Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold511
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: 1668812
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 9 of 12
Found at i:1224691 original size:32 final size:33
Alignment explanation
Indices: 1224631--1224696 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1224621 TTCAACGATT
1224631 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
1224664 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1224696 T
1 T
1224697 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1224755 original size:13 final size:13
Alignment explanation
Indices: 1224737--1224761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1224727 ATTACTCAAA
1224737 TGTATCGATACAT
1 TGTATCGATACAT
1224750 TGTATCGATACA
1 TGTATCGATACA
1224762 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1224826 original size:52 final size:52
Alignment explanation
Indices: 1224770--1224898 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1224760 CACTGATCTT
*
1224770 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
1224822 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1224874 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1224899 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1238596 original size:13 final size:13
Alignment explanation
Indices: 1238578--1238603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1238568 TACAGCAAGT
1238578 ATGTATCGATACA
1 ATGTATCGATACA
1238591 ATGTATCGATACA
1 ATGTATCGATACA
1238604 GAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1238601 original size:32 final size:33
Alignment explanation
Indices: 1238560--1238623 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1238550 TAGCCAAACT
* **
1238560 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACAGAAAAAATTGTATCGATACAA
1238592 TGTATCGATACAGAAAAAATTGTATCGATACA
1 TGTATCGATACAGAAAAAATTGTATCGATACA
1238624 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAGAAAAAATTGTATCGATACAA
Found at i:1240853 original size:21 final size:21
Alignment explanation
Indices: 1240820--1240864 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1240810 TTGCAAGTTG
*
1240820 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1240842 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1240862 AAA
1 AAA
1240865 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1242606 original size:15 final size:15
Alignment explanation
Indices: 1242586--1242616 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1242576 TAAAAATGTC
*
1242586 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1242601 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1242616 C
1 C
1242617 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1244713 original size:13 final size:13
Alignment explanation
Indices: 1244695--1244720 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1244685 ACATTTTTCT
1244695 TTGTATCGATACA
1 TTGTATCGATACA
1244708 TTGTATCGATACA
1 TTGTATCGATACA
1244721 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1244884 original size:20 final size:20
Alignment explanation
Indices: 1244841--1244886 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1244831 AAATCTTTTG
1244841 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1244862 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1244882 CAAAA
1 CAAAA
1244887 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1246539 original size:14 final size:14
Alignment explanation
Indices: 1246520--1246563 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1246510 AAATAAATTT
1246520 TTGATATGAATTAC
1 TTGATATGAATTAC
*
1246534 TTGATA--AATT-T
1 TTGATATGAATTAC
1246545 TTGATATGAATTAC
1 TTGATATGAATTAC
1246559 TTGAT
1 TTGAT
1246564 TAAGGGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (14 bp):
TTGATATGAATTAC
Found at i:1246546 original size:25 final size:25
Alignment explanation
Indices: 1246512--1246563 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1246502 ATATGTGCAA
1246512 ATAAATTTTTGATATGAATTACTTG
1 ATAAATTTTTGATATGAATTACTTG
1246537 ATAAATTTTTGATATGAATTACTTG
1 ATAAATTTTTGATATGAATTACTTG
1246562 AT
1 AT
1246564 TAAGGGGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (25 bp):
ATAAATTTTTGATATGAATTACTTG
Found at i:1246665 original size:30 final size:30
Alignment explanation
Indices: 1246631--1246690 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1246621 ACAATTATTT
1246631 CATTAAGGGGGAGAATGTACAAATTTGTTA
1 CATTAAGGGGGAGAATGTACAAATTTGTTA
1246661 CATTAAGGGGGAGAATGTACAAATTTGTTA
1 CATTAAGGGGGAGAATGTACAAATTTGTTA
1246691 AATTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (30 bp):
CATTAAGGGGGAGAATGTACAAATTTGTTA
Found at i:1247351 original size:13 final size:13
Alignment explanation
Indices: 1247333--1247358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1247323 TACACCAAGT
1247333 ATGTATCGATACA
1 ATGTATCGATACA
1247346 ATGTATCGATACA
1 ATGTATCGATACA
1247359 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1247356 original size:32 final size:33
Alignment explanation
Indices: 1247315--1247378 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1247305 TAGCCAAACT
* **
1247315 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1247347 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1247379 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1248661 original size:33 final size:32
Alignment explanation
Indices: 1248619--1248726 Score: 141
Period size: 33 Copynumber: 3.3 Consensus size: 32
1248609 GTCCTCCGCA
*
1248619 AAAAGAAAAACAACAACAAAAAAAAAACAAAAC
1 AAAACAAAAA-AACAACAAAAAAAAAACAAAAC
*
1248652 AAAATAAAAAAACAACAATAAAAAAAACAAAAC
1 AAAACAAAAAAACAACAA-AAAAAAAACAAAAC
1248685 AAAAC--AAAAA-AACAAAAAAAAAACAACAAC
1 AAAACAAAAAAACAACAAAAAAAAAACAA-AAC
1248715 AACAACAAAAAA
1 AA-AACAAAAAA
1248727 GGGTCCGGAT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
29 11 0.16
30 10 0.15
31 8 0.12
32 8 0.12
33 31 0.46
ACGTcount: A:0.82, C:0.15, G:0.01, T:0.02
Consensus pattern (32 bp):
AAAACAAAAAAACAACAAAAAAAAAACAAAAC
Found at i:1248675 original size:47 final size:47
Alignment explanation
Indices: 1248624--1248726 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
1248614 CCGCAAAAAG
* *
1248624 AAAAACAACAACAA-AAAAAAAACAAAACAAAATAAAAA-AACAACAAT
1 AAAAAAAACAA-AACAAAAAAAA-AAAACAAAAAAAAAACAACAACAAT
* *
1248671 AAAAAAAACAAAACAAAACAAAAAAACAAAAAAAAAACAACAACAAC
1 AAAAAAAACAAAACAAAAAAAAAAAACAAAAAAAAAACAACAACAAT
1248718 AACAAAAAA
1 AA-AAAAAA
1248727 GGGTCCGGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
46 16 0.33
47 27 0.55
48 6 0.12
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.02
Consensus pattern (47 bp):
AAAAAAAACAAAACAAAAAAAAAAAACAAAAAAAAAACAACAACAAT
Found at i:1248719 original size:38 final size:38
Alignment explanation
Indices: 1248618--1248719 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
1248608 CGTCCTCCGC
*
1248618 AAAAAGAAAAACAACAACAAAAAAAAAACAAAACAAAAT
1 AAAAA-AAAAACAACAACAAAAACAAAACAAAACAAAAT
* * *
1248657 AAAAAAACAACAATAAAAAAAACAAAACAAAACAAAA-
1 AAAAAAAAAACAACAACAAAAACAAAACAAAACAAAAT
* *
1248694 AAACAAAAAAAAAACAACAACAACAA
1 AAA-AAAAAAACAACAACAAAAACAA
1248720 CAAAAAAGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
37 3 0.06
38 45 0.85
39 5 0.09
ACGTcount: A:0.82, C:0.15, G:0.01, T:0.02
Consensus pattern (38 bp):
AAAAAAAAAACAACAACAAAAACAAAACAAAACAAAAT
Found at i:1248726 original size:1 final size:1
Alignment explanation
Indices: 1248636--1248707 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
1248626 AAACAACAAC
* * * * * * * * * *
1248636 AAAAAAAAAACAAAACAAAATAAAAAAACAACAATAAAAAAAACAAAACAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1248701 AAAAAAA
1 AAAAAAA
1248708 CAACAACAAC
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:1250190 original size:29 final size:30
Alignment explanation
Indices: 1250151--1250440 Score: 197
Period size: 29 Copynumber: 9.6 Consensus size: 30
1250141 TCACCCTTCA
1250151 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
1250180 AAAGCCCACAAGTCAGTGGCATTTTTTTTTA
1 AAAGCCCACAAGTCAGTGGCA-CTCTTTTTC
1250211 AAAGCCCACAAGTCAGTGGCAAC-C---TTC
1 AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* *
1250238 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
1250268 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
1250297 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * * * *
1250327 TTTTGTAAGCTCACAACTCTA-TAGCACTATTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCACTCTTTTTC
* * *
1250362 TTTTTAAGCCCACAAGTTAGTGGCACAC-TTTTC
1 ----AAAGCCCACAAGTCAGTGGCACTCTTTTTC
*
1250395 AAAAGCCCACAAGTCAGTGGCAAC-C--TTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
1250424 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
1250441 AGCAACCTTC
Statistics
Matches: 212, Mismatches: 33, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.01
27 22 0.10
28 17 0.08
29 47 0.22
30 47 0.22
31 28 0.13
32 1 0.00
33 6 0.03
34 19 0.09
35 23 0.11
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:1250253 original size:27 final size:27
Alignment explanation
Indices: 1250211--1250263 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1250201 TTTTTTTTTA
*
1250211 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
1250238 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
1250264 TTTCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:1250343 original size:35 final size:34
Alignment explanation
Indices: 1250302--1250376 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
1250292 TTTCCAAAGT
* * *
