Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 12 of 311
Found at i:3422460 original size:21 final size:19
Alignment explanation
Indices: 3422423--3422461 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3422413 TTAGACTTCG
*
3422423 TTTTTTTTTTGGTTTATTA
1 TTTTTTTTTTGGCTTATTA
3422442 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGG-CTTATT
3422462 TCTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.10, C:0.03, G:0.13, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTGGCTTATTA
Found at i:3422793 original size:22 final size:21
Alignment explanation
Indices: 3422767--3422824 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 21
3422757 TATATCTCAC
3422767 ATTATAAAATAAGTTAATTTTA
1 ATTATAAAATAA-TTAATTTTA
*
3422789 ATTAT--AAT-ATTTATTTTA
1 ATTATAAAATAATTAATTTTA
3422807 ATTATATAAAT-ATTAATT
1 ATTATA-AAATAATTAATT
3422825 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
20 3 0.10
21 9 0.29
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATAAAATAATTAATTTTA
Found at i:3426107 original size:16 final size:16
Alignment explanation
Indices: 3426083--3426128 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3426073 TATTATAGTG
* *
3426083 AAATTAGTTCATGACT
1 AAATGAGTTCATAACT
*
3426099 AAATGAGTTTATAACT
1 AAATGAGTTCATAACT
*
3426115 AAATGAGTTTATAA
1 AAATGAGTTCATAA
3426129 TTAATATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (16 bp):
AAATGAGTTCATAACT
Found at i:3433108 original size:3 final size:3
Alignment explanation
Indices: 3433102--3433143 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3433092 TTTATTATTA
* *
3433102 TTG TTG TTG TTG CTG TTG TTG TTTG TTG TTG TTA TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG TT
3433144 AAAACTTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.02, C:0.02, G:0.29, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:3433127 original size:22 final size:22
Alignment explanation
Indices: 3433102--3433143 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3433092 TTTATTATTA
*
3433102 TTGTTGTTGTTGCTGTTGTTGT
1 TTGTTGTTGTTACTGTTGTTGT
*
3433124 TTGTTGTTGTTATTGTTGTT
1 TTGTTGTTGTTACTGTTGTT
3433144 AAAACTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.02, G:0.29, T:0.67
Consensus pattern (22 bp):
TTGTTGTTGTTACTGTTGTTGT
Found at i:3433129 original size:19 final size:19
Alignment explanation
Indices: 3433105--3433143 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3433095 ATTATTATTG
*
3433105 TTGTTGTTGCTGTTGTTGT
1 TTGTTGTTGCTATTGTTGT
*
3433124 TTGTTGTTGTTATTGTTGT
1 TTGTTGTTGCTATTGTTGT
3433143 T
1 T
3433144 AAAACTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.28, T:0.67
Consensus pattern (19 bp):
TTGTTGTTGCTATTGTTGT
Found at i:3435874 original size:17 final size:16
Alignment explanation
Indices: 3435831--3435874 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
3435821 CAAATTTTAT
3435831 TTACTTT-CCTTAGAA
1 TTACTTTCCCTTAGAA
3435846 TCTAACTTTCCCTTAAGAA
1 T-T-ACTTTCCCTT-AGAA
3435865 TTACTTTCCC
1 TTACTTTCCC
3435875 ATAAACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 13 0.52
18 5 0.20
19 5 0.20
ACGTcount: A:0.25, C:0.27, G:0.05, T:0.43
Consensus pattern (16 bp):
TTACTTTCCCTTAGAA
Found at i:3440236 original size:38 final size:38
Alignment explanation
Indices: 3440162--3440236 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
3440152 GATCTTCTGA
* * * *
3440162 GCTTTTTGAACTTGTGAATATTTTGAATGGCGAGAAAG
1 GCTTCTTGAACTTGTGAATATATTGAATAGCAAGAAAG
*
3440200 GCTTCTTGAACTTGTGAATATATTGAATAGTAAGAAA
1 GCTTCTTGAACTTGTGAATATATTGAATAGCAAGAAA
3440237 AGATTGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (38 bp):
GCTTCTTGAACTTGTGAATATATTGAATAGCAAGAAAG
Found at i:3441687 original size:19 final size:19
Alignment explanation
Indices: 3441659--3441701 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3441649 TTCAGTAGAT
*
3441659 TTATATATAGGTCAATATA
1 TTATAAATAGGTCAATATA
*
3441678 TTATAAATAGGTCAGTATA
1 TTATAAATAGGTCAATATA
3441697 TTATA
1 TTATA
3441702 TAAGCCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (19 bp):
TTATAAATAGGTCAATATA
Found at i:3441703 original size:21 final size:20
Alignment explanation
Indices: 3441650--3441704 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3441640 CAAATTAGAT
* *
3441650 TCAGTAGATTTATATATAGG
1 TCAGTATATTTATAAATAGG
*
3441670 TCAATATA-TTATAAATAGG
1 TCAGTATATTTATAAATAGG
3441689 TCAGTATATTATATAA
1 TCAGTATATT-TATAA
3441705 GCCAGTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 7 0.24
21 5 0.17
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (20 bp):
TCAGTATATTTATAAATAGG
Found at i:3443469 original size:45 final size:45
Alignment explanation
Indices: 3443419--3443507 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
3443409 AACTCGTAAA
* *
3443419 AGAAAATTCATAGATGTAG-AGAATTCATACATGTGAATTCATAGT
1 AGAAAATTCATAGATATAGCAG-ACTCATACATGTGAATTCATAGT
* *
3443464 AGAAAATTCATAGATATGGCAGACTCATACATGTGGATTCATAG
1 AGAAAATTCATAGATATAGCAGACTCATACATGTGAATTCATAG
3443508 ATATAGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (45 bp):
AGAAAATTCATAGATATAGCAGACTCATACATGTGAATTCATAGT
Found at i:3443504 original size:31 final size:31
Alignment explanation
Indices: 3443468--3443622 Score: 177
Period size: 31 Copynumber: 5.0 Consensus size: 31
3443458 CATAGTAGAA
* *
3443468 AATTCATAGATATGGCAGACTCATACATGTG
1 AATTCATAGATATGGCAAACTCATACATGCG
* * ** * * *
3443499 GATTCATAGATATAGTGAACTTATACATACA
1 AATTCATAGATATGGCAAACTCATACATGCG
*
3443530 AATTCATAGATATGGCAAACTCATACAAGCG
1 AATTCATAGATATGGCAAACTCATACATGCG
* * *
3443561 AATTCATAGATATAGTAAACTCATACATGCT
1 AATTCATAGATATGGCAAACTCATACATGCG
3443592 AATTCATAGATATGGCGAAA-TCATACATGCG
1 AATTCATAGATATGGC-AAACTCATACATGCG
3443623 GACTATGTCA
Statistics
Matches: 99, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
31 96 0.97
32 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (31 bp):
AATTCATAGATATGGCAAACTCATACATGCG
Found at i:3443533 original size:62 final size:62
Alignment explanation
Indices: 3443467--3443622 Score: 215
Period size: 62 Copynumber: 2.5 Consensus size: 62
3443457 TCATAGTAGA
* * * *
3443467 AAATTCATAGATATGGCAGACTCATACATGTGGATTCATAGATATAGTGAACTTATACATAC
1 AAATTCATAGATATGGCAGACTCATACATGCGAATTCATAGATATAGTAAACTCATACATAC
* * *
3443529 AAATTCATAGATATGGCAAACTCATACAAGCGAATTCATAGATATAGTAAACTCATACATGC
1 AAATTCATAGATATGGCAGACTCATACATGCGAATTCATAGATATAGTAAACTCATACATAC
* *
3443591 TAATTCATAGATATGGC-GAAATCATACATGCG
1 AAATTCATAGATATGGCAG-ACTCATACATGCG
3443623 GACTATGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (62 bp):
AAATTCATAGATATGGCAGACTCATACATGCGAATTCATAGATATAGTAAACTCATACATAC
Found at i:3459340 original size:25 final size:25
Alignment explanation
Indices: 3459312--3459367 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
3459302 TTCTAAAAAA
3459312 ATTAAAGAAATATATAA-AAATTAAT
1 ATTAAAGAAATATA-AATAAATTAAT
**
3459337 ATTAAAGAAATATAAATATGTTAAT
1 ATTAAAGAAATATAAATAAATTAAT
3459362 ATTAAA
1 ATTAAA
3459368 TAAAAATCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (25 bp):
ATTAAAGAAATATAAATAAATTAAT
Found at i:3462526 original size:20 final size:20
Alignment explanation
Indices: 3462501--3462540 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3462491 AATATTTTCC
*
3462501 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3462521 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3462541 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3462546 original size:34 final size:34
Alignment explanation
Indices: 3462489--3462554 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
3462479 CAAACACCAG
*
3462489 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
3462524 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
3462555 ATATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:3464385 original size:14 final size:14
Alignment explanation
Indices: 3464366--3464408 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
3464356 AAAATACAGT
*
3464366 AAAATAATAAAATA
1 AAAATAAAAAAATA
3464380 AAAATAAAAAAATA
1 AAAATAAAAAAATA
*
3464394 ATAAACAAAAAAATA
1 A-AAATAAAAAAATA
3464409 GAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:3464394 original size:22 final size:23
Alignment explanation
Indices: 3464366--3464408 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3464356 AAAATACAGT
*
3464366 AAAATAATAAA-ATAAAAATAAA
1 AAAATAATAAACAAAAAAATAAA
3464388 AAAATAATAAACAAAAAAATA
1 AAAATAATAAACAAAAAAATA
3464409 GAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAATAATAAACAAAAAAATAAA
Found at i:3464405 original size:15 final size:14
Alignment explanation
Indices: 3464374--3464408 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3464364 GTAAAATAAT
*
3464374 AAAATAAAAATAAA
1 AAAATAAAAACAAA
3464388 AAAATAATAAACAAA
1 AAAATAA-AAACAAA
3464403 AAAATA
1 AAAATA
3464409 GAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAAACAAA
