Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 10 of 120
Found at i:2773934 original size:19 final size:18
Alignment explanation
Indices: 2773911--2773957 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2773901 TGAAAACTTT
2773911 TTTTTTTAAATTTTAATA
1 TTTTTTTAAATTTTAATA
* *
2773929 TTTTTTGAATTTTTAATA
1 TTTTTTTAAATTTTAATA
*
2773947 ATTTTTTAAAT
1 TTTTTTTAAAT
2773958 GAATCAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTTTAAATTTTAATA
Found at i:2774141 original size:26 final size:24
Alignment explanation
Indices: 2774112--2774159 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2774102 TCCCATGTGG
*
2774112 ATTTTGTCAAAATAATTTTGTGATTT
1 ATTTT-TCAAAA-AATTTGGTGATTT
*
2774138 ATTTTTTAAAAAATTTGGTGAT
1 ATTTTTCAAAAAATTTGGTGAT
2774160 GTAACATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 5 0.25
26 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTTTCAAAAAATTTGGTGATTT
Found at i:2774381 original size:3 final size:3
Alignment explanation
Indices: 2774373--2774412 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2774363 CTTAATCAGG
2774373 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2774413 AGTATACATA
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:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2781262 original size:14 final size:14
Alignment explanation
Indices: 2781243--2781272 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2781233 TTGAAAGAGT
2781243 TGAGATACAATTTG
1 TGAGATACAATTTG
2781257 TGAGATACAATTTG
1 TGAGATACAATTTG
2781271 TG
1 TG
2781273 CATCGAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (14 bp):
TGAGATACAATTTG
Found at i:2781608 original size:6 final size:6
Alignment explanation
Indices: 2781597--2781636 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
2781587 TTAGTGATTT
2781597 AATATA AATATA AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA
2781637 ATTATTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:2787438 original size:2 final size:2
Alignment explanation
Indices: 2787431--2787455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2787421 TCTGTTTTCT
2787431 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2787456 TTTTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2789667 original size:27 final size:26
Alignment explanation
Indices: 2789619--2789671 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2789609 ACAATGCCTT
*
2789619 GCCTGATGAGAAACTTGATTCTACCTG
1 GCCTGATGAAAAACTTGATTCT-CCTG
*
2789646 GCCTGATGAAACAAC-TGGTTCTCCTG
1 GCCTGATGAAA-AACTTGATTCTCCTG
2789672 TAAGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.70
28 3 0.13
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (26 bp):
GCCTGATGAAAAACTTGATTCTCCTG
Found at i:2793847 original size:44 final size:44
Alignment explanation
Indices: 2793793--2793882 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
2793783 TTTCTTTGGG
* * * *
2793793 TTATGGGATATTTGTATTTAGGGGTATTTTGTGTTTATTTGAAT
1 TTATGAGATATTTGTATCTAGAGGTATTTTGTGTTTATTCGAAT
*
2793837 TTATGAGATATTTGTATCTAGAGTTATTTTGTGTTTATTCGAAT
1 TTATGAGATATTTGTATCTAGAGGTATTTTGTGTTTATTCGAAT
2793881 TT
1 TT
2793883 GATGTCGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.22, C:0.02, G:0.21, T:0.54
Consensus pattern (44 bp):
TTATGAGATATTTGTATCTAGAGGTATTTTGTGTTTATTCGAAT
Found at i:2793975 original size:47 final size:47
Alignment explanation
Indices: 2793869--2793980 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 47
2793859 GTTATTTTGT
* * * *
2793869 GTTTATTCGAATTTGATGTCGATATTGATTGTGATTTTTAATTTAGG
1 GTTTATTCGATTTTGATTTCGATATTGATTGTCATTTTTAATTTAAG
* *
2793916 GTTTATTCGATTTTGATTTCGAT-TCTGATTTTCATTTTTGATTTAAG
1 GTTTATTCGATTTTGATTTCGATAT-TGATTGTCATTTTTAATTTAAG
*
2793963 G-TTATTTTGATTTTGATT
1 GTTTA-TTCGATTTTGATT
2793981 GCTACTTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 4 0.07
47 52 0.93
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (47 bp):
GTTTATTCGATTTTGATTTCGATATTGATTGTCATTTTTAATTTAAG
Found at i:2799669 original size:22 final size:21
Alignment explanation
Indices: 2799640--2799701 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
2799630 TTTTTAATTT
*
2799640 ATAAAATTTTAAATTAATAATA
1 ATAAAA-TTTAATTTAATAATA
* *
2799662 TTAAAATTTAACTTTAAAAATA
1 ATAAAATTTAA-TTTAATAATA
2799684 ATAAAAATTTAATTTAAT
1 AT-AAAATTTAATTTAAT
2799702 CTTTTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 5 0.15
22 19 0.58
23 9 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATTTAATTTAATAATA
Found at i:2799682 original size:29 final size:31
Alignment explanation
Indices: 2799650--2799714 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 31
2799640 ATAAAATTTT
*
2799650 AAATTAAT-AATATTAAAATTTAA-C-TTTAA
1 AAATTAATAAAAATT-AAATTTAATCTTTTAA
*
2799679 AAA-TAATAAAAATTTAATTTAATCTTTTAA
1 AAATTAATAAAAATTAAATTTAATCTTTTAA
2799709 AAATTA
1 AAATTA
2799715 CAAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
28 11 0.37
29 9 0.30
30 8 0.27
31 2 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATTAATAAAAATTAAATTTAATCTTTTAA
Found at i:2799697 original size:28 final size:30
Alignment explanation
Indices: 2799666--2799721 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2799656 ATAATATTAA
*
2799666 AATTTAA-C-TTTAAAAATAATAAAAATTT
1 AATTTAATCTTTTAAAAATAACAAAAATTT
*
2799694 AATTTAATCTTTTAAAAATTACAAAAAT
1 AATTTAATCTTTTAAAAATAACAAAAAT
2799722 ATAAACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 1 0.04
30 16 0.67
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
AATTTAATCTTTTAAAAATAACAAAAATTT
Found at i:2808518 original size:29 final size:31
Alignment explanation
Indices: 2808448--2808518 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
2808438 AATCATTTTG
* *
2808448 TTTTTATTTA-AGATAAATAATTGATTTATC
1 TTTTTATTTATCGATAAATAATTAATTTATC
*
2808478 TTTTTATTTATCGATATAT-ATTAATTTAT-
1 TTTTTATTTATCGATAAATAATTAATTTATC
2808507 TTTTTATTTATC
1 TTTTTATTTATC
2808519 TTTAATTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.32
30 19 0.51
31 6 0.16
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (31 bp):
TTTTTATTTATCGATAAATAATTAATTTATC
Found at i:2810818 original size:25 final size:24
Alignment explanation
Indices: 2810758--2810806 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2810748 AGGTCCTGCC
*
2810758 ATATTTTTTTTAATTTTTTTAATA
1 ATATTTATTTTAATTTTTTTAATA
*
2810782 ATATTTATTTTATTTTATTTTAATA
1 ATATTTATTTTAATTT-TTTTAATA
2810807 TTTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
ATATTTATTTTAATTTTTTTAATA
Found at i:2812324 original size:51 final size:51
Alignment explanation
Indices: 2812262--2812442 Score: 274
Period size: 51 Copynumber: 3.5 Consensus size: 51
2812252 GAATCCATAA
* *
2812262 ACTCACGATGACACTTAGCCATCGAACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* * *
2812313 AATCACGATGACACTTAGTTC-TCGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAG-TCATCGGACCTTTAATCCATAAAGGATTCATTT
2812364 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* * *
2812415 GCTCACGATGACATTTACTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
2812443 CTTTCGTTTA
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
50 2 0.02
51 114 0.97
52 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
Found at i:2819539 original size:51 final size:51
Alignment explanation
Indices: 2819476--2819656 Score: 308
Period size: 51 Copynumber: 3.5 Consensus size: 51
2819466 GAATCCATAA
*
2819476 ACTCACGATGACACTTAGTCATTGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* *
2819527 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* *
2819578 AATCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
*
2819629 TCTCACGATGACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
2819657 CTTTCGTTTA
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 120 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
Found at i:2820977 original size:87 final size:87
Alignment explanation
Indices: 2820807--2820980 Score: 242
Period size: 87 Copynumber: 2.0 Consensus size: 87
2820797 CACCCTAAAT
* * * * * *
2820807 TTGAGTTTAATTGCTTGTAATTACACTTATTATTTCAATTTATAGCACAATCACGATTTTAGGTG
1 TTGAGTGTAATTGCTTGTAATCACACTTAGTATTTCAATTTATAACACAATCACGAATTTAAGTG
* *
2820872 AAAAATACATTACATAAAAAAA
66 AAAAACACACTACATAAAAAAA
2820894 TTGAGTGTAATTGCTTGTCAA-CACACTTAGTATTTCAATTTATAACACAATCACGAATTTAAGT
1 TTGAGTGTAATTGCTTGT-AATCACACTTAGTATTTCAATTTATAACACAATCACGAATTTAAGT
* *
2820958 GAAAAACATACTACGTAAAAAAA
65 GAAAAACACACTACATAAAAAAA