1250302 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTATTTTTCTTTT-TAAGC
* *
1250337 TCACAACTCTATAGCACTATTTTTCTTTTTAAGC
1 CCACAACTCCATAGCACTATTTTTCTTTTTAAGC
1250371 CCACAA
1 CCACAA
1250377 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.37
Consensus pattern (34 bp):
CCACAACTCCATAGCACTATTTTTCTTTTTAAGC
Found at i:1250401 original size:30 final size:29
Alignment explanation
Indices: 1250367--1250490 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 29
1250357 TTTTCTTTTT
* *
1250367 AAGCCCACAAGTTAGTGGCACACTTTTCAA
1 AAGCCCACAAGTCAGTGGCA-ACCTTTCAA
1250397 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
1250425 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
1250453 AAGCACACAAGT-TGAT-GCAAACCTTGCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
1250482 AAGCCCACA
1 AAGCCCACA
1250491 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 42 0.51
29 17 0.20
30 19 0.23
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:1250638 original size:52 final size:52
Alignment explanation
Indices: 1250510--1250711 Score: 250
Period size: 49 Copynumber: 3.9 Consensus size: 52
1250500 GGCGTCTCCT
1250510 TTTAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA--
1 TTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
*
1250560 -TTAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
* * *
1250611 TTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CATC
* * * * * *
1250666 TTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1250712 ATCACTTTTC
Statistics
Matches: 131, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
49 45 0.34
50 2 0.02
52 36 0.27
53 5 0.04
54 6 0.05
55 37 0.28
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (52 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
Found at i:1251538 original size:13 final size:13
Alignment explanation
Indices: 1251520--1251544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1251510 CATAAAGTGT
1251520 TGTATCGATACAA
1 TGTATCGATACAA
1251533 TGTATCGATACA
1 TGTATCGATACA
1251545 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1251560 original size:32 final size:33
Alignment explanation
Indices: 1251500--1251565 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1251490 TTCAACGATT
1251500 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
1251533 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1251565 T
1 T
1251566 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1251624 original size:13 final size:13
Alignment explanation
Indices: 1251606--1251631 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1251596 ATTACTCAAA
1251606 TGTATCGATACAT
1 TGTATCGATACAT
1251619 TGTATCGATACAT
1 TGTATCGATACAT
1251632 GCAGGAAAAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1251681 original size:52 final size:52
Alignment explanation
Indices: 1251619--1251747 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1251609 ATCGATACAT
* *
1251619 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
1251671 TGTATCGATACATGCATGCAAATTTGCCCAGATGTATCGATACACTATTTAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1251723 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1251748 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1255364 original size:672 final size:663
Alignment explanation
Indices: 1254146--1255458 Score: 1977
Period size: 672 Copynumber: 2.0 Consensus size: 663
1254136 TTCTTTTATG
* * * *
1254146 TTAATCTTGATGGCATTCGTATTTTAAAACTGGTTTACAAAAACCGTAAAGCAATGTTTCGTGCC
1 TTAATCTTGATGGCACTCATATTTTAAAACTGGTTTACAAAAACCGTAAAGCAATATTCCGTGCC
*
1254211 GGTATCTCTCCAGTGCTTGACACGGAATATCCTATTTCCAAAATAAAATCCAGAGAGCTTTTATA
66 GGTATCTCTCCAGTGCTTGACACGGAATATCCTATTTCCAAAATAAAATCCAGAGAGCCTTTATA
*
1254276 TCTCTATGTTTCCCATCTCTCCGGGGCGCATATGAGATGATCAAAACCTGGATTTATTTTCTTGC
131 TCTCTATGTTTCCCATCTCTCCGGGGCGCATATGAGATGATCAAAACCTGGATTTATTTTCTTAC
* * *
1254341 AAAATTCATACATTTAAAGGGGATCATATCGAAATAATGAGAAACCGAAATCAATGAAATCAACT
196 AAAATTCATACATTCAAAGAGGATCATATCGAAATAATGAGAAACCGAAATCAATGAAATCAACA
* * *
1254406 TTAAGTCAAAGCATTGCTAGTAAGGTATCGATTTCGGGCCTCGCGAGGAGGTTCGTACCTCTTTG
261 TCAAGTCAAAACATTGCTAGTAAGGTACCGATTTCGGGCCTCGCGAGGAGGTTCGTACCTCTTTG
* * **
1254471 CGCGTAGCCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTATGCAGACCACGGGATCGATGTT
326 CGCGTAACCAACTCCCAAACCCAACCGGCGAATCTCTAAAGTACACAGACCACGGGATCGATGTT
* * *
1254536 TTGAGTTTCGTAACTCAAGATATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATC
391 TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGCCATCCGATCATGCCTAGCCCAAAATGATC
* * *
1254601 GGTGGCGACTCCAAAATCTCGGTCACTTCGTAGCGACCATTGAAGATCAAGTAGATGGGCGATTC
456 GATGACGACTCCAAAATCTCGGTCACTTCGTAGCGACCATTGAAGATCAAGTAGATGGGCAATTC
* * * *
1254666 ATCTACTGATCTTCCCCCTTTAATCAACATATTTCCCCTCATGCCATAGAAATCCCCAATCGCGA
521 ATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCATGCCATAAAAATCCCCAATCGCGA
*
1254731 GGGATATTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAGCA
586 GGGATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAGCA
1254796 TGCTTACTCTTTA
651 TGCTTACTCTTTA
* * * **
1254809 TTAATCTTGATGGCACTCATATTTTAAAACTGGTTTACAAAAATCTTAAGGCAATATTCCGTGTT
1 TTAATCTTGATGGCACTCATATTTTAAAACTGGTTTACAAAAACCGTAAAGCAATATTCCGTGCC
* * * *
1254874 TGTATCTCTCCAGTGCTTGACACGGAATATCC-AGTTTTCAAAGTGAAATCCAGAG-GTCACTTT
66 GGTATCTCTCCAGTGCTTGACACGGAATATCCTA-TTTCCAAAATAAAATCCAGAGAG-C-CTTT
* * *
1254937 ATATCTCTATGTTTCCCATTTCTCCGTGGCGCATATGAGATTAAAATTTTATCAAAACCTGGATT
128 ATATCTCTATGTTTCCCATCTCTCCGGGGCGCATATGAG------A--TGATCAAAACCTGGATT
* * * *
1255002 TATTTT-TATACAAAATTCATGCATTCGAAGAGGATCATATCGAAATAATGATAAATCGAAA-CA
185 TATTTTCT-TACAAAATTCATACATTCAAAGAGGATCATATCGAAATAATGAGAAACCGAAATC-
* * *
1255065 AATGTAATCAACATCAAGTCAAAACATTGCTAGTAAGGTACCGATTTTGGGCGTCGCGAGGAGGT
248 AATGAAATCAACATCAAGTCAAAACATTGCTAGTAAGGTACCGATTTCGGGCCTCGCGAGGAGGT
* * * *
1255130 TTGTACCTCTTTGCGCGTAACCAACTCCCAAACCCAACCGGTGAATCTCTAAATTACATAGACCA
313 TCGTACCTCTTTGCGCGTAACCAACTCCCAAACCCAACCGGCGAATCTCTAAAGTACACAGACCA
1255195 CGGGATCGATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGCCATCCGATCATGCCTA
378 CGGGATCGATGTTTTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGCCATCCGATCATGCCTA
* * * *
1255260 GCCCAAAATGATCGATGACGACTCCAAAATTTCGGTCACTTTGTAGTGACCATTGAAGATCAATT
443 GCCCAAAATGATCGATGACGACTCCAAAATCTCGGTCACTTCGTAGCGACCATTGAAGATCAAGT
1255325 AGATGGGCAATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCATGCCATAAAAA
508 AGATGGGCAATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCATGCCATAAAAA
* *
1255390 TCCCCAATCGCGAGGGATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTTGAGTGCA
573 TCCCCAATCGCGAGGGATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCA
1255455 CGTT
638 CGTT
1255459 GCAACAGGGA
Statistics
Matches: 581, Mismatches: 56, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
662 2 0.00
663 106 0.18
664 40 0.07
670 1 0.00
671 2 0.00
672 430 0.74
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (663 bp):
TTAATCTTGATGGCACTCATATTTTAAAACTGGTTTACAAAAACCGTAAAGCAATATTCCGTGCC
GGTATCTCTCCAGTGCTTGACACGGAATATCCTATTTCCAAAATAAAATCCAGAGAGCCTTTATA
TCTCTATGTTTCCCATCTCTCCGGGGCGCATATGAGATGATCAAAACCTGGATTTATTTTCTTAC
AAAATTCATACATTCAAAGAGGATCATATCGAAATAATGAGAAACCGAAATCAATGAAATCAACA
TCAAGTCAAAACATTGCTAGTAAGGTACCGATTTCGGGCCTCGCGAGGAGGTTCGTACCTCTTTG
CGCGTAACCAACTCCCAAACCCAACCGGCGAATCTCTAAAGTACACAGACCACGGGATCGATGTT
TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGCCATCCGATCATGCCTAGCCCAAAATGATC
GATGACGACTCCAAAATCTCGGTCACTTCGTAGCGACCATTGAAGATCAAGTAGATGGGCAATTC
ATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCATGCCATAAAAATCCCCAATCGCGA
GGGATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAGCA
TGCTTACTCTTTA
Found at i:1257919 original size:123 final size:123
Alignment explanation
Indices: 1257700--1257944 Score: 411
Period size: 123 Copynumber: 2.0 Consensus size: 123
1257690 GAGTCTAAAA
*
1257700 TTAACAATTGATATCTTTGTATGTCATGTATGCTTGAAATATTTACATTGTATGAATGTTTGAAC
1 TTAACAATTGATATCTTTGTATGTCATGTATGCTTGAAATATTTACATTGTATGAATCTTTGAAC
** *
1257765 ATGGCTATTAGTTAAATTACCTTGATTGAATTAACTTGACTTAGCTCATAGATCAAAC
66 ATGGCTAGGAGTTAAATTACCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAAC
* * *
1257823 TTAACAATTGATATCTTTGTATGTCGTGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAAC
1 TTAACAATTGATATCTTTGTATGTCATGTATGCTTGAAATATTTACATTGTATGAATCTTTGAAC
1257888 ATGGCTAGGAGTTCAAA-TACCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAA
66 ATGGCTAGGAGTT-AAATTACCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAA
1257945 ATGCCTAATG
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
123 111 0.97
124 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (123 bp):
TTAACAATTGATATCTTTGTATGTCATGTATGCTTGAAATATTTACATTGTATGAATCTTTGAAC
ATGGCTAGGAGTTAAATTACCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAAC
Found at i:1258673 original size:16 final size:16
Alignment explanation
Indices: 1258652--1258683 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1258642 TGTTTTTTTA
1258652 AGCTATAAATCATATG
1 AGCTATAAATCATATG
1258668 AGCTATAAATCATATG
1 AGCTATAAATCATATG
1258684 TTTTAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
AGCTATAAATCATATG
Found at i:1268132 original size:34 final size:35
Alignment explanation
Indices: 1268093--1268165 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
1268083 AATTTCTACA
*
1268093 TTTCAAAGAGCTTTTGTATT-CTTTGTTG-TTATTC
1 TTTCAAAGAGCATTTGTATTCCTTTG-TGCTTATTC
**
1268127 TTTCAAAGCTCATTTGTATTCCTTTGTGCTTATTC
1 TTTCAAAGAGCATTTGTATTCCTTTGTGCTTATTC
1268162 TTTC
1 TTTC
1268166 CACAAACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.55