Found at i:3465034 original size:18 final size:19
Alignment explanation
Indices: 3465013--3465059 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
3465003 ATTAATTTTA
3465013 TTTAAC-ATTAATATTATG
1 TTTAACTATTAATATTATG
* *
3465031 TTT-ACTATTATTATTATT
1 TTTAACTATTAATATTATG
*
3465049 TTTAAATATTA
1 TTTAACTATTA
3465060 GTGTACTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.67
19 6 0.25
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAACTATTAATATTATG
Found at i:3469614 original size:14 final size:14
Alignment explanation
Indices: 3469591--3469625 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3469581 ATTAATAATT
3469591 TTAAAATTAAAAAA
1 TTAAAATTAAAAAA
*
3469605 TTAAATTTAAAAAA
1 TTAAAATTAAAAAA
3469619 TATAAAA
1 T-TAAAA
3469626 CAAATAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAATTAAAAAA
Found at i:3469662 original size:22 final size:19
Alignment explanation
Indices: 3469639--3469677 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
3469629 ATAATCTATA
3469639 AAAATATTAATAATATTATTT
1 AAAATA-TAAT-ATATTATTT
*
3469660 AAATTATAATATATTATT
1 AAAATATAATATATTATT
3469678 ATTATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATATAATATATTATTT
Found at i:3481759 original size:18 final size:18
Alignment explanation
Indices: 3481715--3481759 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3481705 AATAAAAAAA
*
3481715 TATATTTTTTTATTATTT
1 TATATTTTTTTAATATTT
*
3481733 TATAATTTTTTACATATTT
1 TATATTTTTTTA-ATATTT
3481752 T-TATTTTT
1 TATATTTTT
3481760 ATTTTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TATATTTTTTTAATATTT
Found at i:3481773 original size:31 final size:30
Alignment explanation
Indices: 3481716--3481774 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3481706 ATAAAAAAAT
3481716 ATATTTTTTTATTATTTTATAATTTTTTAC
1 ATATTTTTTTATTATTTTATAATTTTTTAC
* *
3481746 ATATTTTTATTTTTATTTTCT-ATTTTTTA
1 ATATTTTT-TTATTATTTTATAATTTTTTA
3481775 AAAAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (30 bp):
ATATTTTTTTATTATTTTATAATTTTTTAC
Found at i:3484047 original size:4 final size:4
Alignment explanation
Indices: 3484038--3484082 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
3484028 ACACTTCTCG
3484038 AAAT AAAT AAAT AAAT AAA- ACAAT CGAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT A-AAT --AAAT AAAT AAAT AAAT AAA
3484083 ACAAAGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.03
4 32 0.86
6 3 0.08
7 1 0.03
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:3484066 original size:26 final size:26
Alignment explanation
Indices: 3484035--3484086 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3484025 AAGACACTTC
3484035 TCGAAATAAATAAATAAATAAAACAA
1 TCGAAATAAATAAATAAATAAAACAA
3484061 TCGAAATAAATAAATAAATAAAACAA
1 TCGAAATAAATAAATAAATAAAACAA
3484087 AGTGAGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (26 bp):
TCGAAATAAATAAATAAATAAAACAA
Found at i:3484710 original size:11 final size:11
Alignment explanation
Indices: 3484696--3484736 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3484686 TGTTTTCTCC
3484696 CTATTTTGCTA
1 CTATTTTGCTA
*
3484707 CTATTTTACTA
1 CTATTTTGCTA
* *
3484718 TTATGTTGCTA
1 CTATTTTGCTA
3484729 CTATTTTG
1 CTATTTTG
3484737 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:3484782 original size:12 final size:11
Alignment explanation
Indices: 3484765--3484795 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
3484755 TGTATAAAAC
3484765 TTATTTTATTA
1 TTATTTTATTA
3484776 TTTATTTTATTA
1 -TTATTTTATTA
3484788 TTATTTTA
1 TTATTTTA
3484796 AAGACATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:3486214 original size:23 final size:23
Alignment explanation
Indices: 3486184--3486275 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
3486174 TGCCTGGGTG
*
3486184 GAATTTTGATTGGCCTTTGTGGC
1 GAATTTTGATTAGCCTTTGTGGC
*
3486207 GAATTTTGGTTAGCCTTTGTGGC
1 GAATTTTGATTAGCCTTTGTGGC
* * *
3486230 GCATTTTG-TTTGACATTTGTGGC
1 GAATTTTGATTAG-CCTTTGTGGC
* *
3486253 AAATTCTGATTAGCCTTTGTGGC
1 GAATTTTGATTAGCCTTTGTGGC
3486276 ATATTCTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 3 0.05
23 51 0.89
24 3 0.05
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.43
Consensus pattern (23 bp):
GAATTTTGATTAGCCTTTGTGGC
Found at i:3486281 original size:23 final size:23
Alignment explanation
Indices: 3486190--3486307 Score: 80
Period size: 23 Copynumber: 5.0 Consensus size: 23
3486180 GGTGGAATTT
* *
3486190 TGATTGGCCTTTGTGGCGA-ATTT
1 TGATTAGCCTTTGTGGC-ATATTC
* ** *
3486213 TGGTTAGCCTTTGTGGCGCATTT
1 TGATTAGCCTTTGTGGCATATTC
* * *
3486236 TG-TTTGACATTTGTGGCAAATTC
1 TGATTAG-CCTTTGTGGCATATTC
3486259 TGATTAGCCTTTGTGGCATATTC
1 TGATTAGCCTTTGTGGCATATTC
*
3486282 TTTATGCTA-CCTTTGTGGCATATTC
1 -TGAT--TAGCCTTTGTGGCATATTC
3486307 T
1 T
3486308 ATATGTTACC
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
22 3 0.04
23 49 0.64
24 7 0.09
25 16 0.21
26 2 0.03
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (23 bp):
TGATTAGCCTTTGTGGCATATTC
Found at i:3486299 original size:25 final size:25
Alignment explanation
Indices: 3486266--3486334 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
3486256 TTCTGATTAG
*
3486266 CCTTTGTGGCATATTCTTTATGCTA
1 CCTTTGTGGCATATTCTATATGCTA
*
3486291 CCTTTGTGGCATATTCTATATGTTA
1 CCTTTGTGGCATATTCTATATGCTA
*
3486316 CCTTTGTGGTATATTCTAT
1 CCTTTGTGGCATATTCTAT
3486335 TTGGCCCTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.49
Consensus pattern (25 bp):
CCTTTGTGGCATATTCTATATGCTA
Found at i:3486399 original size:23 final size:23
Alignment explanation
Indices: 3486366--3486422 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
3486356 GCTAAGTCTA
* *
3486366 TGTGGTAAATTATGTATCGCAAT
1 TGTGGTGAATTATGTATCACAAT
*
3486389 TGTGGTGAATTATGTATCATAAT
1 TGTGGTGAATTATGTATCACAAT
3486412 TGTGGTGAATT
1 TGTGGTGAATT
3486423 CTGGGTACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (23 bp):
TGTGGTGAATTATGTATCACAAT
Found at i:3491974 original size:23 final size:23
Alignment explanation
Indices: 3491940--3492050 Score: 91
Period size: 23 Copynumber: 4.7 Consensus size: 23
3491930 TGTGGCATTT
*
3491940 TGATTGGCCTTTGTGGCGAATTC
1 TGATTAGCCTTTGTGGCGAATTC
* * *
3491963 TGGTTAGCCTTTGTTGCGCATTC
1 TGATTAGCCTTTGTGGCGAATTC
* * *
3491986 T-ATTTGACATTTGTGACGAATTC
1 TGATTAG-CCTTTGTGGCGAATTC
* *
3492009 TGATTAGCCTTTATGGCGTATTC
1 TGATTAGCCTTTGTGGCGAATTC
3492032 TGTATGCTA-CCTTTGTGGC
1 TG-AT--TAGCCTTTGTGGC
3492051 ATATTCTATA
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
22 3 0.04
23 47 0.70
24 6 0.09
25 9 0.13
26 2 0.03
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.42
Consensus pattern (23 bp):
TGATTAGCCTTTGTGGCGAATTC
Found at i:3492050 original size:25 final size:25
Alignment explanation
Indices: 3492016--3492080 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
3492006 TTCTGATTAG
* * *
3492016 CCTTTATGGCGTATTCTGTATGCTA
1 CCTTTGTGGCATATTCTATATGCTA
*
3492041 CCTTTGTGGCATATTCTATATGTTA
1 CCTTTGTGGCATATTCTATATGCTA
3492066 CCTTTGTGGCATATT
1 CCTTTGTGGCATATT
3492081 TTGTTTGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (25 bp):
CCTTTGTGGCATATTCTATATGCTA
Found at i:3496879 original size:37 final size:38
Alignment explanation
Indices: 3496825--3496899 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
3496815 CTGCATCAGG
* *
3496825 AGAAAATTGAGGAAAATTATACAAT-GAAGCACAAAAT
1 AGAAAATAGAGGAAAATTAGACAATGGAAGCACAAAAT
3496862 AGAAAATAGAAGG-AAATTAGACAATGGAAGCACAAAAT
1 AGAAAATAG-AGGAAAATTAGACAATGGAAGCACAAAAT
3496900 CAAGCAGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.57, C:0.08, G:0.19, T:0.16
Consensus pattern (38 bp):
AGAAAATAGAGGAAAATTAGACAATGGAAGCACAAAAT
Found at i:3500039 original size:17 final size:15
Alignment explanation
Indices: 3500001--3500047 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
3499991 AAAAGTACAT
*
3500001 TAAAAATTCAAAAAA
1 TAAAAATTCTAAAAA
*
3500016 TAAAAATTTTAAAAA
1 TAAAAATTCTAAAAA
3500031 TAGATAAATTCTAAAAA
1 TA-A-AAATTCTAAAAA
3500048 AAATTAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 15 0.56
16 1 0.04
17 11 0.41
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (15 bp):
TAAAAATTCTAAAAA
Found at i:3500221 original size:29 final size:28
Alignment explanation
Indices: 3500182--3500246 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
3500172 CTAAAATATT
* * *
3500182 ATTTAAAAAAATCTAAAAATCTTATAAAA
1 ATTTAAAAAAATATAAAAA-ATTACAAAA
*
3500211 TTTTAAAAAAATATAAAAAATTACAAAA
1 ATTTAAAAAAATATAAAAAATTACAAAA
3500239 ATTTAAAA
1 ATTTAAAA
3500247 TTCAACTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
ATTTAAAAAAATATAAAAAATTACAAAA
Found at i:3500225 original size:18 final size:18
Alignment explanation
Indices: 3500204--3500248 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3500194 CTAAAAATCT
3500204 TATAAAATTTTAAAAAAA
1 TATAAAATTTTAAAAAAA
** *
3500222 TATAAAAAATTACAAAAA
1 TATAAAATTTTAAAAAAA
