignment explanation
Indices: 43603166--43603307 Score: 89
Period size: 25 Copynumber: 5.6 Consensus size: 25
43603156 AAAATTATGC
*
43603166 TATGTAAGTTATGTAAGTCATATAAGT
1 TATGTAAGTTATGTAAGT--TGTAAGT
43603193 TATGT-A-TTATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAG-T-TGTAAGT
* * *
43603218 TAT-TTA-TTATGAAAATTAAGTAAGT
1 TATGTAAGTTATGTAAGTT--GTAAGT
* * **
43603243 TATGTAATTTATGAATAA-TT-AAAAA
1 TATGTAAGTTATG--TAAGTTGTAAGT
*
43603268 AATGTAAGTTATGTAAGTTGTAAGT
1 TATGTAAGTTATGTAAGTTGTAAGT
43603293 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
43603308 TAATATTAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
23 4 0.04
24 4 0.04
25 65 0.71
26 4 0.04
27 10 0.11
28 2 0.02
29 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.43
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTGTAAGT
Found at i:43603360 original size:22 final size:21
Alignment explanation
Indices: 43603326--43603425 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
43603316 ATTAACTAAG
*
43603326 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
43603347 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
43603366 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
43603388 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
*
43603409 TTAAAGTAAGTTATGTA
1 TT-ATGTAAGTTATGTA
43603426 ATTTATGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 7 0.11
21 8 0.13
22 36 0.57
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
TTATGTAAGTTATGTATAATA
Found at i:43603360 original size:31 final size:31
Alignment explanation
Indices: 43603286--43603920 Score: 579
Period size: 31 Copynumber: 20.0 Consensus size: 31
43603276 TTATGTAAGT
*
43603286 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
43603317 TTAACTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
43603351 TGTAAGTTATGTAATTTATGTATATTAATTAA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
43603383 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * **
43603413 AGTAAGTTATGTAATTTATGAATAATTAAAAAAA
1 TGTAAGTTATGTAATTTATGTATAA-T--ATTAA
43603447 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAA----T---TTATGTATAATATTAA
*
43603485 TTAACTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
43603519 TGTAAGTTATGTAATTTATGTATATTAATTAA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
43603551 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * **
43603581 AGTAAGTTATGTAATTTATGAATAATTAAAAAAA
1 TGTAAGTTATGTAATTTATGTATAA-T--ATTAA
** *
43603615 TGTAAGTTATGT-AGGT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
** *
43603640 TGTAAGTTATGT-A--TA-ACATTA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
43603666 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
43603696 TGTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * * **
43603727 AGTAAGTTATGT-ATAATATGAATAATTAAAAAAA
1 TGTAAGTTATGTAAT-TTATGTATAA-T--ATTAA
* *
43603761 TGTAAGTTATGTAAGTTGTAAGT-T-AT-GTAA
1 TGTAAGTTATGTAA-TT-TATGTATAATATTAA
*
43603791 GTTGTAAGTTATGTAAGTTATGTATAATATTAA
1 --TGTAAGTTATGTAATTTATGTATAATATTAA
*
43603824 TTAATTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
43603858 TGTAAGTTATGTAATTTATGTATATTAATTAA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
43603890 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
43603920 T
1 T
43603921 TAATTAATTA
Statistics
Matches: 504, Mismatches: 52, Indels: 96
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.00
25 28 0.06
26 3 0.01
28 2 0.00
29 3 0.01
30 33 0.07
31 232 0.46
32 42 0.08
33 9 0.02
34 117 0.23
35 2 0.00
36 4 0.01
37 1 0.00
38 4 0.01
39 1 0.00
40 1 0.00
41 21 0.04
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (31 bp):
TGTAAGTTATGTAATTTATGTATAATATTAA
Found at i:43603435 original size:177 final size:177
Alignment explanation
Indices: 43603219--43603919 Score: 1071
Period size: 168 Copynumber: 4.1 Consensus size: 177
43603209 TATGTAAGTT
*
43603219 ATTTAT-TATGAAAATT-AAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGT
1 ATTTATGTAT-AATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGT
43603282 AAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATA
65 AAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATA
43603347 TTAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
130 TTAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
43603395 ATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAG---T-T-
1 ATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTA
43603455 A--TGTAAG-T-TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAT
66 AGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAT
43603516 TAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
131 TAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
43603563 ATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTA
1 ATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTA
* * *
43603628 GGTTGTAAGTTATGTAAGTTATGTATAACATTAATTAATTAAGTTATGTAATTTATGTATAATAT
66 AGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAT
* *
43603693 TAATGTAAGTTATGTAATTTATGTATAAT-ATTAAAGTAAGTTATGT-
131 TAATGTAAGTTATGTAATTTATGTATATTAATT-AATTAAGTTATGTA
* * * * *
43603739 ATAATATGAAT-A-ATTAAA--AA--AATGTAAGTTATG--TAAGT-------TGTAAGTTATGT
1 AT-TTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGT
*
43603789 AAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
65 AAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATA
43603854 TTAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
130 TTAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