Consensus pattern (35 bp):
TTTCAAAGAGCATTTGTATTCCTTTGTGCTTATTC
Found at i:1269548 original size:13 final size:13
Alignment explanation
Indices: 1269530--1269556 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1269520 ACCAAGGAAA
1269530 TGTATCGATACAT
1 TGTATCGATACAT
1269543 TGTATCGATACAT
1 TGTATCGATACAT
1269556 T
1 T
1269557 ATTCAATGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1271005 original size:19 final size:19
Alignment explanation
Indices: 1270981--1271025 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1270971 AAACAGTAAA
1270981 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
* *
1271000 TGTATCGATATATAAGTTT
1 TGTATCGATACATAAGTGT
1271019 TGTATCG
1 TGTATCG
1271026 CTGCAAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1271088 original size:13 final size:13
Alignment explanation
Indices: 1271070--1271095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1271060 ATTTTTTCAA
1271070 TGTATCGATACAT
1 TGTATCGATACAT
1271083 TGTATCGATACAT
1 TGTATCGATACAT
1271096 CTAGGAAGTT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1273503 original size:48 final size:48
Alignment explanation
Indices: 1273430--1273555 Score: 216
Period size: 48 Copynumber: 2.6 Consensus size: 48
1273420 AAATCTCTAG
* *
1273430 ATTTTTCATCTCGGGGATACTCCAACTCTGGTTTTATTTCTAAAACATCA
1 ATTTTTCA--TCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
1273480 ATTTTTCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
1 ATTTTTCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
1273528 ATTTTTCATCGGGGATACTCCAACCCCG
1 ATTTTTCATCGGGGATACTCCAACCCCG
1273556 TTATTTCCGA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
48 66 0.89
50 8 0.11
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (48 bp):
ATTTTTCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
Found at i:1273657 original size:28 final size:26
Alignment explanation
Indices: 1273617--1273690 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 26
1273607 TTTTTCATAA
1273617 TCAGGGG-TACTCCAACCCTGTTA-TT
1 TCAGGGGATACTCCAACCC-GTTATTT
1273642 TCATCGGGGATACTCCAATCCCGTTATTT
1 TCA--GGGGATACTCCAA-CCCGTTATTT
1273671 TCGAGGGGATACTCCAACCC
1 TC-AGGGGATACTCCAACCC
1273691 CAATTTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
25 3 0.07
27 7 0.16
28 25 0.58
29 7 0.16
30 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (26 bp):
TCAGGGGATACTCCAACCCGTTATTT
Found at i:1273659 original size:81 final size:75
Alignment explanation
Indices: 1273483--1273666 Score: 208
Period size: 81 Copynumber: 2.4 Consensus size: 75
1273473 AACATCAATT
*
1273483 TTTCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTC
1 TTTCATCGGGGATACTCCAACCCC-GTTTTATATCTAAAACATCAATTTTTCATCGGGGATACTC
1273548 CAACCCCGTTA
65 CAACCCCGTTA
*** * * *
1273559 TTTCCGAGGGGATACTCCAACCCCGTCTTTATATCTAAAAATATTATTTTTTTCATAATCAGGGG
1 TTTCATCGGGGATACTCCAACCCCGT-TTTATATCT-AAAACATCA-ATTTTTC---ATC-GGGG
*
1273624 -TACTCCAACCCTGTTA
59 ATACTCCAACCCCGTTA
*
1273640 TTTCATCGGGGATACTCCAATCCCGTT
1 TTTCATCGGGGATACTCCAACCCCGTT
1273667 ATTTTCGAGG
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
75 2 0.02
76 29 0.33
77 7 0.08
78 6 0.07
80 1 0.01
81 40 0.45
82 4 0.04
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (75 bp):
TTTCATCGGGGATACTCCAACCCCGTTTTATATCTAAAACATCAATTTTTCATCGGGGATACTCC
AACCCCGTTA
Found at i:1273736 original size:51 final size:51
Alignment explanation
Indices: 1273675--1273792 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
1273665 TTATTTTCGA
* *
1273675 GGGGATACTCCAACCCCAATTTTA-TTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTTC-AAAACACCAATTTCTCACAATC
* *
1273726 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTCTCACAATC
*
1273777 GGAGATACTCCAACCC
1 GGGGATACTCCAACCC
1273793 TGCTATTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 56 0.93
52 4 0.07
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTCTCACAATC
Found at i:1275830 original size:4 final size:4
Alignment explanation
Indices: 1275821--1275849 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1275811 TATTTTGAGG
1275821 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
1275850 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1283114 original size:19 final size:19
Alignment explanation
Indices: 1283090--1283139 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1283080 ATCGATACCA
1283090 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
1283109 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
1283128 TGTATCGATACA
1 TGTATCGATACA
1283140 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1283246 original size:52 final size:52
Alignment explanation
Indices: 1283168--1283295 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
1283158 ACTGCCAATA
*
1283168 AAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTACG
1 AAATGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTACG
* * *
1283220 AAATGTATCGATAGATACAGGCAAATTTGCCCAGATGTATCGATACATTTC-
1 AAATGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTACG
* *
1283271 ATAGTGTATCGATACATGCAGGCAA
1 A-AATGTATCGATACATACAGGCAA
1283296 CTTTTCGTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 67 0.99
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (52 bp):
AAATGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTACG
Found at i:1297154 original size:29 final size:30
Alignment explanation
Indices: 1297109--1297228 Score: 131
Period size: 29 Copynumber: 4.0 Consensus size: 30
1297099 GGCATCCTCC
1297109 ACAAA-AAAAAAACAACAAAACAAACAAAAA
1 ACAAACAAAAAAA-AACAAAACAAACAAAAA
* *
1297139 A-AAAGAAAAAAAAACAAAACAAAAAAAAA
1 ACAAACAAAAAAAAACAAAACAAACAAAAA
* *
1297168 ACAAACAAACAAAAA-AAAAGAAGA-AAAAA
1 ACAAACAAAAAAAAACAAAACAA-ACAAAAA
*
1297197 ACAAACAAACAAAAACAAAACAACAACAAAAA
1 ACAAACAAAAAAAAACAAAAC-A-AACAAAAA
1297229 GGGTCCGGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
29 46 0.59
30 24 0.31
31 2 0.03
32 6 0.08
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (30 bp):
ACAAACAAAAAAAAACAAAACAAACAAAAA
Found at i:1297162 original size:48 final size:48
Alignment explanation
Indices: 1297109--1297222 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 48
1297099 GGCATCCTCC
1297109 ACAAAAAAAAAACAACAAAACAAACAAAAAAAAAG-AAAAAA-AAACAAA
1 ACAAAAAAAAAACAACAAAACAAA-AAAAAAAAAGAAAAAAACAAAC-AA
*
1297157 ACAAAAAAAAAACAA-ACAAACAAAAAAAAAGAAGAAAAAAACAAACAA
1 ACAAAAAAAAAACAACA-AAACAAAAAAAAAAAAGAAAAAAACAAACAA
*
1297205 ACAAAAACAAAACAACAA
1 ACAAAAAAAAAACAACAA
1297223 CAAAAAGGGT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
47 10 0.17
48 45 0.75
49 5 0.08
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (48 bp):
ACAAAAAAAAAACAACAAAACAAAAAAAAAAAAGAAAAAAACAAACAA
Found at i:1297164 original size:44 final size:44
Alignment explanation
Indices: 1297109--1297228 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 44
1297099 GGCATCCTCC
1297109 ACAAAA-AAAAAACAACAAAACAAACAAAAAAAAAGAA-AAAAAA
1 ACAAAACAAAAAA-AACAAAACAAACAAAAAAAAAGAAGAAAAAA
*
1297152 ACAAAACAAAAAAAAAACAAACAAACAAAAAAAAAGAAGAAAAAA
1 ACAAAACAAAAAAAACA-AAACAAACAAAAAAAAAGAAGAAAAAA
*
1297197 AC-AAACAAACAAAAACAAAAC-AACAACAAAAA
1 ACAAAACAAA-AAAAACAAAACAAACAAAAAAAA
1297229 GGGTCCGGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
43 19 0.27
44 37 0.53
45 14 0.20
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (44 bp):
ACAAAACAAAAAAAACAAAACAAACAAAAAAAAAGAAGAAAAAA
Found at i:1297228 original size:1 final size:1
Alignment explanation
Indices: 1297111--1297216 Score: 68
Period size: 1 Copynumber: 106.0 Consensus size: 1
1297101 CATCCTCCAC
* * * * * * * * *
1297111 AAAAAAAAAACAACAAAACAAACAAAAAAAAAGAAAAAAAAACAAAACAAAAAAAAAACAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1297176 ACAAAAAAAAAGAAGAAAAAAACAAACAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1297217 CAACAACAAA
Statistics
Matches: 73, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1298718 original size:27 final size:28
Alignment explanation
Indices: 1298648--1298816 Score: 200
Period size: 28 Copynumber: 6.0 Consensus size: 28
1298638 CATTCCTCAC
*
1298648 CCTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1298676 CTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
*
1298705 CCTTC-AAAGCCCACAAGTTAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1298732 CCTTCAAAAGCCCACAAGTTAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1298760 CCTTTTTC-AAAGCCCACAAATCGGTGGCAA
1 CC---TTCAAAAGCCCACAAGTCAGTGGCAA
*
1298790 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
1298817 TCTTTTTCCT
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
27 32 0.26
28 43 0.35
29 22 0.18
30 23 0.19
31 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1298788 original size:58 final size:55
Alignment explanation
Indices: 1298648--1298816 Score: 196
Period size: 58 Copynumber: 3.0 Consensus size: 55
1298638 CATTCCTCAC
* * *
1298648 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 CCTTC-AAAGCCCACAAATCAGTGGCAAC--CTTCAAAAGCCCACAAGTCAGTGGCAA
* * * *
1298705 CCTTCAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAC
1 CCTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1298760 CCTTTTTCAAAGCCCACAAATCGGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCA
1 CC---TTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCA
1298817 TCTTTTTCCT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.03
55 22 0.22
56 21 0.21
57 5 0.05
58 47 0.48
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (55 bp):
CCTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1298839 original size:33 final size:33