*
3500240 TTTAAAATT
1 TATAAAATT
3500249 CAACTATCCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAATTTTAAAAAAA
Found at i:3501504 original size:39 final size:39
Alignment explanation
Indices: 3501461--3501546 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
3501451 TGAAGTTGGT
* * *
3501461 GGTGGTTGTGATTGAACTGGTGGATGTGGAGAA-TAGACG
1 GGTGGTGGTGATTGAACTGGTGGAGGTGG-GAAGGAGACG
3501500 GGTGGTGGTGATTGAACTGGTGGAGGTGGGAAGGAGACG
1 GGTGGTGGTGATTGAACTGGTGGAGGTGGGAAGGAGACG
3501539 GGTGGTGG
1 GGTGGTGG
3501547 AGGGGAGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.07
39 40 0.93
ACGTcount: A:0.20, C:0.05, G:0.51, T:0.24
Consensus pattern (39 bp):
GGTGGTGGTGATTGAACTGGTGGAGGTGGGAAGGAGACG
Found at i:3501576 original size:63 final size:62
Alignment explanation
Indices: 3501500--3501786 Score: 270
Period size: 63 Copynumber: 4.5 Consensus size: 62
3501490 AGAATAGACG
*
3501500 GGTGGTGGTGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGAGAGAACTGGT
1 GGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGA-ACGGGTGGTGGAGGGGAGAGAACTGGT
*
3501563 GGTGGTGGAGATTGAACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGAGAGAACTGGT
1 GGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGA-ACGGGTGGTGGAGGGGAGAGAACTGGT
* * * * * * * * * **
3501626 GGAGGTGGAGAGT-AGACGGGTGGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGT
1 GGTGGTGGAGATTGA-ACTGGTGGAGGTGGGAAG-GAACGGGTGGTGGAGGGGAGAGAACTGGT
* ** * * ** * *
3501689 GGAGGTGGAAGGGAGCGAACCGGTGGTGGTGGTGATTGAACTGGTGGAGGTGGAGGGGAGCGAAC
1 GGTGGTGG-A--GATTGAACTGGTGGAGGTGG-GAAGGAAC--G-GGTGGTGGAGGGGAGAGAAC
3501754 TGGT
59 TGGT
3501758 GGTGGTGGAGATTGAACTGGTGGAGGTGG
1 GGTGGTGGAGATTGAACTGGTGGAGGTGG
3501787 AGGGGAGCGA
Statistics
Matches: 183, Mismatches: 31, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
62 1 0.01
63 115 0.63
64 3 0.02
66 35 0.19
67 2 0.01
68 1 0.01
69 26 0.14
ACGTcount: A:0.21, C:0.06, G:0.54, T:0.19
Consensus pattern (62 bp):
GGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAACGGGTGGTGGAGGGGAGAGAACTGGT
Found at i:3501668 original size:21 final size:21
Alignment explanation
Indices: 3501513--3501855 Score: 170
Period size: 21 Copynumber: 15.8 Consensus size: 21
3501503 GGTGGTGATT
* *
3501513 GAACTGGTGGAGGTGGGAAG-
1 GAACTGGTGGTGGTGGGGAGA
* *
3501533 GAGACGGGTGGTGGAGGGGAGA
1 GA-ACTGGTGGTGGTGGGGAGA
* **
3501555 GAACTGGTGGTGGTGGAGATT
1 GAACTGGTGGTGGTGGGGAGA
* **
3501576 GAACTGGTGGAGGTGGAAAG-
1 GAACTGGTGGTGGTGGGGAGA
* *
3501596 GAGACGGGTGGTGGAGGGGAGA
1 GA-ACTGGTGGTGGTGGGGAGA
* *
3501618 GAACTGGTGGAGGTGGAGAGTA
1 GAACTGGTGGTGGTGGGGAG-A
* * *
3501640 G-ACGGGTGGTGGAGGGGAGC
1 GAACTGGTGGTGGTGGGGAGA
* **
3501660 GAACTGGTGGTGGTGGTGATT
1 GAACTGGTGGTGGTGGGGAGA
* *
3501681 GAACTGGTGGAGGTGGAAGGGAGC
1 GAACTGGTGGTGGT-G--GGGAGA
* * **
3501705 GAACCGGTGGTGGTGGTGATT
1 GAACTGGTGGTGGTGGGGAGA
* *
3501726 GAACTGGTGGAGGTGGAGGGGAGC
1 GAACTGGT---GGTGGTGGGGAGA
* **
3501750 GAACTGGTGGTGGTGGAGATT
1 GAACTGGTGGTGGTGGGGAGA
* *
3501771 GAACTGGTGGAGGTGGAGGGGAGC
1 GAACTGGT---GGTGGTGGGGAGA
* * *
3501795 GAACAGGTTGTGGTGGTGGTGA
1 GAACTGGTGGTGGTGG-GGAGA
* *
3501817 GTAGACGGGTGGTGGAGGGGAGA
1 G-A-ACTGGTGGTGGTGGGGAGA
* *
3501840 GAACTTGTTGTGGTGG
1 GAACTGGTGGTGGTGG
3501856 TGTGTGAACG
Statistics
Matches: 239, Mismatches: 66, Indels: 35
0.70 0.19 0.10
Matches are distributed among these distances:
20 5 0.02
21 156 0.65
22 12 0.05
23 7 0.03
24 59 0.25
ACGTcount: A:0.21, C:0.06, G:0.54, T:0.19
Consensus pattern (21 bp):
GAACTGGTGGTGGTGGGGAGA
Found at i:3501690 original size:42 final size:42
Alignment explanation
Indices: 3501500--3501857 Score: 265
Period size: 42 Copynumber: 8.2 Consensus size: 42
3501490 AGAATAGACG
* * * *
3501500 GGTGGTGGTGATTGAACTGGTGGAGGTGGGAAG-GAGACGGGT
1 GGTGGTGGTGATTGAACTGGTGGTGGAGGGGAGCGA-ACTGGT
* * ** * * **
3501542 GGTGGAGGGGAGAGAACTGGTGGTGGTGGAGATTGAACTGGT
1 GGTGGTGGTGATTGAACTGGTGGTGGAGGGGAGCGAACTGGT
* * ** * *
3501584 GGAGGTGG-AAAGGAGACGGGTGGTGGAGGGGAGAGAACTGGT
1 GGTGGTGGTGATTGA-ACTGGTGGTGGAGGGGAGCGAACTGGT
* * * *
3501626 GGAGGTGGAGAGT-AGACGGGTGGTGGAGGGGAGCGAACTGGT
1 GGTGGTGGTGATTGA-ACTGGTGGTGGAGGGGAGCGAACTGGT
* *
3501668 GGTGGTGGTGATTGAACTGGTGGAGGTGGAAGGGAGCGAACCGGT
1 GGTGGTGGTGATTGAACTGGT---GGTGGAGGGGAGCGAACTGGT
3501713 GGTGGTGGTGATTGAACTGGTGGAGGTGGAGGGGAGCGAACTGGT
1 GGTGGTGGTGATTGAACTGGT---GGTGGAGGGGAGCGAACTGGT
* *
3501758 GGTGGTGGAGATTGAACTGGTGGAGGTGGAGGGGAGCGAACAGGTTGT
1 GGTGGTGGTGATTGAACTGGT---GGTGGAGGGGAGCGAAC---TGGT
* * * *
3501806 GGTGGTGGTGAGT-AGACGGGTGGTGGAGGGGAGAGAACTTGT
1 GGTGGTGGTGATTGA-ACTGGTGGTGGAGGGGAGCGAACTGGT
*
3501848 TGTGGTGGTG
1 GGTGGTGGTG
3501858 TGTGAACGGG
Statistics
Matches: 267, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
41 3 0.01
42 122 0.46
43 4 0.01
45 118 0.44
47 1 0.00
48 19 0.07
ACGTcount: A:0.20, C:0.06, G:0.54, T:0.20
Consensus pattern (42 bp):
GGTGGTGGTGATTGAACTGGTGGTGGAGGGGAGCGAACTGGT
Found at i:3501697 original size:45 final size:45
Alignment explanation
Indices: 3501605--3501812 Score: 289
Period size: 45 Copynumber: 4.7 Consensus size: 45
3501595 GGAGACGGGT
* * * * *
3501605 GGTGGAGGGGAGAGAACTGGTGGAGGTGGAGAGT-AGAC--G-GGT
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGA-ACTGGTGGA
3501647 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
* *
3501692 GGTGGAAGGGAGCGAACCGGTGGTGGTGGTGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
*
3501737 GGTGGAGGGGAGCGAACTGGTGGTGGTGGAGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
* *
3501782 GGTGGAGGGGAGCGAACAGGTTGTGGTGGTG
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTG
3501813 GTGAGTAGAC
Statistics
Matches: 149, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
42 32 0.21
43 1 0.01
44 1 0.01
45 115 0.77
ACGTcount: A:0.20, C:0.07, G:0.54, T:0.19
Consensus pattern (45 bp):
GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
Found at i:3501831 original size:45 final size:44
Alignment explanation
Indices: 3501605--3501857 Score: 257
Period size: 45 Copynumber: 5.7 Consensus size: 44
3501595 GGAGACGGGT
* * * *
3501605 GGTGGAGGGGAGAGAACTGGTGGAGGTGGAGAGTAG-AC-G-GGT
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGA-TAGAACGGTGGA
*
3501647 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATAGAAC-GGTGGA
* * *
3501692 GGTGGAAGGGAGCGAACCGGTGGTGGTGGTGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATAGAAC-GGTGGA
* *
3501737 GGTGGAGGGGAGCGAACTGGTGGTGGTGGAGATTGAACTGGTGGA
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATAGAAC-GGTGGA
* *
3501782 GGTGGAGGGGAGCGAACAGGTTGTGGTGGTGGTGAGTAG-AC-G-GGT
1 GGTGGAGGGGAGCGAAC---TGGTGGTGGTGGTGA-TAGAACGGTGGA
* * *
3501827 GGTGGAGGGGAGAGAACTTGTTGTGGTGGTG
1 GGTGGAGGGGAGCGAACTGGTGGTGGTGGTG
3501858 TGTGAACGGG
Statistics
Matches: 187, Mismatches: 16, Indels: 16
0.85 0.07 0.07
Matches are distributed among these distances:
41 2 0.01
42 44 0.24
44 1 0.01
45 122 0.65
46 1 0.01
48 15 0.08
49 2 0.01
ACGTcount: A:0.19, C:0.06, G:0.54, T:0.20
Consensus pattern (44 bp):
GGTGGAGGGGAGCGAACTGGTGGTGGTGGTGATAGAACGGTGGA
Found at i:3501864 original size:90 final size:87
Alignment explanation
Indices: 3501500--3501857 Score: 322
Period size: 90 Copynumber: 4.1 Consensus size: 87
3501490 AGAATAGACG
* * * *
3501500 GGTGGTGGTGATTGAACTGGTGGAGGTGGGAA-GGA--G-ACGGGTGGTGGAGGGGAG-AGAACT
1 GGTGGTGGTGATTGAACTGGTGGAGGT-GGAAGGGAGCGAACCGGTGGTGGTGGTGAGTAG-ACG
* * **
3501560 GGTGGTGGTGGAGATTGAACTGGT
64 GGTGGTGGAGGGGAGCGAACTGGT
* * ** * * * * * *
3501584 GGAGGTGG-AAAGGAGAC--G-GGTGGTGGAGGGGAGAGAACTGGTGGAGGTGGAGAGTAGACGG
1 GGTGGTGGTGATTGA-ACTGGTGGAGGTGGAAGGGAGCGAACCGGTGGTGGTGGTGAGTAGACGG
3501645 GTGGTGGAGGGGAGCGAACTGGT
65 GTGGTGGAGGGGAGCGAACTGGT
*
3501668 GGTGGTGGTGATTGAACTGGTGGAGGTGGAAGGGAGCGAACCGGTGGTGGTGGTGA-TTGAACTG
1 GGTGGTGGTGATTGAACTGGTGGAGGTGGAAGGGAGCGAACCGGTGGTGGTGGTGAGTAG-AC--
*
3501732 GTGGAGGTGGAGGGGAGCGAACTGGT
63 G-GGTGGTGGAGGGGAGCGAACTGGT
* * *
3501758 GGTGGTGGAGATTGAACTGGTGGAGGTGGAGGGGAGCGAACAGGTTGTGGTGGTGGTGAGTAGAC
1 GGTGGTGGTGATTGAACTGGTGGAGGTGGAAGGGAGCGAAC-CG--GTGGTGGTGGTGAGTAGAC
* *
3501823 GGGTGGTGGAGGGGAGAGAACTTGT
63 GGGTGGTGGAGGGGAGCGAACTGGT
*
3501848 TGTGGTGGTG
1 GGTGGTGGTG
3501858 TGTGAACGGG
Statistics
Matches: 220, Mismatches: 36, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
80 3 0.01
81 8 0.04
82 1 0.00
83 4 0.02
84 54 0.25
85 5 0.02
86 3 0.01
87 31 0.14
89 1 0.00
90 91 0.41
91 2 0.01
93 15 0.07
94 2 0.01
ACGTcount: A:0.20, C:0.06, G:0.54, T:0.20
Consensus pattern (87 bp):
GGTGGTGGTGATTGAACTGGTGGAGGTGGAAGGGAGCGAACCGGTGGTGGTGGTGAGTAGACGGG
TGGTGGAGGGGAGCGAACTGGT
Found at i:3507638 original size:42 final size:42
Alignment explanation
Indices: 3507568--3507649 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
3507558 GTGCCCTCAC
**
3507568 CTGTGTAACTCTCTGAGTAGGGTCACACGCTCGTGTGCCAGG
1 CTGTGTAACTCTCTGAGTAGCCTCACACGCTCGTGTGCCAGG
* * *
3507610 CTGTGTAACTCTCTGAGTTGCC-CTACACGGTTGTGTGCCA