43603902 ATTTATGTATAATATTAA
1 ATTTATGTATAATATTAA
43603920 TTAATTAATT
Statistics
Matches: 491, Mismatches: 17, Indels: 46
0.89 0.03 0.08
Matches are distributed among these distances:
162 122 0.25
163 6 0.01
164 5 0.01
168 158 0.32
169 5 0.01
170 6 0.01
171 12 0.02
172 2 0.00
173 3 0.01
174 1 0.00
175 12 0.02
176 18 0.04
177 141 0.29
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (177 bp):
ATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTA
AGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAT
TAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTA
Found at i:43603528 original size:22 final size:21
Alignment explanation
Indices: 43603494--43603593 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
43603484 ATTAACTAAG
*
43603494 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
43603515 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
43603534 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
43603556 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
*
43603577 TTAAAGTAAGTTATGTA
1 TT-ATGTAAGTTATGTA
43603594 ATTTATGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 7 0.11
21 8 0.13
22 36 0.57
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
TTATGTAAGTTATGTATAATA
Found at i:43603782 original size:16 final size:16
Alignment explanation
Indices: 43603761--43603809 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
43603751 ATTAAAAAAA
43603761 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43603777 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43603793 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43603809 T
1 T
43603810 ATGTATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:43603788 original size:25 final size:25
Alignment explanation
Indices: 43603761--43603809 Score: 52
Period size: 25 Copynumber: 2.0 Consensus size: 25
43603751 ATTAAAAAAA
43603761 TGTAAGTTATGTAAG-T-TGTAAGTT
1 TGTAAGTTATGTAAGTTATGTAAG-T
43603785 ATGTAAG-T-TGTAAGTTATGTAAGT
1 -TGTAAGTTATGTAAGTTATGTAAGT
43603809 T
1 T
43603810 ATGTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
23 7 0.32
24 3 0.14
25 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (25 bp):
TGTAAGTTATGTAAGTTATGTAAGT
Found at i:43603953 original size:162 final size:156
Alignment explanation
Indices: 43603322--43603954 Score: 669
Period size: 162 Copynumber: 4.0 Consensus size: 156
43603312 ATTAATTAAC
* * *
43603322 TAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT-ATTAAT
*
43603384 -TAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGAATAATTAA-AAAAA
65 GTAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAATTTATG-ATAATTAATTAAAA
*
43603447 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATAT-
129 T-TAAGTTATGTAA--TG--AG-TATGTA-AGT-TG
** * * *
43603482 TAA-TTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTA
1 TAAGTTATGTAAGTTATGT-A--TA-ATATTA-ATTAAT-TAAGTTATGTAATTTATGTATAAT-
43603546 ATTAAT-TAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAATTTATG--AA-TAAT
59 ATTAATGTAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGATAATTAAT
* *
43603607 TAAAA--AA---ATGTAA-G-TTATGTAGGTTG
124 TAAAATTAAGTTATGTAATGAGTATGTAAGTTG
*
43603633 TAAGTTATGTAAGTTATGTATAACATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
* *
43603698 TAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGT-ATAATATGAATAATTAA-AAAAA
66 TAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAAT-TTATG-ATAATTAATTAAAA
43603761 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTG
129 T-TAAGTTATGTAA--TG--AG-TATGTAAGTTG
43603795 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
* *
43603860 TAAGTTATGTAATTTATGTATATTAATT-AATTAAGTTATGTAATTTATGTATAATATTAATTAA
66 TAAGTTATGTAATTTATGTATAAT-ATTAAAGTAAGTTATGTAATTTATG-AT-A-ATTAATTAA
*
43603924 TTAATTAAGTTATGTAATCGAGGATGTAAGT
127 --AATTAAGTTATGTAAT-GAGTATGTAAGT
43603955 GGATCACTCC
Statistics
Matches: 407, Mismatches: 27, Indels: 76
0.80 0.05 0.15
Matches are distributed among these distances:
145 8 0.02
146 68 0.17
147 6 0.01
148 3 0.01
149 8 0.02
150 4 0.01
151 5 0.01
152 21 0.05
155 6 0.01
156 1 0.00
158 1 0.00
159 18 0.04
160 4 0.01
162 127 0.31
163 12 0.03
164 10 0.02
165 10 0.02
166 12 0.03
167 3 0.01
168 80 0.20
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (156 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
TAAGTTATGTAATTTATGTATAATATTAAAGTAAGTTATGTAATTTATGATAATTAATTAAAATT
AAGTTATGTAATGAGTATGTAAGTTG
Found at i:43604177 original size:18 final size:18
Alignment explanation
Indices: 43604155--43604197 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
43604145 AAAAATCAGA
43604155 AAAAATAACAAAAAATTT
1 AAAAATAACAAAAAATTT
* ** *
43604173 TAAAATTTCAACAAATTT
1 AAAAATAACAAAAAATTT
43604191 AAAAATA
1 AAAAATA
43604198 TTCATAAAAA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATAACAAAAAATTT
Found at i:43604520 original size:18 final size:18
Alignment explanation
Indices: 43604497--43604585 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
43604487 ATATATAAAT
43604497 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
43604515 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
*
43604537 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
43604554 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
43604572 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
43604586 GTAAGTAATG
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.22
18 30 0.48
19 3 0.05
20 3 0.05
21 4 0.06
22 9 0.14