2820981 AGAGATAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
87 74 0.97
88 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (87 bp):
TTGAGTGTAATTGCTTGTAATCACACTTAGTATTTCAATTTATAACACAATCACGAATTTAAGTG
AAAAACACACTACATAAAAAAA
Found at i:2823508 original size:19 final size:20
Alignment explanation
Indices: 2823486--2823586 Score: 66
Period size: 19 Copynumber: 5.2 Consensus size: 20
2823476 TAAAAATATT
*
2823486 AAAAATTAGAAAAAATTAGAA
1 AAAAATTA-TAAAAATTAGAA
* *
2823507 AAAAATTATAAAAATCA-TA
1 AAAAATTATAAAAATTAGAA
* *
2823526 AAAATTTATAAAAATT-GTA
1 AAAAATTATAAAAATTAGAA
***
2823545 AATTTTTATAAAAA-TAGTAA
1 AAAAATTATAAAAATTAG-AA
* *
2823565 AGAAATTATAAATA-TAGAA
1 AAAAATTATAAAAATTAGAA
2823584 AAA
1 AAA
2823587 TATAGAAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
18 1 0.02
19 34 0.54
20 20 0.32
21 8 0.13
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATTAGAA
Found at i:2823509 original size:11 final size:11
Alignment explanation
Indices: 2823486--2823520 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2823476 TAAAAATATT
2823486 AAAAATTAG-A
1 AAAAATTAGAA
2823496 AAAAATTAGAA
1 AAAAATTAGAA
*
2823507 AAAAATTATAA
1 AAAAATTAGAA
2823518 AAA
1 AAA
2823521 TCATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:2823529 original size:10 final size:10
Alignment explanation
Indices: 2823459--2823539 Score: 60
Period size: 10 Copynumber: 8.2 Consensus size: 10
2823449 AAAAGTTATT
*
2823459 AAATTTTAATA
1 AAATTATAA-A
*
2823470 AAAATAT-AA
1 AAATTATAAA
*
2823479 AAA-TATTAA
1 AAATTATAAA
*
2823488 AAATTAGAAA
1 AAATTATAAA
*
2823498 AAATTAGAAAA
1 AAATTA-TAAA
2823509 AAATTAT-AA
1 AAATTATAAA
*
2823518 AAATCATAAA
1 AAATTATAAA
*
2823528 AATTTATAAA
1 AAATTATAAA
2823538 AA
1 AA
2823540 TTGTAAATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
8 3 0.05
9 17 0.30
10 23 0.40
11 14 0.25
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (10 bp):
AAATTATAAA
Found at i:2823540 original size:10 final size:10
Alignment explanation
Indices: 2823474--2823559 Score: 54
Period size: 9 Copynumber: 8.9 Consensus size: 10
2823464 TTAATAAAAA
*
2823474 TATAAAAATA
1 TATAAAAATT
2823484 T-TAAAAA-T
1 TATAAAAATT
* *
2823492 TAGAAAAAAT
1 TATAAAAATT
* *
2823502 TAGAAAAAAAT
1 TA-TAAAAATT
2823513 TATAAAAA-T
1 TATAAAAATT
*
2823522 CATAAAAATT
1 TATAAAAATT
2823532 TATAAAAA-T
1 TATAAAAATT
* **
2823541 TGTAAATTTT
1 TATAAAAATT
2823551 TATAAAAAT
1 TATAAAAAT
2823560 AGTAAAGAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 1 0.02
9 25 0.42
10 24 0.41
11 9 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
TATAAAAATT
Found at i:2823546 original size:9 final size:9
Alignment explanation
Indices: 2823467--2823546 Score: 65
Period size: 9 Copynumber: 8.6 Consensus size: 9
2823457 TTAAATTTTA
2823467 ATAAAAA-T
1 ATAAAAATT
2823475 ATAAAAA-T
1 ATAAAAATT
2823483 ATTAAAAATT
1 A-TAAAAATT
*
2823493 AGAAAAAATT
1 A-TAAAAATT
*
2823503 AGAAAAAAATT
1 --ATAAAAATT
*
2823514 ATAAAAATC
1 ATAAAAATT
2823523 ATAAAAATTT
1 ATAAAAA-TT
2823533 ATAAAAATT
1 ATAAAAATT
*
2823542 GTAAA
1 ATAAA
2823547 TTTTTATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
8 9 0.15
9 26 0.43
10 17 0.28
11 8 0.13
12 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2823577 original size:30 final size:29
Alignment explanation
Indices: 2823449--2823633 Score: 114
Period size: 28 Copynumber: 6.4 Consensus size: 29
2823439 GTCACACCCT
*
2823449 AAAAGTTATTAAATTTTAATAAAAATA-TAA
1 AAAAATTA-TAAATTTT-ATAAAAATAGTAA
* * **
2823479 AAATATTAAAAATTAGA-AAAAATTAG-AA
1 AAAAATTATAAATTTTATAAAAA-TAGTAA
** * * *
2823507 AAAAATTATAAAAATCATAAAAAT-TTAT
1 AAAAATTATAAATTTTATAAAAATAGTAA
*
2823535 AAAAATTGTAAATTTTTATAAAAATAGTAA
1 AAAAATTATAAA-TTTTATAAAAATAGTAA
* * *
2823565 AGAAATTATAAA-TATAGAAAAATA-TAGA
1 AAAAATTATAAATTTTATAAAAATAGTA-A
* * *
2823593 AAAAAATATAAAATTTTAT-AAAGTCGTAA
1 AAAAATTAT-AAATTTTATAAAAATAGTAA
2823622 AAAAATTATAAA
1 AAAAATTATAAA
2823634 AAATGTAAAG
Statistics
Matches: 115, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
27 7 0.06
28 50 0.43
29 35 0.30
30 23 0.20
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATTATAAATTTTATAAAAATAGTAA
Found at i:2823597 original size:58 final size:58
Alignment explanation
Indices: 2823469--2823635 Score: 155
Period size: 57 Copynumber: 2.9 Consensus size: 58
2823459 AAATTTTAAT
* * ** *
2823469 AAAAATATAAAAATATTA-AAAATTAGA-AAAAATTAG-AAAAAAATTATAAAAATCAT
1 AAAAATATAAAAAAAATATAAAATTTTATAAAAA-TAGTAAAAAAATTATAAAAATCAG
* * * * * * *
2823525 AAAAATTTATAAAAATTGTAAATTTTTATAAAAATAGTAAAGAAATTATAAATAT-AG
1 AAAAATATAAAAAAAATATAAAATTTTATAAAAATAGTAAAAAAATTATAAAAATCAG
* *
2823582 AAAAATATAGAAAAAAATATAAAATTTTAT-AAAGTCGTAAAAAAATTATAAAAA
1 AAAAATATA-AAAAAAATATAAAATTTTATAAAAATAGTAAAAAAATTATAAAAA
2823636 ATGTAAAGTA
Statistics
Matches: 88, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
56 14 0.16
57 38 0.43
58 36 0.41
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (58 bp):
AAAAATATAAAAAAAATATAAAATTTTATAAAAATAGTAAAAAAATTATAAAAATCAG
Found at i:2824353 original size:21 final size:22
Alignment explanation
Indices: 2824313--2824353 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2824303 TAAAAATGAT
*
2824313 AAAATTTTAATTTAATCTTTTA
1 AAAATTATAATTTAATCTTTTA
2824335 AAAATTATAATTTAA-CTTT
1 AAAATTATAATTTAATCTTT
2824354 GGTCCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTATAATTTAATCTTTTA
Found at i:2828606 original size:19 final size:19
Alignment explanation
Indices: 2828582--2828618 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2828572 ATATAAATAA
* *
2828582 AAAAATATTAAAATTATTT
1 AAAAATATAAAAAATATTT
2828601 AAAAATATAAAAAATATT
1 AAAAATATAAAAAATATT
2828619 GTTTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATATAAAAAATATTT
Found at i:2829379 original size:31 final size:31
Alignment explanation
Indices: 2829322--2829380 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2829312 TATAACTTTC
* *
2829322 GACCCATAAACTTGATAAGTAGGTCCACATT
1 GACCCATAAACTTGACAAGTAAGTCCACATT
* *
2829353 GACCCCTAAACTTGACAATTAAGTCCAC
1 GACCCATAAACTTGACAAGTAAGTCCAC
2829381 TTTGGTACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.24
Consensus pattern (31 bp):
GACCCATAAACTTGACAAGTAAGTCCACATT
Found at i:2829992 original size:175 final size:177
Alignment explanation
Indices: 2829678--2830035 Score: 433
Period size: 175 Copynumber: 2.0 Consensus size: 177
2829668 AAAAAGTTAA
*
2829678 AAATATAAAATTGAATATACTTTTTTTTTAGATTTTATGATTTAAATTATTTATTTAATTATTGT
1 AAATATAAAATCGAATATACTTTTTTTTTAGATTTTATGATTTAAATTATTTATTTAATTATTGT
*
2829743 TAGTCTGACGATCGAACTGATCGAAATGGTTGAATCGAGAACTGATGGTCTAACATGTTCAATCA
66 TAGTCT-A-GATCG-A--GATCGAAATGGTTGAATCGAGAACTGATGGTCTAACATGTTCAACCA
* * *
2829808 TCAGTTTGGTTATTAAAATATTTAATAGGACACTATGAGATTGTGCCACATC
126 TCAGTTTGGTTATTAAAACATTGAATAGGACACTATGAGATTGTACCACATC
* * *
2829860 AAATATAAAATCGATTTTAC-TTTTTTTTAGATTTTTATGAATTTTTAATTATTTATTTAATTAT
1 AAATATAAAATCGAATATACTTTTTTTTTAGA-TTTTATG-A-TTTAAATTATTTATTTAATTAT
* * *
2829924 TGTT-GATCT-GA-CG-G-TCGAATTGGTTGAATCGAGAACT-AGTGGTTTAACTTGTTCAACCA
63 TGTTAG-TCTAGATCGAGATCGAAATGGTTGAATCGAGAACTGA-TGGTCTAACATGTTCAACCA
** * * *
2829983 TTGGTTTGGTTATTAAAACATTGAATATGACATTCTGAGATTGTACCACATC
126 TCAGTTTGGTTATTAAAACATTGAATAGGACACTATGAGATTGTACCACATC
2830035 A
1 A
2830036 TCATTTAAAT
Statistics
Matches: 155, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
174 1 0.01
175 84 0.54
176 1 0.01
180 2 0.01
181 13 0.08
182 24 0.15
183 2 0.01
184 28 0.18
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (177 bp):
AAATATAAAATCGAATATACTTTTTTTTTAGATTTTATGATTTAAATTATTTATTTAATTATTGT
TAGTCTAGATCGAGATCGAAATGGTTGAATCGAGAACTGATGGTCTAACATGTTCAACCATCAGT
TTGGTTATTAAAACATTGAATAGGACACTATGAGATTGTACCACATC
Found at i:2837834 original size:58 final size:58
Alignment explanation
Indices: 2837763--2838193 Score: 435
Period size: 58 Copynumber: 7.4 Consensus size: 58
2837753 TTTTAACCTT
* * * *
2837763 GAACTTTAC-AAAATTACCATTTTACCCCGAATGTCAAAAAATTCTATTCTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCC
* * ** * ***
2837820 AAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCTGAAAATTCCATTTTTTACTAT
1 GAACTTTCCAAAAATTACCATTTTA-CCCCGAATGTCCAAAAATTCCATTTTTGACCCC
** * ** *
2837879 GAACTTTTTAAAAATTA-CATTTTTACCCTCTAACT-TTAAAAAATTCCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCA-TTTTACCC-CGAA-TGTCCAAAAATTCCATTTTTGACCCC
* * *
2837938 GAACTTTCCAAAAATTACCATTTTACTCCCGAATTTCC-AAAATTTCATTTTTGATCCC