1 CTGTGTAACTCTCTGAGTAGCCTC-ACACGCTCGTGTGCCA
3507650 AGCTATGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (42 bp):
CTGTGTAACTCTCTGAGTAGCCTCACACGCTCGTGTGCCAGG
Found at i:3510187 original size:25 final size:25
Alignment explanation
Indices: 3510159--3510228 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
3510149 AGACCCACCA
* *
3510159 CAGCTCATATGAGCTTATCGATATT
1 CAGCTCGTATGAGCTTACCGATATT
3510184 CAGCTCGTATGAGCTTACCGATATT
1 CAGCTCGTATGAGCTTACCGATATT
*
3510209 CAGCTCGGATGAGCTTACCG
1 CAGCTCGTATGAGCTTACCG
3510229 TTTGTCGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGATATT
Found at i:3513238 original size:50 final size:50
Alignment explanation
Indices: 3513161--3513387 Score: 348
Period size: 50 Copynumber: 4.5 Consensus size: 50
3513151 CCATGGCAAC
* *
3513161 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
3513211 AAGTGATAAGTGATAGCTTCGGTTACACTTATTTGATCAAGGA-AAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TGA
3513261 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
3513311 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
3513362 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
3513388 CTGATCAATG
Statistics
Matches: 162, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
49 2 0.01
50 134 0.83
51 26 0.16
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:3513405 original size:31 final size:31
Alignment explanation
Indices: 3513367--3513425 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
3513357 ATGGCAAGTA
3513367 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
3513398 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
3513426 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:3513433 original size:46 final size:46
Alignment explanation
Indices: 3513380--3513471 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3513370 AGTGGTAGCT
* *
3513380 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
3513426 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
3513472 ATGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:3515341 original size:21 final size:21
Alignment explanation
Indices: 3515315--3515362 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3515305 AGGCCTATAG
*
3515315 CACGGGCGTGTCCCTTAGT-CA
1 CACGGGCGTGTCCCCT-GTCCA
3515336 CACGGGCGTGTCCCCTGTCCA
1 CACGGGCGTGTCCCCTGTCCA
3515357 CACGGG
1 CACGGG
3515363 TTAGGGGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.12, C:0.38, G:0.31, T:0.19
Consensus pattern (21 bp):
CACGGGCGTGTCCCCTGTCCA
Found at i:3516549 original size:12 final size:12
Alignment explanation
Indices: 3516532--3516585 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
3516522 GCTAATAATG
3516532 ATAATGATAGTA
1 ATAATGATAGTA
*
3516544 ATAATGATACTA
1 ATAATGATAGTA
3516556 ATAATG---GTA
1 ATAATGATAGTA
* *
3516565 AAAATAATA-TA
1 ATAATGATAGTA
3516576 ATAATGATAG
1 ATAATGATAG
3516586 CATGAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 6 0.19
11 9 0.28
12 17 0.53
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.31
Consensus pattern (12 bp):
ATAATGATAGTA
Found at i:3516965 original size:21 final size:22
Alignment explanation
Indices: 3516939--3516981 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3516929 ATATTACATA
3516939 TAATAATAATAC-TAAAAATAG
1 TAATAATAATACATAAAAATAG
3516960 TAATAATAATACATTAAAAATA
1 TAATAATAATACA-TAAAAATA
3516982 ATTATGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
TAATAATAATACATAAAAATAG
Found at i:3518188 original size:29 final size:29
Alignment explanation
Indices: 3518156--3518213 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3518146 GATGGGTTAG
*
3518156 TGGGTTTAGGT-ATTGGGTTGTTGGGGTTT
1 TGGGCTTAGGTAATTGGGTT-TTGGGGTTT
**
3518185 TGGGCTTCTGTAATTGGGTTTTGGGGTTT
1 TGGGCTTAGGTAATTGGGTTTTGGGGTTT
3518214 AATGATTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.07, C:0.03, G:0.41, T:0.48
Consensus pattern (29 bp):
TGGGCTTAGGTAATTGGGTTTTGGGGTTT
Found at i:3531850 original size:16 final size:13
Alignment explanation
Indices: 3531818--3531843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3531808 TTTGTTGCCG
3531818 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
3531831 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
3531844 ATTTTCTCAA
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:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:3540551 original size:17 final size:18
Alignment explanation
Indices: 3540510--3540551 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3540500 ATGTAAATTA
*
3540510 TTATATATTATTATATTAT
1 TTAT-TATTATTATACTAT
3540529 TT-TTATTATTA-ACTAT
1 TTATTATTATTATACTAT
3540545 TTATTAT
1 TTATTAT
3540552 GTATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 12 0.57
18 1 0.05
19 2 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATTATTATACTAT
Found at i:3549991 original size:46 final size:46
Alignment explanation
Indices: 3549933--3550116 Score: 305
Period size: 46 Copynumber: 4.0 Consensus size: 46
3549923 TTTCTGTCAT
* *
3549933 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
*
3549979 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
* ** *
3550025 GTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
3550071 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
3550117 AGAGCACACT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATATCAG
Found at i:3552275 original size:16 final size:18
Alignment explanation
Indices: 3552246--3552286 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3552236 TCATCCTTTC
3552246 TTTCTTTTTCTATT-CTT
1 TTTCTTTTTCTATTCCTT
3552263 TTTCTTTTT-TATTCCTT
1 TTTCTTTTTCTATTCCTT
*
3552280 TTACTTT
1 TTTCTTT
3552287 ATATATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTTCTATTCCTT
Found at i:3555820 original size:25 final size:25
Alignment explanation
Indices: 3555786--3555834 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3555776 AACACATGTT
3555786 AAACTCAAAATAGTCTTTATGGAAA
1 AAACTCAAAATAGTCTTTATGGAAA
3555811 AAACTCAAAATAGTCTTTATGGAA
1 AAACTCAAAATAGTCTTTATGGAA
3555835 TTTGTGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (25 bp):
AAACTCAAAATAGTCTTTATGGAAA
Found at i:3556550 original size:44 final size:44
Alignment explanation
Indices: 3556495--3557288 Score: 936
Period size: 44 Copynumber: 18.2 Consensus size: 44
3556485 GTAGATCACC
* * * * * *
3556495 GATAGCTGATTTGGCATCTCTTTATTGTCAGAGAGCAAATTGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
3556539 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3556583 GAT-GACAGATTTGGCATCTCTGTATTGTCAGAAAGCAGATCGAA
1 GATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3556627 GATAACAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3556671 GAT-GACAGATTTGGCGTCCCTGTATTGTCAGAGAGCAGATCAAA
1 GATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* *
3556715 GAT-GATAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* *
3556759 TAT-GACAGATTTGGCGTCTCTGTATT-ATCAGAGAGCAGATCTAA
1 GATAG-CAGATTTGGCGTCTCTGTATTGA-CAGAGAGCAGATCGAA
* *
3556803 GATAACAGATTTGGCGTCTCTGTGTTGACAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3556847 GAT-GACAGATTTGGCGTCTCTGTATTGTCAAAGAACAGATCGAA
1 GATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3556891 GATAACAGATTTGGCGTCTCTGTGTTGACAGAGAGCAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
3556935 GATAGCAGATTTGGCGTCTCTGTATTGAC-GAAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAG-AGAGCAGATCGAA
* *
3556979 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCATATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * * *
3557023 GATAACAGATTTTGCATCTCTGTATTGACAGAGAGCAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* **
3557067 GATAGCAGA--T----T-TCTATATTGATGGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3557104 AATAGCAGATTTGGCATCTCTGTATTGACGGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* *
3557148 GATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
* * *
3557192 GATAACAGATTTGGCGTCT-TAGTATTGACAAAGAGCAGATTGAA
1 GATAGCAGATTTGGCGTCTCT-GTATTGACAGAGAGCAGATCGAA
* * * * * *
3557236 AATAACAGATTTTGCGTCTCTGTGTTAGA-TGTGGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATT-GACAG-AGAGCAGATCGAA
3557281 GATAGCAG
1 GATAGCAG
3557289 CTCTGACATT
Statistics
Matches: 654, Mismatches: 75, Indels: 41
0.85 0.10 0.05
Matches are distributed among these distances:
37 30 0.05
38 1 0.00
39 1 0.00
42 1 0.00
43 4 0.01
44 595 0.91
45 22 0.03
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (44 bp):
GATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAA
Found at i:3557138 original size:81 final size:81
Alignment explanation
Indices: 3557009--3557231 Score: 263
Period size: 81 Copynumber: 2.7 Consensus size: 81
3556999 TGTATTGACA
* *
3557009 GAGAGCATATCAAAGATAACAGATTTTGCATCTCTGTATTGACAGAGAGCAGATCAAAGATAGCA
1 GAGAGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAAGATAGCA
