Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 57 of 117
Found at i:12830583 original size:35 final size:35
Alignment explanation
Indices: 12830471--12830583 Score: 90
Period size: 35 Copynumber: 3.2 Consensus size: 35
12830461 CAGGTCATTA
* *
12830471 TTTATTTCCTGACTTACAGCTTAATCCT-AGTCATTC
1 TTTATTTCTTGACTTACAACTTAATCCTGA-TCA-TC
* * *
12830507 TTTACCTT-TAGACTTACAACTCAAT-CTCGATCAT-
1 TTTA-TTTCTTGACTTACAACTTAATCCT-GATCATC
* *
12830541 TCGTATTTCTTGACTTACAACTTAGTCCTGATCATC
1 T-TTATTTCTTGACTTACAACTTAATCCTGATCATC
12830577 TTTATTT
1 TTTATTT
12830584 TTTAACTTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
34 3 0.05
35 30 0.51
36 23 0.39
37 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (35 bp):
TTTATTTCTTGACTTACAACTTAATCCTGATCATC
Found at i:12830609 original size:35 final size:35
Alignment explanation
Indices: 12830570--12830701 Score: 104
Period size: 35 Copynumber: 3.7 Consensus size: 35
12830560 ACTTAGTCCT
12830570 GATCATCTTTATTTTTTAACTTGCAGTTCAATCTC
1 GATCATCTTTATTTTTTAACTTGCAGTTCAATCTC
* * * ** * *
12830605 GATCATTTTTATTTCTCAACTTGTGGCTCAGTC-C
1 GATCATCTTTATTTTTTAACTTGCAGTTCAATCTC
* * * *
12830639 TAGTCATTTTTTTTATTTTTTAACTTGTAGTTCAATCTT
1 GA-TCA---TCTTTATTTTTTAACTTGCAGTTCAATCTC
* *
12830678 GGTTATCTTTATTTTTTAACTTGC
1 GATCATCTTTATTTTTTAACTTGC
12830702 TATTCAGTCT
Statistics
Matches: 73, Mismatches: 19, Indels: 10
0.72 0.19 0.10
Matches are distributed among these distances:
34 2 0.03
35 46 0.63
38 25 0.34
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.53
Consensus pattern (35 bp):
GATCATCTTTATTTTTTAACTTGCAGTTCAATCTC
Found at i:12830775 original size:19 final size:19
Alignment explanation
Indices: 12830753--12830789 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12830743 GCCTTTATTC
12830753 CTTGACTCACAGTTTAGTT
1 CTTGACTCACAGTTTAGTT
* *
12830772 CTTGTCTCGCAGTTTAGT
1 CTTGACTCACAGTTTAGT
12830790 CCCTATCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
CTTGACTCACAGTTTAGTT
Found at i:12831406 original size:7 final size:7
Alignment explanation
Indices: 12831385--12831476 Score: 53
Period size: 7 Copynumber: 13.0 Consensus size: 7
12831375 TAAAAAATAT
12831385 TAAAAAA
1 TAAAAAA
**
12831392 TATCAAA
1 TAAAAAA
12831399 TAAAAAA
1 TAAAAAA
12831406 TAAAAAA
1 TAAAAAA
* *
12831413 TATAATAG
1 TA-AAAAA
*
12831421 TAATATAA
1 TAA-AAAA
12831429 TAATAAAA
1 TAA-AAAA
**
12831437 TAGTAAA
1 TAAAAAA
*
12831444 TAAATAA
1 TAAAAAA
*
12831451 TAAATAA
1 TAAAAAA
*
12831458 -CAAAAA
1 TAAAAAA
12831464 T-AAAAA
1 TAAAAAA
12831470 TAAAAAA
1 TAAAAAA
12831477 AGAAATGGGC
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
6 10 0.15
7 39 0.59
8 17 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAAAAA
Found at i:12831419 original size:19 final size:20
Alignment explanation
Indices: 12831370--12831476 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 20
12831360 GAAAATCCAA
12831370 ATAAATAAAAAATATTAAAAAAT
1 ATAAAT-AAAAA-A-TAAAAAAT
12831393 ATCAAATAAAAAATAAAAAAT
1 AT-AAATAAAAAATAAAAAAT
*
12831414 ATAATAGTAATATAATAATAAAAT
1 ATAA-A-TAA-AAAATAA-AAAAT
* * *
12831438 AGTAAATAAATAATAAATAAC
1 A-TAAATAAAAAATAAAAAAT
*
12831459 AAAAAT-AAAAATAAAAAA
1 ATAAATAAAAAATAAAAAA
12831477 AGAAATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.14
20 6 0.08
21 15 0.21
22 11 0.15
23 16 0.22
24 11 0.15
25 3 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
ATAAATAAAAAATAAAAAAT
Found at i:12831448 original size:11 final size:11
Alignment explanation
Indices: 12831368--12831473 Score: 59
Period size: 10 Copynumber: 9.9 Consensus size: 11
12831358 ACGAAAATCC
12831368 AAATAAATAAA-
1 AAAT-AATAAAT
*
12831379 AAATATTAAA-
1 AAATAATAAAT
12831389 AAAT-ATCAAAT
1 AAATAAT-AAAT
*
12831400 AAAAAATAAA-
1 AAATAATAAAT
12831410 AAAT-ATAATAGT
1 AAATAATAA-A-T
12831422 AATATAAT-AAT
1 AA-ATAATAAAT
*
12831433 AAAATAGTAAAT
1 -AAATAATAAAT
12831445 AAATAATAAAT
1 AAATAATAAAT
*
12831456 -AACAA-AAAT
1 AAATAATAAAT
12831465 AAA-AATAAA
1 AAATAATAAA
12831474 AAAAGAAATG
Statistics
Matches: 76, Mismatches: 7, Indels: 25
0.70 0.06 0.23
Matches are distributed among these distances:
9 11 0.14
10 25 0.33
11 25 0.33
12 10 0.13
13 3 0.04
14 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:12831472 original size:15 final size:15
Alignment explanation
Indices: 12831369--12831477 Score: 64
Period size: 16 Copynumber: 6.9 Consensus size: 15
12831359 CGAAAATCCA
12831369 AATAAAT-AAAAAAT
1 AATAAATAAAAAAAT
*
12831383 ATTAAA-AAATATCAAAT
1 AATAAATAAA-A--AAAT
*
12831400 AAAAAATAAAAAATAT
1 AATAAATAAAAAA-AT
* *
12831416 AATAGTAATATAATAAT
1 AATA--AATAAAAAAAT
*
12831433 AA-AATAGTAAATAAAT
1 AATAA-A-TAAAAAAAT
12831449 AATAAATAACAAAAAT
1 AATAAATAA-AAAAAT
12831465 AA-AAATAAAAAAA
1 AATAAATAAAAAAA
12831478 GAAATGGGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 24
0.68 0.09 0.22
Matches are distributed among these distances:
14 13 0.18
15 13 0.18
16 22 0.30
17 15 0.21
18 10 0.14
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAAATAAAAAAAT
Found at i:12833403 original size:3 final size:3
Alignment explanation
Indices: 12833395--12833435 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12833385 AAGATAAGTA
12833395 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12833436 ATTTTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12833500 original size:14 final size:14
Alignment explanation
Indices: 12833477--12833518 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12833467 ATCATAAAAG
*
12833477 AAACCTTAAAATTA
1 AAACCCTAAAATTA
12833491 AAACCCT-AAA-TA
1 AAACCCTAAAATTA
*
12833503 AAATCCTAAAATTA
1 AAACCCTAAAATTA
12833517 AA
1 AA
12833519 TTCGAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 6 0.25
14 10 0.42
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAAATTA
Found at i:12834126 original size:16 final size:17
Alignment explanation
Indices: 12834097--12834129 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12834087 GAGAGTTATT
12834097 AATAATTATCATTTTTA
1 AATAATTATCATTTTTA
*
12834114 AATAA-TATTATTTTTA
1 AATAATTATCATTTTTA
12834130 TTTTTCAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
AATAATTATCATTTTTA
Found at i:12837044 original size:3 final size:3
Alignment explanation
Indices: 12837036--12837078 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12837026 TTGACTCCAT
12837036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12837079 CGAAAAGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12837249 original size:28 final size:28
Alignment explanation
Indices: 12837193--12837249 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12837183 ATTCTTTGGC
**
12837193 ATTCTAAGTATTTTTTAGGTGTTTAGTT
1 ATTCTAAGTATTTTTTAGGCATTTAGTT
*
12837221 ATTC-AAGTTATTTTTTAGGCATTTTGTT
1 ATTCTAAG-TATTTTTTAGGCATTTAGTT
12837249 A
1 A
12837250 GGTTTTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (28 bp):
ATTCTAAGTATTTTTTAGGCATTTAGTT
Found at i:12842193 original size:30 final size:30
Alignment explanation
Indices: 12842131--12842212 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
12842121 GGTTATCTCA
*
12842131 TAAT-TGAT-TTTGAATTATAATAAAATATT
1 TAATATGATATTTGAATTATAA-AAAAAATT
*
12842160 TAATATGATATTTGAATTTTAAAAAAAATT
1 TAATATGATATTTGAATTATAAAAAAAATT
12842190 TAATATGATATTTGAATTATAAA
1 TAATATGATATTTGAATTATAAA
12842213 TTTATTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.08
30 33 0.69
31 11 0.23
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (30 bp):
TAATATGATATTTGAATTATAAAAAAAATT
Found at i:12845533 original size:23 final size:23
Alignment explanation
Indices: 12845503--12845549 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12845493 ATACCGATGC
12845503 TTTTTCTTGTCTTAATCGACAAA
1 TTTTTCTTGTCTTAATCGACAAA
12845526 TTTTTCTTGTCTTAATCGACAAA
1 TTTTTCTTGTCTTAATCGACAAA
12845549 T
1 T
12845550 CTCTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTTTCTTGTCTTAATCGACAAA
Found at i:12854517 original size:30 final size:28
Alignment explanation
Indices: 12854435--12854517 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 28
12854425 CATTTTATTT
*
12854435 AAATAAGCTCTTATACTTTT-ATTATACCC
1 AAATAAACTCTTA-ACTTTTAATT-TACCC
* * *
12854464 AAATAAATTTTTAA-TCTTCAATTTACATCC
1 AAATAAACTCTTAACT-TTTAATTTAC--CC
12854494 AAATAAACTCTTAACTTTTAATTT
1 AAATAAACTCTTAACTTTTAATTT
12854518 GTATCTAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.02
28 6 0.14
29 13 0.31
30 21 0.50
31 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (28 bp):
AAATAAACTCTTAACTTTTAATTTACCC
Found at i:12854568 original size:31 final size:31
Alignment explanation
Indices: 12854494--12854569 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
12854484 ATTTACATCC
12854494 AAATAAACTCTTAA-CTTTTAATTTGTATCT
1 AAATAAACTCTTAATCTTTTAATTTGTATCT
* *
12854524 AAAT-AAGTACTTAATC-TTTAATTTGTTTCTT
1 AAATAAACT-CTTAATCTTTTAATTTGTATC-T
12854555 AAATAAACTCTTAAT
1 AAATAAACTCTTAAT
12854570 ATAACCAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 3 0.08
30 21 0.54
31 12 0.31
32 3 0.08
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (31 bp):
AAATAAACTCTTAATCTTTTAATTTGTATCT
Found at i:12854747 original size:66 final size:66
Alignment explanation
Indices: 12854639--12854770 Score: 187