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:43604556 original size:39 final size:37
Alignment explanation
Indices: 43604480--43604585 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 37
43604470 TTTAAGTAAT
*
43604480 GTAATATATATATAAATTTTAAGTAATGTAATATATTTAA
1 GTAATGTA-ATATAAATTTT-AGTAA-GTAATATATTTAA
43604520 GTAATGTAAGTTATAAATTTTAGTAAGTAATATATTTAA
1 GTAATGTAA--TATAAATTTTAGTAAGTAATATATTTAA
43604559 GTAATGTAATAT--ATTTTAGTAAGTAAT
1 GTAATGTAATATAAATTTTAGTAAGTAAT
43604586 GTAAGTAATG
Statistics
Matches: 63, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
35 15 0.24
37 3 0.05
39 23 0.37
40 12 0.19
41 10 0.16
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (37 bp):
GTAATGTAATATAAATTTTAGTAAGTAATATATTTAA
Found at i:43604567 original size:22 final size:22
Alignment explanation
Indices: 43604468--43604594 Score: 85
Period size: 22 Copynumber: 6.0 Consensus size: 22
43604458 AGCTAATTTT
43604468 TATTTAAGTAATGTAA-T-ATA
1 TATTTAAGTAATGTAAGTAATA
* *
43604488 TATATAAATTTTAA-GTAATGTAATA
1 TAT-TTAA--GTAATGTAA-GTAATA
*
43604513 TATTTAAGTAATGTAAGTTATA
1 TATTTAAGTAATGTAAGTAATA
*
43604535 AATTT---T-A-GTAAGTAATA
1 TATTTAAGTAATGTAAGTAATA
43604552 TATTTAAGTAATGTAA-T-ATA
1 TATTTAAGTAATGTAAGTAATA
*
43604572 TTTTAGTAAGTAATGTAAGTAAT
1 TATT--TAAGTAATGTAAGTAAT
43604595 GTAATATATA
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
17 13 0.16
18 1 0.01
19 1 0.01
20 10 0.12
21 5 0.06
22 32 0.39
23 8 0.10
24 6 0.07
25 6 0.07
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTAAGTAATGTAAGTAATA
Found at i:43604619 original size:57 final size:56
Alignment explanation
Indices: 43604472--43604632 Score: 143
Period size: 57 Copynumber: 2.8 Consensus size: 56
43604462 AATTTTTATT
43604472 TAAGTAATGTAATATATATATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAG
1 TAAGTAATGTAATATATATAT-AATTTT-AGTAATGTAATATATTTAAGTAATGTAAG
* * * * *
43604530 TTA-TAAATTTTAGTA-AGTA-ATATATTTAAGTAATGTAATATATTTTAGTAA-GTAATG
1 TAAGT-AA-TGTAATATA-TATATA-ATTTTAGTAATGTAATATATTTAAGTAATGTAA-G
* * *
43604587 TAAGTAATGTAATATATACTGTAATTTTAGTAA-GTCATGTATTTAA
1 TAAGTAATGTAATATATA-TATAATTTTAGTAATGTAATATATTTAA
43604633 CATTCTGTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
56 21 0.26
57 39 0.48
58 14 0.17
59 7 0.09
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.43
Consensus pattern (56 bp):
TAAGTAATGTAATATATATATAATTTTAGTAATGTAATATATTTAAGTAATGTAAG
Found at i:43607374 original size:24 final size:24
Alignment explanation
Indices: 43607332--43607379 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43607322 ACCCCTAAAG
* * *
43607332 CATAACCCTTAACCCTTAAATCCC
1 CATAACCCCTAAACATTAAATCCC
43607356 CATAACCCCTAAACATTAAATCCC
1 CATAACCCCTAAACATTAAATCCC
43607380 AAACCCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (24 bp):
CATAACCCCTAAACATTAAATCCC
Found at i:43607803 original size:114 final size:114
Alignment explanation
Indices: 43607582--43607818 Score: 330
Period size: 114 Copynumber: 2.1 Consensus size: 114
43607572 AATTATTTTC
* * * * *
43607582 AATCCTTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAACTCAGAAAACGG
1 AATCCCTGAGCATTAGCGGCACTTTCCTAAAAACACCGCTAAAACCCCGACAACTCAGAAAACAG
* * **
43607647 CGTCGTTGGTCTTAGGTATTTTTGAAGCGCTTTCCCAAAAACGCTGCTA
66 CGTCGTTGGTCTTAGGTATTTTTGAAGCGCTTACACAAAAACGCCACTA
* *
43607696 AATCCCTGAGCATTAGCGGCACTTTTCTAAAAACACCGCTAAAACCCCGACAGCTCAGAAAACAG
1 AATCCCTGAGCATTAGCGGCACTTTCCTAAAAACACCGCTAAAACCCCGACAACTCAGAAAACAG
** * * *
43607761 CGTCGTTGGTCTTAGGTATTTTTGCGGCTCTTACATAGAAACGCCACTA
66 CGTCGTTGGTCTTAGGTATTTTTGAAGCGCTTACACAAAAACGCCACTA
43607810 AATCCCTGA
1 AATCCCTGA
43607819 CAGCTCAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (114 bp):
AATCCCTGAGCATTAGCGGCACTTTCCTAAAAACACCGCTAAAACCCCGACAACTCAGAAAACAG
CGTCGTTGGTCTTAGGTATTTTTGAAGCGCTTACACAAAAACGCCACTA
Found at i:43607876 original size:73 final size:73
Alignment explanation
Indices: 43607724--43607889 Score: 215
Period size: 73 Copynumber: 2.3 Consensus size: 73
43607714 GCACTTTTCT
* * * * *
43607724 AAAAACACCGCTAAAACCCCGACAGCTCAGAAAACAGCGTCGTTGGTCTTAGGTATTTTTGCGGC
1 AAAAACGCCGCTAAATCCCTGACAGCTCAAAAAACAGCATCGTTGGTCTTAGGTATTTTTGCGGC
* *
43607789 TCTTACAT
66 GCTTACAC
* * *
43607797 AGAAACGCCACTAAATCCCTGACAGCTCAAAAAACGGCATCGTTGGTCTTAGGTATTTTTGCGGC
1 AAAAACGCCGCTAAATCCCTGACAGCTCAAAAAACAGCATCGTTGGTCTTAGGTATTTTTGCGGC
* *
43607862 GCTTTCCC
66 GCTTACAC
*
43607870 AAAAACGCCGTTAAATCCCT
1 AAAAACGCCGCTAAATCCCT
43607890 AAGCATTAGC
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCTGACAGCTCAAAAAACAGCATCGTTGGTCTTAGGTATTTTTGCGGC
GCTTACAC
Found at i:43607924 original size:114 final size:114
Alignment explanation
Indices: 43607784--43608093 Score: 442
Period size: 114 Copynumber: 2.7 Consensus size: 114
43607774 AGGTATTTTT
* * * * *
43607784 GCGGCTCTTACATAGAAACGCCACTAAATCCCTGACAGCTCAAAAAACGGCATCGTTGGTCTTAG
1 GCGGCGCTTACATAGAAATGCCACTAAATCCCCGACAGCTCAAAAAACGGCGTCGTTGGCCTTAG
* *
43607849 GTATTTTTGCGGCGCTTTCCCAAAAACGCCGTTAAATCCCTAAGCATTA
66 GTATTTTTGTGGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTA
* * *
43607898 GCGGCGCTTACCTAGAAATGCCACTAAATCCCCGACAGCTCAGAAAACAGCGTCGTTGGCCTTAG
1 GCGGCGCTTACATAGAAATGCCACTAAATCCCCGACAGCTCAAAAAACGGCGTCGTTGGCCTTAG
* *
43607963 GTATTTTTGTGGTGCTTTCCCAAAAACGCCGCTAAATCCCTGAGCATTA
66 GTATTTTTGTGGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTA
* * * * * * *
43608012 GCAGCGCTTACTTAGAAATGCCATTAAATCCCCGAAAGCTCCAAAAACGGTGTCGTTGGGCTTAG
1 GCGGCGCTTACATAGAAATGCCACTAAATCCCCGACAGCTCAAAAAACGGCGTCGTTGGCCTTAG
43608077 GT-TTTTTGTGGCGCTTT