1 GAACTTTCCAAAAATTACCATTTTAC-CCCGAATGTCCAAAAATTCCATTTTTGACCCC
* * * *
2837996 GAACTTTCCAAAAATTACCATTTTACTCCTGAATTTCC-AAAATTCTATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTAC-CCCGAATGTCCAAAAATTCCATTTTTGACCCC
* * *
2838054 GAACTTTCCAAAAATTACCATTTTACTCTCGAATTTCCAAAAATTCCATTTTTGACCCT
1 GAACTTTCCAAAAATTACCATTTTAC-CCCGAATGTCCAAAAATTCCATTTTTGACCCC
* * * *
2838113 GAACTTT-CAAAAATTACCATTTTACCCTTGGATGTCCAAAAATTACATTTTTGCCCCC
1 GAACTTTCCAAAAATTACCATTTTACCC-CGAATGTCCAAAAATTCCATTTTTGACCCC
* *
2838171 G-AGTGTCCAAAAATTACCATTTT
1 GAACTTTCCAAAAATTACCATTTT
2838194 GCTCATGAAG
Statistics
Matches: 313, Mismatches: 50, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
57 10 0.03
58 186 0.59
59 112 0.36
60 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (58 bp):
GAACTTTCCAAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCC
Found at i:2838152 original size:29 final size:29
Alignment explanation
Indices: 2837705--2838193 Score: 221
Period size: 29 Copynumber: 16.8 Consensus size: 29
2837695 AAGGTCCCTA
* *
2837705 AACTGTCTAAAAATTA-CATTTTGGCCCTCG
1 AACTGTCCAAAAATTACCATTTT-ACCC-CG
* * **
2837735 AACTCTTCAAAAATTA-CATTTTAACCTTG
1 AACTGTCCAAAAATTACCATTTT-ACCCCG
* *
2837764 AACTTTAC-AAAATTACCATTTTACCCCG
1 AACTGTCCAAAAATTACCATTTTACCCCG
* * *
2837792 AA-TGTCAAAAAATT-CTATTCTTGACCCCA
1 AACTGTCCAAAAATTACCATT-TT-ACCCCG
* *
2837821 AAATTTCCAAAAATTACCATTTTACCCCCG
1 AACTGTCCAAAAATTACCATTTTA-CCCCG
** ***
2837851 AA-TGTCTGAAAATT-CCATTTTTTACTATG
1 AACTGTCCAAAAATTACCA--TTTTACCCCG
* ** *
2837880 AACTTTTTAAAAATTA-CATTTTTACCCTCT
1 AACTGTCCAAAAATTACCA-TTTTACCC-CG
** *
2837910 AACT-TTAAAAAATT-CCATTTTTGACCTCG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCCG
*
2837939 AACTTTCCAAAAATTACCATTTTACTCCCG
1 AACTGTCCAAAAATTACCATTTTAC-CCCG
* * *
2837969 AA-TTTCC-AAAATT-TCATTTTTGATCCCG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCCG
* *
2837997 AACTTTCCAAAAATTACCATTTTACTCCTG
1 AACTGTCCAAAAATTACCATTTTAC-CCCG
* * *
2838027 AA-TTTCC-AAAATT-CTATTTTTGACCTCG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCCG
* *
2838055 AACTTTCCAAAAATTACCATTTTACTCTCG
1 AACTGTCCAAAAATTACCATTTTAC-CCCG
* *
2838085 AA-TTTCCAAAAATT-CCATTTTTGACCCTG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCCG
* *
2838114 AACT-TTCAAAAATTACCATTTTACCCTTG
1 AACTGTCCAAAAATTACCATTTTACCC-CG
* *
2838143 GA-TGTCCAAAAATTA-CATTTTTGCCCCCG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCCG
*
2838172 -AGTGTCCAAAAATTACCATTTT
1 AACTGTCCAAAAATTACCATTTT
2838194 GCTCATGAAG
Statistics
Matches: 365, Mismatches: 55, Indels: 79
0.73 0.11 0.16
Matches are distributed among these distances:
27 10 0.03
28 65 0.18
29 158 0.43
30 121 0.33
31 11 0.03
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (29 bp):
AACTGTCCAAAAATTACCATTTTACCCCG
Found at i:2838213 original size:116 final size:115
Alignment explanation
Indices: 2837744--2838214 Score: 481
Period size: 116 Copynumber: 4.1 Consensus size: 115
2837734 GAACTCTTCA
* * * *
2837744 AAAATTACA-TTTTAACCTTGAACTTT-ACAAAATTACCATTTTACCCCGAATGTCAAAAAATTC
1 AAAATTCCATTTTTGACCCTGAACTTTCA-AAAATTACCATTTTACCCTGAATGTCAAAAAATTC
* * * * *
2837807 TATTCTTGACCCCAAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCTG
65 TATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACTCCCGAATGTC-C
* ** * * *
2837859 AAAATTCCATTTTTTACTATGAACTTTTTAAAAATTA-CATTTTTACCCTCTAACT-TTAAAAAA
1 AAAATTCCATTTTTGACCCTGAAC-TTTCAAAAATTACCA-TTTTACCCT-GAA-TGTCAAAAAA
* * *
2837922 TTCCATTTTTGACCTCGAACTTTCCAAAAATTACCATTTTACTCCCGAATTTCC
62 TTCTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACTCCCGAATGTCC
* * *
2837976 AAAATTTCATTTTTGATCCC-GAACTTTCCAAAAATTACCATTTTACTCCTGAATTTC-CAAAAT
1 AAAATTCCATTTTTGA-CCCTGAACTTT-CAAAAATTACCATTTTAC-CCTGAATGTCAAAAAAT
* * *
2838039 TCTATTTTTGACCTCGAACTTTCCAAAAATTACCATTTTACTCTCGAATTTCC
63 TCTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACTCCCGAATGTCC
* *
2838092 AAAAATTCCATTTTTGACCCTGAACTTTCAAAAATTACCATTTTACCCTTGGATGTCCAAAAATT
1 -AAAATTCCATTTTTGACCCTGAACTTTCAAAAATTACCATTTTACCC-TGAATGTCAAAAAATT
* * * * **
2838157 AC-ATTTTTGCCCCCG-AGTGTCCAAAAATTACCATTTTGCTCATGAAGTGTCC
64 -CTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACTCCCGAA-TGTCC
2838209 AAAATT
1 AAAATT
2838215 ACTGTTTTAC
Statistics
Matches: 302, Mismatches: 37, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
115 10 0.03
116 132 0.44
117 96 0.32
118 63 0.21
119 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.37
Consensus pattern (115 bp):
AAAATTCCATTTTTGACCCTGAACTTTCAAAAATTACCATTTTACCCTGAATGTCAAAAAATTCT
ATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACTCCCGAATGTCC
Found at i:2838238 original size:58 final size:58
Alignment explanation
Indices: 2837944--2838242 Score: 183
Period size: 58 Copynumber: 5.2 Consensus size: 58
2837934 CCTCGAACTT
* * * * * *
2837944 TCCAAAAATTACCATTTTACTCC-CGAATTTCC-AAAATTTCATTTTTGATCCC-GAACTT
1 TCCAAAAATTACCATTTTAC-CCATGAATGTCCAAAAATTACATTTTT-ACCCCAG-AGTA
* * * *
2838002 TCCAAAAATTACCATTTTACTCC-TGAATTTCC-AAAATT-CTATTTTTGACCTC-GAACTT
1 TCCAAAAATTACCATTTTAC-CCATGAATGTCCAAAAATTAC-ATTTTT-ACCCCAG-AGTA
* * * * *
2838060 TCCAAAAATTACCATTTTACTC-TCGAATTTCCAAAAATTCCATTTTTGA-CCCTGAACT-
1 TCCAAAAATTACCATTTTACCCAT-GAATGTCCAAAAATTACATTTTT-ACCCCAG-AGTA
* * * * * *
2838118 TTCAAAAATTACCATTTTACCCTTGGATGTCCAAAAATTACATTTTTGCCCCCGAGTG
1 TCCAAAAATTACCATTTTACCCATGAATGTCCAAAAATTACATTTTTACCCCAGAGTA
* *
2838176 TCCAAAAATTACCATTTTGCTCATGAAGTGTCC-AAAATTAC-TGTTTTACCCCTAG-GTA
1 TCCAAAAATTACCATTTTACCCATGAA-TGTCCAAAAATTACAT-TTTTACCCC-AGAGTA
2838234 TCCAAAAAT
1 TCCAAAAAT
2838243 CGCATTTTTT
Statistics
Matches: 209, Mismatches: 21, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
57 6 0.03
58 176 0.84
59 26 0.12
60 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCATGAATGTCCAAAAATTACATTTTTACCCCAGAGTA
Found at i:2843690 original size:19 final size:18
Alignment explanation
Indices: 2843641--2843692 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
2843631 TCGATGAGAG
* *
2843641 ATAAAAAAAATTAAATTA
1 ATAAAAAAAATTGAATAA
**
2843659 ATATAAATTAATTGAATCAA
1 ATA-AAAAAAATTGAAT-AA
2843679 ATAAAAAAAATTGA
1 ATAAAAAAAATTGA
2843693 TTAATCTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
ATAAAAAAAATTGAATAA
Found at i:2857590 original size:19 final size:19
Alignment explanation
Indices: 2857555--2857600 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2857545 GATAATTGTG
2857555 AAAAATAATAAAATAAA-T
1 AAAAATAATAAAATAAATT
* *
2857573 AATAAATAATACATTAAATT
1 AA-AAATAATAAAATAAATT
2857593 AAAAATAA
1 AAAAATAA
2857601 CTCTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 19 0.79
20 3 0.12
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATAATAAAATAAATT
Found at i:2859320 original size:30 final size:30
Alignment explanation
Indices: 2859285--2859345 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2859275 CCTGAATTTG
*
2859285 TTTTATCAGAATGTTGTTGCAAACTTGACT
1 TTTTATCAGAATGTTATTGCAAACTTGACT
2859315 TTTTATCAGAATGTTATTGCAAACTTGACT
1 TTTTATCAGAATGTTATTGCAAACTTGACT
2859345 T
1 T
2859346 CCAAGCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (30 bp):
TTTTATCAGAATGTTATTGCAAACTTGACT
Found at i:2860627 original size:31 final size:31
Alignment explanation
Indices: 2860591--2860652 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2860581 CTTAACAATC
2860591 CAGTGACTTAAATAAAAACTTTCAAATAGTT
1 CAGTGACTTAAATAAAAACTTTCAAATAGTT
* **
2860622 CAGTGACTTAAATGAAAACTTTTGAATAGTT
1 CAGTGACTTAAATAAAAACTTTCAAATAGTT
2860653 AATGACCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCAAATAGTT
Found at i:2867789 original size:39 final size:42
Alignment explanation
Indices: 2867706--2867790 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 42
2867696 AGTACATTAA
** *
2867706 ATTTTATTTATATTAAAGAACACAACTATAAATATAATAAAT
1 ATTTTATTTATATTAAAGAACACAAAAATAAAAATAATAAAT
* *
2867748 ATTTTA-TTATATTAAA-AA-ATAAAAATAAAAATAATATAT
1 ATTTTATTTATATTAAAGAACACAAAAATAAAAATAATAAAT
2867787 ATTT
1 ATTT
2867791 GTTGTATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 20 0.53
40 2 0.05
41 10 0.26
42 6 0.16
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (42 bp):
ATTTTATTTATATTAAAGAACACAAAAATAAAAATAATAAAT
Found at i:2869453 original size:23 final size:20
Alignment explanation
Indices: 2869406--2869446 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2869396 AAAACGCATA
* *
2869406 AAAAATAACATCCAAACAAC
1 AAAAATAACAGCAAAACAAC
2869426 AAAAATAACAGCAAAACAAC
1 AAAAATAACAGCAAAACAAC