Period size: 66 Copynumber: 2.0 Consensus size: 66
12854629 TATTTGGGTA
* * * *
12854639 TAATAAAAATATAAAGGTCTATTTAAATATAGTTGAATAATTCAAGAGTTTTTTTTTTTAAGTAT
1 TAATAAAAATATAAAGCTCTATTTAAATAAAATTGAATAATTCAA-AGATTTTTTTTTT-AGTAT
12854704 TTT
64 TTT
*
12854707 TAAT-AAAATATAAAGCT-TATTTCAATAAAATTGAATAATTCAAAGATTTTTTTTTTAGTATTT
1 TAATAAAAATATAAAGCTCTATTTAAATAAAATTGAATAATTCAAAGATTTTTTTTTTAGTATTT
12854770 T
66 T
12854771 AGTTGAACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 8 0.14
65 12 0.20
66 23 0.39
67 12 0.20
68 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (66 bp):
TAATAAAAATATAAAGCTCTATTTAAATAAAATTGAATAATTCAAAGATTTTTTTTTTAGTATTT
T
Found at i:12855356 original size:2 final size:2
Alignment explanation
Indices: 12855349--12855377 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12855339 AAAACATCAT
12855349 TA TA 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 TA TA T
12855378 CAGAATCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12857989 original size:25 final size:26
Alignment explanation
Indices: 12857950--12858009 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
12857940 TTGAATAAAT
** *
12857950 AACTTTAACCAAAATTATTATATTCA
1 AACTTTAAATAAATTTATTATATTCA
*
12857976 AACTTTAAATAAATTTATTATATTTA
1 AACTTTAAATAAATTTATTATATTCA
*
12858002 AATTTTAA
1 AACTTTAA
12858010 TTTAATGTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
AACTTTAAATAAATTTATTATATTCA
Found at i:12858448 original size:77 final size:78
Alignment explanation
Indices: 12858321--12858476 Score: 235
Period size: 77 Copynumber: 2.0 Consensus size: 78
12858311 AAATTATGAA
* * *
12858321 TAAATCACTATTTAGTTATCATATGCAATACATGATGAATAACTAA-TTTTTTAATAGTGTGATT
1 TAAATCACCATTTAATTATCATATGCAATACACGATGAATAACTAATTTTTTTAATAGTGTGATT
12858385 ATATAACT-TGATT
66 ATATAA-TATGATT
* * *
12858398 TAAATCACCATTTAATTATCATATGTAATACACGATGAGTAATTAATTTTTTTAATAGTGTGATT
1 TAAATCACCATTTAATTATCATATGCAATACACGATGAATAACTAATTTTTTTAATAGTGTGATT
12858463 ATATAATATGATT
66 ATATAATATGATT
12858476 T
1 T
12858477 GAATGTAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
77 41 0.58
78 30 0.42
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (78 bp):
TAAATCACCATTTAATTATCATATGCAATACACGATGAATAACTAATTTTTTTAATAGTGTGATT
ATATAATATGATT
Found at i:12867938 original size:36 final size:34
Alignment explanation
Indices: 12867876--12867944 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
12867866 ATGGAATTTT
* *
12867876 AAAAATATCTGATAACCTAGAATTTTTTAAAAAC
1 AAAAAAATCTCATAACCTAGAATTTTTTAAAAAC
*
12867910 AAAAAAATCTCATAAGCTAAGAATTTTTTTAAAAA
1 AAAAAAATCTCATAACCT-AGAA-TTTTTTAAAAA
12867945 ATTTATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 15 0.50
35 4 0.13
36 11 0.37
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (34 bp):
AAAAAAATCTCATAACCTAGAATTTTTTAAAAAC
Found at i:12868347 original size:25 final size:25
Alignment explanation
Indices: 12868317--12868372 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
12868307 TTAAAAGTAT
12868317 ATATTTTAAATTTAATATTTAACAA
1 ATATTTTAAATTTAATATTTAACAA
* *
12868342 ATATTTTAAATTTAATGTTTAATAA
1 ATATTTTAAATTTAATATTTAACAA
12868367 ATATTT
1 ATATTT
12868373 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATATTTTAAATTTAATATTTAACAA
Found at i:12868378 original size:16 final size:15
Alignment explanation
Indices: 12868359--12868393 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
12868349 AAATTTAATG
12868359 TTTAATAAATATTTAT
1 TTTAATAAATATTT-T
*
12868375 TTTAATATATATTTT
1 TTTAATAAATATTTT
12868390 TTTA
1 TTTA
12868394 GAAATAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATAAATATTTT
Found at i:12874093 original size:16 final size:17
Alignment explanation
Indices: 12874062--12874095 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12874052 ATAGGCCCAA
*
12874062 ATTTAAAAAGTTAAAAT
1 ATTTAAAAAGTGAAAAT
12874079 ATTTAAAAAG-GAAAAT
1 ATTTAAAAAGTGAAAAT
12874095 A
1 A
12874096 AAGAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
ATTTAAAAAGTGAAAAT
Found at i:12875069 original size:24 final size:24
Alignment explanation
Indices: 12875041--12875086 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12875031 ATAAGTAACA
12875041 AAAAG-AAAATGAAAAAAAAAAAGC
1 AAAAGCAAAA-GAAAAAAAAAAAGC
*
12875065 AAAAGCAAAAGAAAAATAAAAA
1 AAAAGCAAAAGAAAAAAAAAAA
12875087 TAAAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (24 bp):
AAAAGCAAAAGAAAAAAAAAAAGC
Found at i:12875074 original size:18 final size:19
Alignment explanation
Indices: 12875040--12875080 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
12875030 AATAAGTAAC
12875040 AAAAAGAAAATGAAAAA-A
1 AAAAAGAAAATGAAAAAGA
*
12875058 AAAAAGCAAAA-GCAAAAGA
1 AAAAAG-AAAATGAAAAAGA
12875077 AAAA
1 AAAA
12875081 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAATGAAAAAGA
Found at i:12875879 original size:16 final size:14
Alignment explanation
Indices: 12875835--12875892 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
12875825 ATTATCTAAT
*
12875835 TAAAAAAAACAAAAA
1 TAAAAAAGA-AAAAA
* *
12875850 TTAAAAAGAAAATA
1 TAAAAAAGAAAAAA
*
12875864 TGAAAAAGAAAAAA
1 TAAAAAAGAAAAAA
*
12875878 TAAAAAAGAAGAAA
1 TAAAAAAGAAAAAA
12875892 T
1 T
12875893 CGAGTTGCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
14 29 0.81
15 7 0.19
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.12
Consensus pattern (14 bp):
TAAAAAAGAAAAAA
Found at i:12877011 original size:26 final size:27
Alignment explanation
Indices: 12876958--12877012 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
12876948 ATATTGAGTG
12876958 TTGTGTATTTTGTGATTTTGATTGTGA
1 TTGTGTATTTTGTGATTTTGATTGTGA
*
12876985 TTGTGTATTTT-T-AGTTTTGATTTTGA
1 TTGTGTATTTTGTGA-TTTTGATTGTGA
12877011 TT
1 TT
12877013 TTTTTCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 14 0.54
27 11 0.42
ACGTcount: A:0.15, C:0.00, G:0.22, T:0.64
Consensus pattern (27 bp):
TTGTGTATTTTGTGATTTTGATTGTGA
Found at i:12877645 original size:20 final size:21
Alignment explanation
Indices: 12877617--12877658 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
12877607 ATAGTTATAG
12877617 ATTGATATT-ATATTATATAAA
1 ATTGATATTAATATT-TATAAA
12877638 ATTG-TATTAATATTTATAAA
1 ATTGATATTAATATTTATAAA
12877658 A
1 A
12877659 GGAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTGATATTAATATTTATAAA
Found at i:12877650 original size:21 final size:20
Alignment explanation
Indices: 12877604--12877658 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
12877594 GATAATGTTA
* *
12877604 ATTATAGTTAT-AGATTGAT
1 ATTATATTTATAAAATTGAT
12877623 ATTATATTATATAAAATTG-T
1 ATTATATT-TATAAAATTGAT
12877643 ATTAATATTTATAAAA
1 ATT-ATATTTATAAAA
12877659 GGAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 7 0.23
20 14 0.45
21 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTATATTTATAAAATTGAT
Found at i:12878521 original size:3 final size:3
Alignment explanation
Indices: 12878513--12878539 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12878503 CTAAAAAACT
12878513 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
12878540 CTCAATTCAT
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:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12881140 original size:12 final size:12
Alignment explanation
Indices: 12881123--12881148 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12881113 TAGAGGGAAG
12881123 AGCTCAAAGATA
1 AGCTCAAAGATA
12881135 AGCTCAAAGATA
1 AGCTCAAAGATA
12881147 AG
1 AG
12881149 AGTGAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (12 bp):
AGCTCAAAGATA
Found at i:12882081 original size:19 final size:20
Alignment explanation
Indices: 12882048--12882098 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12882038 ATTTGATTAG
*
12882048 GTTAATC-TCTTTTAGCTAA
1 GTTAATCTTTTTTTAGCTAA
* *
12882067 GTTGAT-TTTTTTTAGCTGA
1 GTTAATCTTTTTTTAGCTAA
12882086 GTTAATCTTTTTT
1 GTTAATCTTTTTT
12882099 GGATGAACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (20 bp):
GTTAATCTTTTTTTAGCTAA
Found at i:12882669 original size:19 final size:19
Alignment explanation
Indices: 12882645--12882684 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12882635 TAGGCGAGTG
*
12882645 GGTCGAAATGAGCGTTTTT
1 GGTCGAAATAAGCGTTTTT
* *
12882664 GGTCGAAGTAAGCTTTTTT
1 GGTCGAAATAAGCGTTTTT
12882683 GG
1 GG
12882685 CTGAGGTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.38
Consensus pattern (19 bp):
GGTCGAAATAAGCGTTTTT
Found at i:12883226 original size:24 final size:24
Alignment explanation
Indices: 12883199--12883245 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12883189 GTATGAACTT
12883199 TTTGGTCGAGTTAGGTTCGAGCTC
1 TTTGGTCGAGTTAGGTTCGAGCTC
* * *
12883223 TTTGGTTGAGTTGGGTTTGAGCT
1 TTTGGTCGAGTTAGGTTCGAGCT
12883246 TTTTTGCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.36, T:0.43
Consensus pattern (24 bp):
TTTGGTCGAGTTAGGTTCGAGCTC
Found at i:12890182 original size:3 final size:3
Alignment explanation
Indices: 12890174--12890218 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
12890164 CTCATATGTT
* * *
12890174 TCA TCA TCA TCG TCA TCA TCA TTCA TCA TTA TTA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA TCA TCA TCA TCA TC