Alignment explanation
Indices: 1298797--1298886 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 33
1298787 CAACCTTCAA
*
1298797 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
1298830 AAGCCCACAACTCCATGGC-TCCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
1298862 AAGTCCACAACTCCGTGGCAGCTTT
1 AAGCCCACAACTCCGTGGCATCTTT
1298887 AAGCCTAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 28 0.58
33 20 0.42
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.33
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
Found at i:1298985 original size:35 final size:35
Alignment explanation
Indices: 1298926--1299026 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
1298916 ATATTGGCAC
*
1298926 CTTTTCTTTTTTAAGTCCACAACTCCGT-GC-CACTT
1 CTTTTC-TTTTTAAGCCCACAACTCCGTGGCACAC-T
*
1298961 CTTTTCTTTTGTAAGCCCATAACTCCGTGGCACACT
1 CTTTTCTTTT-TAAGCCCACAACTCCGTGGCACACT
* * *
1298997 -TTTTCCTTTTAAGCCCACAAGTCGGTGGCA
1 CTTTTCTTTTTAAGCCCACAACTCCGTGGCA
1299027 TCTTTTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 22 0.39
35 29 0.51
36 3 0.05
37 3 0.05
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (35 bp):
CTTTTCTTTTTAAGCCCACAACTCCGTGGCACACT
Found at i:1299311 original size:39 final size:40
Alignment explanation
Indices: 1299257--1299629 Score: 241
Period size: 39 Copynumber: 8.6 Consensus size: 40
1299247 CTAATGTCGA
*
1299257 TGGCCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGC
1 TGGCCTTGAATCAGCATATTGGCATTAAGCCCAATATCGC
* *
1299296 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCAC
1 TGGCCTTGAATCAGCATATTGG------CA---TTAAGCCCAATATCGC
* * * *
1299345 TGGCTTTGAATCAGCATATTGGCACCTTATCTTTAAGACTAATGTCGC
1 TGGCCTTGAATCAGCATATTGG---C--A---TTAAGCCCAATATCGC
* *
1299393 TGGCCTTGATTCAGCACATTGGCA-TAAGCCCAATATCGC
1 TGGCCTTGAATCAGCATATTGGCATTAAGCCCAATATCGC
* * *
1299432 TGACCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCATATTGGCA--------TTAAGCCCAATATCGC
* ** *
1299480 TGGCCTTGAATCAACGCATTAGCA-TAAGCCCAATATCGC
1 TGGCCTTGAATCAGCATATTGGCATTAAGCCCAATATCGC
* * *
1299519 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGT
1 TGGCCTTGAATCAGCATATTGGCA--------TTAAGCCCAATATCGC
*
1299567 TGGCCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGC
1 TGGCCTTGAATCAGCATATTGGCATTAAGCCCAATATCGC
1299606 TGGCCTTGAATCAGCATATTGGCA
1 TGGCCTTGAATCAGCATATTGGCA
1299630 CCTTGTCTTT
Statistics
Matches: 264, Mismatches: 40, Indels: 60
0.73 0.11 0.16
Matches are distributed among these distances:
39 122 0.46
43 1 0.00
45 3 0.01
46 2 0.01
48 102 0.39
49 34 0.13
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (40 bp):
TGGCCTTGAATCAGCATATTGGCATTAAGCCCAATATCGC
Found at i:1299397 original size:136 final size:136
Alignment explanation
Indices: 1299158--1299492 Score: 546
Period size: 136 Copynumber: 2.5 Consensus size: 136
1299148 GACCAATGTT
* * **
1299158 GCTGGCCTTGAATCAACACATTGGCTTCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCAG
*
1299223 CATATTGGCACCTTGTCTCTAAGACTAATGTCGATGGCCTTGAATCAGCACATTGGCATAAGCCC
66 CATATTGGCACCTTATCTCTAAGACTAATGTCGATGGCCTTGAATCAGCACATTGGCATAAGCCC
1299288 AATATC
131 AATATC
*
1299294 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCTTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCAG
* * *
1299359 CATATTGGCACCTTATCTTTAAGACTAATGTCGCTGGCCTTGATTCAGCACATTGGCATAAGCCC
66 CATATTGGCACCTTATCTCTAAGACTAATGTCGATGGCCTTGAATCAGCACATTGGCATAAGCCC
1299424 AATATC
131 AATATC
* * * *
1299430 GCTGACCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGTCCAATGTCGCTGGCCTTGAATCA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCA
1299493 ACGCATTAGC
Statistics
Matches: 185, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
135 29 0.16
136 156 0.84
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (136 bp):
GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCAG
CATATTGGCACCTTATCTCTAAGACTAATGTCGATGGCCTTGAATCAGCACATTGGCATAAGCCC
AATATC
Found at i:1299446 original size:87 final size:87
Alignment explanation
Indices: 1299330--1299677 Score: 570
Period size: 87 Copynumber: 4.0 Consensus size: 87
1299320 CCTTCATCTT
* * * * * *
1299330 TAAGTCCAATATCACTGGCTTTGAATCAGCATATTGGCACCTTATCTTTAAGACTAATGTCGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
* *
1299395 GCCTTGATTCAGCACATTGGCA
66 GCCTTGAATCAACACATTGGCA
*
1299417 TAAGCCCAATATCGCTGACCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
* *
1299482 GCCTTGAATCAACGCATTAGCA
66 GCCTTGAATCAACACATTGGCA
*
1299504 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGTTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
*
1299569 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAACACATTGGCA
*
1299591 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATATCGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
1299656 GCCTTGAATCAACACATTGGCA
66 GCCTTGAATCAACACATTGGCA
1299678 CCTTCATCTT
Statistics
Matches: 242, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 242 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (87 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTCGCTG
GCCTTGAATCAACACATTGGCA
Found at i:1300597 original size:13 final size:13
Alignment explanation
Indices: 1300579--1300603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1300569 ATTACTCAAA
1300579 TGTATCGATACAT
1 TGTATCGATACAT
1300592 TGTATCGATACA
1 TGTATCGATACA
1300604 CTGATCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1301453 original size:13 final size:13
Alignment explanation
Indices: 1301435--1301460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1301425 CAATTTTTTG
1301435 TGTATCGATACAT
1 TGTATCGATACAT
1301448 TGTATCGATACAT
1 TGTATCGATACAT
1301461 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1309361 original size:52 final size:52
Alignment explanation
Indices: 1309283--1309411 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1309273 CAAAATATGA
* *
1309283 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1309335 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1309387 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1309412 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1309424 original size:52 final size:51
Alignment explanation
Indices: 1309283--1309431 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
1309273 CAAAATATGA
*
1309283 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1309335 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1309387 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1309432 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1309438 original size:13 final size:13
Alignment explanation
Indices: 1309420--1309444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1309410 CAAAGATCAG
1309420 TGTATCGATACAA
1 TGTATCGATACAA
1309433 TGTATCGATACA
1 TGTATCGATACA
1309445 TTTGAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1309463 original size:34 final size:34
Alignment explanation
Indices: 1309420--1309499 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
1309410 CAAAGATCAG
*
1309420 TGTATCGATACAATGTATCGATACATTTGAGTGA
1 TGTATCGATACAAAGTATCGATACATTTGAGTGA
1309454 TGTATCGATACAAAGTATCGATACATTTGAGTGA
1 TGTATCGATACAAAGTATCGATACATTTGAGTGA
1309488 TGTATCGATACA
1 TGTATCGATACA
1309500 TTTTTTGGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (34 bp):
TGTATCGATACAAAGTATCGATACATTTGAGTGA
Found at i:1309559 original size:33 final size:33
Alignment explanation
Indices: 1309522--1309585 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1309512 AGCTTAAATT
1309522 GTATCGATACAAAAAAATATGTATCGATACATA
1 GTATCGATACAAAAAAATATGTATCGATACATA
* ***
1309555 GTATCGATACAACACTTTATGTATCGATACA
1 GTATCGATACAAAAAAATATGTATCGATACA
1309586 AATCGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (33 bp):
GTATCGATACAAAAAAATATGTATCGATACATA
Found at i:1311844 original size:1 final size:1
Alignment explanation
Indices: 1311840--1311902 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
1311830 ATTCTTTTTC
* * * * * * *
1311840 AAAAAAAAAACAAAAAAACAAAAAAAAACAAAAACAAAAAAAAAACAAAACAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1311903 GAGAAAAGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1311864 original size:17 final size:16
Alignment explanation
Indices: 1311842--1311902 Score: 86
Period size: 16 Copynumber: 3.7 Consensus size: 16
1311832 TCTTTTTCAA
1311842 AAAAAAAACAAAAAAAC
1 AAAAAAAA-AAAAAAAC
*
1311859 AAAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAC
*
1311875 AAAAAAAAAACAAAAC
1 AAAAAAAAAAAAAAAC
1311891 AAAGAAAAAAAA
1 AAA-AAAAAAAA
1311903 GAGAAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 24 0.62
17 15 0.38
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:1317347 original size:52 final size:52
Alignment explanation
Indices: 1317256--1317383 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1317246 CGATATATGA
* *
1317256 AAATTTACCTGCATGTAT-GATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1317307 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1317359 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1317384 AAGATTAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 17 0.23
52 56 0.77
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1317484 original size:20 final size:20
Alignment explanation
Indices: 1317455--1317512 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1317445 GCAGTAGCTT
1317455 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1317474 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1317494 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1317513 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1317595 original size:24 final size:21