3557074 GATTTCTATATTGATG
66 GATTTCTATATTGATG
* * *
3557090 GAGAGCAGATCGAAA-ATAGCAGATTTGGCATCTCTGTATTGACGGAGAGCAGATCGAAGATAGC
1 GAGAGCAGATC-AAAGATAACAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAAGATAGC
*
3557154 AGATTTGGC-ATCTCTGTATTG
65 AGATTT--CTATAT-TG-A-TG
* *
3557175 ACAGAGAGCAGATCAAAGATAACAGATTTGGCGTCT-TAGTATTGACAAAGAGCAGAT
1 ---GAGAGCAGATCAAAGATAACAGATTTGGCATCTCT-GTATTGACAGAGAGCAGAT
3557232 TGAAAATAAC
Statistics
Matches: 121, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
81 61 0.50
82 6 0.05
83 3 0.02
84 1 0.01
85 2 0.02
87 4 0.03
88 44 0.36
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (81 bp):
GAGAGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAAGATAGCA
GATTTCTATATTGATG
Found at i:3559075 original size:21 final size:21
Alignment explanation
Indices: 3559051--3559105 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3559041 CTTATAAATT
3559051 TTTATTATATATACATTTTAC
1 TTTATTATATATACATTTTAC
**
3559072 TTTA-TATATTATTTATTTTAC
1 TTTATTATA-TATACATTTTAC
*
3559093 TATATTTATATAT
1 TTTA-TTATATAT
3559106 GTTCCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 3 0.11
23 4 0.14
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATATATACATTTTAC
Found at i:3566652 original size:29 final size:29
Alignment explanation
Indices: 3566594--3566652 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
3566584 TAAAATGGAC
* * *
3566594 TCAAAATAGAAAAAAATAAAAACAGGAAA
1 TCAAAAAAGAAAAAAAGAAAAACAGAAAA
*
3566623 TCAAAAAAGAAAAAAACGAGAAA-AGAAAA
1 TCAAAAAAGAAAAAAA-GAAAAACAGAAAA
3566652 T
1 T
3566653 TACAATAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.08
Consensus pattern (29 bp):
TCAAAAAAGAAAAAAAGAAAAACAGAAAA
Found at i:3571359 original size:27 final size:27
Alignment explanation
Indices: 3571318--3571372 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3571308 TGTCAAGAAG
3571318 ATCAGTTTCAAGTTTCTGTGTGCAGTT
1 ATCAGTTTCAAGTTTCTGTGTGCAGTT
*
3571345 ATCAGTTTCAGGTTTCTGTGTGCAGTT
1 ATCAGTTTCAAGTTTCTGTGTGCAGTT
3571372 A
1 A
3571373 GGAGACTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (27 bp):
ATCAGTTTCAAGTTTCTGTGTGCAGTT
Found at i:3578228 original size:29 final size:30
Alignment explanation
Indices: 3578195--3578251 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
3578185 AACCAAAAAT
*
3578195 AAAATATTTA-CAACAATGACCT-AAATTCA
1 AAAATAATTATCAA-AATGACCTGAAATTCA
*
3578224 AAAATAATTATTAAAATGACCTGAAATT
1 AAAATAATTATCAAAATGACCTGAAATT
3578252 AATAATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAATAATTATCAAAATGACCTGAAATTCA
Found at i:3582944 original size:28 final size:28
Alignment explanation
Indices: 3582912--3582968 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3582902 TAATTTTTAC
3582912 TCAAATTAAATTAAAGTACGTGAAAAGA
1 TCAAATTAAATTAAAGTACGTGAAAAGA
3582940 TCAAATTAAATTAAAGTACGTGAAAAGA
1 TCAAATTAAATTAAAGTACGTGAAAAGA
3582968 T
1 T
3582969 TTTATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (28 bp):
TCAAATTAAATTAAAGTACGTGAAAAGA
Found at i:3584865 original size:24 final size:25
Alignment explanation
Indices: 3584838--3584895 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
3584828 TACATTGATG
*
3584838 ATTTTAAATTG-TTTCATACTATTT
1 ATTTTAAATTGCTTTCATAATATTT
**
3584862 ATTTTAAATTGCTTTTTGTAATATTT
1 ATTTTAAATTGC-TTTCATAATATTT
3584888 ATTTTAAA
1 ATTTTAAA
3584896 CGTGTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.38
26 18 0.62
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (25 bp):
ATTTTAAATTGCTTTCATAATATTT
Found at i:3584912 original size:27 final size:27
Alignment explanation
Indices: 3584852--3584913 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
3584842 TAAATTGTTT
* *
3584852 CATACTATTTATTTTAAATTGCTTTTTG
1 CATA-TATTTATTTTAAAGTGCTTTTTA
*
3584880 TA-ATATTTATTTTAAACGTG-TTTTTA
1 CATATATTTATTTTAAA-GTGCTTTTTA
3584906 CATATATT
1 CATATATT
3584914 ACTCATCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 19 0.68
27 8 0.29
28 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (27 bp):
CATATATTTATTTTAAAGTGCTTTTTA
Found at i:3586284 original size:27 final size:28
Alignment explanation
Indices: 3586240--3586294 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3586230 AAATGTGTTA
*
3586240 AATTTTTAAAATAAAAAAAATATT-AACAC
1 AATTTGTAAAAT--AAAAAATATTCAACAC
3586269 AATTTGTAAAAT-AAAAATATTCAACA
1 AATTTGTAAAATAAAAAATATTCAACA
3586295 TAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 4 0.17
29 11 0.46
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (28 bp):
AATTTGTAAAATAAAAAATATTCAACAC
Found at i:3587316 original size:8 final size:7
Alignment explanation
Indices: 3587259--3587318 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
3587249 TAACAAGGAC
3587259 AATAATA
1 AATAATA
3587266 AATAATA
1 AATAATA
*
3587273 ATTAAT-
1 AATAATA
*
3587279 AATACTA
1 AATAATA
* *
3587286 AATTAGTT
1 AA-TAATA
3587294 AATAATAA
1 AATAAT-A
3587302 AATAATA
1 AATAATA
3587309 AATAAATA
1 AAT-AATA
3587317 AA
1 AA
3587319 CACAAAAAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
6 4 0.10
7 21 0.50
8 17 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:3587443 original size:3 final size:3
Alignment explanation
Indices: 3587423--3587741 Score: 79
Period size: 3 Copynumber: 102.7 Consensus size: 3
3587413 AAACATACAC
* * * * * *
3587423 TAA TAT TAA TAA TGA TAA TAA TAC TAA CAA TAG TAA TGA -AA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
3587468 AAA AAA GTAA -ATA TAA T-A TAA TAA TAA TAT TAA -AA TAA GTAA TTAA
1 TAA TAA -TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA -TAA
* * *
3587514 AAA TAA TAC T-A TATA TAAA TATA TATA TACA TATA TAA TAA -AA CATA
1 TAA TAA TAA TAA TA-A T-AA TA-A TA-A TA-A TA-A TAA TAA TAA TA-A
* * * *
3587561 TAC TAA TAT TAA TAA TAA TAA TAA TAC TAGA -AA TAA TAA TGA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * * *
3587605 TACA AAA AAA TAA AAA TAA -ACA TAA T-A TAA TAA TAA TAT TAA -AT
1 TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
3587649 TAA -AG TAA TTAA AAA TAA TAC T-A TATA TAA TATA TATA TACC TATA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TA-A TAA TA-A TA-A TA-A TA-A
* * *
3587695 TAA TAA AACA TACA CTAA TAA TAA TAA TAA TAA CAA TAG TAA TAA TA
1 TAA TAA TA-A TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3587742 TTGAAATACA
Statistics
Matches: 231, Mismatches: 56, Indels: 58
0.67 0.16 0.17
Matches are distributed among these distances:
2 17 0.07
3 156 0.68
4 55 0.24
5 3 0.01
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3587472 original size:146 final size:139
Alignment explanation
Indices: 3587337--3587820 Score: 658
Period size: 146 Copynumber: 3.4 Consensus size: 139
3587327 GGAAGGCATG
3587337 TAATATAATAATAATATTAAAATAAAGTAATTAAAAA-AATACTATATATAAATATATGTATATA
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAAATATA--TATATA
*
3587401 CACATATAATAAAAACATACACTAATATTAATAATGATAATAATACTAACAATAGTAATGAAATA
64 CACATATAAT-AAAACATACACTAATATTAATAATAATAATAATACTAA-AATA-TAATGAAATA
3587466 CAAAAAAAGTAAATA
126 C-AAAAAAGTAAATA
3587481 TAATATAATAATAATATTAAAAT-AAGTAATTAAAAATAATACTATATATAAATATATATATACA
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAAATATATATATACA
* *
3587545 TATATAATAAAACATATACTAATATTAATAATAATAATAATACTAGAAATAATAATGAAATACAA
66 CATATAATAAAACATACACTAATATTAATAATAATAATAATACTA-AAAT-ATAATGAAATACAA
*
3587610 AAAAATAAAAATAAACA
129 AAAAGT--AAAT----A
*
3587627 TAATATAATAATAATATTAAATTAAAGTAATTAAAAATAATACTATATAT-AATATATATATAC-
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAAATATATATATACA
* * *
3587690 CTATATAATAAAACATACACTAATAATAATAATAATAACAATAGTAATAATAT--TGAAATAC-A
66 C-ATATAATAAAACATACACTAATATTAATAATAATAATAATACTAA-AATATAATGAAATACAA
* *
3587752 AAAAGCAAATG
129 AAAAGTAAATA
* *
3587763 TAATATAATAAAAATATTAAAATAAAGTAATTAAAAAATAATACTATGTATAAATATA
1 TAATATAATAATAATATTAAAATAAAGTAATT-AAAAATAATACTATATATAAATATA
3587821 AATACATATA
Statistics
Matches: 310, Mismatches: 16, Indels: 34
0.86 0.04 0.09
Matches are distributed among these distances:
136 30 0.10
137 17 0.05
138 6 0.02
140 11 0.04
141 49 0.16
142 26 0.08
143 21 0.07
144 42 0.14
145 3 0.01
146 79 0.25
147 26 0.08
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (139 bp):
TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAAATATATATATACA
CATATAATAAAACATACACTAATATTAATAATAATAATAATACTAAAATATAATGAAATACAAAA
AAGTAAATA
Found at i:3587830 original size:146 final size:136
Alignment explanation
Indices: 3587337--3587884 Score: 609
Period size: 143 Copynumber: 3.8 Consensus size: 136
3587327 GGAAGGCATG
3587337 TAATATAATAATAATATTAAAATAAAGTAATTAAAAA-AATACTATATATAAATATATGTATATA
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATAT-AATATA--TATATA
* * * * *
3587401 CACATATAATAAAAACATACACTAATATTAATAATGATAATAATACTAACAATAGTAATGAAATA
63 C-TATATAAT-AAAACATACACTAATAATAATAATAATAATAATAGTAATAATA-T--TGAAATA
*