12890219 GTAATCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:12890198 original size:22 final size:22
Alignment explanation
Indices: 12890173--12890217 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12890163 ACTCATATGT
*
12890173 TTCATCATCATCGTCATCATCA
1 TTCATCATCATCATCATCATCA
* *
12890195 TTCATCATTATTATCATCATCA
1 TTCATCATCATCATCATCATCA
12890217 T
1 T
12890218 CGTAATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (22 bp):
TTCATCATCATCATCATCATCA
Found at i:12893418 original size:131 final size:131
Alignment explanation
Indices: 12893181--12893420 Score: 321
Period size: 132 Copynumber: 1.8 Consensus size: 131
12893171 CTCAATTAGA
12893181 TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
1 TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
* *
12893246 GTATTATAGCAATTTTCAAATAAAATTTCACAAGTCAAATTTCTATGAAATGATGATAGAGGTAT
66 GTATTATAACAATTTTCAAATAAAATCTCACAAGTCAAATTTCTATGAAATGATGATAGAGGTAT
12893311 T
131 T
* *
12893312 TTAGTAATTTAATATGT-GATTAATTCTATATTATTATGTTAAAATTTAATATGTA-AA-TTAA-
1 TTAGTAATTTAAAATGTAG-TTAATT-T-TA-TATTATGTTAAAATTTAATATATATAACTTAAT
* * *
12893373 AAGGGGTATTATAATAATTTTCAAATAAAATGCT-ACATGTC-AATTTCT
62 AA-GAGTATTATAACAATTTTCAAATAAAAT-CTCACAAGTCAAATTTCT
12893421 TAGGAAGCAA
Statistics
Matches: 96, Mismatches: 7, Indels: 12
0.83 0.06 0.10
Matches are distributed among these distances:
130 1 0.01
131 31 0.32
132 36 0.38
133 5 0.05
134 23 0.24
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (131 bp):
TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
GTATTATAACAATTTTCAAATAAAATCTCACAAGTCAAATTTCTATGAAATGATGATAGAGGTAT
T
Found at i:12893450 original size:131 final size:131
Alignment explanation
Indices: 12893181--12893451 Score: 297
Period size: 132 Copynumber: 2.1 Consensus size: 131
12893171 CTCAATTAGA
12893181 TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
1 TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
* * * ** * *
12893246 GTATTATAGCAATTTTCAAATAAAATTTCACAAGTCAAATTTCTATGAAATGATGATAGAGGTAT
66 GTATTATAACAATTTTCAAATAAAATCTCACAAGTCAAATTTCTAGGAAACAATCATAGAGGCAT
12893311 T
131 T
* *
12893312 TTAGTAATTTAATATGT-GATTAATTCTATATTATTATGTTAAAATTTAATATGTA-AA-TTAA-
1 TTAGTAATTTAAAATGTAG-TTAATT-T-TA-TATTATGTTAAAATTTAATATATATAACTTAAT
* * * *
12893373 AAGGGGTATTATAATAATTTTCAAATAAAATGCT-ACATGTC-AATTTCTTAGGAAGCAATCATA
62 AA-GAGTATTATAACAATTTTCAAATAAAAT-CTCACAAGTCAAATTTC-TAGGAAACAATCATA
12893436 -AGGACATT
124 GAGG-CATT
12893444 TT-GTAATT
1 TTAGTAATT
12893452 ATGGTAAAGA
Statistics
Matches: 119, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
130 1 0.01
131 39 0.33
132 51 0.43
133 5 0.04
134 23 0.19
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (131 bp):
TTAGTAATTTAAAATGTAGTTAATTTTATATTATGTTAAAATTTAATATATATAACTTAATAAGA
GTATTATAACAATTTTCAAATAAAATCTCACAAGTCAAATTTCTAGGAAACAATCATAGAGGCAT
T
Found at i:12893689 original size:30 final size:29
Alignment explanation
Indices: 12893655--12893747 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 29
12893645 TACCACAATA
*
12893655 ATTTAACATTTATAGGAGGGTATTTTTGTC
1 ATTTAACAATTATA-GAGGGTATTTTTGTC
* * * **
12893685 ATTTAA-AACGTA-AG-GGGCATTATAATC
1 ATTTAACAA-TTATAGAGGGTATTTTTGTC
*
12893712 ATTTAACAATTATAAGAGGGTATTTTTGTA
1 ATTTAACAATTAT-AGAGGGTATTTTTGTC
12893742 ATTTAA
1 ATTTAA
12893748 GATAGGAAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
27 17 0.37
28 3 0.07
29 4 0.09
30 22 0.48
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.41
Consensus pattern (29 bp):
ATTTAACAATTATAGAGGGTATTTTTGTC
Found at i:12893761 original size:57 final size:56
Alignment explanation
Indices: 12893655--12893804 Score: 169
Period size: 57 Copynumber: 2.6 Consensus size: 56
12893645 TACCACAATA
* * *
12893655 ATTTAACATTTATAGGAGGGTATTTTTGTCATTTAAAACGTAAGGGGCATTATAAT
1 ATTTAACATTTATAAGAGGGTATTTTTGTCATTTAAAACGGAAGAGGCATTATAAT
* * *
12893711 CATTTAACAATTATAAGAGGGTATTTTTGTAATTTAAGATA-GGAA-AGGCATTATAGT
1 -ATTTAACATTTATAAGAGGGTATTTTTGTCATTTAA-A-ACGGAAGAGGCATTATAAT
* *
12893768 AGTTTATCATTTAAAAGAAGGGTATTTTTGTCATTTA
1 A-TTTAACATTTATAAG-AGGGTATTTTTGTCATTTA
12893805 CTATTGGAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 55 0.70
58 22 0.28
59 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (56 bp):
ATTTAACATTTATAAGAGGGTATTTTTGTCATTTAAAACGGAAGAGGCATTATAAT
Found at i:12894106 original size:186 final size:185
Alignment explanation
Indices: 12893722--12894254 Score: 863
Period size: 186 Copynumber: 2.9 Consensus size: 185
12893712 ATTTAACAAT
* * *
12893722 TATAAGAGGG-TATTTTTGTAATTTAAGATAGGAAAGGCATTATAGTAGTTTATCATTTAAAAGA
1 TATAAGAGGGATATTTTTGTAATTTAAGA-AAGTAAGGCATTATAGCAGTTTATCATTTAAAAG-
* * *** *
12893786 AGG-GTATTTTTGTCATTTACTATTGGAGGGGCATTGTTGTCTTTTTGGATAGGTGTCAAGCAAT
64 AGGTGTATTTTTTTCATTTAATATAAAAGGGG-ATTATTGTCTTTTT-GATAGGTGTCAAGCAAT
* *
12893850 TGGTAAAAAAATTGGAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGATATT
127 TGGT-AAAAAATTGAAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGATATA
12893910 TATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTATCATTTAAAAGAG
1 TATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTATCATTTAAAAGAG
* * *
12893975 GTGTATTTTTTTCATTTAATATAAAAAGGGGGTTATTGTCTTTATGACAGGTGTCAAGCAATTGG
66 GTGTATTTTTTTCATTTAATAT-AAAAGGGGATTATTGTCTTTTTGATAGGTGTCAAGCAATTGG
12894040 TAAAAAATTGAAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGATATA
130 TAAAAAATTGAAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGATATA
12894096 TATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTATCATTTAAAAGAG
1 TATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTATCATTTAAAAGAG
*
12894161 GTGTATTTTTTTCATTTAATATAAAAGGGCATTATTGTCTTTTTGATAGGTGTCAAGCAATTGGT
66 GTGTATTTTTTTCATTTAATATAAAAGGGGATTATTGTCTTTTTGATAGGTGTCAAGCAATTGGT
12894226 AAAAAATTGAAAGGGTAAAATGGTCATTT
131 AAAAAATTGAAAGGGTAAAATGGTCATTT
12894255 GATATTTATA
Statistics
Matches: 324, Mismatches: 18, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
185 68 0.21
186 140 0.43
187 23 0.07
188 70 0.22
189 23 0.07
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (185 bp):
TATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTATCATTTAAAAGAG
GTGTATTTTTTTCATTTAATATAAAAGGGGATTATTGTCTTTTTGATAGGTGTCAAGCAATTGGT
AAAAAATTGAAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGATATA
Found at i:12894400 original size:165 final size:165
Alignment explanation
Indices: 12894083--12894411 Score: 461
Period size: 165 Copynumber: 2.0 Consensus size: 165
12894073 TAGCATTAGA
* *
12894083 GTCATTTGATATATATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTA
1 GTCATTTGATATATATAAGAGGGATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTTA
* * * * **
12894148 TCATTTAAAAGAGGTGTATTTTTTTCATTTAATATAAAAGGGCATTATTGTCTTTTTGATAGGTG
66 TCATTTAAAAGAGGTGTATATTTATCATTTAATATAAAAGGGCATTATTGTCTTTTGGAAAAATG
12894213 TCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATG
131 TCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATG
*
12894248 GTCATTTGATATTTATAAGAGGTG-TA-TTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTT
1 GTCATTTGATATATATAAGAGG-GATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTT
** *
12894311 ATCATTTAAAAGAAGG-GTATATTTATCATTTAATATAGGAGGGTCATTGGCTT-T-TTTTGGAA
65 ATCATTTAAAAG-AGGTGTATATTTATCATTTAATATAAAAGGG-CATT--ATTGTCTTTTGGAA
*
12894373 AAATGTCAAGCAATTGGTAAGAAATTGAAAGGGTAAAAT
126 AAATGTCAAGCAATTGGTAAAAAATTGAAAGGGTAAAAT
12894412 AATCATTTTG
Statistics
Matches: 146, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
164 70 0.48
165 72 0.49
166 2 0.01
167 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (165 bp):
GTCATTTGATATATATAAGAGGGATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTTA
TCATTTAAAAGAGGTGTATATTTATCATTTAATATAAAAGGGCATTATTGTCTTTTGGAAAAATG
TCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATG
Found at i:12894439 original size:350 final size:352
Alignment explanation
Indices: 12893897--12894601 Score: 901
Period size: 350 Copynumber: 2.0 Consensus size: 352
12893887 TAGCATTAGA
* *
12893897 GTCATTTGATATTTATAAGAGGGATATTTTTGTAATTTAAGAAAGTAAGGCATTATAGCAGTTTA
1 GTCATTTGATATTTATAAGAGGGATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTTA
* * * * **
12893962 TCATTTAAAAGAGGTGTATTTTTTTCATTTAATATAAAAAGGGGGTTATTGTCTTTATGACAGGT
66 TCATTTAAAAGAGGTGTATATTTATCATTTAATAT---AAGGGGGTCATTGTCTTTATGAAAAAT
** *
12894027 GTCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATGGTCATTTTGCTAGCATTAGAGTCATTTGA
128 GTCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATAATCATTTTGCTAGCAGTAGAGTCATTTGA
* *
12894092 TATATATAAGAGG-GATATTTTTGTAATTTAAGAA-AGTAAGG-CATTATAGCAGTTTATCATTT
193 TATATATAAGAGGAG-TATTTTTGTAATTTAAGAAGA-AAAGGACATTATAACAGTTTATCATTT
* * **
12894154 AAAAGAGGTGTATTTTTT-TCATTTAATATA-AAAGGGCATTAT-TGTCTTTTT-GATAGGTGTC
256 AAAAGAGGGGTATTTTTTGTCATTTAATACAGAAAGGGCATTATCAAT-TTTTTGGATAGGTGTC
*
12894215 AAGCAATTGGTAAAAAATTGAAAGGGTAAAATG
320 AAGCAATTGATAAAAAATTGAAAGGGTAAAATG
12894248 GTCATTTGATATTTATAAGAGGTG-TA-TTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTT
1 GTCATTTGATATTTATAAGAGG-GATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTT
* *
12894311 ATCATTTAAAAGAAGG-GTATATTTATCATTTAATAT-AGGAGGGTCATTGGCTTTTTTTGGAAA