Alignment explanation
Indices: 1317548--1317596 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1317538 GTTGGGATCT
*
1317548 TGTATCGATACATTCTAAAAA
1 TGTATCGATACATTATAAAAA
1317569 TGTATCGATACATTTGGATAAAAA
1 TGTATCGATACA-TT--ATAAAAA
1317593 TGTA
1 TGTA
1317597 ATTTTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
24 10 0.42
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTATAAAAA
Found at i:1318246 original size:13 final size:13
Alignment explanation
Indices: 1318228--1318255 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1318218 CGTTACAAGC
1318228 CAATGTATCGATA
1 CAATGTATCGATA
1318241 CAATGTATCGATA
1 CAATGTATCGATA
1318254 CA
1 CA
1318256 TATTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1318354 original size:20 final size:21
Alignment explanation
Indices: 1318307--1318359 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1318297 GCCAATGACC
**
1318307 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
1318328 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
1318348 TGTATCGATACA
1 TGTATCGATACA
1318360 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:1318365 original size:13 final size:13
Alignment explanation
Indices: 1318347--1318375 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1318337 ACATTTGGTC
1318347 ATGTATCGATACA
1 ATGTATCGATACA
1318360 ATGTATCGATACA
1 ATGTATCGATACA
1318373 ATG
1 ATG
1318376 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1318386 original size:20 final size:20
Alignment explanation
Indices: 1318361--1318411 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1318351 ATCGATACAA
*
1318361 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * * *
1318381 TGTATCAATACATTTAAATG
1 TGTATCGATACAATGAAATC
1318401 TGTATCGATAC
1 TGTATCGATAC
1318412 TTTTCAGGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:1320728 original size:20 final size:21
Alignment explanation
Indices: 1320699--1320739 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1320689 TATTTTTGTT
1320699 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1320718 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1320740 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1320900 original size:13 final size:13
Alignment explanation
Indices: 1320870--1320908 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1320860 TATAATCTCC
*
1320870 TTGTATCGATGCA
1 TTGTATCGATACA
* *
1320883 CTGTATTGATACA
1 TTGTATCGATACA
1320896 TTGTATCGATACA
1 TTGTATCGATACA
1320909 AAGAATTCTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1323499 original size:22 final size:22
Alignment explanation
Indices: 1323474--1323518 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1323464 TCTTCCAATG
1323474 TCCGATTTTTCCTTTCAACGAC
1 TCCGATTTTTCCTTTCAACGAC
*
1323496 TCCGATTTTTCCTTTCAAGGAC
1 TCCGATTTTTCCTTTCAACGAC
1323518 T
1 T
1323519 TTTTTTGTTC
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:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (22 bp):
TCCGATTTTTCCTTTCAACGAC
Found at i:1325136 original size:28 final size:27
Alignment explanation
Indices: 1325069--1325141 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
1325059 CTTCAAAATC
**
1325069 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
1325096 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
*
1325124 GGGGATATTCCAACCCCG
1 GGGGATACTCCAACCCCG
1325142 ACTTTCTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:1325187 original size:51 final size:51
Alignment explanation
Indices: 1325124--1325345 Score: 219
Period size: 52 Copynumber: 4.3 Consensus size: 51
1325114 TTATTTCCGA
* * * * *** *
1325124 GGGGATATTCCAACCCCGACTTTCTTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * *
1325175 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT-CACAATC
* * * * * **
1325227 GGGGATACTTCAACCCTGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATC
* *
1325279 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATC
*
1325331 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1325346 TCGTTATTTC
Statistics
Matches: 138, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 36 0.26
52 88 0.64
53 14 0.10
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:1325390 original size:28 final size:28
Alignment explanation
Indices: 1325333--1325395 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1325323 TCACAATCGA
* * **
1325333 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1325361 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1325389 GGATACT
1 GGATACT
1325396 TTTTCCCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1326994 original size:33 final size:33
Alignment explanation
Indices: 1326954--1327314 Score: 196
Period size: 34 Copynumber: 11.3 Consensus size: 33
1326944 AAGCCCACGG
1326954 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
* * * * * **
1326987 TTTAGTGGCATC--TCTTTC-CAAAGCCCACGG
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
1327017 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
* * * * * **
1327050 TTTAGTGGCATC--TCTTTC-CAAAGCCCACGG
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
1327080 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
* * *
1327113 CTCCGTGGCA-C--T-CTTTTTAAAGCCCACAA
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
* *
1327142 CTCCGTGGCACTCTTTTTCCTTC-T-AAGCCCACAA
1 CTCAGTGGCA-TC--TTTCCTTCTTAAAGTCCACAA
*
1327176 CTCCGTGGCACTCTTTTTCCTTC-T-AAGTCCACAA
1 CTCAGTGGCA-TC--TTTCCTTCTTAAAGTCCACAA
* * *
1327210 CTTAGTGGCA-C---CCGT-TT-AAGCCCACAA
1 CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
*
1327237 CTCCGTGGCACTCTTTTTCCTTC-T-AAGTCCACAA
1 CTCAGTGGCA-TC--TTTCCTTCTTAAAGTCCACAA
*
1327271 CTCCA-TGGCACTCTTTTTCCTTCTT--AGTGCACAA
1 CT-CAGTGGCA-TC--TTTCCTTCTTAAAGTCCACAA
*
1327305 CTCTGTGGCA
1 CTCAGTGGCA
1327315 CCTTCTTCTA
Statistics
Matches: 259, Mismatches: 44, Indels: 49
0.74 0.12 0.14
Matches are distributed among these distances:
27 21 0.08
29 26 0.10
30 37 0.14
31 11 0.04
32 12 0.05
33 46 0.18
34 99 0.38
35 4 0.02
36 3 0.01
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (33 bp):
CTCAGTGGCATCTTTCCTTCTTAAAGTCCACAA
Found at i:1327026 original size:30 final size:31
Alignment explanation
Indices: 1326933--1327110 Score: 137
Period size: 33 Copynumber: 5.6 Consensus size: 31
1326923 AATTCTTCAA
1326933 ATCT-CTTCTCAAAGCCCACGGCTCAGTGGC
1 ATCTCCTTCTCAAAGCCCACGGCTCAGTGGC
* * *** *
1326963 ATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATC--TCCTTCTCAAAGCCCACGGCTCAGTGGC
*
1326996 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGC
1 ATCTCCTTCTCAAAGCCCACGGCTCAGTGGC
* * *** *
1327026 ATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATC--TCCTTCTCAAAGCCCACGGCTCAGTGGC
*
1327059 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGC
1 ATCTCCTTCTCAAAGCCCACGGCTCAGTGGC
* *
1327089 ATCTTTCCTTCTTAAAGTCCAC
1 ATC--TCCTTCTCAAAGCCCAC
1327111 AACTCCGTGG
Statistics
Matches: 109, Mismatches: 30, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
30 39 0.36
31 10 0.09
32 11 0.10
33 49 0.45
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (31 bp):
ATCTCCTTCTCAAAGCCCACGGCTCAGTGGC
Found at i:1327032 original size:63 final size:63
Alignment explanation
Indices: 1326933--1327157 Score: 346
Period size: 63 Copynumber: 3.6 Consensus size: 63
1326923 AATTCTTCAA
1326933 ATCTC-TTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1326996 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
* **
1327059 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAACTCCGTGGC
1 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
** ** *
1327122 A-CTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCA-TCTTT
1327158 TTCCTTCTAA
Statistics
Matches: 152, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
62 24 0.16
63 125 0.82
64 3 0.02
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.31
Consensus pattern (63 bp):
ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
Found at i:1327175 original size:34 final size:34
Alignment explanation
Indices: 1327092--1327315 Score: 247
Period size: 34 Copynumber: 6.9 Consensus size: 34
1327082 CAGTGGCATC
1327092 TTTCCTTCTTAAAGTCCACAACTCCGTGGCACTC--
1 TTTCCTTC-T-AAGTCCACAACTCCGTGGCACTCTT
* *
1327126 TTT--TT-AAAGCCCACAACTCCGTGGCACTCTT
1 TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
*
1327157 TTTCCTTCTAAGCCCACAACTCCGTGGCACTCTT
1 TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
**
1327191 TTTCCTTCTAAGTCCACAACTTAGTGGCAC-C--
1 TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
* *
1327222 ---CGTT-TAAGCCCACAACTCCGTGGCACTCTT
1 TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
*
1327252 TTTCCTTCTAAGTCCACAACTCCATGGCACTCTT
1 TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
* * *
1327286 TTTCCTTCTTAGTGCACAACTCTGTGGCAC
1 TTTCCTTCTAAGTCCACAACTCCGTGGCAC
1327316 CTTCTTCTAA
Statistics
Matches: 161, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
27 19 0.12
28 4 0.02
29 22 0.14
31 3 0.02
32 2 0.01
33 6 0.04
34 105 0.65
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTCCTTCTAAGTCCACAACTCCGTGGCACTCTT
Found at i:1327184 original size:126 final size:127
Alignment explanation
Indices: 1326933--1327191 Score: 341
Period size: 126 Copynumber: 2.1 Consensus size: 127
1326923 AATTCTTCAA
* *
1326933 ATCTC-TTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGCA
1 ATCTCTTTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAACTCAGTGGCA
** * * *
1326997 TCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