66 GTATTTTTGTGGCGCTTT
43608094 TCTGGAAACG
Statistics
Matches: 174, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
113 14 0.08
114 160 0.92
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTACATAGAAATGCCACTAAATCCCCGACAGCTCAAAAAACGGCGTCGTTGGCCTTAG
GTATTTTTGTGGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTA
Found at i:43607992 original size:187 final size:188
Alignment explanation
Indices: 43607597--43608005 Score: 581
Period size: 187 Copynumber: 2.2 Consensus size: 188
43607587 TTGAGCATTA
* * *
43607597 GCGGC-GCTTTCCTAAAAACGCCGCTAAATCCCCGACAACTCAGAAAACGGCGTCGTTGGTCTTA
1 GCGGCTGCTTTCCTAAAAACGCCGCTAAATCCCTGACAACTCAAAAAACGGCATCGTTGGTCTTA
* * **
43607661 GGTATTTTTGAAGCGCTTTCCCAAAAACGCTGCTAAATCCCTGAGCATTAGCGGCACTTTTCTAA
66 GGTATTTTTGAAGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACTTACCTAA
* *
43607726 AAACACCGCTAAAACCCCGACAGCTCAGAAAACAGCGTCGTTGGTCTTAGGTATTTTT
131 AAACACCACTAAAACCCCGACAGCTCAGAAAACAGCGTCGTTGGCCTTAGGTATTTTT
* * * * *
43607784 GCGGCT-CTTACATAGAAACGCCACTAAATCCCTGACAGCTCAAAAAACGGCATCGTTGGTCTTA
1 GCGGCTGCTTTCCTAAAAACGCCGCTAAATCCCTGACAACTCAAAAAACGGCATCGTTGGTCTTA
** * * *
43607848 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGTTAAATCCCTAAGCATTAGCGGCGCTTACCTAG
66 GGTATTTTTGAAGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACTTACCTAA
** *
43607913 AAATGCCACTAAATCCCCGACAGCTCAGAAAACAGCGTCGTTGGCCTTAGGTATTTTT
131 AAACACCACTAAAACCCCGACAGCTCAGAAAACAGCGTCGTTGGCCTTAGGTATTTTT
* *
43607971 GTGG-TGCTTTCCCAAAAACGCCGCTAAATCCCTGA
1 GCGGCTGCTTTCCTAAAAACGCCGCTAAATCCCTGA
43608006 GCATTAGCAG
Statistics
Matches: 192, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
186 1 0.01
187 191 0.99
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (188 bp):
GCGGCTGCTTTCCTAAAAACGCCGCTAAATCCCTGACAACTCAAAAAACGGCATCGTTGGTCTTA
GGTATTTTTGAAGCGCTTTCCCAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACTTACCTAA
AAACACCACTAAAACCCCGACAGCTCAGAAAACAGCGTCGTTGGCCTTAGGTATTTTT
Found at i:43611378 original size:26 final size:26
Alignment explanation
Indices: 43611349--43611402 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
43611339 CTCAGTACAA
* *
43611349 TTTCAGAAAGAAGTAACTATAGTGTT
1 TTTCAAAAAGAACTAACTATAGTGTT
**
43611375 TTTCAAAAAGTTCTAACTATAGTGTT
1 TTTCAAAAAGAACTAACTATAGTGTT
43611401 TT
1 TT
43611403 CTAAATTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (26 bp):
TTTCAAAAAGAACTAACTATAGTGTT
Found at i:43615820 original size:26 final size:25
Alignment explanation
Indices: 43615764--43615826 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
43615754 TAGCTCTTAT
* *
43615764 GAGCTTACCATTATTTAGGTCGGAG
1 GAGCTTACCATTATTTAGCTCAGAG
* *
43615789 GAGCTTATCGTTATTTCAGCTCAGAG
1 GAGCTTACCATTATTT-AGCTCAGAG
43615815 GAGCTTACCATT
1 GAGCTTACCATT
43615827 TACAGCTCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTACCATTATTTAGCTCAGAG
Found at i:43616423 original size:56 final size:56
Alignment explanation
Indices: 43616356--43616544 Score: 132
Period size: 56 Copynumber: 3.2 Consensus size: 56
43616346 TGATTTGGCT
*
43616356 TGTGTTTTGGTATATTTTGCTATGTAGATATATAAATGGTCTTATCATGTTTGATG
1 TGTGGTTTGGTATATTTTGCTATGTAGATATATAAATGGTCTTATCATGTTTGATG
* * * * * * * * * *
43616412 TGTGGTTTGGTATGGTTAATGATA-GCCTACATGTTTTATTAT-GTTTTAGCCATTTGATTTGGC
1 TGTGGTTTGGTAT-ATT-TTGCTATG--TAGAT-ATATA-AATGGTCTTA-TCA--TG-TTT-GA
43616475 T-
55 TG
* * *
43616476 TGTGTTTTGGTATATTTTGCTATGTAGATATATAAATGGCCTAATCATGTTTGATG
1 TGTGGTTTGGTATATTTTGCTATGTAGATATATAAATGGTCTTATCATGTTTGATG
43616532 TGTGGTTTGGTAT
1 TGTGGTTTGGTAT
43616545 GGTTAACATG
Statistics
Matches: 94, Mismatches: 25, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
55 2 0.02
56 27 0.29
57 5 0.05
58 4 0.04
59 8 0.09
60 14 0.15
61 8 0.09
62 4 0.04
63 5 0.05
64 15 0.16
65 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (56 bp):
TGTGGTTTGGTATATTTTGCTATGTAGATATATAAATGGTCTTATCATGTTTGATG
Found at i:43616463 original size:120 final size:120
Alignment explanation
Indices: 43616304--43616550 Score: 476
Period size: 120 Copynumber: 2.1 Consensus size: 120
43616294 ATAGTTATTT
43616304 TGGTTAATGATAGCCTACATGTTTTATTATGTTTTAGCCATTTGATTTGGCTTGTGTTTTGGTAT
1 TGGTTAATGATAGCCTACATGTTTTATTATGTTTTAGCCATTTGATTTGGCTTGTGTTTTGGTAT
* *
43616369 ATTTTGCTATGTAGATATATAAATGGTCTTATCATGTTTGATGTGTGGTTTGGTA
66 ATTTTGCTATGTAGATATATAAATGGCCTAATCATGTTTGATGTGTGGTTTGGTA
43616424 TGGTTAATGATAGCCTACATGTTTTATTATGTTTTAGCCATTTGATTTGGCTTGTGTTTTGGTAT
1 TGGTTAATGATAGCCTACATGTTTTATTATGTTTTAGCCATTTGATTTGGCTTGTGTTTTGGTAT
43616489 ATTTTGCTATGTAGATATATAAATGGCCTAATCATGTTTGATGTGTGGTTTGGTA
66 ATTTTGCTATGTAGATATATAAATGGCCTAATCATGTTTGATGTGTGGTTTGGTA
43616544 TGGTTAA
1 TGGTTAA
43616551 CATGTAAATT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (120 bp):
TGGTTAATGATAGCCTACATGTTTTATTATGTTTTAGCCATTTGATTTGGCTTGTGTTTTGGTAT
ATTTTGCTATGTAGATATATAAATGGCCTAATCATGTTTGATGTGTGGTTTGGTA
Found at i:43617062 original size:15 final size:15
Alignment explanation
Indices: 43617044--43617080 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
43617034 TTAGCTGTGT
43617044 GTGACACACAGCTAG
1 GTGACACACAGCTAG
*
43617059 GTGATACACAGCTAG
1 GTGACACACAGCTAG
43617074 GTGACAC
1 GTGACAC
43617081 GGCCATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.16
Consensus pattern (15 bp):
GTGACACACAGCTAG
Found at i:43619020 original size:19 final size:20
Alignment explanation
Indices: 43618996--43619034 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43618986 CATATGTATT
*
43618996 TTTTGC-ACATTTGAAATTC
1 TTTTGCTACATTTAAAATTC
43619015 TTTTGCTTACATTTAAAATT