2869446 A
1 A
2869447 TTAAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.22, G:0.02, T:0.07
Consensus pattern (20 bp):
AAAAATAACAGCAAAACAAC
Found at i:2869455 original size:20 final size:20
Alignment explanation
Indices: 2869406--2869461 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2869396 AAAACGCATA
* *
2869406 AAAAATAACATCCAAACAAC
1 AAAAATAACAACAAAACAAC
*
2869426 AAAAATAACAGCAAAACAAC
1 AAAAATAACAACAAAACAAC
*
2869446 ATTAAA-AACAACAAAA
1 A-AAAATAACAACAAAA
2869462 ATAACAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:2869460 original size:32 final size:31
Alignment explanation
Indices: 2869419--2869484 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 31
2869409 AATAACATCC
*
2869419 AAACAACAAAAATAACAGCAAAACAACATTAA
1 AAACAACAAAAATAACAGCAAAA-AACATGAA
2869451 AAACAACAAAAATAACAGCAAAAAACATGAA
1 AAACAACAAAAATAACAGCAAAAAACATGAA
2869482 AAA
1 AAA
2869485 ATAACCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.08
Consensus pattern (31 bp):
AAACAACAAAAATAACAGCAAAAAACATGAA
Found at i:2869485 original size:32 final size:32
Alignment explanation
Indices: 2869419--2869494 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
2869409 AATAACATCC
*
2869419 AAACAACAAAAATAACAGCAAAACAACATTAA
1 AAACAACAAAAATAACAGCAAAACAACATAAA
2869451 AAACAACAAAAATAACAGCAAAA-AACATGAAA
1 AAACAACAAAAATAACAGCAAAACAACAT-AAA
* *
2869483 AAATAACCAAAA
1 AAACAACAAAAA
2869495 CAGTAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 5 0.12
32 35 0.88
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (32 bp):
AAACAACAAAAATAACAGCAAAACAACATAAA
Found at i:2869494 original size:19 final size:20
Alignment explanation
Indices: 2869480--2869558 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
2869470 AAAAAACATG
*
2869480 AAAAAATAAC-CAAAACAGT
1 AAAAAACAACACAAAACAGT
*
2869499 AAAAAACAACACAAAAACAAT
1 AAAAAACAACAC-AAAACAGT
2869520 AAAAATAGCAAC-CAAAACAGT
1 AAAAA-A-CAACACAAAACAGT
2869541 AAAAAAGC-AC-CAAAACAG
1 AAAAAA-CAACACAAAACAG
2869559 CAATATAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
19 19 0.36
20 4 0.08
21 24 0.45
22 2 0.04
23 4 0.08
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.06
Consensus pattern (20 bp):
AAAAAACAACACAAAACAGT
Found at i:2869545 original size:61 final size:63
Alignment explanation
Indices: 2869438--2869558 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 63
2869428 AAATAACAGC
* * *
2869438 AAAACAACATTAAAAACAACAAAAATAACAGCAAAAAACATGAAAAAATAACCAAAACAGTAA
1 AAAACAACATCAAAAACAACAAAAATAACAACAAAAAACATGAAAAAAGAACCAAAACAGTAA
* * * *
2869501 AAAACAACA-CAAAAACAATAAAAATAGCAAC-CAAAACA-GTAAAAAAGCACCAAAACAG
1 AAAACAACATCAAAAACAACAAAAATAACAACAAAAAACATG-AAAAAAGAACCAAAACAG
2869559 CAATATAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.02
61 22 0.44
62 18 0.36
63 9 0.18
ACGTcount: A:0.69, C:0.18, G:0.06, T:0.07
Consensus pattern (63 bp):
AAAACAACATCAAAAACAACAAAAATAACAACAAAAAACATGAAAAAAGAACCAAAACAGTAA
Found at i:2870951 original size:17 final size:17
Alignment explanation
Indices: 2870929--2870977 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
2870919 TACCCCCATA
2870929 CTCATCTTCATCTCAAC
1 CTCATCTTCATCTCAAC
* *
2870946 CTCATCTTCATCTTTACC
1 CTCATCTTCATC-TCAAC
*
2870964 CTCATCTTCGTCTC
1 CTCATCTTCATCTC
2870978 CATCTTCTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.16, C:0.41, G:0.02, T:0.41
Consensus pattern (17 bp):
CTCATCTTCATCTCAAC
Found at i:2871289 original size:12 final size:12
Alignment explanation
Indices: 2871272--2871301 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2871262 GATGCTGCAG
*
2871272 TGGTGCATAGTA
1 TGGTGCATAATA
2871284 TGGTGCATAATA
1 TGGTGCATAATA
2871296 TGGTGC
1 TGGTGC
2871302 TTGTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (12 bp):
TGGTGCATAATA
Found at i:2872816 original size:16 final size:17
Alignment explanation
Indices: 2872797--2872832 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2872787 TTATATCAAC
*
2872797 AAAAT-AAAATATTTTA
1 AAAATAAAAAAATTTTA
2872813 AAAATAAAAAAATTTTA
1 AAAATAAAAAAATTTTA
2872830 AAA
1 AAA
2872833 TTAACTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAAAAAATTTTA
Found at i:2876211 original size:6 final size:6
Alignment explanation
Indices: 2876200--2876263 Score: 101
Period size: 6 Copynumber: 10.7 Consensus size: 6
2876190 GAGCGTGTTG
*
2876200 CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGC
1 CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT CCCTGT
* *
2876248 CCCTGC CCCTGC CCCT
1 CCCTGT CCCTGT CCCT
2876264 ACACCAATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.56, G:0.16, T:0.28
Consensus pattern (6 bp):
CCCTGT
Found at i:2878806 original size:18 final size:19
Alignment explanation
Indices: 2878775--2878816 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2878765 TATTTTCAAA
2878775 TAAAATTTTATAAA-ATAT
1 TAAAATTTTATAAAGATAT
*
2878793 TAAAA-TTTATTAAAGTTAT
1 TAAAATTTTA-TAAAGATAT
2878812 TAAAA
1 TAAAA
2878817 ATGATAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAATTTTATAAAGATAT
Found at i:2878880 original size:11 final size:12
Alignment explanation
Indices: 2878864--2878889 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2878854 ATTATAAATT
2878864 AAAAAAATTTAA
1 AAAAAAATTTAA
2878876 AAAAAAATTTAA
1 AAAAAAATTTAA
2878888 AA
1 AA
2878890 TTTATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:2888560 original size:39 final size:41
Alignment explanation
Indices: 2888492--2888578 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 41
2888482 AAAGTATTTG
*
2888492 TATTAAAAAACATTACCATAAATATAATAAATGA-TTTATTA
1 TATTAAAAAACATTACAATAAATATAATAAAT-ATTTTATTA
*
2888533 TATTAAAAAACA-TA-AATAAATATAATAAATATTTTATTG
1 TATTAAAAAACATTACAATAAATATAATAAATATTTTATTA
2888572 TATTAAA
1 TATTAAA
2888579 TATAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 1 0.02
39 28 0.65
40 2 0.05
41 12 0.28
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTAAAAAACATTACAATAAATATAATAAATATTTTATTA
Found at i:2888689 original size:6 final size:6
Alignment explanation
Indices: 2888678--2888706 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2888668 TTAGTTACTT
2888678 AATATA AATATA AATATA AATATA AATAT
1 AATATA AATATA AATATA AATATA AATAT
2888707 CTATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:2888974 original size:6 final size:6
Alignment explanation
Indices: 2888952--2888993 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
2888942 ATATCAAAAA
*
2888952 TATATT TATTCATT TATATT TATATT TATATT TATACT TATA
1 TATATT TA-T-ATT TATATT TATATT TATATT TATATT TATA
2888994 AGTAGAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 26 0.79
7 2 0.06
8 5 0.15
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:2896711 original size:14 final size:14
Alignment explanation
Indices: 2896692--2896722 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2896682 ATAAAGTGCA
2896692 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
2896706 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
2896720 TTT
1 TTT
2896723 ATAGCTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTCTTTCTTTTTT
Found at i:2904407 original size:141 final size:141
Alignment explanation
Indices: 2904127--2904503 Score: 474
Period size: 141 Copynumber: 2.7 Consensus size: 141
2904117 AATCTCATCT
* *
2904127 CATTATATGTTTTAATAATATCTGCTCTTTTGATACAATGCTTAGAACTATACATAA--CTTTTC
1 CATTATATGTTTTAATAATATCTGCTCTTTTGATACAATGCTTAGAACTACACATAATCCTTTCC
* * * *** *
2904190 AATTCATAAATAGGAGGATAATGCACTTCAATGTATTCGAACTCACGTCTTCTTGCATTAACAAT
66 AACTCATAAATAAGAGGATAATACACTTCAACACATTCAAACTCACGTCTTCTTGCATTAACAAT
2904255 AATACCCATGC
131 AATACCCATGC
* * * *
2904266 CATTATATGTTTTAATAATATATGCTCTTTTGATACAATACCT-GAACTACATATAATCCTTTCC
1 CATTATATGTTTTAATAATATCTGCTCTTTTGATACAATGCTTAGAACTACACATAATCCTTTCC
** * * *
2904330 AAACTCATAAATAAGAGGATAATACGTTTCAACACATTCAAACTCGCGTTCTTC-TGCTTTGACA
66 -AACTCATAAATAAGAGGATAATACACTTCAACACATTCAAACTCACG-TCTTCTTGCATTAACA
*
2904394 ATAATACCTATGC
129 ATAATACCCATGC
* *
2904407 CATTATATGTTTTAATAATATCTGATTTTTTGTATACAATGCTTAGAACTACACATAATCCCTTT
1 CATTATATGTTTTAATAATATCTGCTCTTTTG-ATACAATGCTTAGAACTACACATAAT-CCTTT
* * *
2904472 CCAACTCATAAATATGAAGATAATGCACTTCA
64 CCAACTCATAAATAAGAGGATAATACACTTCA
2904504 GCATACTCGA
Statistics
Matches: 201, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
138 11 0.05
139 40 0.20
140 5 0.02
141 86 0.43
142 14 0.07
143 38 0.19
144 7 0.03
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (141 bp):
