Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 134 of 135
Found at i:43218081 original size:59 final size:57
Alignment explanation
Indices: 43218012--43218225 Score: 196
Period size: 59 Copynumber: 3.6 Consensus size: 57
43218002 ATTTTTGGAA
43218012 TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAATTTTTAGGGTCAAAAATGAAAT
1 TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAATTTTT-GGGT-AAAAATGAAAT
* * * * * *
43218071 TTTTGGAAGTTTG-GGGATAAAAATATAATTTTTTTGATTTTTTGGGGTTAACATGCAAT
1 TTTTGGAAGTTCGAGGG-TAAAAATATAA-TTTTTGGAATTTTT-GGGTAAAAATGAAAT
** ** * * *
43218130 TTTCTAAAAGTTTTAGGGTAACAAATATAATTTTTAGAAGTTTTGGGTAAAAATGTAAT
1 TTT-TGGAAGTTCGAGGGTAA-AAATATAATTTTTGGAATTTTTGGGTAAAAATGAAAT
* * * *
43218189 TTTGGAGAAGTTCAAGGGTCAAAATACAATTTTTGGA
1 TTTTG-GAAGTTCGAGGGTAAAAATATAATTTTTGGA
43218226 CAGTTTAGGG
Statistics
Matches: 125, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
58 17 0.14
59 60 0.48
60 37 0.30
61 11 0.09
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (57 bp):
TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAATTTTTGGGTAAAAATGAAAT
Found at i:43220383 original size:20 final size:21
Alignment explanation
Indices: 43220351--43220392 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
43220341 TTAGGGTTCG
43220351 AAGTTTGGAGTTCAAAATTCA
1 AAGTTTGGAGTTCAAAATTCA
*
43220372 AAGTTT-GAGTTCAATATTCA
1 AAGTTTGGAGTTCAAAATTCA
43220392 A
1 A
43220393 GGTTCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
AAGTTTGGAGTTCAAAATTCA
Found at i:43220402 original size:20 final size:20
Alignment explanation
Indices: 43220359--43220407 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
43220349 CGAAGTTTGG
**
43220359 AGTTCAAAATTCAAAGTTTG
1 AGTTCAAAATTCAAAGTTCA
* *
43220379 AGTTCAATATTCAAGGTTCA
1 AGTTCAAAATTCAAAGTTCA
*
43220399 AGTTTAAAA
1 AGTTCAAAA
43220408 AAATTATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
AGTTCAAAATTCAAAGTTCA
Found at i:43225398 original size:6 final size:6
Alignment explanation
Indices: 43225387--43225411 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43225377 CAAACAGCTA
43225387 GTTGCT GTTGCT GTTGCT GTTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT G
43225412 GTTTTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTGCT
Found at i:43232835 original size:2 final size:2
Alignment explanation
Indices: 43232828--43232852 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43232818 TTTTCACTTT
43232828 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
43232853 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43233160 original size:2 final size:2
Alignment explanation
Indices: 43233147--43233180 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43233137 TTACCAGTAA
*
43233147 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43233181 TTAAATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43234286 original size:17 final size:16
Alignment explanation
Indices: 43234264--43234295 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
43234254 GATTTAGAAG
43234264 TGATTTTTTTCGTGGAA
1 TGATTTTTTT-GTGGAA
43234281 TGATTTTTTTGTGGA
1 TGATTTTTTTGTGGA
43234296 CCCTGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.03, G:0.25, T:0.56
Consensus pattern (16 bp):
TGATTTTTTTGTGGAA
Found at i:43234882 original size:5 final size:6
Alignment explanation
Indices: 43234859--43234889 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
43234849 CCAATATTAC
43234859 CAAAATA CAAAAA CAAAAA CAAAAA CAAAAA
1 CAAAA-A CAAAAA CAAAAA CAAAAA CAAAAA
43234890 AACATGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (6 bp):
CAAAAA
Found at i:43236960 original size:2 final size:2
Alignment explanation
Indices: 43236947--43236980 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43236937 ACTTGCACAT
*
43236947 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43236981 AATTAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:43252471 original size:30 final size:30
Alignment explanation
Indices: 43252435--43252528 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