1 TTTTGC-TACATTTAAAATT
43619035 TGGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTGCTACATTTAAAATTC
Found at i:43619481 original size:30 final size:31
Alignment explanation
Indices: 43619422--43619485 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43619412 ACTTAACAAG
*
43619422 CAAATGCCTCTAAAATAATAACAAAAATTAA
1 CAAATGACTCTAAAATAATAACAAAAATTAA
*
43619453 CAAATGACTTTAAAATAATAAC-AAAATTAA
1 CAAATGACTCTAAAATAATAACAAAAATTAA
43619483 CAA
1 CAA
43619486 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.23
Consensus pattern (31 bp):
CAAATGACTCTAAAATAATAACAAAAATTAA
Found at i:43621069 original size:17 final size:19
Alignment explanation
Indices: 43621042--43621076 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43621032 CAAATTGAAA
43621042 ATACATTAAAA-AATATTC
1 ATACATTAAAACAATATTC
43621060 ATAC-TTAAAACAATATT
1 ATACATTAAAACAATATT
43621077 AAGGACGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (19 bp):
ATACATTAAAACAATATTC
Found at i:43621347 original size:21 final size:22
Alignment explanation
Indices: 43621298--43621361 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
43621288 ATATCCAAAT
* ***
43621298 AATAACAACAAAATAGTTGCAA
1 AATAATAACAAAATAGCAACAA
*
43621320 TATAATAACAAAATA-CAACAA
1 AATAATAACAAAATAGCAACAA
**
43621341 AATAATAGTAAAATAGCAACA
1 AATAATAACAAAATAGCAACA
43621362 GAAAAAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (22 bp):
AATAATAACAAAATAGCAACAA
Found at i:43621712 original size:3 final size:3
Alignment explanation
Indices: 43621704--43621743 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
43621694 GGAAATCCAC
43621704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43621744 TTTTCTACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43622312 original size:16 final size:17
Alignment explanation
Indices: 43622238--43622314 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 17
43622228 TAAGATAACA
43622238 TTTAAATAAATATAT-GT
1 TTTAAA-AAATATATAGT
* *
43622255 TTTAAAAATTATTTAGT
1 TTTAAAAAATATATAGT
*
43622272 TTTAAAACAAAGAAATATCAGT
1 TTT--AA-AAA-ATATAT-AGT
43622294 TTTAAAAAATATATA-T
1 TTTAAAAAATATATAGT
43622310 TTTAA
1 TTTAA
43622315 GAATATTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.25
17 12 0.25
18 5 0.10
19 5 0.10
20 5 0.10
21 3 0.06
22 6 0.12
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (17 bp):
TTTAAAAAATATATAGT
Found at i:43623031 original size:15 final size:14
Alignment explanation
Indices: 43623011--43623051 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
43623001 AAGGTTGGGT
43623011 TTTAGGGTTTATATA
1 TTTAGGGTTTAT-TA
43623026 TTTAGGGGTCTTATTA
1 TTTA-GGGT-TTATTA
43623042 TTTAGGGTTT
1 TTTAGGGTTT
43623052 GAGGGTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 10 0.42
17 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATTA
Found at i:43623623 original size:22 final size:21
Alignment explanation
Indices: 43623597--43623696 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 21
43623587 TCAAGATAAA
43623597 TATTAAATTAAATATTAAATCT
1 TATTAAATTAAATATTAAAT-T
*
43623619 TATTAAATT-AATA-GAATATT
1 TATTAAATTAAATATTAA-ATT
* * *
43623639 TATTTACAAGATAAACAATAAATT
1 TA-TTA-AA-TTAAATATTAAATT
*
43623663 AAATTAAATTAAATATTAAATCT
1 -TATTAAATTAAATATTAAAT-T
43623686 TATTAAATTAA
1 TATTAAATTAA
43623697 TAAAATATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.08
21 9 0.15
22 31 0.51
23 4 0.07
24 9 0.15
25 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTAAATTAAATATTAAATT
Found at i:43623666 original size:57 final size:57
Alignment explanation
Indices: 43623565--43623737 Score: 192
Period size: 67 Copynumber: 2.9 Consensus size: 57
43623555 ATCATTTTAA
* * *
43623565 TATTAAATTAATATAAGATTTA--T-CAAGATAAATATTAAATTAAATATTAAATCT
1 TATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATTAAATATTAAATCT
*
43623619 TATTAAATTAATAGAATATTTATTTACAAGATAAACAATAAATTAAATTAAATTAAATATTAAAT
1 TATTAAATTAATAAAATATTTATTTACAAGATAAAC----------ATTAAATTAAATATTAAAT
43623684 CT
56 CT
43623686 TATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATTAAAT-TTAA
1 TATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATTAAATATTAA
43623738 TATTAAGATA
Statistics
Matches: 102, Mismatches: 4, Indels: 24
0.78 0.03 0.18
Matches are distributed among these distances:
54 20 0.20
56 5 0.05
57 21 0.21
67 56 0.55
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (57 bp):
TATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATTAAATATTAAATCT
Found at i:43623672 original size:67 final size:67
Alignment explanation
Indices: 43623598--43623743 Score: 256
Period size: 67 Copynumber: 2.1 Consensus size: 67
43623588 CAAGATAAAT
*
43623598 ATTAAATTAAATATTAAATCTTATTAAATTAATAGAATATTTATTTACAAGATAAACAATAAATT
1 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
43623663 AA
66 AA
*
43623665 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACATTAAATT
1 ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
43623730 AA
66 AA
43623732 ATTTAATATTAA
1 A-TTAA-ATTAA
43623744 GATAATTACT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 66 0.88
68 4 0.05
69 5 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (67 bp):
ATTAAATTAAATATTAAATCTTATTAAATTAATAAAATATTTATTTACAAGATAAACAATAAATT
AA
Found at i:43624209 original size:19 final size:19
Alignment explanation
Indices: 43624185--43624221 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43624175 AAAATATCAT
43624185 ATTAATTTTAA-TTAATTTG
1 ATTAA-TTTAATTTAATTTG
43624204 ATTAATTTAATTTAATTT
1 ATTAATTTAATTTAATTT