65 ATCATTTAAAAG-AGGTGTATATTTATCATTTAATATAAGG-GGGTCATT-G-TCTTTAT-GAAA
* * ** * *
12894374 AATGTCAAGCAATTGGTAAGAAATTGAAAGGGTAAAATAATCATTTTGCTTGGGGTGGCGTCATT
125 AATGTCAAGCAATTGGTAAAAAATTGAAAGGGTAAAATAATCATTTTGCTAGCAGTAGAGTCATT
* * * * *
12894439 TGATATTTATAAGAGTAGTATTTTTGTAATTTATGAAGAAAAGGATATTATAATAGTTTATCATT
190 TGATATATATAAGAGGAGTATTTTTGTAATTTAAGAAGAAAAGGACATTATAACAGTTTATCATT
* * * *
12894504 TAAAATAGGGGTATTTTTTGTCATTTAATACAGGAGGGGTATTATCAATTTTTTGGATAGGTGTC
255 TAAAAGAGGGGTATTTTTTGTCATTTAATACAGAAAGGGCATTATCAATTTTTTGGATAGGTGTC
*
12894569 AAGCAATTGATAAGAAATTGAAAGGGTAAAATG
320 AAGCAATTGATAAAAAATTGAAAGGGTAAAATG
12894602 ATTATTTTGC
Statistics
Matches: 305, Mismatches: 36, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
346 3 0.01
347 7 0.02
348 1 0.00
349 5 0.02
350 158 0.52
351 63 0.21
352 12 0.04
353 14 0.05
354 42 0.14
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (352 bp):
GTCATTTGATATTTATAAGAGGGATATTTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTTA
TCATTTAAAAGAGGTGTATATTTATCATTTAATATAAGGGGGTCATTGTCTTTATGAAAAATGTC
AAGCAATTGGTAAAAAATTGAAAGGGTAAAATAATCATTTTGCTAGCAGTAGAGTCATTTGATAT
ATATAAGAGGAGTATTTTTGTAATTTAAGAAGAAAAGGACATTATAACAGTTTATCATTTAAAAG
AGGGGTATTTTTTGTCATTTAATACAGAAAGGGCATTATCAATTTTTTGGATAGGTGTCAAGCAA
TTGATAAAAAATTGAAAGGGTAAAATG
Found at i:12894585 original size:189 final size:185
Alignment explanation
Indices: 12894248--12894618 Score: 487
Period size: 189 Copynumber: 2.0 Consensus size: 185
12894238 GGGTAAAATG
*
12894248 GTCATTTGATATTTATAAGAGGTGTATTTTGTAATTTAAGAAAGGAAGGCATTATAACAGTTTAT
1 GTCATTTGATATTTATAAGAGGTGTATTTTGTAATTTAAGAAAGAAAGGCATTATAACAGTTTAT
* * *
12894313 CATTTAAAAGAAGGGTATATTTATCATTTAATATAGGAGGGTCATTGGCTTTTTTTGGAAAAATG
66 CATTTAAAAGAAGGGTATATTTATCATTTAATACAGGAGGGTCATTAGCATTTTTTGGAAAAATG
* *
12894378 TCAAGCAATTGGTAAGAAATTGAAAGGGTAAAATAATCATTTTGCTTGGGGTGGC
131 TCAAGCAATTGATAAGAAATTGAAAGGGTAAAATAATCATTTTGCTAGGGGTGGC
* * *
12894433 GTCATTTGATATTTATAAGA-GTAGTATTTTTGTAATTTATG-AAGAAAAGGATATTATAATAGT
1 GTCATTTGATATTTATAAGAGGT-GTA-TTTTGTAATTTAAGAAAG-AAAGG-CATTATAACAGT
* * * * *
12894496 TTATCATTTAAAATAGGGGTATTTTTTGTCATTTAATACAGGAGGGGT-ATTATCAATTTTTTGG
62 TTATCATTTAAAAGAAGGGTA-TATTTATCATTTAATACAGGA-GGGTCATTAGC-ATTTTTTGG
* ** * *
12894560 ATAGGTGTCAAGCAATTGATAAGAAATTGAAAGGGTAAAATGATTATTTTGCTAGGGGT
124 AAAAATGTCAAGCAATTGATAAGAAATTGAAAGGGTAAAATAATCATTTTGCTAGGGGT
12894619 TTACTACTAT
Statistics
Matches: 160, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
184 2 0.01
185 26 0.16
186 17 0.11
187 29 0.18
188 22 0.14
189 64 0.40
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (185 bp):
GTCATTTGATATTTATAAGAGGTGTATTTTGTAATTTAAGAAAGAAAGGCATTATAACAGTTTAT
CATTTAAAAGAAGGGTATATTTATCATTTAATACAGGAGGGTCATTAGCATTTTTTGGAAAAATG
TCAAGCAATTGATAAGAAATTGAAAGGGTAAAATAATCATTTTGCTAGGGGTGGC
Found at i:12895430 original size:19 final size:19
Alignment explanation
Indices: 12895406--12895451 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12895396 ATTATTAATG
12895406 TAAAAAAAATTAAAAAATA
1 TAAAAAAAATTAAAAAATA
* **
12895425 TAAAAATAATTTTAAAATA
1 TAAAAAAAATTAAAAAATA
*
12895444 GAAAAAAA
1 TAAAAAAA
12895452 GTAAGATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAAAAATTAAAAAATA
Found at i:12898605 original size:32 final size:32
Alignment explanation
Indices: 12898569--12898635 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
12898559 AAAATGAAGA
*
12898569 TGACTAGATTGAACCAAGGTCGAAGATAAAGG
1 TGACTAGATTGAACCAAAGTCGAAGATAAAGG
* *
12898601 TGACTAGATTGAATCAAAGTCGAATATAAAGG
1 TGACTAGATTGAACCAAAGTCGAAGATAAAGG
12898633 TGA
1 TGA
12898636 TTGGACTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.22
Consensus pattern (32 bp):
TGACTAGATTGAACCAAAGTCGAAGATAAAGG
Found at i:12899734 original size:15 final size:16
Alignment explanation
Indices: 12899714--12899753 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
12899704 TTTTCCCTTA
*
12899714 TTTTTATTTTTTATT-
1 TTTTTATTTTTCATTC
12899729 TTTTTATTTTTCATTC
1 TTTTTATTTTTCATTC
12899745 TTTTT-TTTT
1 TTTTTATTTT
12899754 CTTTTTGCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTATTTTTCATTC
Found at i:12899735 original size:21 final size:21
Alignment explanation
Indices: 12899711--12899753 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12899701 TTCTTTTCCC
*
12899711 TTATTTTT-ATTTTTTATTTTT
1 TTATTTTTCATTCTTT-TTTTT
12899732 TTATTTTTCATTCTTTTTTTT
1 TTATTTTTCATTCTTTTTTTT
12899753 T
1 T
12899754 CTTTTTGCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.84
Consensus pattern (21 bp):
TTATTTTTCATTCTTTTTTTT
Found at i:12903969 original size:20 final size:20
Alignment explanation
Indices: 12903929--12903978 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
12903919 CAAAAAATAT
12903929 TACCAAAATAA-ATAAATAAA
1 TACCAAAA-AATATAAATAAA
12903949 TACCATAAAAATATAAA-AAA
1 TACCA-AAAAATATAAATAAA
12903969 TACCAAAAAA
1 TACCAAAAAA
12903979 AAAAGCCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.18
20 15 0.54
21 8 0.29
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (20 bp):
TACCAAAAAATATAAATAAA
Found at i:12905031 original size:24 final size:23
Alignment explanation
Indices: 12904976--12905057 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 23
12904966 AATAATTATG
*
12904976 AAATTAAGATAAAAGGGATAAAATAA
1 AAATAAAGAT-AAA-GGAT-AAATAA
12905002 AAATAAAGATAAATGGATAAATAA
1 AAATAAAGATAAA-GGATAAATAA
** *
12905026 GCATAAAAATACAAGGATAAATATA
1 AAATAAAGATA-AAGGATAAATA-A
12905051 ATAATAA
1 A-AATAA
12905058 TAATAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 23 0.50
25 10 0.22
26 13 0.28
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (23 bp):
AAATAAAGATAAAGGATAAATAA
Found at i:12905056 original size:3 final size:3
Alignment explanation
Indices: 12905048--12905072 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12905038 AAGGATAAAT
12905048 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12905073 ATACATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12905057 original size:12 final size:12
Alignment explanation
Indices: 12905042--12905113 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
12905032 AAATACAAGG
12905042 ATAAATATAATA
1 ATAAATATAATA
12905054 ATAATAATAATAATA
1 AT-A-AAT-ATAATA
* *
12905069 ATAAATACATTTA
1 ATAAATATA-ATA
*
12905082 A-AAATATAAAA
1 ATAAATATAATA
12905093 ATAAA-ATAA-A
1 ATAAATATAATA
12905103 ATAAAATATAA
1 AT-AAATATAA
12905114 CAATTGGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
10 3 0.06
11 9 0.19
12 17 0.35
13 7 0.15
14 4 0.08
15 8 0.17
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAATATAATA
Found at i:12905707 original size:16 final size:17
Alignment explanation
Indices: 12905677--12905711 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12905667 ACCTCAAAAT
*
12905677 AAAAAAGTAACAAAACA
1 AAAAAAATAACAAAACA
12905694 AAAAAAATAA-AAAACA
1 AAAAAAATAACAAAACA
12905710 AA
1 AA
12905712 TGAAGCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.83, C:0.09, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAATAACAAAACA
Found at i:12909216 original size:47 final size:47
Alignment explanation
Indices: 12909162--12909255 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
12909152 AGGTAAGTTT
* * *
12909162 GACTTGCAAGAGAAGAATTATAAGAGGAAAGAGATTTTTAATAGGCA
1 GACTTGCAAAAGAAGAATTATAAAAGGAAAGAGATTCTTAATAGGCA
* *
12909209 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGTGATTCTTAATAGGCA
1 GACTTGCAAAAGAAGAATTATAAAAGGAAAGAGATTCTTAATAGGCA
12909256 AGTTTGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (47 bp):
GACTTGCAAAAGAAGAATTATAAAAGGAAAGAGATTCTTAATAGGCA
Found at i:12919786 original size:14 final size:16
Alignment explanation
Indices: 12919755--12919786 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12919745 CACAAATTTA
12919755 AAATTTTATTTGTGAT
1 AAATTTTATTTGTGAT
12919771 AAATTTT-TTT-TGAT
1 AAATTTTATTTGTGAT
12919785 AA
1 AA
12919787 GTTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
AAATTTTATTTGTGAT
Found at i:12935893 original size:48 final size:49
Alignment explanation
Indices: 12935806--12935947 Score: 137
Period size: 48 Copynumber: 2.9 Consensus size: 49
12935796 AAATATGATG
* * * *
12935806 AGATTTATAAAGTTTTTTAGCTTTTATTTA-GAAGAAGCTTTTTCAAATA
1 AGATTTTTAAAGTTATTTACCCTTTATTTAGGAAG-AGCTTTTTCAAATA
* * * *
12935855 AGATTTTTAAAGTTATTTA-CCTTTATTTAGGATGAGCTTGTCCAAATG
1 AGATTTTTAAAGTTATTTACCCTTTATTTAGGAAGAGCTTTTTCAAATA
* * * *
12935903 AGATTTTTAAAATTGTTTACCCTTTGTATA-GAAGGAGCTTTTTCA
1 AGATTTTTAAAGTTATTTACCCTTTATTTAGGAA-GAGCTTTTTCA
12935948 GTTAAAAATT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
48 39 0.51
49 37 0.49
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (49 bp):
AGATTTTTAAAGTTATTTACCCTTTATTTAGGAAGAGCTTTTTCAAATA
Found at i:12936192 original size:81 final size:83
Alignment explanation
Indices: 12936021--12936281 Score: 228
Period size: 81 Copynumber: 3.2 Consensus size: 83
12936011 AGACTTTCGG
* * * * *
12936021 GCATAGTCTATAAGTTCTTCGAGCAAGATCTATAAGT-TTTTCAAGCTAAATCTGTTTTGGTGTC
1 GCATAGTCTCTAAG-TCTTCGGGCAAGATTTATAAGTCTTTT-GAGCTAAATCTATTTTGGTGTC
* *
12936085 ACAATTTATAAGACCTCCGA
64 ACAATTTATAAGACCTACAA
* * * *
12936105 GCATAGTGTCT-A-TCTTCGGGCAAGATTTGTAAGTCTTTTGAGTTAAATCTATTTTGGTGTCAT