66 TCTCTTTCCAAAGCCCACAACTCAGTGGCATCTTTCCTTCTTAAAGCCCACAACTCAGTGGC
*
1327059 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAACTCCGTGGCA
1 ATCTCTTTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAACTCAGTGGCA
** * *
1327123 -CTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC-T-AAGCCCACAACTCCGTGGC
66 TCTCTTTCCAAAGCCCACAACTCAGTGGCA-TC--TTTCCTTCTTAAAGCCCACAACTCAGTGGC
1327185 A-CTCTTT
1 ATCTCTTT
1327192 TTCCTTCTAA
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
125 30 0.26
126 75 0.64
127 4 0.03
128 8 0.07
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (127 bp):
ATCTCTTTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAACTCAGTGGCA
TCTCTTTCCAAAGCCCACAACTCAGTGGCATCTTTCCTTCTTAAAGCCCACAACTCAGTGGC
Found at i:1327250 original size:95 final size:95
Alignment explanation
Indices: 1327092--1327333 Score: 326
Period size: 95 Copynumber: 2.5 Consensus size: 95
1327082 CAGTGGCATC
* **
1327092 TTTCCTTCTTAAAGTCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTCCTTC-T-AAGTCCACAACT-TGTGGCAC-CCGTTTAAAGCCCACAACTCCGTGGCACTCTT
*
1327157 TTTCCTTCTAAGCCCACAACTCCGTGGCACTCTT
62 TTTCCTTCTAAGCCCACAACTCCATGGCACTCTT
1327191 TTTCCTTCTAAGTCCACAACTTAGTGGCACCCGTTT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 TTTCCTTCTAAGTCCACAACTT-GTGGCACCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
1327255 CCTTCTAAGTCCACAACTCCATGGCACTCTT
65 CCTTCTAAGCCCACAACTCCATGGCACTCTT
* *
1327286 TTTCCTTCTTAGTGCACAACTCTGTGGCACCTTC-TTCTAAAGCCCACA
1 TTTCCTTCTAAGTCCACAACT-TGTGGCACC--CGTT-TAAAGCCCACA
1327334 CAAGTCGGTG
Statistics
Matches: 130, Mismatches: 7, Indels: 13
0.87 0.05 0.09
Matches are distributed among these distances:
95 84 0.65
96 7 0.05
97 21 0.16
98 10 0.08
99 8 0.06
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (95 bp):
TTTCCTTCTAAGTCCACAACTTGTGGCACCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
CTTCTAAGCCCACAACTCCATGGCACTCTT
Found at i:1327280 original size:61 final size:61
Alignment explanation
Indices: 1327165--1327281 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
1327155 TTTTTCCTTC
*
1327165 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTAGTGGCACCCGTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCAGTGGCACCCGTT
1327226 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCA-TGGCAC
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACT-CAGTGGCAC
1327282 TCTTTTTCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
61 53 0.98
62 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (61 bp):
TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCAGTGGCACCCGTT
Found at i:1327398 original size:33 final size:33
Alignment explanation
Indices: 1327315--1327681 Score: 598
Period size: 33 Copynumber: 11.2 Consensus size: 33
1327305 CTCTGTGGCA
1327315 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327349 CCTTCTC-AAAGCCCACACAAGTTGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327381 CATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1327414 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327447 CCTTCTC-AAAGCCCACACAAGTTGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327479 CATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1327512 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1327545 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1327577 CCTTCTTCCAAAGCCCACACAAGTCGGTGGCAAG
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * *
1327611 CC-TCTCTAAAGCCCATATAAGTTGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327643 CATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1327676 CCTTCT
1 CCTTCT
1327682 AAGCCCAATA
Statistics
Matches: 309, Mismatches: 19, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
32 89 0.29
33 213 0.69
34 7 0.02
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1327423 original size:98 final size:99
Alignment explanation
Indices: 1327315--1327681 Score: 607
Period size: 98 Copynumber: 3.7 Consensus size: 99
1327305 CTCTGTGGCA
*
1327315 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCCACACAAGTTGGTGGCA
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1327379 ACCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
65 ACCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1327414 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCCACACAAGTTGGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1327478 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
66 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1327512 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
* *
1327577 CC-TTCTTCCAAAGCCCACACAAGTCGGTGGCAAG
66 CCATTC-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * * *
1327611 CC-TCTCTAAAGCCCATATAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1327675 CCCTTCT
66 CCATTCT
1327682 AAGCCCAATA
Statistics
Matches: 258, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
98 197 0.76
99 61 0.24
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (99 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1327519 original size:131 final size:129
Alignment explanation
Indices: 1327300--1327681 Score: 608
Period size: 131 Copynumber: 2.9 Consensus size: 129
1327290 CTTCTTAGTG
* *
1327300 CACAACTCTGTGGC-ACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCC
1 CACAAGTCGGTGGCAACCTTC-TC-AAAGCCCACACAAGTCGGTGGCAA-CCTTCTCTAAAGCCC
1327363 ACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCC
63 ACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCC
1327428 CA
128 CA
*
1327430 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTCTCAAAGCCCACACAAGTCGGTGGCAACC-TTCTCTAAAGCCCA
* *
1327495 CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCC
64 CACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCC
1327560 A
129 A
1327561 CACAAGTCGGTGGCAACCTTCTTCCAAAGCCCACACAAGTCGGTGGCAAGCC-TCTCTAAAGCCC
1 CACAAGTCGGTGGCAACCTTC-T-CAAAGCCCACACAAGTCGGTGGCAA-CCTTCTCTAAAGCCC
* *
1327625 ATATAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
63 ACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1327682 AAGCCCAATA
Statistics
Matches: 235, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
129 2 0.01
130 45 0.19
131 157 0.67
132 29 0.12
133 2 0.01
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (129 bp):
CACAAGTCGGTGGCAACCTTCTCAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACA
CAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
Found at i:1327792 original size:43 final size:43
Alignment explanation
Indices: 1327727--1328000 Score: 325
Period size: 43 Copynumber: 6.1 Consensus size: 43
1327717 GCACCTTCTT
* * *
1327727 CTTTAAATCCAATGTAGTTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1327770 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
1327817 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
1327862 CTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCA----C
* *
1327909 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGGAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1327954 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1327997 CTTT
1 CTTT
1328001 TCCATCTTTA
Statistics
Matches: 200, Mismatches: 17, Indels: 28
0.82 0.07 0.11
Matches are distributed among these distances:
43 118 0.59
44 1 0.00
45 2 0.01
47 2 0.01
48 1 0.00
49 76 0.38
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1327843 original size:92 final size:92
Alignment explanation
Indices: 1327676--1328053 Score: 596
Period size: 92 Copynumber: 4.1 Consensus size: 92
1327666 CGGTGGCAAC
* * *
1327676 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCTTCTTTAAATCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATG
*
1327741 TAGTTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
1327769 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGT
1327834 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1327861 CCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 CCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATG
*
1327925 TAGCTGGCCTTGAATCAGCACATTGGGA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1327953 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACC--TT-CATCTTTAAGTCCAA
*
1328018 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1328048 TCCTTT
1 -CCTTT
1328054 TTCTCATCTT
Statistics
Matches: 265, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
91 1 0.00
92 212 0.80
93 4 0.02
94 2 0.01
95 41 0.15
96 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1327864 original size:21 final size:21
Alignment explanation
Indices: 1327840--1327907 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
1327830 ATGTAGCTGG
1327840 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
1327861 CCTTTAAGTCCAATATCACTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
1327883 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
1327904 CCTT
1 CCTT
1327908 CTTCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:1328032 original size:52 final size:53
Alignment explanation
Indices: 1327954--1328107 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 53
1327944 ACATTGGGAC
1327954 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTCTCAT
* * * * *
1328006 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCA-CC-TTTTCTCAT
* * * *
1328061 CTTTAAG-CCTAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAACATATTGGCACCTTT
1328108 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
52 37 0.44
53 5 0.06
54 7 0.08
55 35 0.42
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTCTCAT
Found at i:1328883 original size:13 final size:13
Alignment explanation
Indices: 1328865--1328889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1328855 CATAAAGTGT
1328865 TGTATCGATACAA
1 TGTATCGATACAA
1328878 TGTATCGATACA
1 TGTATCGATACA
1328890 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1328900 original size:32 final size:33
Alignment explanation
Indices: 1328845--1328906 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
1328835 TTCAACGATT
1328845 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1328878 TGTATCGATACAT-AAGTGTTGTATCGATA
1 TGTATCGATACATAAAGTGTTGTATCGATA
1328907 TATAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1328902 original size:19 final size:19
Alignment explanation
Indices: 1328844--1328927 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
1328834 TTTCAACGAT
1328844 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
1328864 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1328878 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
* *
1328896 TTGTATCGATATATAAGTT
1 TTGTATCGATACATAAGTG
1328915 TTGTATCGATACA
1 TTGTATCGATACA
1328928 ATGTAAGCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 28 0.51
20 12 0.22
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1328988 original size:13 final size:13
Alignment explanation
Indices: 1328970--1328997 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1328960 ATTACTCAAA
1328970 TGTATCGATACAT
1 TGTATCGATACAT
1328983 TGTATCGATACAT
1 TGTATCGATACAT
1328996 TG
1 TG
1328998 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1329059 original size:52 final size:52
Alignment explanation
Indices: 1329003--1329130 Score: 238
Period size: 52 Copynumber: 2.5 Consensus size: 52
1328993 CATTGATCTT
1329003 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1329055 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1329107 TGTATCGATACATGCAGGCAAATT
1 TGTATCGATACATGCAGGCAAATT
1329131 CTCATATTTC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1332298 original size:41 final size:41
Alignment explanation
Indices: 1332220--1332644 Score: 243
Period size: 41 Copynumber: 10.3 Consensus size: 41
1332210 CCTATAGACT
* * * * *
1332220 TCTTTTGTCTGCTCATCGGCTTTAACCTGGGAGACTTCTTTA
1 TCTTTT-TCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
** * * * *
1332262 TCTTTTTCTGCCCATTAACTTTGACTCGGGAAACTTCTATA
1 TCTTTTTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
* * * * ** * *
1332303 CCCTATGTCTGCCTATCGGTTTTGACCCGACAGACTTCTTTT
1 -TCTTTTTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
* * * *
1332345 TCTTTTGTCTACCTAT-TAGCTTTGACCTGAGAGACTTCTTTA
1 TCTTTT-TCTGCCCATCGA-CTTTGACCCGAGAGACTTCTTTA
* * * * * *
1332387 CCCTTTGTCTACTCGA-CGACTTTG-CCTCGACAGACTTCTTTT
1 -TCTTTTTCTGC-CCATCGACTTTGACC-CGAGAGACTTCTTTA
* * * *
1332429 TCTTTTGTCTACCCATCGACTTTGACTCGGGAGA-TTTTTTA
1 TCTTTT-TCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
*** * *
1332470 TCTTTGTT-TGCTTGTCGACTTTCACCCGGGAGACTTCTTTA
1 TCTTT-TTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
* * * * * *
1332511 TCTTTTTCTACTCATTGACTTTGACTCGAAAGACTT-TTTT
1 TCTTTTTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
* * *
1332551 TCTTTTTTTTGCCTATC-AGCTTTGACCCGAGAGACTTTTTTA
1 TC-TTTTTCTGCCCATCGA-CTTTGACCCGAGAGACTTCTTTA
* * * *
1332593 TCTTTGTCTGCCCATCGACATTGACCCAAGAAACTTCTTTA
1 TCTTTTTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
1332634 TCTTTTTCTGC
1 TCTTTTTCTGC
1332645 TTGTCAACTT
Statistics
Matches: 286, Mismatches: 80, Indels: 35
0.71 0.20 0.09
Matches are distributed among these distances:
40 27 0.09
41 144 0.50
42 107 0.37
43 8 0.03
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (41 bp):
TCTTTTTCTGCCCATCGACTTTGACCCGAGAGACTTCTTTA
Found at i:1332354 original size:42 final size:42
Alignment explanation
Indices: 1332219--1332644 Score: 234
Period size: 42 Copynumber: 10.3 Consensus size: 42
1332209 CCCTATAGAC
* * * *
1332219 TTCTTTTGTCTG-CTCATCGGCTTTAACCTGGGAGACTTCTTT
1 TTCTTTTGTCTGCCT-ATCGACTTTGACCCGAGAGACTTCTTT
* * ** * * * *
1332261 ATCTTTT-TCTGCCCATTAACTTTGACTCGGGAAACTTCTAT
1 TTCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
** * * ** *
1332302 ACCCTATGTCTGCCTATCGGTTTTGACCCGACAGACTTCTTT
1 TTCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
* * *
1332344 TTCTTTTGTCTACCTAT-TAGCTTTGACCTGAGAGACTTCTTT
1 TTCTTTTGTCTGCCTATCGA-CTTTGACCCGAGAGACTTCTTT
** * * * *
1332386 ACCCTTTGTCTACTCGA-CGACTTTG-CCTCGACAGACTTCTTT
1 TTCTTTTGTCTGC-CTATCGACTTTGACC-CGAGAGACTTCTTT
* * * *
1332428 TTCTTTTGTCTACCCATCGACTTTGACTCGGGAGA-TT-TTT
1 TTCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
* * * * *
1332468 TATC-TTTGTTTGCTTGTCGACTTTCACCCGGGAGACTTCTTT
1 T-TCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
* * * * *
1332510 ATCTTTT-TCT-ACTCATTGACTTTGACTCGAAAGACTT-TTT
1 TTCTTTTGTCTGCCT-ATCGACTTTGACCCGAGAGACTTCTTT
* *
1332550 TTCTTTTTTTTGCCTATC-AGCTTTGACCCGAGAGACTT-TTT
1 TTCTTTTGTCTGCCTATCGA-CTTTGACCCGAGAGACTTCTTT
* * * *
1332591 TATC-TTTGTCTGCCCATCGACATTGACCCAAGAAACTTCTTT
1 T-TCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
*
1332633 ATCTTTT-TCTGC
1 TTCTTTTGTCTGC
1332645 TTGTCAACTT
Statistics
Matches: 287, Mismatches: 77, Indels: 41
0.71 0.19 0.10
Matches are distributed among these distances:
40 39 0.14
41 115 0.40
42 129 0.45
43 4 0.01
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (42 bp):
TTCTTTTGTCTGCCTATCGACTTTGACCCGAGAGACTTCTTT
Found at i:1332539 original size:123 final size:123
Alignment explanation
Indices: 1332374--1332642 Score: 301
Period size: 123 Copynumber: 2.2 Consensus size: 123
1332364 CTTTGACCTG
* * * *
1332374 AGAGACTTCTTTACCCTTTGTCTACTCGACGACTTTGCCTCGACAGACTTCTTTTTCTTTTGTCT
1 AGAGACTTCTTTA-TCTTTTTCTACTCGACGACTTTGACTCGAAAGACTT-TTTTTCTTTTGTCT
* * * *** * *
1332439 ACCCATC-GACTTTGACTCGGGAGA-TTTTTTATCTTTGTTTGCTTGTCGACTTTCACCCG
64 ACCCATCAG-CTTTGACCCGAGAGACTTTTTTATCTTTGTCTGCCCATCGACATTCACCCA
* * * * *
1332498 GGAGACTTCTTTATCTTTTTCTACTC-ATTGACTTTGACTCGAAAGACTTTTTTTCTTTTTTTTG
1 AGAGACTTCTTTATCTTTTTCTACTCGA-CGACTTTGACTCGAAAGACTTTTTTTCTTTTGTCTA
* *
1332562 CCTATCAGCTTTGACCCGAGAGACTTTTTTATCTTTGTCTGCCCATCGACATTGACCCA
65 CCCATCAGCTTTGACCCGAGAGACTTTTTTATCTTTGTCTGCCCATCGACATTCACCCA
*
1332621 AGAAACTTCTTTATCTTTTTCT
1 AGAGACTTCTTTATCTTTTTCT
1332643 GCTTGTCAAC
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
122 31 0.26
123 78 0.64
124 12 0.10
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (123 bp):
AGAGACTTCTTTATCTTTTTCTACTCGACGACTTTGACTCGAAAGACTTTTTTTCTTTTGTCTAC
CCATCAGCTTTGACCCGAGAGACTTTTTTATCTTTGTCTGCCCATCGACATTCACCCA
Found at i:1333421 original size:13 final size:13
Alignment explanation
Indices: 1333403--1333428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1333393 CAATTTTTTG
1333403 TGTATCGATACAT
1 TGTATCGATACAT
1333416 TGTATCGATACAT
1 TGTATCGATACAT
1333429 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1333513 original size:20 final size:20
Alignment explanation
Indices: 1333488--1333560 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1333478 CAACTTTTTT
1333488 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1333508 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1333529 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1333549 ATGTATCGATAC
1 ATGTATCGATAC
1333561 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1333526 original size:41 final size:41
Alignment explanation
Indices: 1333467--1333560 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1333457 CTGCCAAGAA
*
1333467 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1333508 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1333549 ATGTATCGATAC
1 ATGTATCGATAC
1333561 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1333542 original size:21 final size:21
Alignment explanation
Indices: 1333467--1333542 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1333457 CTGCCAAGAA
* *
1333467 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1333488 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1333508 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1333529 ATGTATCGATACAT
1 ATGTATCGATACAT
1333543 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1336008 original size:13 final size:13
Alignment explanation
Indices: 1335990--1336028 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1335980 ATAATCACCC
*
1335990 TGTATCGATACAG
1 TGTATCGATACAA
1336003 TGTATCGATACAA
1 TGTATCGATACAA
1336016 TGTATCGATACAA
1 TGTATCGATACAA
1336029 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1336039 original size:20 final size:20
Alignment explanation
Indices: 1336014--1336092 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1336004 GTATCGATAC
1336014 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1336034 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1336059 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1336079 CATGTATCGATACA
1 AATGTATCGATACA
1336093 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1338128 original size:15 final size:15
Alignment explanation
Indices: 1338108--1338138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1338098 ATTTCGTTTG
*
1338108 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1338123 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1338138 G
1 G
1338139 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1342220 original size:13 final size:13
Alignment explanation
Indices: 1342202--1342227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1342192 CAATTTTTTG
1342202 TGTATCGATACAT
1 TGTATCGATACAT
1342215 TGTATCGATACAT
1 TGTATCGATACAT