43624222 AATTTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTAATTTAATTTAATTTG
Found at i:43624215 original size:5 final size:5
Alignment explanation
Indices: 43624186--43624226 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
43624176 AAATATCATA
*
43624186 TTAATT TTAA- TTAAT TTGA- TTAAT TTAAT TTAAT TTAAT TT
1 TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
43624227 TATCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 7 0.23
5 20 0.65
6 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:43624226 original size:10 final size:9
Alignment explanation
Indices: 43624185--43624225 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
43624175 AAAATATCAT
43624185 ATTAATTTTA
1 ATTAA-TTTA
*
43624195 ATTAATTTG
1 ATTAATTTA
43624204 ATTAATTTA
1 ATTAATTTA
43624213 ATTTAATTTA
1 A-TTAATTTA
43624223 ATT
1 ATT
43624226 TTATCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
ATTAATTTA
Found at i:43631795 original size:14 final size:14
Alignment explanation
Indices: 43631776--43631802 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43631766 ATATTTTTTT
43631776 TCCATAAATTGAAA
1 TCCATAAATTGAAA
43631790 TCCATAAATTGAA
1 TCCATAAATTGAA
43631803 CCATCCATTA
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:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
TCCATAAATTGAAA
Found at i:43632437 original size:24 final size:24
Alignment explanation
Indices: 43632392--43632437 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43632382 TAACAGTTTT
* *
43632392 AGAAGGAGCTGGTGAAGTAGGATC
1 AGAAGGAGCTAGTGAAGCAGGATC
*
43632416 AGAAGGAGCTAGTGGAGCAGGA
1 AGAAGGAGCTAGTGAAGCAGGA
43632438 GTTGCTGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.43, T:0.13
Consensus pattern (24 bp):
AGAAGGAGCTAGTGAAGCAGGATC
Found at i:43636372 original size:50 final size:50
Alignment explanation
Indices: 43636308--43636503 Score: 221
Period size: 50 Copynumber: 3.9 Consensus size: 50
43636298 CATTGAGATC
* *
43636308 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * *
43636358 ACGAAAGGTCCCATGTAAGACCATGTCCGGAACATGGCGTTCGCACCGAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * * * * *
43636408 ATGAGAGGTCCCCTGTAAGATCATGTATGGGACATGGCATGGGCACCGAT
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * *
43636458 ATGAGAACATCCCATGTAAAACCATGTCTAGGACATGGCTTTGGCA
1 ATGA-AAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
43636504 TGTTGTTATC
Statistics
Matches: 118, Mismatches: 27, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 87 0.74
51 31 0.26
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:43638735 original size:29 final size:31
Alignment explanation
Indices: 43638697--43638755 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
43638687 GGAGGTGGGA
*
43638697 TGGGAAGGGAATAAAAGTTTT-AGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
* *
43638727 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
43638756 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:43638925 original size:21 final size:21
Alignment explanation
Indices: 43638891--43638931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43638881 GGGGGAAAGT
*
43638891 GGGAAGGAGTAAAAGTTTTGA
1 GGGAAGGAGTAAAAGGTTTGA
43638912 GGGAA-GAGTAAAAAGGTTTG
1 GGGAAGGAGT-AAAAGGTTTG
43638932 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (21 bp):
GGGAAGGAGTAAAAGGTTTGA
Found at i:43638983 original size:9 final size:9
Alignment explanation
Indices: 43638969--43639005 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43638959 TATAGTTTGA
43638969 TATTCGAAT
1 TATTCGAAT
43638978 TATTCGAAT
1 TATTCGAAT
*
43638987 TATTCGAGT
1 TATTCGAAT
43638996 TATTCGAAT
1 TATTCGAAT
43639005 T
1 T
43639006 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43639075 original size:9 final size:9
Alignment explanation
Indices: 43639059--43639089 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43639049 TCGAGTTGAT
43639059 TCGAATAAC
1 TCGAATAAC
*
43639068 TTGAATAAC
1 TCGAATAAC
43639077 TCGAATAAC
1 TCGAATAAC
43639086 TCGA
1 TCGA
43639090 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43639275 original size:4 final size:4
Alignment explanation
Indices: 43639266--43639311 Score: 74
Period size: 4 Copynumber: 11.2 Consensus size: 4
43639256 GTGATAAACA
*
43639266 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AATAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT A
43639312 AACATTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 36 0.92
5 3 0.08
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:43639394 original size:22 final size:19
Alignment explanation
Indices: 43639382--43639428 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
43639372 CATGACATAT
43639382 GTAATATACAAACATAATA
1 GTAATATACAAACATAATA
* *
43639401 GTAATATA-ACACATAACA
1 GTAATATACAAACATAATA
43639419 --AATATACAAA
1 GTAATATACAAA
43639429 TATACATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 8 0.33
19 8 0.33
ACGTcount: A:0.60, C:0.13, G:0.04, T:0.23
Consensus pattern (19 bp):
GTAATATACAAACATAATA
Found at i:43639416 original size:18 final size:18
Alignment explanation
Indices: 43639331--43639416 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 18
43639321 AAACAGTCAT
43639331 ACACATAATAGTAATATA
1 ACACATAATAGTAATATA
* *
43639349 CCATATAATA-TACATACATTA
1 ACACATAATAGTA-AT--A-TA
43639370 A-ACATGACATATGTAATATA
1 ACACAT-A-ATA-GTAATATA
*
43639390 CAAACATAATAGTAATATA
1 -ACACATAATAGTAATATA
43639409 ACACATAA
1 ACACATAA
43639417 CAAATATACA
Statistics