1 GCATAGTCTCTAAGTCTTCGGGCAAGATTTATAAGTCTTTTGAGCTAAATCTATTTTGGTGTCAC
* * *
12936168 GATTTATAAGACTTATAA
66 AATTTATAAGACCTACAA
* * * * * * *
12936186 GTATAGTCTCTAAGTCCTTTGGGCAAGACTTATAAGTCTTTCGAGCAAAATCTA---TAGTGTTA
1 GCATAGTCTCTAAGT-CTTCGGGCAAGATTTATAAGTCTTTTGAGCTAAATCTATTTTGGTGTCA
***
12936248 CAATTTATAAGACCTTTGA
65 CAATTTATAAGACCTACAA
*
12936267 GCATAGTCTTTAAGT
1 GCATAGTCTCTAAGT
12936282 TTTCCAAACA
Statistics
Matches: 142, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
81 94 0.66
82 5 0.04
83 2 0.01
84 41 0.29
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (83 bp):
GCATAGTCTCTAAGTCTTCGGGCAAGATTTATAAGTCTTTTGAGCTAAATCTATTTTGGTGTCAC
AATTTATAAGACCTACAA
Found at i:12936678 original size:20 final size:19
Alignment explanation
Indices: 12936637--12936679 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12936627 AGAGTTTTTC
*
12936637 AAATAAAAAAAAAACACAA
1 AAATAAAAAAAAAAAACAA
12936656 AAATAAAAAAAAAAGAAGCAA
1 AAATAAAAAAAAAA-AA-CAA
12936677 AAA
1 AAA
12936680 GAGAGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 1 0.05
21 6 0.29
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.05
Consensus pattern (19 bp):
AAATAAAAAAAAAAAACAA
Found at i:12937204 original size:36 final size:36
Alignment explanation
Indices: 12937164--12937242 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
12937154 AGATTTGAAC
*
12937164 CTATTTGAGCACTTTAATTGGATTTATTTTCTTAGG
1 CTATTTGAGCACTTTAATTGAATTTATTTTCTTAGG
*
12937200 CTATTTGAGCACTTTAATTGAATTTATTTTTTTAGG
1 CTATTTGAGCACTTTAATTGAATTTATTTTCTTAGG
12937236 CTATTTG
1 CTATTTG
12937243 GGATTTATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (36 bp):
CTATTTGAGCACTTTAATTGAATTTATTTTCTTAGG
Found at i:12945785 original size:16 final size:16
Alignment explanation
Indices: 12945761--12945821 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
12945751 CAAATAAATC
*
12945761 TTAAATAATTTTAATT
1 TTAAATAATTTGAATT
*
12945777 TTAATTAATTTGAA-T
1 TTAAATAATTTGAATT
* *
12945792 TTAAGATGA-TTCAATT
1 TTAA-ATAATTTGAATT
*
12945808 TTAAATACTTTGAA
1 TTAAATAATTTGAA
12945822 AGACTAATCC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (16 bp):
TTAAATAATTTGAATT
Found at i:12946224 original size:2 final size:2
Alignment explanation
Indices: 12946217--12946241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12946207 TATGTGACAA
12946217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12946242 ATGTGTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12947963 original size:21 final size:22
Alignment explanation
Indices: 12947938--12947994 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
12947928 GAATAGCATT
*
12947938 AAATATTCATTAAT-TAAACA-A
1 AAATATTCATGAATATAAA-AGA
12947959 AAATA-TCATGAATATAAAAGA
1 AAATATTCATGAATATAAAAGA
*
12947980 AAA-ATTCATGCATAT
1 AAATATTCATGAATAT
12947995 TCAATTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (22 bp):
AAATATTCATGAATATAAAAGA
Found at i:12949412 original size:2 final size:2
Alignment explanation
Indices: 12949405--12949435 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12949395 GACCAGACCA
12949405 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12949436 GCTATGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12950721 original size:11 final size:12
Alignment explanation
Indices: 12950707--12950744 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12950697 AATAAAAATA
12950707 TATTTTT-TATT
1 TATTTTTATATT
*
12950718 TATTTTTATTTT
1 TATTTTTATATT
12950730 TATTTTGTATATT
1 TATTTT-TATATT
12950743 TA
1 TA
12950745 GATAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 7 0.30
12 9 0.39
13 7 0.30
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:12950776 original size:24 final size:24
Alignment explanation
Indices: 12950749--12950795 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12950739 TATTTAGATA
* *
12950749 ATTTTTTTATAAATATATATTAAC
1 ATTTTTCTATAAAAATATATTAAC
12950773 ATTTTTCTATAAAAATATATTAA
1 ATTTTTCTATAAAAATATATTAA
12950796 TTCTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTTCTATAAAAATATATTAAC
Found at i:12951849 original size:12 final size:12
Alignment explanation
Indices: 12951832--12951856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12951822 TAAGATTTTA
12951832 TTATAAAAATAT
1 TTATAAAAATAT
12951844 TTATAAAAATAT
1 TTATAAAAATAT
12951856 T
1 T
12951857 ATTTTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATAAAAATAT
Found at i:12952246 original size:25 final size:25
Alignment explanation
Indices: 12952191--12952247 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
12952181 ATAATAATAA
*
12952191 AAAAAAAGTTAAAAATAAAAATGAG
1 AAAAAAACTTAAAAATAAAAATGAG
* *
12952216 ATAAAAACTT-AAAATATAAAATGAT
1 AAAAAAACTTAAAAATA-AAAATGAG
12952241 AAAAAAA
1 AAAAAAA
12952248 ATAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (25 bp):
AAAAAAACTTAAAAATAAAAATGAG
Found at i:12952248 original size:19 final size:16
Alignment explanation
Indices: 12952226--12952283 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
12952216 ATAAAAACTT
*
12952226 AAAATATAAAATGATAA
1 AAAAAATAAAATGA-AA
*
12952243 AAAAAATAAAATCAAAAA
1 AAAAAATAAAAT--GAAA
*
12952261 ATAAAAATAAAATGAAC
1 A-AAAAATAAAATGAAA
12952278 AAAAAA
1 AAAAAA
12952284 CCTACAATCG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 5 0.15
17 14 0.41
18 3 0.09
19 12 0.35
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAATAAAATGAAA
Found at i:12952252 original size:24 final size:24
Alignment explanation
Indices: 12952171--12952254 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
12952161 AAATTAGTAG
*
12952171 AATAAAATA-AATAATAATAAAAAAA
1 AATAAAATATAA-AATGAT-AAAAAA
*
12952196 AAGTTAAAA-ATAAAAATGAGATAAAAA
1 AA--TAAAATAT-AAAATGATA-AAAAA
**
12952223 CTTAAAATATAAAATGATAAAAAA
1 AATAAAATATAAAATGATAAAAAA
12952247 AATAAAAT
1 AATAAAAT
12952255 CAAAAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
24 11 0.24
25 15 0.33
26 4 0.09
27 14 0.30
28 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (24 bp):
AATAAAATATAAAATGATAAAAAA
Found at i:12952260 original size:24 final size:23
Alignment explanation
Indices: 12952171--12952267 Score: 72
Period size: 24 Copynumber: 4.0 Consensus size: 23
12952161 AAATTAGTAG
*
12952171 AATAAAATAAATAATAATAAAAAAA
1 AATAAAATAAA-AATGAT-AAAAAA
*
12952196 AAGTTAAAAATAAAAATGAGATAAAAA
1 AA--T-AAAATAAAAATGATA-AAAAA
**
12952223 CTTAAAATATAAAATGATAAAAAA
1 AATAAAATA-AAAATGATAAAAAA
12952247 AATAAAATCAAAAA--ATAAAAA
1 AATAAAAT-AAAAATGATAAAAA
12952268 TAAAATGAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
22 7 0.12
24 21 0.36
25 12 0.20
26 1 0.02
27 10 0.17
28 8 0.14
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (23 bp):
AATAAAATAAAAATGATAAAAAA
Found at i:12953110 original size:3 final size:3
Alignment explanation
Indices: 12953100--12953203 Score: 83
Period size: 3 Copynumber: 36.0 Consensus size: 3
12953090 ATGATGATGG
* *
12953100 TAA T-A TAA TAA T-A TAA T-A TAA TAA T-A TAA T-A TGA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
12953143 TAC CAA TAA TAA CAAA TAA TAA TAA TAA TAA CAA AAA TAA TAA TAG
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12953189 TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA
12953204 AAATCAACCT
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
2 10 0.13
3 67 0.85
4 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12953118 original size:13 final size:13
Alignment explanation
Indices: 12953100--12953172 Score: 67
Period size: 13 Copynumber: 5.4 Consensus size: 13
12953090 ATGATGATGG
12953100 TAATATAATAATA
1 TAATATAATAATA
12953113 TAATATAATAATA
1 TAATATAATAATA
* *
12953126 TAATATGATATTAA
1 TAATATAATAAT-A
*
12953140 TAATACCAATAATA
1 TAATA-TAATAATA
*
12953154 -ACAAATAATAATAA
1 TA-ATATAATAAT-A
12953168 TAATA
1 TAATA
12953173 ACAAAAATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
13 30 0.64
14 12 0.26
15 5 0.11
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (13 bp):
TAATATAATAATA
Found at i:12953121 original size:18 final size:18
Alignment explanation
Indices: 12953107--12953202 Score: 63
Period size: 19 Copynumber: 5.1 Consensus size: 18
12953097 TGGTAATATA
12953107 ATAATATAATATAATAAT
1 ATAATATAATATAATAAT
*
12953125 ATAATATGATATTAATAAT
1 ATAATATAATA-TAATAAT
* *
12953144 ACCAATAATAACA-AATAAT
1 A-TAAT-ATAATATAATAAT
*
12953163 AATAATAATAACA-AA-AAT
1 -ATAAT-ATAATATAATAAT
12953181 AATAATAGTAATAGTAATAAT
1 -ATAATA-TAATA-TAATAAT
12953202 A
1 A
12953203 AAAATCAACC
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.02
18 23 0.36
19 26 0.41
20 7 0.11
21 7 0.11
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAATATAATATAATAAT
Found at i:12953160 original size:19 final size:19
Alignment explanation
Indices: 12953138--12953187 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
12953128 ATATGATATT
*
12953138 AATAATACCAATAATAACA
1 AATAATAACAATAATAACA
*
12953157 AATAATAATAATAATAACA
1 AATAATAACAATAATAACA
*
12953176 AA-AATAATAATA
1 AATAATAACAATA
12953188 GTAATAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAACAATAATAACA
Found at i:12954729 original size:44 final size:44
Alignment explanation
Indices: 12954635--12954785 Score: 151