CATTATATGTTTTAATAATATCTGCTCTTTTGATACAATGCTTAGAACTACACATAATCCTTTCC
AACTCATAAATAAGAGGATAATACACTTCAACACATTCAAACTCACGTCTTCTTGCATTAACAAT
AATACCCATGC
Found at i:2905029 original size:31 final size:32
Alignment explanation
Indices: 2904993--2905054 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
2904983 AGTAAAGCTG
*
2904993 TAAATTG-AAA-ATTAATTTTCATACCAATTTT
1 TAAATTGCAAATATTAACTTTCATA-CAATTTT
*
2905024 TAAATTGCAAATATTAACTTTCCTACAATTT
1 TAAATTGCAAATATTAACTTTCATACAATTT
2905055 AATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 7 0.26
32 9 0.33
33 11 0.41
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (32 bp):
TAAATTGCAAATATTAACTTTCATACAATTTT
Found at i:2907108 original size:22 final size:22
Alignment explanation
Indices: 2907082--2907131 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2907072 TATAGATTGA
2907082 TTGAACTGATTAAAAAAACTGG
1 TTGAACTGATTAAAAAAACTGG
*
2907104 TTGAACTGATTAAAAAAATTGG
1 TTGAACTGATTAAAAAAACTGG
2907126 TTGAAC
1 TTGAAC
2907132 CAGTTTAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (22 bp):
TTGAACTGATTAAAAAAACTGG
Found at i:2912339 original size:76 final size:76
Alignment explanation
Indices: 2912190--2912341 Score: 216
Period size: 76 Copynumber: 2.0 Consensus size: 76
2912180 ATGGTTACGG
* * * *
2912190 GTAGTTTTAGATTTTGTATAAAAAATGACAGATATGATCAAAACCTATAATGAGATTGCTCATTA
1 GTAGTTCTAGATTTTATATAAAAAATGACAGATATGATCAAAACCTATAATGAAATTACTCATTA
2912255 CTTTTACTTTT
66 CTTTTACTTTT
* * * *
2912266 GTAGTTCTAGATTTTATATAAAAAATGACATATATGATCAAAACTTATAATGAAATTATTTATTA
1 GTAGTTCTAGATTTTATATAAAAAATGACAGATATGATCAAAACCTATAATGAAATTACTCATTA
2912331 -TTTCTACTTTT
66 CTTT-TACTTTT
2912342 CTAAATTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 3 0.04
76 64 0.96
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (76 bp):
GTAGTTCTAGATTTTATATAAAAAATGACAGATATGATCAAAACCTATAATGAAATTACTCATTA
CTTTTACTTTT
Found at i:2917715 original size:158 final size:158
Alignment explanation
Indices: 2917427--2917743 Score: 445
Period size: 158 Copynumber: 2.0 Consensus size: 158
2917417 GACTTCAGGA
* * * ** * *
2917427 ATTACAGGTTATATGCGTGTTGGTCTTAGATGTTTTATCGATGGCTGAGATCCGATAGTTATTGC
1 ATTACAGGTCATATGAGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGACAGTTATTGC
* * * * * *
2917492 AAATTTTCCATAGCTCGTGTGAGCAGCATCGTGTAACCCAACATCTCGATCCACAGCTCGTGTGA
66 AAATTCTCCACAACTCATGTGAGCAGCATCGTGTAACCCAACATCTCAACCCACAGCTCGTGTGA
2917557 GCAGGCCCACTTCACAGCTCGTGTGAGC
131 GCAGGCCCACTTCACAGCTCGTGTGAGC
* *
2917585 ATTACAGGTCATATGAGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGGCATTTATTGC
1 ATTACAGGTCATATGAGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGACAGTTATTGC
** * *
2917650 GGATTCTCCACAACTCATGTGAGCAGCATCGTGTAGCCCAACATCTCAACCCATAGCTCGTGTGA
66 AAATTCTCCACAACTCATGTGAGCAGCATCGTGTAACCCAACATCTCAACCCACAGCTCGTGTGA
* *
2917715 GCAGGCCCATTTCACAGCTTGTGTGAGC
131 GCAGGCCCACTTCACAGCTCGTGTGAGC
2917743 A
1 A
2917744 ATACGCGATA
Statistics
Matches: 138, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 138 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (158 bp):
ATTACAGGTCATATGAGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGACAGTTATTGC
AAATTCTCCACAACTCATGTGAGCAGCATCGTGTAACCCAACATCTCAACCCACAGCTCGTGTGA
GCAGGCCCACTTCACAGCTCGTGTGAGC
Found at i:2920869 original size:24 final size:26
Alignment explanation
Indices: 2920842--2920893 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2920832 TAACTAATTT
*
2920842 AATTT-ATAA-ATAACATTATTATAA
1 AATTTCATAATATAACAATATTATAA
* *
2920866 AATTTCATAATATTATAATATTATAA
1 AATTTCATAATATAACAATATTATAA
2920892 AA
1 AA
2920894 ATTAACCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 14 0.61
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTTCATAATATAACAATATTATAA
Found at i:2922710 original size:31 final size:31
Alignment explanation
Indices: 2922669--2922731 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
2922659 TTACAATTTA
*
2922669 TCATTTAATTATTCGAAAA-TTTTTATTTAAG
1 TCATTGAATTATTC-AAAAGTTTTTATTTAAG
2922700 TCATTGAATTATTCAAAAGTTTTTATTTAAG
1 TCATTGAATTATTCAAAAGTTTTTATTTAAG
2922731 T
1 T
2922732 TACTGAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (31 bp):
TCATTGAATTATTCAAAAGTTTTTATTTAAG
Found at i:2922743 original size:31 final size:31
Alignment explanation
Indices: 2922675--2922743 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
2922665 TTTATCATTT
*
2922675 AATTATTCGAAAATTTTTATTTAAGTCATTG
1 AATTATTCGAAAATTTTTATTTAAGTCACTG
*
2922706 AATTATTC-AAAAGTTTTTATTTAAGTTACTG
1 AATTATTCGAAAA-TTTTTATTTAAGTCACTG
*
2922737 AGTTATT
1 AATTATT
2922744 AAATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (31 bp):
AATTATTCGAAAATTTTTATTTAAGTCACTG
Found at i:2923789 original size:18 final size:18
Alignment explanation
Indices: 2923749--2923791 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2923739 GTTCAAAATG
2923749 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
2923767 GAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
2923785 TAATTAA
1 TAATTAA
2923792 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:2936940 original size:48 final size:49
Alignment explanation
Indices: 2936857--2936958 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 49
2936847 TGCGTTCTTT
* **
2936857 TTTTTTTTTTTACATTTTTATAATTTCAGAAAATATTT-AATTTTTTAA
1 TTTTTATTTTTACATTTTTATAATTTCAGAAAATATTTAAACCTTTTAA
*
2936905 TTTTTATTTTTATGATTTTTATAATTT-A-AATAATATTTAAACCTTTTAA
1 TTTTTATTTTTA-CATTTTTATAATTTCAGAA-AATATTTAAACCTTTTAA
2936954 TTTTT
1 TTTTT
2936959 TAAAACAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 2 0.04
48 19 0.40
49 26 0.55
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (49 bp):
TTTTTATTTTTACATTTTTATAATTTCAGAAAATATTTAAACCTTTTAA
Found at i:2942919 original size:29 final size:27
Alignment explanation
Indices: 2942866--2942931 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
2942856 TTAAAAATTA
* *
2942866 TAAAAAAAATATTAAAATATTAAATAT
1 TAAAAAAATTATTAAAATATAAAATAT
*
2942893 TAAAAAAATTATGTAAACCTATAAAATAT
1 TAAAAAAATTAT-TAAA-ATATAAAATAT
*
2942922 TATAAAAATT
1 TAAAAAAATT
2942932 TCATAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 11 0.33
28 4 0.12
29 18 0.55
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAAAAATTATTAAAATATAAAATAT
Found at i:2942947 original size:31 final size:31
Alignment explanation
Indices: 2942912--2942995 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
2942902 TATGTAAACC
*
2942912 TATAAAATATTATAAAAATTTCATAAAAGTT
1 TATAAAATATTATAAAAATTTCATAAAAGTG
* ***
2942943 TATAAAATATAATAAAAAAAAC-TAAAAGTG
1 TATAAAATATTATAAAAATTTCATAAAAGTG
*
2942973 TATTAAAATATT-TAAAACTTTCA
1 TA-TAAAATATTATAAAAATTTCA
2942996 CAGAACTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.35
Consensus pattern (31 bp):
TATAAAATATTATAAAAATTTCATAAAAGTG
Found at i:2943443 original size:9 final size:10
Alignment explanation
Indices: 2943420--2943444 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2943410 TAACCTTAAT
2943420 TTTTTTGAAA
1 TTTTTTGAAA
2943430 TTTTTTGAAA
1 TTTTTTGAAA
2943440 TTTTT
1 TTTTT
2943445 CTTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:2945205 original size:9 final size:9
Alignment explanation
Indices: 2945182--2945221 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
2945172 AATTTTTTTA
2945182 ATAAAAT-T
1 ATAAAATAT
2945190 ATAAAATAT
1 ATAAAATAT
*
2945199 TTAAAATAT
1 ATAAAATAT
2945208 ATAAAAT-T
1 ATAAAATAT
2945216 ATAAAA
1 ATAAAA
2945222 AAAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAAAATAT
Found at i:2945727 original size:14 final size:15
Alignment explanation
Indices: 2945696--2945733 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2945686 TTAAATAATT
* *
2945696 TTTTTATAATTTACA
1 TTTTTATAAATGACA
2945711 TTTTTATAAATGA-A
1 TTTTTATAAATGACA
2945725 TTTTTATAA
1 TTTTTATAA
2945734 GTTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTATAAATGACA
Found at i:2945912 original size:17 final size:15
Alignment explanation
Indices: 2945890--2945929 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2945880 TCTATGATTA
2945890 TTTATGAATTTTATAAT
1 TTTATGAA-TTTA-AAT
2945907 TTTATGAATTTAAAT
1 TTTATGAATTTAAAT
2945922 TATTATGA
1 T-TTATGA
2945930 TCAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTATGAATTTAAAT
Found at i:2946750 original size:25 final size:25
Alignment explanation
Indices: 2946722--2946793 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
2946712 ATTTTTAGTA
*