3587466 CAAAAAAAGTAAATA
123 C-AAAAAAGAAAATA
3587481 TAATATAATAATAATATTAAAAT-AAGTAATTAAAAATAATACTATATATAAATATATATATACA
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATAT-AATATATATATAC-
* * * *
3587545 TATATAATAAAACATATACTAATATTAATAATAATAATAATACTAGAAATAATAATGAAATACAA
64 TATATAATAAAACATACACT-A-A-TAATAATAATAATAATAATAGTAATAATATTGAAATAC-A
*
3587610 AAAAATAAAAATAAACA
125 AAAAA-GAAAAT----A
*
3587627 TAATATAATAATAATATTAAATTAAAGTAATTAAAAATAATACTATATATAATATATATATACCT
1 TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAATATATATATA-CT
*
3587692 ATATAATAAAACATACACTAATAATAATAATAATAACAATAGTAATAATATTGAAATAC-AAAAA
65 ATATAATAAAACATACACTAATAATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAA
* *
3587756 GCAAATG
130 GAAAATA
* *
3587763 TAATATAATAAAAATATTAAAATAAAGTAATTAAAAAATAATACTATGTATAAATATAAATACAT
1 TAATATAATAATAATATTAAAATAAAGTAATT-AAAAATAATACTATATAT-AATAT--AT--AT
* * * *
3587828 ATACGTATATAATAAAAAAATATA-TACTCATATATAATAATAATAATAGTAATAATA
60 ATAC-TATATAAT-AAAACATACACTAATAATA-ATAATAATAATAATAGTAATAATA
3587885 ATAATATAAA
Statistics
Matches: 356, Mismatches: 28, Indels: 41
0.84 0.07 0.10
Matches are distributed among these distances:
136 30 0.08
137 17 0.05
138 5 0.01
140 6 0.02
141 32 0.09
142 39 0.11
143 79 0.22
144 66 0.19
145 1 0.00
146 54 0.15
147 27 0.08
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (136 bp):
TAATATAATAATAATATTAAAATAAAGTAATTAAAAATAATACTATATATAATATATATATACTA
TATAATAAAACATACACTAATAATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAAG
AAAATA
Found at i:3587848 original size:25 final size:25
Alignment explanation
Indices: 3587790--3587867 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
3587780 TAAAATAAAG
* *
3587790 TAATTAAAAAATA-ATACT-ATGTA
1 TAATAAAAAAATACATACTCATATA
* * *
3587813 TAA-ATATAAATACATA-TACGTATA
1 TAATAAAAAAATACATACT-CATATA
*
3587837 TAATAAAAAAATATATACTCATATA
1 TAATAAAAAAATACATACTCATATA
3587862 TAATAA
1 TAATAA
3587868 TAATAATAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
22 7 0.17
23 6 0.15
24 6 0.15
25 21 0.51
26 1 0.02
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (25 bp):
TAATAAAAAAATACATACTCATATA
Found at i:3587852 original size:23 final size:23
Alignment explanation
Indices: 3587790--3587885 Score: 60
Period size: 23 Copynumber: 4.3 Consensus size: 23
3587780 TAAAATAAAG
* *
3587790 TAATTAAAAAATAATACTATGTATA
1 TAATAAAAAAAT-ATA-TACGTATA
* * *
3587815 -AATATAAATACATATACGTATA
1 TAATAAAAAAATATATACGTATA
3587837 TAATAAAAAAATATATAC-TCATA
1 TAATAAAAAAATATATACGT-ATA
*
3587860 T-ATAATAATAATA-ATA-GTA-A
1 TAATAA-AAAAATATATACGTATA
3587880 TAATAA
1 TAATAA
3587886 TAATATAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
20 2 0.04
21 5 0.09
22 16 0.28
23 27 0.47
24 7 0.12
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (23 bp):
TAATAAAAAAATATATACGTATA
Found at i:3587869 original size:3 final size:3
Alignment explanation
Indices: 3587861--3587907 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3587851 ATACTCATAT
* * *
3587861 ATA ATA ATA ATA ATA GTA ATA ATA ATA AT- ATA AAA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3587908 GTGTTAGACA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3589507 original size:30 final size:30
Alignment explanation
Indices: 3589471--3589535 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
3589461 CAACTTAACA
*
3589471 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
* * *
3589501 AACAAATGTATTTAAAATAATAACCAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
3589531 AACAA
1 AACAA
3589536 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCATCTAAAATAATAACAAAATT
Found at i:3590286 original size:14 final size:14
Alignment explanation
Indices: 3590241--3590286 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
3590231 TTATGAAGAA
3590241 TATTTATATTTTTT
1 TATTTATATTTTTT
*
3590255 T-TTCTATAATTTTGT
1 TATT-TAT-ATTTTTT
3590270 TATTTATATTTTTT
1 TATTTATATTTTTT
3590284 TAT
1 TAT
3590287 CGAATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 13 0.48
15 10 0.37
16 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (14 bp):
TATTTATATTTTTT
Found at i:3591173 original size:10 final size:10
Alignment explanation
Indices: 3591160--3591184 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3591150 TTGTACTTTT
3591160 TTTTTATATA
1 TTTTTATATA
3591170 TTTTTATATA
1 TTTTTATATA
3591180 TTTTT
1 TTTTT
3591185 GGATTTTTTT
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:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:3594421 original size:22 final size:24
Alignment explanation
Indices: 3594370--3594422 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3594360 TTTTTATGAC
3594370 TAAATTATTGTTATTAAATATGCTT
1 TAAATTATTGTTATTAAATAT-CTT
* *
3594395 GAAATTATTG-TATTATATAT-TT
1 TAAATTATTGTTATTAAATATCTT
3594417 TAAATT
1 TAAATT
3594423 GAATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (24 bp):
TAAATTATTGTTATTAAATATCTT
Found at i:3596900 original size:20 final size:19
Alignment explanation
Indices: 3596875--3596918 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3596865 GAGGAAATTT
*
3596875 TTTTTGTACTTTTTTATATA
1 TTTTTGGACTTTTTTATA-A
* *
3596895 TTTTTGGATTTTTTTTTAA
1 TTTTTGGACTTTTTTATAA
3596914 TTTTT
1 TTTTT
3596919 TTAGACGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTGGACTTTTTTATAA
Found at i:3598513 original size:22 final size:23
Alignment explanation
Indices: 3598464--3598513 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
3598454 TAATCGACCT
*
3598464 TCGACTGAATTAGATCGATTAAA
1 TCGACTGAATTAGACCGATTAAA
3598487 T-GACTG-ATTA-ACCGAATTAAA
1 TCGACTGAATTAGACCG-ATTAAA
3598508 TCGACT
1 TCGACT
3598514 CGATCGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 9 0.38
23 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (23 bp):
TCGACTGAATTAGACCGATTAAA
Found at i:3598899 original size:2 final size:2
Alignment explanation
Indices: 3598892--3598916 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3598882 TTACAAAGGT
3598892 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
3598917 GAATCTAGAA
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:3599626 original size:11 final size:11
Alignment explanation
Indices: 3599592--3599632 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3599582 TATTTCAAGT
*
3599592 ATAAATATATA
1 ATAAATATTTA
*
3599603 TTAAA-ATTT-
1 ATAAATATTTA
3599612 ATAAATATTTA
1 ATAAATATTTA
3599623 ATAAATATTT
1 ATAAATATTT
3599633 TATAGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 4 0.16
10 7 0.28
11 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAAATATTTA
Found at i:3599627 original size:20 final size:21
Alignment explanation
Indices: 3599591--3599632 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3599581 ATATTTCAAG
*
3599591 TATAAATATATATTAAA-ATT
1 TATAAATATATAATAAATATT
*
3599611 TATAAATATTTAATAAATATT
1 TATAAATATATAATAAATATT
3599632 T
1 T
3599633 TATAGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATAAATATATAATAAATATT
Found at i:3601572 original size:24 final size:24
Alignment explanation
Indices: 3601543--3601588 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3601533 CAATTAAACA
3601543 AACTAGTTAAATTCTATTAAAAGG
1 AACTAGTTAAATTCTATTAAAAGG
3601567 AACTAGTTAAATTCTATTAAAA
1 AACTAGTTAAATTCTATTAAAA
3601589 CTCTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (24 bp):
AACTAGTTAAATTCTATTAAAAGG
Found at i:3603577 original size:24 final size:25
Alignment explanation
Indices: 3603549--3603605 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
3603539 TACTACTAAT
3603549 TTGATA-AATTATT-TAATATCATAA
1 TTGATATAATTATTGTAATA-CATAA
*
3603573 TTGATATAATTTTTGTAATACAT-A
1 TTGATATAATTATTGTAATACATAA
*
3603597 TTTATATAA
1 TTGATATAA
3603606 ATAATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.52
25 9 0.31
26 5 0.17
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (25 bp):
TTGATATAATTATTGTAATACATAA
Found at i:3636416 original size:61 final size:60
Alignment explanation
Indices: 3636288--3636416 Score: 163
Period size: 61 Copynumber: 2.1 Consensus size: 60
3636278 GTGGGAAATC
* *
3636288 AACACGGCCTGGACTTCCTTACATGGGTAGACCACACAGCTAAGTAGTTTTAGCAGACTCT
1 AACACGGCCTGGACTTCCTTACATGGGTAGACCACACAGC-AAGTAGTTTTAACAGACTCA
* * *
3636349 AGCACGGCCTGGACTTCCTTACATGGGTAGACCACACGGC-CGT-GTCTATTCAACAGACTCA
1 AACACGGCCTGGACTTCCTTACATGGGTAGACCACACAGCAAGTAGT-T-TT-AACAGACTCA
3636410 AACACGG
1 AACACGG
3636417 TTTGAAGCAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
58 2 0.03
59 3 0.05
60 2 0.03
61 52 0.88
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (60 bp):
AACACGGCCTGGACTTCCTTACATGGGTAGACCACACAGCAAGTAGTTTTAACAGACTCA
Found at i:3640395 original size:15 final size:16
Alignment explanation
Indices: 3640358--3640397 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3640348 GAAAAGGTTA
3640358 AAAAGGATATCAAATG
1 AAAAGGATATCAAATG
*