Matches: 53, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
17 2 0.04
18 17 0.32
19 8 0.15
20 9 0.17
21 6 0.11
22 7 0.13
23 2 0.04
24 2 0.04
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (18 bp):
ACACATAATAGTAATATA
Found at i:43639432 original size:43 final size:43
Alignment explanation
Indices: 43639384--43639472 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 43
43639374 TGACATATGT
43639384 AATATACAAACATAATAGTA-ATATAAC-ACATAACAAATATACA
1 AATATACAAACATAATA-TATATATAACAACAT-ACAAATATACA
*
43639427 AATATACATACATAATATATATATAACATACATACAAATATACA
1 AATATACAAACATAATATATATATAACA-ACATACAAATATACA
43639471 AA
1 AA
43639473 CATAACATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 2 0.05
43 23 0.55
44 13 0.31
45 4 0.10
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.26
Consensus pattern (43 bp):
AATATACAAACATAATATATATATAACAACATACAAATATACA
Found at i:43639441 original size:25 final size:24
Alignment explanation
Indices: 43639403--43639486 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 24
43639393 ACATAATAGT
*
43639403 AATATA-ACACATAACAAATATACA
1 AATATACATACAT-ACAAATATACA
*
43639427 AATATACATACAT---AATATATA
1 AATATACATACATACAAATATACA
*
43639448 TATA-ACATACATACAAATATACA
1 AATATACATACATACAAATATACA
*
43639471 AACATAACATACATAC
1 AATAT-ACATACATAC
43639487 TTAACAGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.17
21 10 0.21
23 9 0.19
24 6 0.12
25 15 0.31
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (24 bp):
AATATACATACATACAAATATACA
Found at i:43639449 original size:60 final size:60
Alignment explanation
Indices: 43639333--43639486 Score: 134
Period size: 60 Copynumber: 2.5 Consensus size: 60
43639323 ACAGTCATAC
* * * * * *
43639333 ACATAATAGTAATATACCATATAATATACATACATTAAACATGACATATGTAATATACAA
1 ACATAATAGTAATATAACACATAACAAACATACAATAAACATGACATATATAATATACAA
* * *
43639393 ACATAATAGTAATATAACACATAACAAATATACAAATATACAT-ACATA-ATATATATA-TA
1 ACATAATAGTAATATAACACATAACAAACATAC-AATAAACATGACATATATA-ATATACAA
** * *
43639452 ACATACATACAAATATACAAACATAACATACATAC
1 ACATA-ATAGTAATATA-ACACATAACAAACATAC
43639487 TTAACAGTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
59 8 0.11
60 47 0.62
61 21 0.28
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (60 bp):
ACATAATAGTAATATAACACATAACAAACATACAATAAACATGACATATATAATATACAA
Found at i:43640237 original size:21 final size:21
Alignment explanation
Indices: 43640185--43640244 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
43640175 AGAGTTTTGA
* *
43640185 GTTTAGAGTTCATGGTTTACT
1 GTTTAGTGTTTATGGTTTACT
* *
43640206 G-TTCGTGGTTTATGGTTTAGT
1 GTTTAGT-GTTTATGGTTTACT
43640227 GTTTAGTGTTTAGTGGTT
1 GTTTAGTGTTTA-TGGTT
43640245 AGAAGCATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.10
21 19 0.61
22 9 0.29
ACGTcount: A:0.13, C:0.05, G:0.30, T:0.52
Consensus pattern (21 bp):
GTTTAGTGTTTATGGTTTACT
Found at i:43640277 original size:22 final size:22
Alignment explanation
Indices: 43640252--43640303 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
43640242 GTTAGAAGCA
**
43640252 TAGGGTTTA-GGGGTTATGGGCT
1 TAGGGTTTAGGGGGTCGT-GGCT
*
43640274 TAGGGTCTAGGGGGTCGTGGCT
1 TAGGGTTTAGGGGGTCGTGGCT
43640296 TAGGGTTT
1 TAGGGTTT
43640304 TGGATTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.12, C:0.08, G:0.46, T:0.35
Consensus pattern (22 bp):
TAGGGTTTAGGGGGTCGTGGCT
Found at i:43640334 original size:23 final size:22
Alignment explanation
Indices: 43640302--43640364 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
43640292 GGCTTAGGGT
*
43640302 TTTGGATTTAAGGGTTTATAGG
1 TTTGGGTTTAAGGGTTTATAGG
*
43640324 TTATGGGTTT-AGTGGTTTATTGG
1 TT-TGGGTTTAAG-GGTTTATAGG
43640347 TTTAGGGTTTAA-GGTTTA
1 TTT-GGGTTTAAGGGTTTA
43640365 AAGTTTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 11 0.31
23 23 0.66
24 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (22 bp):
TTTGGGTTTAAGGGTTTATAGG
Found at i:43640348 original size:16 final size:15
Alignment explanation
Indices: 43640324--43640357 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
43640314 GGTTTATAGG
43640324 TTATGGGTTTAGTGGT
1 TTATGGGTTTAG-GGT
*
43640340 TTATTGGTTTAGGGT
1 TTATGGGTTTAGGGT
43640355 TTA
1 TTA
43640358 AGGTTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (15 bp):
TTATGGGTTTAGGGT
Found at i:43640364 original size:14 final size:14
Alignment explanation
Indices: 43640329--43640566 Score: 71
Period size: 14 Copynumber: 17.0 Consensus size: 14
43640319 ATAGGTTATG
*
43640329 GGTTTAGTGGTTTATT
1 GGTTTAG-GGTTTA-A
43640345 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
**
43640359 GGTTTAAAGTTTAA
1 GGTTTAGGGTTTAA
*
43640373 AGTTTAGGG-TTAA
1 GGTTTAGGGTTTAA
43640386 --TTTAGGGTTTACA
1 GGTTTAGGGTTTA-A
* *
43640399 -GTTTAAGGTGT-A
1 GGTTTAGGGTTTAA
* * *
43640411 TGTTTAGCGTATAA
1 GGTTTAGGGTTTAA
* * *
43640425 AGTTTAAGGTTTAT
1 GGTTTAGGGTTTAA
* **
43640439 GATTTAATG-TTAA
1 GGTTTAGGGTTTAA
* *
43640452 GAGTTTAGTGTTTAC
1 G-GTTTAGGGTTTAA
*
43640467 GGTGTA-GGTTTATA
1 GGTTTAGGGTTTA-A
* *
43640481 -GTCTAGGGTTTAT
1 GGTTTAGGGTTTAA
**
43640494 TATTTAGGGTTTAGAA
1 GGTTTAGGGTTT--AA
*
43640510 GG-TTAGAGTTTAA
1 GGTTTAGGGTTTAA
* * *
43640523 GGGTTACGAGTTTAG
1 GGTTTA-GGGTTTAA
* * *
43640538 GGTTTAAAGGCTTAT
1 GGTTT-AGGGTTTAA
43640553 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
43640567 ATTTTATTTT
Statistics
Matches: 164, Mismatches: 43, Indels: 32
0.69 0.18 0.13
Matches are distributed among these distances:
11 7 0.04
12 4 0.02
13 30 0.18
14 76 0.46
15 38 0.23
16 9 0.05