Period size: 44 Copynumber: 3.4 Consensus size: 44
12954625 GAACTCTTTT
* * * * * *
12954635 TTTTTTTTTTGCTCAAGCTG-TCTTTTCAGATTTTCAACTTGAAC
1 TTTTTTTTTAGCTCAAGCCGCACTTTTGAG-TTTTTAACATGAAC
* *
12954679 TATTTTTTTTAGATCAAGCCGCACTTTTGAGTTTTTAACATGAAT
1 T-TTTTTTTTAGCTCAAGCCGCACTTTTGAGTTTTTAACATGAAC
* ** * * *
12954724 TTTTTTTTTTGCTCAAGTTGCCCTTTTGGGTTTTTAACTTGAAC
1 TTTTTTTTTAGCTCAAGCCGCACTTTTGAGTTTTTAACATGAAC
12954768 TTTTTTTTTAGCTCAAGC
1 TTTTTTTTTAGCTCAAGC
12954786 AAAGTATTTC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
44 52 0.60
45 28 0.32
46 7 0.08
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (44 bp):
TTTTTTTTTAGCTCAAGCCGCACTTTTGAGTTTTTAACATGAAC
Found at i:12961042 original size:10 final size:10
Alignment explanation
Indices: 12961027--12961054 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12961017 TGATCTTGTG
12961027 GTCCTTTTGA
1 GTCCTTTTGA
12961037 GTCCTTTTGA
1 GTCCTTTTGA
12961047 GTCCTTTT
1 GTCCTTTT
12961055 CAACTGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.21, G:0.18, T:0.54
Consensus pattern (10 bp):
GTCCTTTTGA
Found at i:12969502 original size:15 final size:14
Alignment explanation
Indices: 12969493--12969574 Score: 76
Period size: 14 Copynumber: 5.5 Consensus size: 14
12969483 TAAAATAGAT
12969493 AATAAAAAAATAAA
1 AATAAAAAAATAAA
12969507 AATAAAAATGAGATAAA
1 AATAAAAA--A-ATAAA
*
12969524 AACTAAAAATATAAA
1 AA-TAAAAAAATAAA
*
12969539 ATGATAAAAGAAT-AA
1 A--ATAAAAAAATAAA
*
12969554 AATTAAAAAATAAA
1 AATAAAAAAATAAA
12969568 AATAAAA
1 AATAAAA
12969575 TGGAAAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.15
14 16 0.29
15 9 0.16
16 8 0.15
17 8 0.15
18 6 0.11
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:12969553 original size:16 final size:13
Alignment explanation
Indices: 12969522--12969574 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
12969512 AAATGAGATA
*
12969522 AAAACTAAAAATAT
1 AAAATTAAAAA-AT
12969536 AAAATGATAAAAGAAT
1 AAAAT--TAAAA-AAT
12969552 AAAATTAAAAAAT
1 AAAATTAAAAAAT
*
12969565 AAAAATAAAA
1 AAAATTAAAA
12969575 TGGAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.35
14 9 0.26
16 12 0.35
17 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATTAAAAAAT
Found at i:12969563 original size:24 final size:24
Alignment explanation
Indices: 12969479--12969565 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 24
12969469 AAAATTTAGT
12969479 AAAATAAAATAGATA-ATAAAAAAATA
1 AAAATAAAA-A-ATAGAT-AAAAAATA
*
12969505 AAAAT-AAAAATGAGATAAAAACTA
1 AAAATAAAAAAT-AGATAAAAAATA
*
12969529 AAAATATAAAAT-GATAAAAGAATA
1 AAAATAAAAAATAGATAAAA-AATA
*
12969553 AAATTAAAAAATA
1 AAAATAAAAAATA
12969566 AAAATAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
23 9 0.18
24 27 0.53
25 10 0.20
26 5 0.10
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAATAAAAAATAGATAAAAAATA
Found at i:12969575 original size:5 final size:6
Alignment explanation
Indices: 12969498--12969574 Score: 59
Period size: 6 Copynumber: 12.7 Consensus size: 6
12969488 TAGATAATAA
* * * *
12969498 AAAAAT AAAAAT AAAAAT -GAGAT AAAAACT AAAAAT ATAAAAT GATAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA-T AAAAAT A-AAAAT AAAAAT
* *
12969546 AAGAAT AAAATT AAAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT -AAAAAT AAAAAT AAAA
12969575 TGGAAAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
5 6 0.11
6 33 0.60
7 16 0.29
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:12969581 original size:19 final size:18
Alignment explanation
Indices: 12969544--12969586 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12969534 ATAAAATGAT
* *
12969544 AAAAGAATAAAATTAAAA
1 AAAAAAATAAAATGAAAA
12969562 AATAAAAATAAAATGGAAAA
1 AA-AAAAATAAAAT-GAAAA
12969582 AAAAA
1 AAAAA
12969587 CCTACGTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 13 0.62
20 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAAATAAAATGAAAA
Found at i:12970332 original size:3 final size:3
Alignment explanation
Indices: 12970326--12970422 Score: 52
Period size: 3 Copynumber: 35.7 Consensus size: 3
12970316 ATGAAAGAAG
*
12970326 AAT AAT AA- AAT AA- AAT AA- AAT AAA AAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * *
12970368 -AT TTT AAT AAT GAT AAT -AT AAT AAT -AT AAT -AT GAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
12970412 ACC AAT AAT AA
1 AAT AAT AAT AA
12970423 CAATTATTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 20
0.67 0.13 0.19
Matches are distributed among these distances:
2 20 0.29
3 50 0.71
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12970358 original size:5 final size:5
Alignment explanation
Indices: 12970327--12970409 Score: 53
Period size: 5 Copynumber: 16.2 Consensus size: 5
12970317 TGAAAGAAGA
* * * * **
12970327 ATAAT AAAAT AAAAT AAAAT AAAAAT ATAAT ATAAT ATAAT ATTTT AATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
*
12970379 GATAAT AT-A- ATAAT ATAAT ATGAT ATTAAT A
1 -ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT A
12970410 ATACCAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 43 0.67
6 17 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:12970431 original size:3 final size:3
Alignment explanation
Indices: 12970425--12970464 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12970415 AATAATAACA
12970425 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12970465 ATTGTAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12971720 original size:18 final size:18
Alignment explanation
Indices: 12971696--12971741 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12971686 GTTGGTTTAC
12971696 TTTTTCTTTTTC-TTTCT
1 TTTTTCTTTTTCTTTTCT
12971713 TCTTTTC-TTTTCTTTTCT
1 T-TTTTCTTTTTCTTTTCT
*
12971731 TTTTTGTTTTT
1 TTTTTCTTTTT
12971742 AAGTTATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTCT
Found at i:12975130 original size:2 final size:2
Alignment explanation
Indices: 12975123--12975157 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12975113 AAACCTTCTC
12975123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12975158 AAGGATCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12978421 original size:8 final size:7
Alignment explanation
Indices: 12978395--12978420 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12978385 TTATTAAAAT
12978395 TTTTTAA
1 TTTTTAA
12978402 TTTTTAA
1 TTTTTAA
12978409 TTTTTAA
1 TTTTTAA
12978416 TTTTT
1 TTTTT
12978421 TGGAACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:12979724 original size:15 final size:15
Alignment explanation
Indices: 12979701--12979730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12979691 ACTTCACAAC
12979701 TTATGTTTATTTTTT
1 TTATGTTTATTTTTT
*
12979716 TTATTTTTATTTTTT
1 TTATGTTTATTTTTT
12979731 ACAAACTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTATGTTTATTTTTT
Found at i:12979976 original size:26 final size:26
Alignment explanation
Indices: 12979937--12979996 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
12979927 ATAAAAAGTA
* * *
12979937 ATTTTTTCCATTTTTGTTTTTGT-TTT
1 ATTTTTTGCATTTTTATTTTT-TAATT
*
12979963 ATTTTTTGCTTTTTTATTTTTTAATT
1 ATTTTTTGCATTTTTATTTTTTAATT
12979989 ATTTTTTG
1 ATTTTTTG
12979997 ATGAGATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (26 bp):
ATTTTTTGCATTTTTATTTTTTAATT
Found at i:12980927 original size:53 final size:56
Alignment explanation
Indices: 12980804--12980942 Score: 155
Period size: 53 Copynumber: 2.5 Consensus size: 56
12980794 GAAAATCAAA
* * * *
12980804 ATTTTAACT-TTTTCCTTAATATTTTAAAAATAATTTTACTTTAAGAAAATATTGAT
1 ATTTCAACTATTTT-CTTAACATTTTCAAAACAATTTTACTTTAAGAAAATATTGAT
*
12980860 ATTTCAACTATTTTCTT-A-ATTTTCAAAACAATTTT-TTTTAAAGAAAA-ATT-AGT
1 ATTTCAACTATTTTCTTAACATTTTCAAAACAATTTTACTTT-AAGAAAATATTGA-T
*
12980913 ATTTCAACTCTTTTCTTAACATTTTCAAAA
1 ATTTCAACTATTTTCTTAACATTTTCAAAA
12980943 TTTAATTCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
52 1 0.01
53 23 0.32
54 23 0.32
55 11 0.15
56 11 0.15
57 4 0.05
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (56 bp):
ATTTCAACTATTTTCTTAACATTTTCAAAACAATTTTACTTTAAGAAAATATTGAT
Found at i:12983198 original size:22 final size:22
Alignment explanation
Indices: 12983172--12983217 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12983162 TGATCAAAAT
* *
12983172 TTTTTAATTTGAAATTTAAAGA
1 TTTTTAATCTAAAATTTAAAGA
*
12983194 TTTTTAATCTAAAATTTAATGA
1 TTTTTAATCTAAAATTTAAAGA
12983216 TT
1 TT
12983218 CACAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTTAATCTAAAATTTAAAGA
Found at i:12983323 original size:19 final size:19
Alignment explanation
Indices: 12983269--12983331 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
12983259 TTATTTTGAT
12983269 TTTAAAGATTCATAAAATA
1 TTTAAAGATTCATAAAATA
* *
12983288 TTCAAAGATACATAAAATA
1 TTTAAAGATTCATAAAATA
* * *
12983307 TTTAAAGATTTACAAAAGA
1 TTTAAAGATTCATAAAATA
12983326 TTTAAA
1 TTTAAA
12983332 ATTTATAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (19 bp):
TTTAAAGATTCATAAAATA
Found at i:12983605 original size:20 final size:20
Alignment explanation
Indices: 12983573--12983623 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
12983563 AGATTCACAG
*
12983573 TTTTAAAAATCACAAAT-AA
1 TTTTAAAATTCACAAATAAA
12983592 TTTCTAAAATTCACAAATGAAA