3640374 AAAAGGATATCAATTG
1 AAAAGGATATCAAATG
3640390 -AAAGGATA
1 AAAAGGATA
3640398 GCATTGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAAGGATATCAAATG
Found at i:3643164 original size:42 final size:42
Alignment explanation
Indices: 3643051--3643174 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
3643041 GTACAATACT
** *
3643051 AATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCATGTC
1 AATGCCATATCCCAGATATGGTCTTACA-CAAAGTCTCATATC
* * * *
3643093 AATGCCAATAGCCTAGCTGTGGTCTTACACAAAGTCTCATATC
1 AATGCC-ATATCCCAGATATGGTCTTACACAAAGTCTCATATC
* * **
3643136 GATGTCATATCCCAGATATGGTCTTACACGTAGTCTCAT
1 AATGCCATATCCCAGATATGGTCTTACACAAAGTCTCAT
3643175 TAACCCTAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
42 35 0.54
43 30 0.46
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
AATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATC
Found at i:3644275 original size:10 final size:10
Alignment explanation
Indices: 3644262--3644415 Score: 75
Period size: 10 Copynumber: 15.2 Consensus size: 10
3644252 AAAAATCAAT
3644262 AAAATTTATA
1 AAAATTTATA
*
3644272 AAAAATTATA
1 AAAATTTATA
*
3644282 AAATTTTAATA
1 AAAATTT-ATA
3644293 AATAATATT-T-
1 AA-AAT-TTATA
* *
3644303 AGAAGTTATTA
1 AAAATTTA-TA
*
3644314 AAAA-TTAGAA
1 AAAATTTA-TA
*
3644324 AAAAATTATA
1 AAAATTTATA
* *
3644334 AAAATATGTA
1 AAAATTTATA
*
3644344 AAATTTTATA
1 AAAATTTATA
*
3644354 AAAA-TCATA
1 AAAATTTATA
3644363 AAATATTTATA
1 AAA-ATTTATA
*
3644374 AAAATATATA
1 AAAATTTATA
* *
3644384 GAAATATATAA
1 AAAATTTAT-A
*
3644395 AAAAATTAT-
1 AAAATTTATA
*
3644404 AAATTTTATA
1 AAAATTTATA
3644414 AA
1 AA
3644416 GTCGTAAGAA
Statistics
Matches: 107, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
8 2 0.02
9 16 0.15
10 59 0.55
11 26 0.24
12 2 0.02
13 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (10 bp):
AAAATTTATA
Found at i:3644412 original size:40 final size:38
Alignment explanation
Indices: 3644250--3644415 Score: 138
Period size: 40 Copynumber: 4.1 Consensus size: 38
3644240 TGATTAAAAA
3644250 ATAAAAATCA-ATAAAATTTATAAAAAATTATAAAATTTT
1 ATAAAAAT-ATATAAAA-TTATAAAAAATTATAAAATTTT
* * * * **
3644289 AATAAATAATATTTAGAAGTTATTAAAAATTAGAAAAAAATT
1 -ATAAA-AATATATA-AAATTATAAAAAATTA-TAAAATTTT
* * *
3644331 ATAAAAATATGTAAAATTTTATAAAAATCATAAAATATTT
1 ATAAAAATATATAAAATTATA-AAAAATTATAAAAT-TTT
3644371 ATAAAAATATATAGAAATATATAAAAAAATTAT-AAATTTT
1 ATAAAAATATATA-AAAT-TAT-AAAAAATTATAAAATTTT
3644411 ATAAA
1 ATAAA
3644416 GTCGTAAGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
39 9 0.09
40 42 0.42
41 30 0.30
42 18 0.18
43 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (38 bp):
ATAAAAATATATAAAATTATAAAAAATTATAAAATTTT
Found at i:3644437 original size:60 final size:60
Alignment explanation
Indices: 3644263--3644451 Score: 145
Period size: 60 Copynumber: 3.1 Consensus size: 60
3644253 AAAATCAATA
* * * ** * * * *
3644263 AAATTTATAAAAAATTATAAAATTTTAATAAATAAT-ATTTAGAAGTTATTAAAAATTAGAAAA
1 AAATATATAAAAAAATGTAAAATTTT-ATAAA-AATCATAAAAAATTTA-TAAAAA-TATAAAG
* * *
3644326 AAAT-TATAAAAATATGTAAAATTTTATAAAAATCATAAAATATTTATAAAAATATATAG
1 AAATATATAAAAAAATGTAAAATTTTATAAAAATCATAAAAAATTTATAAAAATATAAAG
* * *
3644385 AAATATATAAAAAAAT-TATAAATTTTAT-AAAGTCGTAAGAAAA-TTATAAAAAATGTAAAG
1 AAATATATAAAAAAATGTA-AAATTTTATAAAAATCATAA-AAAATTTAT-AAAAATATAAAG
3644445 AAATATA
1 AAATATA
3644452 AAATTCATAA
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
59 22 0.21
60 48 0.46
61 12 0.12
62 18 0.17
63 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (60 bp):
AAATATATAAAAAAATGTAAAATTTTATAAAAATCATAAAAAATTTATAAAAATATAAAG
Found at i:3644944 original size:16 final size:16
Alignment explanation
Indices: 3644923--3644953 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3644913 TTTTATAATA
3644923 TTTTTACAATTTTATG
1 TTTTTACAATTTTATG
*
3644939 TTTTTACTATTTTAT
1 TTTTTACAATTTTAT
3644954 AAAAAAATTC
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:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTACAATTTTATG
Found at i:3645074 original size:16 final size:17
Alignment explanation
Indices: 3645038--3645075 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3645028 TTTACGATTT
3645038 TTTTATAATTTTTGTGA
1 TTTTATAATTTTTGTGA
*
3645055 -TTTATAATTTTT-TTA
1 TTTTATAATTTTTGTGA
3645070 TTTTAT
1 TTTTAT
3645076 GATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTATAATTTTTGTGA
Found at i:3645101 original size:21 final size:21
Alignment explanation
Indices: 3645077--3645162 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
3645067 TTATTTTATG
*
3645077 ATAAATTTTAAATATTTTTCT
1 ATAAATTTTTAATATTTTTCT
* *
3645098 ATAAATTTTTTATATTTTT-A
1 ATAAATTTTTAATATTTTTCT
** * *
3645118 ATATGTTTCT-ATATTTTTTT
1 ATAAATTTTTAATATTTTTCT
*
3645138 ATAAATTTTTAATAATTTTCT
1 ATAAATTTTTAATATTTTTCT
3645159 ATAA
1 ATAA
3645163 CTTTATTGAT
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 8 0.16
20 14 0.27
21 29 0.57
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
ATAAATTTTTAATATTTTTCT
Found at i:3645118 original size:31 final size:31
Alignment explanation
Indices: 3645080--3645162 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
3645070 TTTTATGATA
*
3645080 AATTTTAAATATTTTTCTATAAATTTTTTAT
1 AATTTTTAATATTTTTCTATAAATTTTTTAT
* *
3645111 -ATTTTTAATATGTTTCTAT-ATTTTTTTAT
1 AATTTTTAATATTTTTCTATAAATTTTTTAT
*
3645140 AAATTTTTAATAATTTTCTATAA
1 -AATTTTTAATATTTTTCTATAA
3645163 CTTTATTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 9 0.20
30 17 0.39
31 17 0.39
32 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (31 bp):
AATTTTTAATATTTTTCTATAAATTTTTTAT
Found at i:3647099 original size:21 final size:21
Alignment explanation
Indices: 3647073--3647121 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3647063 CAATTCGTGC
* *
3647073 ATTCAATTGTATTGGTTCCGT
1 ATTCAATTGTACTAGTTCCGT
*
3647094 ATTCAATTGTACTAGTTCCTT
1 ATTCAATTGTACTAGTTCCGT
3647115 ATTCAAT
1 ATTCAAT
3647122 AAAAGACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTCAATTGTACTAGTTCCGT
Found at i:3649054 original size:36 final size:36
Alignment explanation
Indices: 3648989--3649091 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 36
3648979 GATTCTGGGT
* *
3648989 ATAGTCAGGATTTGCCCCTTGCCCAAAATTCTGCCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * *
3649025 ATAGCCAGGATTTGCCCCCTGTCCGAAATTTTGTCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * ** *
3649061 ATAACCAGAACTTGGTCCCTGCCCATAATTC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTC
3649092 CCACCTTGTG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (36 bp):
ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
Found at i:3650958 original size:30 final size:33
Alignment explanation
Indices: 3650923--3650993 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 33
3650913 AATAAAATTC
*
3650923 AATAAAAATA-TAAAAAAATTAT-TAAATTT-T
1 AATAAAAATATTAAAAAAATTATAAAAATTTAT
* *
3650953 AATAAAAA-ATTATAAAAATTGTAAAAATTTAT
1 AATAAAAATATTAAAAAAATTATAAAAATTTAT
3650985 AATAAAAAT
1 AATAAAAAT
3650994 TGTAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 18 0.53
31 6 0.18
32 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (33 bp):
AATAAAAATATTAAAAAAATTATAAAAATTTAT
Found at i:3650967 original size:10 final size:10
Alignment explanation
Indices: 3650926--3651119 Score: 72
Period size: 10 Copynumber: 19.9 Consensus size: 10
3650916 AAAATTCAAT
3650926 AAAAA-TATAA
1 AAAAATTAT-A
*
3650936 AAAAATTATT
1 AAAAATTATA
**
3650946 AAATTTTAATA
1 AAAAATT-ATA
3650957 AAAAATTAT-
1 AAAAATTATA
*
3650966 AAAAATTGTA
1 AAAAATTATA
*
3650976 AAAATTTATAA
1 AAAAATTAT-A
*
3650987 TAAAAATTGTA
1 -AAAAATTATA
**
3650998 AAATTTTAT-
1 AAAAATTATA
*
3651007 AAAAATCATA
1 AAAAATTATA
3651017 AAAAA-TAT-
1 AAAAATTATA
3651025 AAAAA-TATA
1 AAAAATTATA
**
3651034 GGGGAAATTAT-
1 --AAAAATTATA
*
3651045 -AAAATTTTA
1 AAAAATTATA
* * *
3651054 TAGAATTGTA
1 AAAAATTATA
3651064 AGAAAATTATA
1 A-AAAATTATA
3651075 AAAAATTA-A
1 AAAAATTATA
*
3651084 AGAAATT-T-
1 AAAAATTATA
3651092 -AAAATTCATA
1 AAAAATT-ATA
3651102 AAAAATTAT-
1 AAAAATTATA
*
3651111 GAAAATTAT
1 AAAAATTAT
3651120 TGTAACAAAA
Statistics
Matches: 136, Mismatches: 30, Indels: 37
0.67 0.15 0.18
Matches are distributed among these distances:
7 5 0.04
8 14 0.10
9 32 0.24
10 46 0.34
11 29 0.21
12 10 0.07
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:3650970 original size:31 final size:32
Alignment explanation
Indices: 3650923--3651012 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
3650913 AATAAAATTC
*
3650923 AATAAAAA-TATAAAAAAATTAT-TAAATTT-T
1 AATAAAAATTAT-AAAAAATTATAAAAATTTAT
*
3650953 AATAAAAAATTAT-AAAAATTGTAAAAATTTAT
1 AAT-AAAAATTATAAAAAATTATAAAAATTTAT
* **
3650985 AATAAAAATTGTAAAATTTTATAAAAAT
1 AATAAAAATTATAAAAAATTATAAAAAT
3651013 CATAAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
30 11 0.22
31 19 0.39
32 19 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