ACGTcount: A:0.25, C:0.03, G:0.29, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:43640396 original size:7 final size:7
Alignment explanation
Indices: 43640212--43640383 Score: 51
Period size: 7 Copynumber: 23.6 Consensus size: 7
43640202 TACTGTTCGT
*
43640212 GGTTTAT
1 GGTTTAG
43640219 GGTTTAG
1 GGTTTAG
*
43640226 TGTTTAG
1 GGTTTAG
*
43640233 TGTTTAG
1 GGTTTAG
43640240 TGG-TTAG
1 -GGTTTAG
* **
43640247 AAGCATAG
1 -GGTTTAG
43640255 GGTTTAG
1 GGTTTAG
*
43640262 GGGTTATG
1 GGTTTA-G
*
43640270 GGCTTAG
1 GGTTTAG
*
43640277 GGTCTAG
1 GGTTTAG
** *
43640284 GGGGTCG
1 GGTTTAG
*
43640291 TGGCTTAG
1 -GGTTTAG
*
43640299 GGTTTTG
1 GGTTTAG
*
43640306 GATTTAAG
1 GGTTT-AG
*
43640314 GGTTTATA
1 GGTTTA-G
43640322 GG-TTATG
1 GGTTTA-G
43640329 GGTTTAG
1 GGTTTAG
*
43640336 TGGTTTATT
1 -GGTTTA-G
43640345 GGTTTAG
1 GGTTTAG
*
43640352 GGTTTAA
1 GGTTTAG
*
43640359 GGTTTAA
1 GGTTTAG
* *
43640366 AGTTTAA
1 GGTTTAG
*
43640373 AGTTTAG
1 GGTTTAG
43640380 GGTT
1 GGTT
43640384 AATTTAGGGT
Statistics
Matches: 124, Mismatches: 32, Indels: 18
0.71 0.18 0.10
Matches are distributed among these distances:
7 88 0.71
8 36 0.29
ACGTcount: A:0.19, C:0.03, G:0.36, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:43640537 original size:22 final size:21
Alignment explanation
Indices: 43640512--43640566 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
43640502 GTTTAGAAGG
* *
43640512 TTAGAGTTTAAGGGTTACGAGT
1 TTAGGGTTTAAGGCTTACG-GT
*
43640534 TTAGGGTTTAAAGGCTTATGGT
1 TTAGGGTTT-AAGGCTTACGGT
43640556 TTAGGGTTTAA
1 TTAGGGTTTAA
43640567 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 19 0.66
23 8 0.28
ACGTcount: A:0.25, C:0.04, G:0.31, T:0.40
Consensus pattern (21 bp):
TTAGGGTTTAAGGCTTACGGT
Found at i:43640994 original size:115 final size:116
Alignment explanation
Indices: 43640740--43641150 Score: 513
Period size: 115 Copynumber: 3.6 Consensus size: 116
43640730 AGCATAATGG
* * * *
43640740 TGTCG-TTTTATCTGCGTTTTTAGTGGCGTTTTTGCTAAAACACTGCAAAAGGATATGTATTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
* *
43640804 GGCGTTTTTACAAAAAATGCCGCAATTATGTTTTTAGTCTTTGGTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* ** *
43640855 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACCAAAATGCCGTAAAAGGATATGTGTTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
** * *
43640920 GGCGTTTTTA-GGAAAACGCCGCAATTGTATTATTAGTCTTTGGTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* * * * * *
43640970 TGTCGTTTTTATCTACATTATTAGTGGC-TTTTTACTAAAACGCCGCGAAAGGTTATGTGGTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
* * * * * *
43641034 GGCGTTTTTACAAAAAACGTCGCAATTATGTTATAATTGTTCGCTAAACGT
66 GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
* * * ** *
43641085 TGTCATTTTTATCTACGTTTTTAGTGGTGTTTGTACTAAAACACCGGTAAAGGATATGTTTTAGT
1 TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
43641150 G
66 G
43641151 CGGTAATTAC
Statistics
Matches: 250, Mismatches: 43, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
114 40 0.16
115 119 0.48
116 91 0.36
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (116 bp):
TGTCGTTTTTATCTACGTTTTTAGTGGCGTTTTTACTAAAACACCGCAAAAGGATATGTGTTAGT
GGCGTTTTTACAAAAAACGCCGCAATTATGTTATTAGTCTTTGGTAAACGT
Found at i:43641405 original size:24 final size:24
Alignment explanation
Indices: 43641378--43641434 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
43641368 TTTTATTTCC
*
43641378 CCCCAATTCCT-TTTCCCACAATTT
1 CCCCAATTCCTATTTCCCA-AAATT
*
43641402 CCCCAATT-TTATTTCCCAAAATT
1 CCCCAATTCCTATTTCCCAAAATT
*
43641425 CCCAAATTCC
1 CCCCAATTCC
43641435 CAAATTCCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (24 bp):
CCCCAATTCCTATTTCCCAAAATT
Found at i:43641433 original size:8 final size:8
Alignment explanation
Indices: 43641414--43641443 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
43641404 CCAATTTTAT
43641414 TTCCCAAAA
1 TTCCC-AAA
43641423 TTCCCAAA
1 TTCCCAAA
43641431 TTCCCAAA
1 TTCCCAAA
43641439 TTCCC
1 TTCCC
43641444 CCTATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (8 bp):
TTCCCAAA
Found at i:43644521 original size:21 final size:20
Alignment explanation
Indices: 43644497--43644591 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 20
43644487 CTACAACTTA
**
43644497 AAGCAGATGCAGCAGCGAGGG
1 AAGCAGA-GCAGCAGCGAGAC
43644518 AAGCAGAGGCAGCAGCGAGAC
1 AAGCAGA-GCAGCAGCGAGAC
*
43644539 AAGCAGAGGCTA-CAGCAAGAC
1 AAGCAGA-GC-AGCAGCGAGAC
**
43644560 AAGCAGAGACTA-CAGCGAGGG
1 AAGCAGAG-C-AGCAGCGAGAC
43644581 AAGCAGAGCAG
1 AAGCAGAGCAG
43644592 AGCAAAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 60 0.94
22 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.37, T:0.03
Consensus pattern (20 bp):
AAGCAGAGCAGCAGCGAGAC
Found at i:43645029 original size:84 final size:85
Alignment explanation
Indices: 43644925--43645084 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 85
43644915 TTTGTGGGAG
* * * *
43644925 AAGCGCCGCTAAAAGTCATGATCTATAGTGACGTTTATGGG-GTAAGCGTCGCTAAAAGTCATGA
1 AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTATGGGAG-AAGCGCCGCTAAAAGTCATAA
*
43644989 TCTATAGCGGCGCTTTTATAC
65 CCTATAGCGGCGCTTTTATAC
** *
43645010 AAGCGCC-CTAAAAGTCATGACCTATAGCGGTGTTTGTGGGAGAAGCGCCGCTAAAAGTCATAAC
1 AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTATGGGAGAAGCGCCGCTAAAAGTCATAAC
43645074 CTATAGCGGCG
66 CTATAGCGGCG
43645085 TTTGTCGGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 58 0.88
85 8 0.12
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (85 bp):
AAGCGCCGCTAAAAGTCATGACCTATAGCGACGTTTATGGGAGAAGCGCCGCTAAAAGTCATAAC
CTATAGCGGCGCTTTTATAC
Done.