1 TTT-TAAAATTCACAAAT-AAA
12983614 TTTTAAAATT
1 TTTTAAAATT
12983624 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 7 0.25
22 5 0.18
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTTAAAATTCACAAATAAA
Found at i:12988769 original size:7 final size:7
Alignment explanation
Indices: 12988757--12988857 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 7
12988747 AAAGTGTTTG
12988757 GAAAGAA
1 GAAAGAA
12988764 GAAAGAAA
1 GAAAG-AA
12988772 GAAAGAA
1 GAAAGAA
*
12988779 AAAAGAA
1 GAAAGAA
12988786 -AAAGAGA
1 GAAAGA-A
12988793 GAAGAGAA
1 GAA-AGAA
*
12988801 -AATGAA
1 GAAAGAA
12988807 -AAAGAA
1 GAAAGAA
12988813 -AAATGGAA
1 GAAA--GAA
12988821 GAAA-AGA
1 GAAAGA-A
12988828 GAAA-AA
1 GAAAGAA
12988834 -AAAGAA
1 GAAAGAA
12988840 -AAAGAGA
1 GAAAGA-A
12988847 GAAA-AA
1 GAAAGAA
12988853 GAAAG
1 GAAAG
12988858 GTTTCTTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 24
0.75 0.03 0.23
Matches are distributed among these distances:
5 3 0.04
6 30 0.38
7 24 0.30
8 16 0.20
9 6 0.08
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (7 bp):
GAAAGAA
Found at i:12988795 original size:21 final size:21
Alignment explanation
Indices: 12988758--12988857 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 21
12988748 AAGTGTTTGG
12988758 AAAGAAGAAAGAAAGAA-AGAAA
1 AAAGAA-AAAGAAAGAAGAG-AA
*
12988780 AAAGAAAAAGAGAGAAGAGAA
1 AAAGAAAAAGAAAGAAGAGAA
*
12988801 AATGAAAAAGAAA-AATGGAAGAA
1 AAAGAAAAAGAAAGAA--G-AGAA
12988824 AAGAGAAAAA-AAAGAA-A-AA
1 AA-AGAAAAAGAAAGAAGAGAA
*
12988843 GAGAGAAAAAGAAAG
1 -AAAGAAAAAGAAAG
12988858 GTTTCTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
19 9 0.14
20 8 0.12
21 22 0.34
22 9 0.14
23 9 0.14
24 8 0.12
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAGAAAGAAGAGAA
Found at i:12988852 original size:27 final size:26
Alignment explanation
Indices: 12988769--12988856 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 26
12988759 AAGAAGAAAG
12988769 AAAGAAAGAAAAAAGAAAAAGAGAG-A
1 AAAGAAA-AAAAAAGAAAAAGAGAGAA
*
12988795 AGAGAAAATGAAAAAGAAAAATG-GA-AGA
1 AAAGAAAA--AAAAAGAAAAA-GAGAGA-A
12988823 AAAGAGAAAAAAAAGAAAAAGAGAGAA
1 AAAGA-AAAAAAAAGAAAAAGAGAGAA
12988850 AAAGAAA
1 AAAGAAA
12988857 GGTTTCTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
25 1 0.02
26 9 0.17
27 32 0.62
28 7 0.13
29 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (26 bp):
AAAGAAAAAAAAAGAAAAAGAGAGAA
Found at i:12990131 original size:12 final size:12
Alignment explanation
Indices: 12990114--12990180 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
12990104 AGGAAAGAAG
12990114 AAAAAGAAAAAA
1 AAAAAGAAAAAA
12990126 AAAAAGAAAAAA
1 AAAAAGAAAAAA
* * *
12990138 TAGAAGAACAAA
1 AAAAAGAAAAAA
*
12990150 AGAAA-AAAAAA
1 AAAAAGAAAAAA
** *
12990161 AGGAAG-AAAAG
1 AAAAAGAAAAAA
12990172 AAAAAGAAA
1 AAAAAGAAA
12990181 TAAATTATTG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 17 0.40
12 25 0.60
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:12990145 original size:58 final size:57
Alignment explanation
Indices: 12990066--12990180 Score: 128
Period size: 58 Copynumber: 2.0 Consensus size: 57
12990056 AAAAAAAGTT
* ** * *
12990066 AAAAAAAAATAAAATGTAAGAA-AAGGGAAAGGAAATAAAGGAA-AGAAGAAAAAGAAA
1 AAAAAAAAAAAAAATGTAAGAACAAAAGAAA--AAAAAAAGGAAGAAAAGAAAAAGAAA
12990123 AAAAAAAAGAAAAAATAG-AAGAACAAAAGAAAAAAAAAAGGAAGAAAAGAAAAAGAAA
1 AAAAAAAA-AAAAAAT-GTAAGAACAAAAGAAAAAAAAAAGGAAGAAAAGAAAAAGAAA
12990181 TAAATTATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
57 18 0.37
58 24 0.49
59 7 0.14
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (57 bp):
AAAAAAAAAAAAAATGTAAGAACAAAAGAAAAAAAAAAGGAAGAAAAGAAAAAGAAA
Found at i:12990150 original size:20 final size:20
Alignment explanation
Indices: 12990102--12990176 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
12990092 GAAAGGAAAT
*
12990102 AAAGGAA-AGAAGAAAAAGAA
1 AAAGGAACAAAAGAAAAA-AA
12990122 AAA--AA-AAAAGAAAAAATA
1 AAAGGAACAAAAGAAAAAA-A
*
12990140 GAA-GAACAAAAGAAAAAAA
1 AAAGGAACAAAAGAAAAAAA
*
12990159 AAAGGAAGAAAAGAAAAA
1 AAAGGAACAAAAGAAAAA
12990177 GAAATAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 14 0.30
19 5 0.11
20 27 0.57
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAGGAACAAAAGAAAAAAA
Found at i:12990456 original size:138 final size:138
Alignment explanation
Indices: 12990188--12990453 Score: 362
Period size: 138 Copynumber: 1.9 Consensus size: 138
12990178 AAATAAATTA
* * *
12990188 TTGAGTGGAAAGCATTGGAAAATGAAAAGACAAATGCCCCTAAAGCGTATCCTTCAAATGAAAGA
1 TTGAGTGGAAAGAATGGGAAAATGAAAAGACAAATGCCCCTAAAGCGAATCCTTCAAATGAAAGA
*
12990253 ATGATCCTTCGTTTAGATCATCCTTAAAGCTTATTTTGGGCTTAACTATCCCTTTTTTTGAAAAC
66 ATGATCCTTCGTTTAGATCATCCTTAAAGCTTATTTTGGGCTTAACTATCCCTTTTTTTAAAAAC
12990318 CTTGAACC
131 CTTGAACC
* * *
12990326 TTGAGTGGAAAGAATGGGAAAATGAAAGGACAAATGCCTCC-AAAGTGAATCCTTTAAATGAAAG
1 TTGAGTGGAAAGAATGGGAAAATGAAAAGACAAATGCC-CCTAAAGCGAATCCTTCAAATGAAAG
* ** *
12990390 AATGATCCTT-GATTTATATCA-CCTTTAAATGCTTA-TTTGGGCTTATTTAT-TCTTTTTTTAA
65 AATGATCCTTCG-TTTAGATCATCC-TTAAA-GCTTATTTTGGGCTTAACTATCCCTTTTTTTAA
12990451 AAA
127 AAA
12990454 ACCCCAAACC
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
137 15 0.13
138 91 0.81
139 7 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (138 bp):
TTGAGTGGAAAGAATGGGAAAATGAAAAGACAAATGCCCCTAAAGCGAATCCTTCAAATGAAAGA
ATGATCCTTCGTTTAGATCATCCTTAAAGCTTATTTTGGGCTTAACTATCCCTTTTTTTAAAAAC
CTTGAACC
Found at i:12990675 original size:11 final size:11
Alignment explanation
Indices: 12990658--12990688 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12990648 AATAATCTAA
12990658 AAAAAAAGAGGC
1 AAAAAAA-AGGC
12990670 AAAAAAAAGGC
1 AAAAAAAAGGC
12990681 AAAAAAAA
1 AAAAAAAA
12990689 AGAAGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGC
Found at i:12990675 original size:13 final size:12
Alignment explanation
Indices: 12990657--12990690 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12990647 TAATAATCTA
12990657 AAAAAAAAGAGGC
1 AAAAAAAA-AGGC
12990670 -AAAAAAAAGGC
1 AAAAAAAAAGGC
12990681 AAAAAAAAAG
1 AAAAAAAAAG
12990691 AAGAGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:12992108 original size:27 final size:26
Alignment explanation
Indices: 12992077--12992135 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
12992067 TCATCTACAT
12992077 AAAAAGAACATTGGCATCTGCATCATG
1 AAAAAG-ACATTGGCATCTGCATCATG
* * * *
12992104 AAAAAGTCATTTGCATTTGCATGATG
1 AAAAAGACATTGGCATCTGCATCATG
12992130 AAAAAG
1 AAAAAG
12992136 TTTTGTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (26 bp):
AAAAAGACATTGGCATCTGCATCATG
Found at i:12992114 original size:26 final size:26
Alignment explanation
Indices: 12992085--12992136 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12992075 ATAAAAAGAA
12992085 CATTGGCATCTGCATCATGAAAAAGT
1 CATTGGCATCTGCATCATGAAAAAGT
* * *
12992111 CATTTGCATTTGCATGATGAAAAAGT
1 CATTGGCATCTGCATCATGAAAAAGT
12992137 TTTGTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
CATTGGCATCTGCATCATGAAAAAGT
Found at i:12992943 original size:31 final size:31
Alignment explanation
Indices: 12992810--12992943 Score: 128
Period size: 31 Copynumber: 4.3 Consensus size: 31
12992800 TGGCACTAAG
*
12992810 GAGAATTAAGCCTAGTTTAGCTAGCTCCT-AT
1 GAGAATTAAGCCTAGTTTAGCTAGC-ACTGAT
* ** *
12992841 GAAAATTTAAG-CTAGTTTAGCTAGCACCAAG
1 GAGAA-TTAAGCCTAGTTTAGCTAGCACTGAT
* * * * *
12992872 GAGAATTAAGCCCAATTTAACTGGCACTGAC
1 GAGAATTAAGCCTAGTTTAGCTAGCACTGAT
*
12992903 GAGAATTAAGCCTAGTTTAGCTAGCATTGAT
1 GAGAATTAAGCCTAGTTTAGCTAGCACTGAT
*
12992934 GAGATTTAAG
1 GAGAATTAAG
12992944 TCTGGAATAG
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
30 6 0.07
31 70 0.86
32 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (31 bp):
GAGAATTAAGCCTAGTTTAGCTAGCACTGAT
Found at i:12993519 original size:49 final size:49
Alignment explanation
Indices: 12993453--12993699 Score: 243
Period size: 49 Copynumber: 5.0 Consensus size: 49
12993443 CTCTTTGTAG
12993453 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAA
1 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAA
* * *
12993502 ACG-AGCTTTTCAAATTTGGGATTTTTAAAGTTTTCTAACCTTTCTTTAA
1 A-GAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAA
** * * *
12993551 A-AGAGCTTTTCAAAGGTGGGATTTTTATAGTTTCCTATCC-TTCTTTTAA
1 AGA-AGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTC-TTTAA
* ** *
12993600 AGAAGCTTTTCAAAGTT-AGGATTTTTAAAGTTTAATAGCCTCTCTTTAGA
1 AGAAGCTTTTCAAATTTGA-GATTTTTAAAGTTTCCTAGCCTTTCTTTA-A
* * * *** *
12993650 GGAAGTTTTTCAAATTTAAGA-TTTTAAAGTTTAAAAGCCTTTGTTTAA
1 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAA
12993698 AG
1 AG
12993700 GAGTTTCTCA
Statistics
Matches: 167, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
48 5 0.03
49 140 0.84
50 21 0.13
51 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (49 bp):
AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAA
Found at i:12993560 original size:98 final size:99
Alignment explanation
Indices: 12993453--12993681 Score: 277
Period size: 98 Copynumber: 2.3 Consensus size: 99
12993443 CTCTTTGTAG
12993453 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTT-TCTTTAAACG-AGCTTTTCAAA
1 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTCT-TTTAAA-GAAGCTTTTCAAA