AATAAAAATTATAAAAAATTATAAAAATTTAT
Found at i:3650971 original size:9 final size:9
Alignment explanation
Indices: 3650924--3651119 Score: 69
Period size: 9 Copynumber: 20.2 Consensus size: 9
3650914 ATAAAATTCA
3650924 ATAAAAATAT
1 ATAAAAAT-T
*
3650934 AAAAAAATT
1 ATAAAAATT
**
3650943 ATTAAATTTT
1 A-TAAAAATT
3650953 AATAAAAAATT
1 -AT-AAAAATT
3650964 ATAAAAATT
1 ATAAAAATT
*
3650973 GTAAAAATTTAT
1 ATAAAAA--T-T
3650985 AATAAAAATT
1 -ATAAAAATT
* *
3650995 GTAAAATTTT
1 ATAAAA-ATT
*
3651005 ATAAAAATC
1 ATAAAAATT
*
3651014 ATAAAAAAT
1 ATAAAAATT
3651023 ATAAAAA-T
1 ATAAAAATT
*
3651031 ATAGGGGAAATT
1 ATA---AAAATT
3651043 AT-AAAATT
1 ATAAAAATT
* *
3651051 TTATAGAATT
1 ATA-AAAATT
*
3651061 GTAAGAAAATT
1 AT-A-AAAATT
3651072 ATAAAAAATT
1 AT-AAAAATT
3651082 A-AAGAAATT
1 ATAA-AAATT
3651091 -T-AAAATT
1 ATAAAAATT
3651098 CATAAAAAATT
1 -AT-AAAAATT
*
3651109 ATGAAAATT
1 ATAAAAATT
3651118 AT
1 AT
3651120 TGTAACAAAA
Statistics
Matches: 141, Mismatches: 24, Indels: 43
0.68 0.12 0.21
Matches are distributed among these distances:
7 5 0.04
8 13 0.09
9 49 0.35
10 38 0.27
11 26 0.18
12 4 0.03
13 6 0.04
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3650977 original size:19 final size:19
Alignment explanation
Indices: 3650955--3651030 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
3650945 TAAATTTTAA
3650955 TAAAAAATTATAAAAATTG
1 TAAAAAATTATAAAAATTG
*
3650974 TAAAAATTTATAATAAAAATTG
1 TAAAAA---ATTATAAAAATTG
** **
3650996 TAAAATTTTATAAAAATCA
1 TAAAAAATTATAAAAATTG
3651015 TAAAAAA-TATAAAAAT
1 TAAAAAATTATAAAAAT
3651031 ATAGGGGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
18 9 0.20
19 20 0.43
22 17 0.37
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTG
Found at i:3650989 original size:22 final size:22
Alignment explanation
Indices: 3650964--3651008 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3650954 ATAAAAAATT
3650964 ATAAAAATTGTAAAAATTTATA
1 ATAAAAATTGTAAAAATTTATA
*
3650986 ATAAAAATTGTAAAATTTTATA
1 ATAAAAATTGTAAAAATTTATA
3651008 A
1 A
3651009 AAATCATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAAAATTGTAAAAATTTATA
Found at i:3651009 original size:51 final size:50
Alignment explanation
Indices: 3650924--3651030 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
3650914 ATAAAATTCA
* * *
3650924 ATAAAAA--TATAAAAAAATTATTAAATTTTAATAAAAAATTATAAAAATT
1 ATAAAAATTTATAAAAAAATTATAAAATTTTAAT-AAAAATCATAAAAAAT
* *
3650973 GTAAAAATTTATAATAAAAATTGTAAAATTTT-ATAAAAATCATAAAAAAT
1 ATAAAAATTTATAA-AAAAATTATAAAATTTTAATAAAAATCATAAAAAAT
3651023 ATAAAAAT
1 ATAAAAAT
3651031 ATAGGGGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 6 0.12
50 21 0.43
51 7 0.14
52 15 0.31
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (50 bp):
ATAAAAATTTATAAAAAAATTATAAAATTTTAATAAAAATCATAAAAAAT
Found at i:3651311 original size:9 final size:9
Alignment explanation
Indices: 3651297--3651355 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
3651287 TTGATGCATG
3651297 TTATAATTT
1 TTATAATTT
3651306 TTATAAATTT
1 TTAT-AATTT
*
3651316 TTACAATTT
1 TTATAATTT
*
3651325 TTACAATTT
1 TTATAATTT
*
3651334 TTTTACTATTT
1 TTATA--ATTT
3651345 TTATAATTT
1 TTATAATTT
3651354 TT
1 TT
3651356 TTCTAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 27 0.63
10 8 0.19
11 8 0.19
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATAATTT
Found at i:3651326 original size:20 final size:19
Alignment explanation
Indices: 3651301--3651376 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
3651291 TGCATGTTAT
3651301 AATTTTTATAAATTTTTAC
1 AATTTTTATAAATTTTTAC
* *
3651320 AATTTTTACAATTTTTTTAC
1 AATTTTTATAA-ATTTTTAC
* * *
3651340 TATTTTTATAATTTTTTTC
1 AATTTTTATAAATTTTTAC
3651359 TAATTTTTAATAAATTTT
1 -AATTTTT-ATAAATTTT
3651377 AAATACTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.36
20 22 0.47
21 8 0.17
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTATAAATTTTTAC
Found at i:3651386 original size:29 final size:30
Alignment explanation
Indices: 3651353--3651426 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
3651343 TTTTATAATT
* *
3651353 TTTTTCTAATTTTTAATAAATTTTAA-ATAC
1 TTTTTATAATTTTTAATAAAATTTAATA-AC
* * *
3651383 TTTTTGTATTTTTTATTAAAATTTAATAAC
1 TTTTTATAATTTTTAATAAAATTTAATAAC
*
3651413 -TTTTATAACTTTTA
1 TTTTTATAATTTTTA
3651427 TTGGTTTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 11 0.31
30 24 0.67
31 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTTTATAATTTTTAATAAAATTTAATAAC
Found at i:3651387 original size:30 final size:30
Alignment explanation
Indices: 3651353--3651416 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3651343 TTTTATAATT
*
3651353 TTTTTCTAATTTTTAATAAATTTTAA-ATAC
1 TTTTTCTAATTTTTAATAAAATTTAATA-AC
* * *
3651383 TTTTTGTATTTTTTATTAAAATTTAATAAC
1 TTTTTCTAATTTTTAATAAAATTTAATAAC
3651413 TTTT
1 TTTT
3651417 ATAACTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTTCTAATTTTTAATAAAATTTAATAAC
Found at i:3656437 original size:19 final size:18
Alignment explanation
Indices: 3656397--3656437 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3656387 TAATTTACAC
*
3656397 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
3656415 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
3656434 ATTT
1 ATTT
3656438 TGATTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:3657038 original size:16 final size:18
Alignment explanation
Indices: 3657007--3657052 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
3656997 TTAATAACTC
*
3657007 TTAATTTCACAAAATTTA
1 TTAATTTCACAAAATTAA
3657025 TTAATTT-A-AAAATTAA
1 TTAATTTCACAAAATTAA
*
3657041 TTAATTACACAA
1 TTAATTTCACAA
3657053 CTAACTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 13 0.54
17 2 0.08
18 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAATTTCACAAAATTAA
Found at i:3662292 original size:21 final size:22
Alignment explanation
Indices: 3662266--3662312 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3662256 CTCTGCTCAA
*
3662266 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3662287 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3662309 ACTC
1 ACTC
3662313 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3667796 original size:3 final size:3
Alignment explanation
Indices: 3667788--3667814 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3667778 CATATTAAAA
3667788 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
3667815 CTTTTGTTGC
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3676728 original size:10 final size:10
Alignment explanation
Indices: 3676713--3676737 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3676703 TATAGTTTGT
3676713 ATTTACTATA
1 ATTTACTATA
3676723 ATTTACTATA
1 ATTTACTATA
3676733 ATTTA
1 ATTTA
3676738 TTTAACTTGA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTACTATA
Found at i:3677861 original size:13 final size:14
Alignment explanation
Indices: 3677834--3677863 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3677824 GATTTAGGTT
3677834 TTTATTTTTAGAAA
1 TTTATTTTTAGAAA
3677848 TTTATTTTTA-AAA
1 TTTATTTTTAGAAA
3677861 TTT
1 TTT
3677864 TAAAATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTATTTTTAGAAA
Found at i:3679596 original size:22 final size:22
Alignment explanation
Indices: 3679571--3679616 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3679561 AATAAAATAA
* *
3679571 TATTTTTA-AAAATTCATATTAT
1 TATTTTAACAAAATTAAT-TTAT
3679593 TATTTTAACAAAATTAATTTAT
1 TATTTTAACAAAATTAATTTAT
3679615 TA
1 TA
3679617 ATAACATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTTAACAAAATTAATTTAT
Found at i:3679976 original size:3 final size:3
Alignment explanation
Indices: 3679968--3679994 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3679958 ATAGACGTGG
3679968 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3679995 GAGATCATGA
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:3681019 original size:24 final size:25
Alignment explanation
Indices: 3680971--3681022 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
3680961 TACTTGTAAA
*
3680971 AAATTATTATTTTAAGTAAAATATT
1 AAATTATTATTTTAAGAAAAATATT
3680996 AAATTATTA-TTTAA-AAAAATTATT
1 AAATTATTATTTTAAGAAAAA-TATT
3681020 AAA
1 AAA
3681023 AAAAATCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 12 0.48
25 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATTATTATTTTAAGAAAAATATT
Found at i:3685227 original size:15 final size:15
Alignment explanation
Indices: 3685207--3685250 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3685197 AGAAGATGGG
3685207 GATGCA-AAGGAAGAA
1 GATGCAGAA-GAAGAA
3685222 GATGCAGAAGAAGAA
1 GATGCAGAAGAAGAA
3685237 G-T--AGAAGAAGAA
1 GATGCAGAAGAAGAA
3685249 GA
1 GA
3685251 CGAAGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.41
14 1 0.04
15 13 0.48
16 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.07
Consensus pattern (15 bp):
GATGCAGAAGAAGAA
Done.