2946722 ATTTTATATAAATTTATTTATTTAT
1 ATTTTTTATAAATTTATTTATTTAT
**
2946747 ATTTTTTACGAATTTATATT-TTTAT
1 ATTTTTTATAAATTTAT-TTATTTAT
*
2946772 -TTATTTTATAAATTTATATATT
1 ATT-TTTTATAAATTTATTTATT
2946794 GAAAATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
25 33 0.87
26 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (25 bp):
ATTTTTTATAAATTTATTTATTTAT
Found at i:2947336 original size:5 final size:5
Alignment explanation
Indices: 2947326--2947360 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
2947316 AAAGACTTGG
2947326 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
2947361 AATATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2947388 original size:30 final size:30
Alignment explanation
Indices: 2947357--2947414 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2947347 TTTATTTTAT
*
2947357 TTTAAATATATT-TTTATTAGGATTTAATA
1 TTTAAAGATATTATTTATTAGGATTTAATA
* *
2947386 TTTAAAGATATTATTTATTTGTATTTAAT
1 TTTAAAGATATTATTTATTAGGATTTAAT
2947415 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (30 bp):
TTTAAAGATATTATTTATTAGGATTTAATA
Found at i:2958847 original size:15 final size:14
Alignment explanation
Indices: 2958827--2958874 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
2958817 CCGAGTTAAG
2958827 TTTTTTAAATTCTAT
1 TTTTTTAAATT-TAT
*
2958842 TTTTTTACATTTAT
1 TTTTTTAAATTTAT
* *
2958856 AATTTTCAAATTTAT
1 -TTTTTTAAATTTAT
2958871 TTTT
1 TTTT
2958875 AAAAAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTAAATTTAT
Found at i:2961082 original size:12 final size:12
Alignment explanation
Indices: 2961065--2961089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2961055 GAAATAAAGT
2961065 TTATTATTAATA
1 TTATTATTAATA
2961077 TTATTATTAATA
1 TTATTATTAATA
2961089 T
1 T
2961090 AATATGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:2962130 original size:20 final size:21
Alignment explanation
Indices: 2962105--2962149 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2962095 TAAATATTCT
2962105 AAAATTCAAACCCTAATA-AA
1 AAAATTCAAACCCTAATATAA
**
2962125 AAAATTCAAACTTTAATATAA
1 AAAATTCAAACCCTAATATAA
2962146 AAAA
1 AAAA
2962150 ATTGTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATTCAAACCCTAATATAA
Found at i:2962848 original size:21 final size:21
Alignment explanation
Indices: 2962827--2962866 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2962817 TAATATTTTA
*
2962827 AATAT-AAATAATTAAAAATT
1 AATATGAAATAAATAAAAATT
*
2962847 AATCTGAAATAAATAAAAAT
1 AATATGAAATAAATAAAAAT
2962867 GATTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AATATGAAATAAATAAAAATT
Found at i:2968236 original size:9 final size:9
Alignment explanation
Indices: 2968219--2968257 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
2968209 TGAATTTTAC
*
2968219 AATTTGAAT
1 AATTCGAAT
2968228 AATTCGAAT
1 AATTCGAAT
*
2968237 AATTTGAAT
1 AATTCGAAT
2968246 AATTCGAAT
1 AATTCGAAT
2968255 AAT
1 AAT
2968258 AGAGTGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2968242 original size:18 final size:18
Alignment explanation
Indices: 2968219--2968257 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2968209 TGAATTTTAC
2968219 AATTTGAATAATTCGAAT
1 AATTTGAATAATTCGAAT
2968237 AATTTGAATAATTCGAAT
1 AATTTGAATAATTCGAAT
2968255 AAT
1 AAT
2968258 AGAGTGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (18 bp):
AATTTGAATAATTCGAAT
Found at i:2968360 original size:19 final size:19
Alignment explanation
Indices: 2968343--2968378 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2968333 CAAAAAATAA
2968343 ATTT-TAAAATTC-AAAAT
1 ATTTATAAAATTCTAAAAT
2968360 ATTTATAAAATTCTAAAAT
1 ATTTATAAAATTCTAAAAT
2968379 TTATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTATAAAATTCTAAAAT
Found at i:2968380 original size:17 final size:17
Alignment explanation
Indices: 2968341--2968383 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2968331 TACAAAAAAT
2968341 AAATTT-TAAAATTCAA
1 AAATTTATAAAATTCAA
*
2968357 AATATTTATAAAATTCTA
1 AA-ATTTATAAAATTCAA
2968375 AAATTTATA
1 AAATTTATA
2968384 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 11 0.46
18 11 0.46
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTATAAAATTCAA
Found at i:2972059 original size:16 final size:17
Alignment explanation
Indices: 2972040--2972083 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2972030 TCAAAATTCG
2972040 AAAATTATAAAAATT-A
1 AAAATTATAAAAATTGA
*
2972056 AAAATTAT-CAAATTGA
1 AAAATTATAAAAATTGA
2972072 AAAA-TATAAAAA
1 AAAATTATAAAAA
2972084 AAAATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATTATAAAAATTGA
Found at i:2974472 original size:14 final size:15
Alignment explanation
Indices: 2974449--2974489 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2974439 ATCTATTTGT
2974449 TAAA-TTAATATTCA
1 TAAATTTAATATTCA
*
2974463 -AAATTTAATATACA
1 TAAATTTAATATTCA
*
2974477 TAAATTAAATATT
1 TAAATTTAATATT
2974490 TATTGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 10 0.45
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTTAATATTCA
Found at i:2976033 original size:20 final size:19
Alignment explanation
Indices: 2975997--2976038 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2975987 CACATTATTT
**
2975997 TTTATAATATATTTTTAGTA
1 TTTATAATATAACTTTAG-A
2976017 TTTATAATATAACTTTAGA
1 TTTATAATATAACTTTAGA
2976036 TTT
1 TTT
2976039 TTTATCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTATAATATAACTTTAGA
Found at i:2976085 original size:29 final size:29
Alignment explanation
Indices: 2976043--2976110 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2976033 AGATTTTTTA
* * *
2976043 TCATAATCATCTCAAATATTCATACGTTG
1 TCATAATTATCTCAAACATTCATACATTG
*
2976072 TCATAATTATCTCAAACATTCATACATTT
1 TCATAATTATCTCAAACATTCATACATTG
*
2976101 TCATACTTAT
1 TCATAATTAT
2976111 AATACAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
TCATAATTATCTCAAACATTCATACATTG
Found at i:2976394 original size:30 final size:30
Alignment explanation
Indices: 2976358--2976422 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
2976348 AATAGTTTAT
*
2976358 ATTTTTATATTTTTTAAAAAATTAAATCA-A
1 ATTTTTATATTTTTTAAAAAATAAAAT-ATA
2976388 ATTTTTATATTTTTTAAAAAATAAAATATA
1 ATTTTTATATTTTTTAAAAAATAAAATATA
2976418 ATTTT
1 ATTTT
2976423 ATCATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTTATATTTTTTAAAAAATAAAATATA
Found at i:2978235 original size:36 final size:36
Alignment explanation
Indices: 2978187--2978256 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2978177 CGAACAAGTT
* *
2978187 GCTCGAGTGAAAAAGAGAATGTTATTCATCCTAGTG
1 GCTCCAGTGAAAAAGAGAATGCTATTCATCCTAGTG
*
2978223 GCTCCAGTGAAAAAGAGGATGCTATTCATCCTAG
1 GCTCCAGTGAAAAAGAGAATGCTATTCATCCTAG
2978257 GGATCTCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (36 bp):
GCTCCAGTGAAAAAGAGAATGCTATTCATCCTAGTG
Found at i:2989961 original size:49 final size:50
Alignment explanation
Indices: 2989876--2989970 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 50
2989866 TTTAATTTAA
*
2989876 TTTTTAAAATTTTAAAACTATTTTAAGAATAATTTTTAT-AATTTTATTG
1 TTTTTAAAATTTTAAAAATATTTTAAGAATAATTTTTATAAATTTTATTG
* * * *
2989925 TTTTTAAATTTTTAAAAATAGTTTTAA-TATATTTTTTTTAAATTTT
1 TTTTTAAAATTTTAAAAATA-TTTTAAGAATAATTTTTATAAATTTT
2989971 CAAATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 27 0.69
50 12 0.31
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (50 bp):
TTTTTAAAATTTTAAAAATATTTTAAGAATAATTTTTATAAATTTTATTG
Found at i:2990267 original size:11 final size:11
Alignment explanation
Indices: 2990251--2990275 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2990241 TAAACTGTCG
2990251 ATATTAAAAAA
1 ATATTAAAAAA
2990262 ATATTAAAAAA
1 ATATTAAAAAA
2990273 ATA
1 ATA
2990276 AATAAGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATTAAAAAA
Found at i:2990743 original size:18 final size:19
Alignment explanation
Indices: 2990702--2990744 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2990692 AATACAAGTT
2990702 TTAAAATTAAAAAAAATGA
1 TTAAAATTAAAAAAAATGA
* *
2990721 -AAAAATTAAATAAAA-GA
1 TTAAAATTAAAAAAAATGA
2990738 TTAAAAT
1 TTAAAAT
2990745 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
TTAAAATTAAAAAAAATGA
Found at i:3000481 original size:16 final size:17
Alignment explanation
Indices: 3000457--3000497 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3000447 GATAAATATT
*
3000457 TGATGAACA-ATAAAAA
1 TGATAAACAGATAAAAA
*
3000473 TGATAAACAGATAAACA
1 TGATAAACAGATAAAAA
3000490 -GATAAACA
1 TGATAAACA