1342228 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1342312 original size:20 final size:20
Alignment explanation
Indices: 1342287--1342359 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1342277 CAACTTTTTT
1342287 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1342307 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1342328 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1342348 ATGTATCGATAC
1 ATGTATCGATAC
1342360 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1342325 original size:41 final size:41
Alignment explanation
Indices: 1342266--1342359 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1342256 CTGCCAAGAA
*
1342266 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1342307 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1342348 ATGTATCGATAC
1 ATGTATCGATAC
1342360 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1342341 original size:21 final size:21
Alignment explanation
Indices: 1342266--1342341 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1342256 CTGCCAAGAA
* *
1342266 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1342287 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1342307 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1342328 ATGTATCGATACAT
1 ATGTATCGATACAT
1342342 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1342735 original size:42 final size:42
Alignment explanation
Indices: 1342652--1342787 Score: 116
Period size: 42 Copynumber: 3.2 Consensus size: 42
1342642 ATCCTAACAA
* ** *
1342652 ACTTTGACCC-AGGAAACTTTTTTACCTTTTGTTTGCTTGTCG
1 ACTTTGACCCTA-GAAACTTCTTTACCTTTTGCCTGCCTGTCG
* *
1342694 ATTTTGACCCTAGATACTTCTTTACCTTTTGCCTGCCTGTCG
1 ACTTTGACCCTAGAAACTTCTTTACCTTTTGCCTGCCTGTCG
* * * * * *
1342736 GCTTTGACCTTAGAGACTT-TTATA-TTCTTTGTCTGCCAGTCG
1 ACTTTGACCCTAGAAACTTCTT-TACCT-TTTGCCTGCCTGTCG
1342778 ACTTTGACCC
1 ACTTTGACCC
1342788 AGGAGACTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
41 3 0.04
42 72 0.95
43 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (42 bp):
ACTTTGACCCTAGAAACTTCTTTACCTTTTGCCTGCCTGTCG
Found at i:1342794 original size:42 final size:41
Alignment explanation
Indices: 1342721--1342810 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
1342711 TTCTTTACCT
* * *
1342721 TTTGCCTGCCTGTCGGCTTTGACCTTAGAGACTTTTATATTC
1 TTTGCCTGCCAGTCGACTTTGACCTCAGAGACTTTTATA-TC
* *
1342763 TTTGTCTGCCAGTCGACTTTGACC-CAGGAGACTTTTTTATC
1 TTTGCCTGCCAGTCGACTTTGACCTCA-GAGACTTTTATATC
1342804 TTTGCCT
1 TTTGCCT
1342811 ACCGGTTGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 9 0.22
42 32 0.78
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (41 bp):
TTTGCCTGCCAGTCGACTTTGACCTCAGAGACTTTTATATC
Found at i:1343103 original size:20 final size:20
Alignment explanation
Indices: 1343078--1343119 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1343068 CATTCCAGAC
1343078 ATGTATCAATACATTCACTT
1 ATGTATCAATACATTCACTT
** *
1343098 ATGTATTGATATATTCACTT
1 ATGTATCAATACATTCACTT
1343118 AT
1 AT
1343120 TTAATCGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:1348984 original size:115 final size:115
Alignment explanation
Indices: 1348782--1348999 Score: 357
Period size: 115 Copynumber: 1.9 Consensus size: 115
1348772 GTTATCTTTG
* * **
1348782 TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATGTTTGAACATGGTTATTAGTTAAATTA
1 TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTAAATTA
* *
1348847 CCTTGATTGAATTAACTTGACTTGGCTCATAGATCAAACTTAACAATTGA
66 CCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAACTTAACAATTGA
1348897 TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTCAAA-T
1 TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTT-AAATT
*
1348961 ACCTTGATTGAGTTAACTTGACTTAGCTCATAAATCAAA
65 ACCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAA
1349000 ATGCCTATTG
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 92 0.97
116 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (115 bp):
TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTAAATTA
CCTTGATTGAATTAACTTGACTTAGCTCATAAATCAAACTTAACAATTGA
Found at i:1350103 original size:23 final size:23
Alignment explanation
Indices: 1350077--1350130 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
1350067 CAGCTGCTGA
*
1350077 AATGAAATAAGAGAA-ACAACTGC
1 AATGAAAGAAGA-AACACAACTGC
1350100 AATGAAAGAAGAAATCGACAACTGC
1 AATGAAAGAAGAAA-C-ACAACTGC
1350125 AATGAA
1 AATGAA
1350131 GAAAGCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 11 0.41
25 14 0.52
ACGTcount: A:0.56, C:0.13, G:0.19, T:0.13
Consensus pattern (23 bp):
AATGAAAGAAGAAACACAACTGC
Found at i:1350621 original size:57 final size:55
Alignment explanation
Indices: 1350556--1350667 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 55
1350546 TTCCTTTGTT
* * *
1350556 TTTCTTCATGTCGTGAGCTTGTTTTCATTGCTTGATTTTCCTTTGTTGCA-TGTTTTC
1 TTTCTTCATGTCGTAAGCTTGTCTTCATTGCTTG-TTTT-CTTTCTT-CATTGTTTTC
*
1350613 TTTCTTCATGTCGTAAGCTTGTCTTCCTTGCTTGTTTTCTTTCTTCATTGTTTTC
1 TTTCTTCATGTCGTAAGCTTGTCTTCATTGCTTGTTTTCTTTCTTCATTGTTTTC
1350668 CTTTGTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 2 0.04
55 13 0.26
56 4 0.08
57 31 0.62
ACGTcount: A:0.08, C:0.20, G:0.15, T:0.57
Consensus pattern (55 bp):
TTTCTTCATGTCGTAAGCTTGTCTTCATTGCTTGTTTTCTTTCTTCATTGTTTTC
Found at i:1359502 original size:20 final size:20
Alignment explanation
Indices: 1359477--1359553 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1359467 GAAAAAAGAC
1359477 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1359497 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
1359517 TA-CATGTATCGATGCACTGA
1 -AGAATGTATCGATACATTGA
* *
1359537 AAAATATATCGATACAT
1 AGAATGTATCGATACAT
1359554 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1360451 original size:26 final size:26
Alignment explanation
Indices: 1360396--1360452 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1360386 AAATTAATAA
* *
1360396 TTGATATATTTGTATGTCATGCATGC
1 TTGAAATATTTGTATGTCATGAATGC
* *
1360422 TTGAAATATTTGCTTTGT-ATGAATGT
1 TTGAAATATTTG-TATGTCATGAATGC
1360448 TTGAA
1 TTGAA
1360453 CATGGCTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (26 bp):
TTGAAATATTTGTATGTCATGAATGC
Found at i:1360610 original size:115 final size:115
Alignment explanation
Indices: 1360408--1360625 Score: 350
Period size: 115 Copynumber: 1.9 Consensus size: 115
1360398 GATATATTTG
* **
1360408 TATGTCATGCATGCTTGAAATATTTGCTTTGTATGAATGTTTGAACATGGCTATTAGTTAAATTA
1 TATGTCATGCATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTAAATTA
*
1360473 CCTTGATTGATTTAACTTGACTTAGCTCATAGATCAAACTTAACAATTGA
66 CCTTGATTGATTTAACTTGACTTAGCTCATAAATCAAACTTAACAATTGA
*
1360523 TATGTCATGTATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTCAAA-T
1 TATGTCATGCATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTT-AAATT
*
1360587 ACCTTGATTG-TGTTGACTTGACTTAGCTCATAAATCAAA
65 ACCTTGATTGAT-TTAACTTGACTTAGCTCATAAATCAAA
1360626 ATGCCTAATG
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
114 1 0.01
115 91 0.96
116 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (115 bp):
TATGTCATGCATGCTTGAAATATTTGCTTTGTATGAATCTTTGAACATGGCTAGGAGTTAAATTA
CCTTGATTGATTTAACTTGACTTAGCTCATAAATCAAACTTAACAATTGA
Found at i:1361774 original size:23 final size:23
Alignment explanation
Indices: 1361747--1361808 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
1361737 CAGCTGCTGA
*
1361747 AATGAAATAAGAGAA-ACAACTGC
1 AATGAAAGAAGA-AACACAACTGC
1361770 AATGAAAGAAGAAATCGACAACTGC
1 AATGAAAGAAGAAA-C-ACAACTGC
1361795 AATG-AAGAAAGAAA
1 AATGAAAG-AAGAAA
1361809 AAAAACAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 2 0.06
23 11 0.32
24 3 0.09
25 18 0.53
ACGTcount: A:0.58, C:0.11, G:0.19, T:0.11
Consensus pattern (23 bp):
AATGAAAGAAGAAACACAACTGC
Found at i:1361815 original size:51 final size:51
Alignment explanation
Indices: 1361725--1361826 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
1361715 AATGAATAAG
* * * *
1361725 AGAAGAAATCGACAGCTGCTGAAATGAAATAAGAGAAACAACTGCAATGAA
1 AGAAGAAATCGACAACTGCTGAAATGAAAGAAAAAAAACAACTGCAATGAA
*
1361776 AGAAGAAATCGACAACTGCAATG-AA-GAAAGAAAAAAAACAGCTGCAATGAA
1 AGAAGAAATCGACAACTGC--TGAAATGAAAGAAAAAAAACAACTGCAATGAA
1361827 GAAAACAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
51 40 0.91
52 2 0.05
53 2 0.05
ACGTcount: A:0.54, C:0.14, G:0.21, T:0.12
Consensus pattern (51 bp):
AGAAGAAATCGACAACTGCTGAAATGAAAGAAAAAAAACAACTGCAATGAA
Found at i:1362326 original size:57 final size:55
Alignment explanation
Indices: 1362257--1362371 Score: 151
Period size: 57 Copynumber: 2.1 Consensus size: 55
1362247 TTCCTTTGTT
* * *
1362257 TTTCTTCATGTCGTGAGATTGTTTTCATTGCTTGATTTTCCTTTGTTGCA-TGTTTTC
1 TTTCTTCATGTCGTAAGATTGTCTTCATTGCTTG-TTTT-CTTTCTT-CATTGTTTTC
* *
1362314 TTTCTTCGTGTCGTAAGCTTGTCTTCATTGCTTGTTTTCTTTCTTCATTGTTTTC
1 TTTCTTCATGTCGTAAGATTGTCTTCATTGCTTGTTTTCTTTCTTCATTGTTTTC
1362369 TTT
1 TTT
1362372 TGTTTTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 2 0.04
55 16 0.31
56 4 0.08
57 30 0.58
ACGTcount: A:0.09, C:0.17, G:0.16, T:0.58
Consensus pattern (55 bp):
TTTCTTCATGTCGTAAGATTGTCTTCATTGCTTGTTTTCTTTCTTCATTGTTTTC
Found at i:1365597 original size:20 final size:20
Alignment explanation
Indices: 1365555--1365608 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1365545 TTCAACAATT
1365555 TGTATCGATACAATAAGGTAA
1 TGTATCGATAC-ATAAGGTAA
*
1365576 TGTATTGATACATAA-GTGAA
1 TGTATCGATACATAAGGT-AA
1365596 TGTATCGATACAT
1 TGTATCGATACAT
1365609 GCTTGAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 18 0.60
21 10 0.33
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGGTAA
Done.