* * ** *
12993516 TTTGGGATTTTTAAAGTTTTCTAACCTTTCTTTAAA
64 GTTAGGATTTTTAAAGTTTAATAACCTCTCTTTAAA
** * * *
12993552 AG-AGCTTTTCAAAGGTGGGATTTTTATAGTTTCCTATCCTTCTTTTAAAGAAGCTTTTCAAAGT
1 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTCTTTTAAAGAAGCTTTTCAAAGT
* *
12993616 TAGGATTTTTAAAGTTTAATAGCCTCTCTTTAGA
66 TAGGATTTTTAAAGTTTAATAACCTCTCTTTAAA
* * *
12993650 GGAAGTTTTTCAAATTTAAGA-TTTTAAAGTTT
1 AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTT
12993682 AAAAGCCTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
97 1 0.01
98 91 0.84
99 16 0.15
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (99 bp):
AGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTCTTTTAAAGAAGCTTTTCAAAGT
TAGGATTTTTAAAGTTTAATAACCTCTCTTTAAA
Found at i:12993697 original size:98 final size:96
Alignment explanation
Indices: 12993450--12993721 Score: 271
Period size: 98 Copynumber: 2.8 Consensus size: 96
12993440 GGTCTCTTTG
12993450 TAGAGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAAACGAGCTTTTCAA
1 TAGAGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTT-TTTAAA-GAGCTTTTCAA
* * ** *
12993515 ATTTGGGATTTTTAAAGTTTTCTAACCTTTCTT
64 AGTTAGGATTTTTAAAGTTTAATAACCTCTCTT
* ** * * *
12993548 TA-AAAGAGCTTTTCAAAGGTGGGATTTTTATAGTTTCCTATCCTTCTTTTAAAGAAGCTTTTCA
1 TAGAGA-AGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTT-TTTTAAAG-AGCTTTTCA
*
12993612 AAGTTAGGATTTTTAAAGTTTAATAGCCTCTCTT
63 AAGTTAGGATTTTTAAAGTTTAATAACCTCTCTT
* * ***
12993646 TAGAGGAAGTTTTTCAAATTTAAGA-TTTTAAAGTTTAAAAGCCTTTGTTTAAAGGAG-TTTCTC
1 TAGA-GAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTT-TTTAAA-GAGCTTT-TC
*
12993709 AAAAGTTAAGATT
62 -AAAGTTAGGATT
12993722 GTTTTTAAAG
Statistics
Matches: 141, Mismatches: 24, Indels: 17
0.77 0.13 0.09
Matches are distributed among these distances:
97 7 0.05
98 106 0.75
99 27 0.19
100 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (96 bp):
TAGAGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTTTTAAAGAGCTTTTCAAAG
TTAGGATTTTTAAAGTTTAATAACCTCTCTT
Found at i:12993697 original size:147 final size:148
Alignment explanation
Indices: 12993444--12993711 Score: 339
Period size: 147 Copynumber: 1.8 Consensus size: 148
12993434 CTTTCTGGTC
* * ** *
12993444 TCTTTGTAGAGAAGCTTTTCAAATTTGAGATTTTTAAAGTTTCCTAGCCTTTCTTTAAACGAGCT
1 TCTTTGTAAAGAAGCTTTTCAAATTAGAGATTTTTAAAGTTTAATAGCCTCTCTTTAAACGAGCT
** **
12993509 TTTCAAATTTGGGATTTTTAAAGTTTTCTAACCTTTCTTTAAAAGAGCTTT-TCAAAGGTGGGAT
66 TTTCAAATTTAAGATTTTTAAAGTTTTAAAACCTTTCTTTAAAAGAG-TTTCTCAAAGGTGGGAT
12993573 TTTTATAGTTTCCTATCCT
130 TTTTATAGTTTCCTATCCT
* *
12993592 TCTTT-TAAAGAAGCTTTTCAAAGTTAG-GATTTTTAAAGTTTAATAGCCTCTCTTTAGAGGAAG
1 TCTTTGTAAAGAAGCTTTTCAAA-TTAGAGATTTTTAAAGTTTAATAGCCTCTCTTTAAACG-AG
* * *
12993655 TTTTTCAAATTTAAGA-TTTTAAAG-TTTAAAAGCCTTTGTTTAAAGGAGTTTCTCAAA
64 CTTTTCAAATTTAAGATTTTTAAAGTTTTAAAA-CCTTTCTTTAAAAGAGTTTCTCAAA
12993712 AGTTAAGATT
Statistics
Matches: 102, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
146 8 0.08
147 71 0.70
148 23 0.23
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (148 bp):
TCTTTGTAAAGAAGCTTTTCAAATTAGAGATTTTTAAAGTTTAATAGCCTCTCTTTAAACGAGCT
TTTCAAATTTAAGATTTTTAAAGTTTTAAAACCTTTCTTTAAAAGAGTTTCTCAAAGGTGGGATT
TTTATAGTTTCCTATCCT
Found at i:12993718 original size:49 final size:47
Alignment explanation
Indices: 12993595--12993721 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 47
12993585 CTATCCTTCT
* * *
12993595 TTTAAAGAAGCTTTTCAAAGTTAGGATTTTTAAAGTTTAATAGCCTCTC
1 TTTAAAGGAG-TTTTCAAAGTTAAGA-TTTTAAAGTTTAAAAGCCTCTC
* * * *
12993644 TTTAGAGGAAGTTTTTCAAATTTAAGATTTTAAAGTTTAAAAGCCTTTG
1 TTTAAAGG-AG-TTTTCAAAGTTAAGATTTTAAAGTTTAAAAGCCTCTC
12993693 TTTAAAGGAGTTTCTCAAAAGTTAAGATT
1 TTTAAAGGAGTTT-TC-AAAGTTAAGATT
12993722 GTTTTTAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
47 3 0.05
48 4 0.06
49 43 0.66
50 15 0.23
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (47 bp):
TTTAAAGGAGTTTTCAAAGTTAAGATTTTAAAGTTTAAAAGCCTCTC
Found at i:12994759 original size:144 final size:142
Alignment explanation
Indices: 12994350--12994785 Score: 411
Period size: 143 Copynumber: 3.0 Consensus size: 142
12994340 CAATTGATGA
* * * * *
12994350 ATTTTTATACATTGAAAACCTTGATTGCACCTTGAGAGGTGTGATATTACCAAAATACATTTTTA
1 ATTTTTATGCATTAAAAACTTTGATTGCACCTTGAAAGGTGTGATATTACCAAAATAC-TCTTTA
* * * * * * * * * **
12994415 -GAATAATTTCATAAATTGACC-TCCCTAGATTGATTTTTTGA-GAAAACCTCTAGATCATGACT
65 GGAGTATTTTTATAATTTGACCTTCTCAAGGTCGATTTTTT-ATGAAAA-CTCTAAATCATGTTT
* *
12994477 TGATATTATTTGATG
128 TGAAATTATTTTATG
* * * *
12994492 ATTTTTAGTGTATTAAAAA-TCTTGATTGCACCTTGATA-GTGTGATATTACTAAAATGCTCATT
1 ATTTTTA-TGCATTAAAAACT-TTGATTGCACCTTGAAAGGTGTGATATTACCAAAATACTC-TT
* * * **
12994555 T-GCAGTATTTTTGTAATTTGACCTTTTTGAGGTCGATTTTTTATGAAACACTCTAAATCATGTT
63 TAGGAGTATTTTTATAATTTGACCTTCTCAAGGTCGATTTTTTATGAAA-ACTCTAAATCATGTT
12994619 TTGAAATTATTTTATG
127 TTGAAATTATTTTATG
* *
12994635 ATTTTTGATGCATTAAAAACTTTGATTGCACCTTGAAAGGTTTGAAATTACCAAAATACTCTTTA
1 ATTTTT-ATGCATTAAAAACTTTGATTGCACCTTGAAAGGTGTGATATTACCAAAATACTCTTTA
* * *
12994700 GGAGTATTTTTATAATTTGACCTTCTCAAGGTC-AGTTTTTTATGAAAACTTTTATATCATAATT
65 GGAGTATTTTTATAATTTGACCTTCTCAAGGTCGA-TTTTTTATGAAAAC-TCTAAATCAT-GTT
* *
12994764 TT-AACTTATTTTAAG
127 TTGAAATTATTTTATG
12994779 ATTTTTA
1 ATTTTTA
12994786 GTGCTTTCAA
Statistics
Matches: 239, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
141 1 0.00
142 44 0.18
143 104 0.44
144 86 0.36
145 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (142 bp):
ATTTTTATGCATTAAAAACTTTGATTGCACCTTGAAAGGTGTGATATTACCAAAATACTCTTTAG
GAGTATTTTTATAATTTGACCTTCTCAAGGTCGATTTTTTATGAAAACTCTAAATCATGTTTTGA
AATTATTTTATG
Found at i:12996674 original size:19 final size:19
Alignment explanation
Indices: 12996642--12996693 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
12996632 ATTTCGCTTG
*
12996642 AAAAAAAAAGAAAAAAACAT
1 AAAAAATAA-AAAAAAACAT
* *
12996662 AAAACATAAAAAAAAAGAT
1 AAAAAATAAAAAAAAACAT
12996681 AAAAAATAAAAAA
1 AAAAAATAAAAAA
12996694 GAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.85, C:0.04, G:0.04, T:0.08
Consensus pattern (19 bp):
AAAAAATAAAAAAAAACAT
Found at i:12996684 original size:27 final size:26
Alignment explanation
Indices: 12996641--12996708 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 26
12996631 TATTTCGCTT
*
12996641 GAAAAAAAAAGAAAAAAACATAAAACA
1 GAAAAAAAAAGAAAAAAA-ATAAAAAA
* *
12996668 TAAAAAAAAAGATAAAAAATAAAAAA
1 GAAAAAAAAAGAAAAAAAATAAAAAA
12996694 GAAAAAAAAGAGAAA
1 GAAAAAAAA-AGAAA
12996709 TGATTCAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (26 bp):
GAAAAAAAAAGAAAAAAAATAAAAAA
Found at i:12996702 original size:16 final size:16
Alignment explanation
Indices: 12996672--12996702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12996662 AAAACATAAA
*
12996672 AAAAAAGATAAAAAAT
1 AAAAAAGAAAAAAAAT
12996688 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
12996703 GAGAAATGAT
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:0.87, C:0.00, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAT
Found at i:12997399 original size:11 final size:11
Alignment explanation
Indices: 12997376--12997416 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12997366 ATCTGATATA
*
12997376 AAAAAAAAAAG
1 AAAAAAGAAAG
*
12997387 AAAGAAGAAAG
1 AAAAAAGAAAG
*
12997398 AAAAAAAAAAG
1 AAAAAAGAAAG
12997409 AAAAAAGA
1 AAAAAAGA
12997417 GATAGAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:12997403 original size:18 final size:18
Alignment explanation
Indices: 12997375--12997416 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12997365 TATCTGATAT
*
12997375 AAAAA-AAAAAAGAAAGA
1 AAAAAGAAAAAAAAAAGA
*
12997392 AGAAAGAAAAAAAAAAGA
1 AAAAAGAAAAAAAAAAGA
12997410 AAAAAGA
1 AAAAAGA
12997417 GATAGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:12997404 original size:22 final size:24
Alignment explanation
Indices: 12997376--12997425 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
12997366 ATCTGATATA
*
12997376 AAAAAAAAAAGAAAGAAGA-A-AG
1 AAAAAAAAAAGAAAAAAGAGATAG
12997398 AAAAAAAAAAGAAAAAAGAGATAG
1 AAAAAAAAAAGAAAAAAGAGATAG
12997422 AAAA
1 AAAA
12997426 CATATAGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.72
23 1 0.04
24 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAAGAGATAG
Found at i:12997407 original size:24 final size:24
Alignment explanation
Indices: 12997375--12997425 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
12997365 TATCTGATAT
*
12997375 AAAAAAAAA-AAGAAAGAAGAAAGA
1 AAAAAAAAAGAAAAAAG-AGAAAGA
*
12997399 AAAAAAAAAGAAAAAAGAGATAGA
1 AAAAAAAAAGAAAAAAGAGAAAGA
12997423 AAA
1 AAA
12997426 CATATAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAGAAAAAAGAGAAAGA
Found at i:12997414 original size:7 final size:7
Alignment explanation
Indices: 12997375--12997416 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12997365 TATCTGATAT
12997375 AAAAA-A
1 AAAAAGA
12997381 AAAAAGA
1 AAAAAGA
*
12997388 AAGAAGA
1 AAAAAGA
*
12997395 AAGAAAAA
1 AA-AAAGA
12997403 AAAAAGA
1 AAAAAGA
12997410 AAAAAGA
1 AAAAAGA
12997417 GATAGAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 5 0.17
7 20 0.67
8 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Done.