3000498 TTTGATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (17 bp):
TGATAAACAGATAAAAA
Found at i:3007301 original size:89 final size:88
Alignment explanation
Indices: 3007133--3007316 Score: 250
Period size: 89 Copynumber: 2.1 Consensus size: 88
3007123 ACTTAGATAT
* * *
3007133 TTGAAATTTCAAAATGCATCAAAAAGATCCATAATTTTTTTAAAAAAAGCAATTAAGCCCTTACG
1 TTGAACTTTCAAAATGCATCAAAAAGATCCATAACTTTTTCAAAAAAAGCAATTAAGCCCTTACG
*
3007198 TTTATTGTGCACTCAATTGGGTAC
66 TTTATTGT-CACTCAATTAGGTAC
3007222 TTGAACTTTCAAAATGCATCAAAAAGATCC-TCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTG
1 TTGAACTTTCAAAATGCATCAAAAAGATCCAT--AACTTTTTCAAAAAAAGCAATTAAGCCCTT-
3007286 ATTC-TTT-TTGT-ACTCAATTAGGTAC
63 A--CGTTTATTGTCACTCAATTAGGTAC
3007311 TTGAAC
1 TTGAAC
3007317 CACCCTTATT
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
88 1 0.01
89 48 0.56
90 28 0.33
91 5 0.06
92 3 0.03
93 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (88 bp):
TTGAACTTTCAAAATGCATCAAAAAGATCCATAACTTTTTCAAAAAAAGCAATTAAGCCCTTACG
TTTATTGTCACTCAATTAGGTAC
Found at i:3007737 original size:87 final size:87
Alignment explanation
Indices: 3007571--3007763 Score: 192
Period size: 89 Copynumber: 2.2 Consensus size: 87
3007561 TGTTAATGTA
* * * *
3007571 TTTGACAGTTCAAGTACCCAATTGAATGCAAAAAAATCAAGGGCTTAATAGCTTTTTTTTTTAAA
1 TTTGAAAGTTCAAGTACACAATTGAATGAAAAAAAAGCAAGGGCTTAATAGCTTTTTTTTTTAAA
* *
3007636 TTTGAGGGCTTTTTTTATGCAT
66 TTTGAGAGCATTTTTTATGCAT
* *
3007658 TTTGAAAGTTCAAGTACACAATTGAGTGTAAAATAAAAGC-AGAGGCTTAAT-TCTTTTTTTTTT
1 TTTGAAAGTTCAAGTACACAATTGAATG-AAAA-AAAAGCAAG-GGCTTAATAGC-TTTTTTTTT
* *** *
3007721 TAAGTTTGAAGATTTTTTTTTATGTAT
62 TAAATTTG-AGAGCATTTTTTATGCAT
* *
3007748 TTTTAAAGTTTAAGTA
1 TTTGAAAGTTCAAGTA
3007764 TCCAAGTGAG
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
87 25 0.28
88 6 0.07
89 29 0.33
90 28 0.32
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (87 bp):
TTTGAAAGTTCAAGTACACAATTGAATGAAAAAAAAGCAAGGGCTTAATAGCTTTTTTTTTTAAA
TTTGAGAGCATTTTTTATGCAT
Found at i:3007992 original size:23 final size:23
Alignment explanation
Indices: 3007962--3008006 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3007952 CAATTACATA
3007962 ATCATCATCTCTAGCATCAGCTC
1 ATCATCATCTCTAGCATCAGCTC
*
3007985 ATCATCATCTCTAGTATCAGCT
1 ATCATCATCTCTAGCATCAGCT
3008007 TGCATGTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (23 bp):
ATCATCATCTCTAGCATCAGCTC
Found at i:3009952 original size:13 final size:13
Alignment explanation
Indices: 3009934--3009960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3009924 ACCATACTGT
3009934 CCATTCAAATCCA
1 CCATTCAAATCCA
3009947 CCATTCAAATCCA
1 CCATTCAAATCCA
3009960 C
1 C
3009961 ACTTAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (13 bp):
CCATTCAAATCCA
Found at i:3010342 original size:3 final size:3
Alignment explanation
Indices: 3010334--3010362 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3010324 TTAATACTTC
3010334 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3010363 GTAGGGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3012749 original size:20 final size:21
Alignment explanation
Indices: 3012726--3012775 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3012716 AAAAGATTGA
*
3012726 AAAACATTAAAAT-TAGATAG-
1 AAAA-ATTAAAATATAAATAGC
3012746 AAAAA-TAAAATATAAATAGC
1 AAAAATTAAAATATAAATAGC
3012766 AAAAATTAAA
1 AAAAATTAAA
3012776 TTGAAACGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.23
19 7 0.27
20 9 0.35
21 4 0.15
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (21 bp):
AAAAATTAAAATATAAATAGC
Found at i:3015559 original size:200 final size:202
Alignment explanation
Indices: 3015204--3015590 Score: 538
Period size: 200 Copynumber: 1.9 Consensus size: 202
3015194 AAATGCACTC
* * *
3015204 TCATTTAACTGATTTGTAGCTTGAAATTGACATTTTTTCTTTTTCTCTTAGTCGATTTTAATTTT
1 TCATATAACTGATTTGTAGCTTGAAATTGACATTTTTTCCTTTTCTCTTAGTCAATTTTAATTTT
* *
3015269 CTCATTGTAACTTTAGGAGATAAACCTTGGTAATGAATTTGGTATTATGTGTTTGTGTGGTTAAC
66 CTCATTGTAACTTTA-GAGAGAAACCTTGGAAATGAATTTGGTATTATGTGTTTGTGTGGTTAAC
* * *
3015334 AGGTATTGAAATGAATGGGATTCAGCA-AAGGAAAGGTCAGAATTTTGAGAAA-TTTCCTGGAAT
130 AGGTATTGAAATGAATAGAATTCAGCACAA-GAAAGGTCAGAATATTGA-AAAGTTTCCTGGAAT
3015397 GACTGTGCTG
193 GACTGTGCTG
* *
3015407 TCATATAAGCTGATTTGTAGCTTGAATTTGACA-TTTTTCCTTTTCTCTTAGTTAATTTTAATTT
1 TCATATAA-CTGATTTGTAGCTTGAAATTGACATTTTTTCCTTTTCTCTTAGTCAATTTTAATTT
** *
3015471 TCTTTTTGT-A-TGTT-GAGAGAAACCTTGGAAATGAATTTGGTGCTT-T-TGATTTGTGTGGTT
65 TCTCATTGTAACT-TTAGAGAGAAACCTTGGAAATGAATTTGGT-ATTATGTG-TTTGTGTGGTT
3015531 AACAGGTATTGAAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCC
127 AACAGGTATTGAAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCC
3015591 AGGATGCCTG
Statistics
Matches: 165, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
199 5 0.03
200 87 0.53
201 5 0.03
202 3 0.02
203 42 0.25
204 23 0.14
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (202 bp):
TCATATAACTGATTTGTAGCTTGAAATTGACATTTTTTCCTTTTCTCTTAGTCAATTTTAATTTT
CTCATTGTAACTTTAGAGAGAAACCTTGGAAATGAATTTGGTATTATGTGTTTGTGTGGTTAACA
GGTATTGAAATGAATAGAATTCAGCACAAGAAAGGTCAGAATATTGAAAAGTTTCCTGGAATGAC
TGTGCTG
Found at i:3015822 original size:5 final size:5
Alignment explanation
Indices: 3015812--3015836 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3015802 TCCATTTTTT
3015812 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
3015837 AGTTCAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:3030314 original size:21 final size:21
Alignment explanation
Indices: 3030290--3030334 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3030280 AAATTACAAA
**
3030290 AAAAAAATTAAAATAATTTTC
1 AAAAAAAGCAAAATAATTTTC
*
3030311 -AAAAAAGCAAAATAATTTTT
1 AAAAAAAGCAAAATAATTTTC
3030331 AAAA
1 AAAA
3030335 TTCCAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAAGCAAAATAATTTTC
Found at i:3030341 original size:20 final size:20
Alignment explanation
Indices: 3030299--3030359 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
3030289 AAAAAAAATT
***
3030299 AAAATAATTTTCAAAAAAGC
1 AAAATAATTTTCAAAATTCC
*
3030319 AAAATAATTTTTAAAATTCC
1 AAAATAATTTTCAAAATTCC
*
3030339 -AAAT-ATTTACAAAATTCC
1 AAAATAATTTTCAAAATTCC
3030357 AAA
1 AAA
3030360 TTTTCTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 12 0.35
19 6 0.18
20 16 0.47
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATAATTTTCAAAATTCC
Found at i:3030346 original size:18 final size:18
Alignment explanation
Indices: 3030320--3030369 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3030310 CAAAAAAGCA
*
3030320 AAATAATTTTTAAAATTCC
1 AAAT-ATTTATAAAATTCC
*
3030339 AAATATTTACAAAATTCC
1 AAATATTTATAAAATTCC
*
3030357 AAAT-TTTCTAAAA
1 AAATATTTATAAAA
3030370 AAATATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTTATAAAATTCC
Found at i:3030626 original size:15 final size:15
Alignment explanation
Indices: 3030606--3030644 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3030596 ACAATTTCAG
3030606 TCCATTCGACTTGAC
1 TCCATTCGACTTGAC
3030621 TCCATTCGACTTGAC
1 TCCATTCGACTTGAC
3030636 TCCATTCGA
1 TCCATTCGA
3030645 AAAAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (15 bp):
TCCATTCGACTTGAC
Found at i:3044485 original size:193 final size:195
Alignment explanation
Indices: 3044195--3044567 Score: 522
Period size: 201 Copynumber: 1.9 Consensus size: 195
3044185 CTGTACTATA
* * * *
3044195 AACTGTTCCCTAACAATGCTGCTCACACGAGCTGTTGAGAGTATGCAATAAGCATAGTCCTAGCC
1 AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCTAGCC
*
3044260 ATCGTAGGGCCTGTAATCCATTTAGAATCC-A-TA-TCTC-TTTCCCGAATCACGATGTTGCTCG
66 ATCGTAGGGCCTGTAATCCATTTAGAATCCAATTATTCTCATTTCCCGAATCACGATGTTGATCG
*
3044321 CACGAGCTATCGAGAACTCGCAACATATGCGGTACCTCAGCCATCGATACGGTATCTATGCATAT
131 CACGAGCTATCGAGAACTCGCAACATATGCGGTACCTCAACCATCGATACGGTATCTATGCATAT
* * * *
3044386 AACTGTTCCCTAATAATACTGCTCACACGAGCTGTCGAGAATGTGCACTTATGCATAAAT-CTCA
1 AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCA-ATAAGCAT-AATCCT-A
* *
3044450 GCCATCGTAGGGCCTGTAATCCATTTAGGATCCATATTTATTTTCTCATTTCCCGACTCACGATG
63 GCCATCGTAGGGCCTGTAATCCATTTAGAATCCA-A-TTA--TTCTCATTTCCCGAATCACGATG
* *
3044515 TTGATCGCACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCG
124 TTGATCGCACGAGCTATCGAGAACTCGCAACATATGCGGTACCTCAACCATCG
3044568 CGTCAGTTTC
Statistics
Matches: 157, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
191 42 0.27
192 8 0.05
193 35 0.22
195 1 0.01
197 2 0.01
200 4 0.03
201 65 0.41
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (195 bp):
AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCTAGCC
ATCGTAGGGCCTGTAATCCATTTAGAATCCAATTATTCTCATTTCCCGAATCACGATGTTGATCG
CACGAGCTATCGAGAACTCGCAACATATGCGGTACCTCAACCATCGATACGGTATCTATGCATAT
Found at i:3050375 original size:40 final size:39
Alignment explanation
Indices: 3050289--3050380 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
3050279 TTAAAATTTA
* * *
3050289 TATTGAATAAAATAAAATATTTATTATATTTATTTGTGTT
1 TATTTAATATAATAAAATATTTATTATATTTA-TTGTGTG
*
3050329 TTTTTAATATAATAAAATATTTATTATATTTA-TGATAGTG
1 TATTTAATATAATAAAATATTTATTATATTTATTG-T-GTG
3050369 TATTTAATATAA
1 TATTTAATATAA
3050381 AAACTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 42 0.93
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (39 bp):
TATTTAATATAATAAAATATTTATTATATTTATTGTGTG
Found at i:3054972 original size:2 final size:2
Alignment explanation
Indices: 3054967--3055002 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3054957 TAGTACCTTC
3054967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3055003 TAGGATCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3057821 original size:67 final size:67
Alignment explanation
Indices: 3057738--3057871 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
3057728 TTTTCCATTG
* *
3057738 ATGAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTTATAAGCTTAGTTGTTAGATTTGATTATT
1 ATGAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTTATAAGCTTAGTTATTAAATTTGATTATT
3057803 TT
66 TT
3057805 ATGAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTTATAAGCTTAGTTATTAAATTTGATTATT
1 ATGAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTTATAAGCTTAGTTATTAAATTTGATTATT
3057870 TT
66 TT
3057872 GTAAAGTAGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.48
Consensus pattern (67 bp):
ATGAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTTATAAGCTTAGTTATTAAATTTGATTATT
TT
Found at i:3057849 original size:33 final size:33
Alignment explanation
Indices: 3057742--3057849 Score: 107
Period size: 33 Copynumber: 3.2 Consensus size: 33
3057732 CCATTGATGA
3057742 ATAAGCTTGTTCTTGAAAGTTTATGTAAGATTT
1 ATAAGCTTGTTCTTGAAAGTTTATGTAAGATTT
* * **
3057775 ATAAGCTTAGTTGTT-AGA-TTTGAT-T-ATTTTAT
1 ATAAGCTT-GTTCTTGAAAGTTT-ATGTAAGATT-T
3057807 GAATAAGCTTGTTCTTGAAAGTTTATGTAAGATTT
1 --ATAAGCTTGTTCTTGAAAGTTTATGTAAGATTT
3057842 ATAAGCTT
1 ATAAGCTT
3057850 AGTTATTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
31 3 0.05
32 5 0.09
33 25 0.43
34 17 0.29
35 5 0.09
36 3 0.05
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.46
Consensus pattern (33 bp):
ATAAGCTTGTTCTTGAAAGTTTATGTAAGATTT
Found at i:3058677 original size:28 final size:28
Alignment explanation
Indices: 3058633--3058687 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3058623 AAATGAGCAT
*
3058633 CATGACCTTTAGATCAACAGGGAGTAAG
1 CATGACCTTTAGATCAACAAGGAGTAAG
* *
3058661 CATGACCTTTGGGTCAACAAGGAGTAA
1 CATGACCTTTAGATCAACAAGGAGTAA
3058688 ATCGAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (28 bp):
CATGACCTTTAGATCAACAAGGAGTAAG
Found at i:3059379 original size:23 final size:23
Alignment explanation
Indices: 3059353--3059399 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3059343 GAATACTTGT
3059353 ATTGGTAAAAGTTGTAAGGAAAA
1 ATTGGTAAAAGTTGTAAGGAAAA
3059376 ATTGGTAAAAGTTGTAAGGAAAA
1 ATTGGTAAAAGTTGTAAGGAAAA
3059399 A
1 A
3059400 CTTCTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (23 bp):
ATTGGTAAAAGTTGTAAGGAAAA
Found at i:3065775 original size:3 final size:3
Alignment explanation
Indices: 3065767--3065815 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
3065757 GTATCTAACA
* *
3065767 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3065815 A
1 A
3065816 ACTAGGGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3074100 original size:19 final size:19
Alignment explanation
Indices: 3074078--3074115 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3074068 CATCGTCACC
*
3074078 CACCGTAATTAAATTTGTT
1 CACCGTAATCAAATTTGTT
3074097 CACCGTAATCAAATTTGTT
1 CACCGTAATCAAATTTGTT
3074116 ATTAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
CACCGTAATCAAATTTGTT
Found at i:3080380 original size:20 final size:20
Alignment explanation
Indices: 3080357--3080394 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3080347 CTATCGGTAA
3080357 AACTTCACTTCTACCGATGC
1 AACTTCACTTCTACCGATGC
*
3080377 AACTTCAGTTCTACCGAT
1 AACTTCACTTCTACCGAT
3080395 ACCTTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (20 bp):
AACTTCACTTCTACCGATGC
Found at i:3080648 original size:20 final size:20
Alignment explanation
Indices: 3080600--3080637 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3080590 TGGTAGAACT
3080600 TCACTTCTATCGATACAACG
1 TCACTTCTATCGATACAACG
*
3080620 TCAATTCTATCGATACAA
1 TCACTTCTATCGATACAA
3080638 GTATGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (20 bp):
TCACTTCTATCGATACAACG
Found at i:3081735 original size:22 final size:22
Alignment explanation
Indices: 3081710--3081753 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3081700 CCCAAACCAT
*
3081710 TTTTACTTTGAAATTTAATTTA
1 TTTTAATTTGAAATTTAATTTA
* *
3081732 TTTTAATTTTAAATTTATTTTA
1 TTTTAATTTGAAATTTAATTTA
3081754 AATTCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAATTTGAAATTTAATTTA
Found at i:3081742 original size:6 final size:6
Alignment explanation
Indices: 3081723--3081786 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
3081713 TACTTTGAAA
* * *
3081723 TTTAA- TTT-AT TTTAAT TTTAAA TTT-AT TTTAAA TTCAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
* *
3081768 TTGAA- TTTAAT TTAAAT TT
1 TTTAAT TTTAAT TTTAAT TT
3081787 AATATTATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
4 1 0.02
5 14 0.30
6 31 0.67
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (6 bp):
TTTAAT
Found at i:3081751 original size:4 final size:5
Alignment explanation
Indices: 3081721--3081789 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
3081711 TTTACTTTGA
* * *
3081721 AATTT AATTT ATTTT AATTTT AAATTT ATTTT AAATTC AATTTT AATTT
1 AATTT AATTT AATTT AA-TTT -AATTT AATTT -AATTT AA-TTT AATTT
3081770 GAATTT AATTT AAATTT AAT
1 -AATTT AATTT -AATTT AAT
3081790 ATTATTATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 27 0.52
6 23 0.44
7 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:3081763 original size:12 final size:11
Alignment explanation
Indices: 3081734--3081804 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
3081724 TTAATTTATT
3081734 TTAATTTTAAA
1 TTAATTTTAAA
*
3081745 TTTATTTTAAA
1 TTAATTTTAAA
*
3081756 TTCAATTTTAAT
1 TT-AATTTTAAA
*
3081768 TTGAA-TTTAAT
1 TT-AATTTTAAA
*
3081779 TTAAATTTAATA
1 TTAATTTTAA-A
*
3081791 TT-ATTATAAA
1 TTAATTTTAAA
3081801 TTAA
1 TTAA
3081805 AAAAAGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 5 0.10
11 31 0.63
12 13 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:3081765 original size:17 final size:17
Alignment explanation
Indices: 3081710--3081780 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
3081700 CCCAAACCAT
*
3081710 TTTTACTTTGAAATTTAA
1 TTTTA-TTTTAAATTTAA
*
3081728 -TTTATTTTAATTTTAA
1 TTTTATTTTAAATTTAA
* *
3081744 ATTTATTTTAAATTCAA
1 TTTTATTTTAAATTTAA
* *
3081761 TTTTAATTTGAATTTAA
1 TTTTATTTTAAATTTAA
3081778 TTT
1 TTT
3081781 AAATTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 10 0.23
17 34 0.77
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTATTTTAAATTTAA
Found at i:3081789 original size:11 final size:11
Alignment explanation
Indices: 3081720--3081788 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
3081710 TTTTACTTTG
3081720 AAATTTAATTT
1 AAATTTAATTT
*
3081731 -ATTTTAATTTT
1 AAATTTAA-TTT
*
3081742 AAATTTATTTT
1 AAATTTAATTT
*
3081753 AAATTCAATTT
1 AAATTTAATTT
*
3081764 TAATTTGAATTT
1 AAATTT-AATTT
3081776 -AATTTAAATTT
1 AAATTT-AATTT
3081787 AA
1 AA
3081789 TATTATTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
10 6 0.13
11 29 0.63
12 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3081892 original size:36 final size:37
Alignment explanation
Indices: 3081826--3081895 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
3081816 CCAAAATGTC
*
3081826 CAAAGTCCAAATACATGGCCCAATTGGGCCCAAAACT
1 CAAAGTCCAAATACAAGGCCCAATTGGGCCCAAAACT
3081863 CAAA-TCCAACATACAAGGCCCAATT-GGCCCAAA
1 CAAAGTCCAA-ATACAAGGCCCAATTGGGCCCAAA
3081896 CACCCCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (37 bp):
CAAAGTCCAAATACAAGGCCCAATTGGGCCCAAAACT
Done.