43252425 CAACTTAACA
* *
43252435 AACAAATGTCTTTAAAATAGTAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
*
43252465 AACAAATGTCTCTAAAATAATAATAAAAAATT
1 AACAAATGTCTCTAAAATAAT-A-ACAAAATT
43252497 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
43252527 AA
1 AA
43252529 TAATAAAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.48
31 2 0.03
32 28 0.48
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:43253020 original size:92 final size:92
Alignment explanation
Indices: 43252863--43253054 Score: 384
Period size: 92 Copynumber: 2.1 Consensus size: 92
43252853 CACTTTTGAG
43252863 AAACATTCCTAAACTAGGCCAAGTGGTAGTATTCTTACTCACTAATGCCATATAAGGGTTTGGGT
1 AAACATTCCTAAACTAGGCCAAGTGGTAGTATTCTTACTCACTAATGCCATATAAGGGTTTGGGT
43252928 TTCAACCCTACCAAGGTCATAATGCTA
66 TTCAACCCTACCAAGGTCATAATGCTA
43252955 AAACATTCCTAAACTAGGCCAAGTGGTAGTATTCTTACTCACTAATGCCATATAAGGGTTTGGGT
1 AAACATTCCTAAACTAGGCCAAGTGGTAGTATTCTTACTCACTAATGCCATATAAGGGTTTGGGT
43253020 TTCAACCCTACCAAGGTCATAATGCTA
66 TTCAACCCTACCAAGGTCATAATGCTA
43253047 AAACATTC
1 AAACATTC
43253055 TCGATGGGTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 100 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (92 bp):
AAACATTCCTAAACTAGGCCAAGTGGTAGTATTCTTACTCACTAATGCCATATAAGGGTTTGGGT
TTCAACCCTACCAAGGTCATAATGCTA
Found at i:43254670 original size:17 final size:17
Alignment explanation
Indices: 43254623--43254672 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
43254613 ATTTTTTATA
43254623 TAAAAAC-TTAAAA-AT
1 TAAAAACATTAAAATAT
* *
43254638 TATAATACATAAAAAATAT
1 TA-AAAACAT-TAAAATAT
43254657 TAAAAACATTAAAATA
1 TAAAAACATTAAAATA
43254673 AATGTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 4 0.15
17 7 0.26
18 10 0.37
19 4 0.15
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAACATTAAAATAT
Found at i:43256311 original size:16 final size:16
Alignment explanation
Indices: 43256290--43256335 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
43256280 TTTGGTTCGC
43256290 TGTAATGGAATAGAGA
1 TGTAATGGAATAGAGA
*
43256306 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGA
*
43256322 TGTAATGCAATAGA
1 TGTAATGGAATAGA
43256336 ATTGTAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.28, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:43256341 original size:16 final size:15
Alignment explanation
Indices: 43256290--43256348 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
43256280 TTTGGTTCGC
*
43256290 TGTAATGGAATAGAGA
1 TGTAATGCAATAGA-A
* *
43256306 TGTAATGGAATAGAGC
1 TGTAATGCAATAGA-A
43256322 TGTAATGCAATAGAA
1 TGTAATGCAATAGAA
43256337 TTGTAAT-CAATA
1 -TGTAATGCAATA
43256349 ATTCAATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 5 0.13
16 34 0.87
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (15 bp):
TGTAATGCAATAGAA
Found at i:43257911 original size:12 final size:12
Alignment explanation
Indices: 43257870--43257913 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
43257860 TTTAGTTTAC
43257870 TGCAAGTAAACA
1 TGCAAGTAAACA
43257882 TGC-AGTATTAAGCA
1 TGCAAGTA--AA-CA
43257896 TGCAAGTAAACA
1 TGCAAGTAAACA
43257908 TGCAAG
1 TGCAAG
43257914 AAAATGTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.14
12 11 0.39
13 4 0.14
14 5 0.18
15 4 0.14
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (12 bp):
TGCAAGTAAACA
Found at i:43275229 original size:24 final size:25
Alignment explanation
Indices: 43275189--43275235 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
43275179 CAAATGCACG
*
43275189 TAAACAACTCCATTATAA-TACATT
1 TAAACAACTCCAATATAACTACATT
*
43275213 TAAACAACTCTAATATAACTACA
1 TAAACAACTCCAATATAACTACA
43275236 AAACTCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAACAACTCCAATATAACTACATT
Found at i:43298380 original size:12 final size:12
Alignment explanation
Indices: 43298340--43298383 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
43298330 AGGGTTTAAT
*
43298340 GAGAGATGAAGGT
1 GAGAGA-GAAGGA
43298353 GAGAGTAGAAGGA
1 GAGAG-AGAAGGA
*
43298366 GAGAGAGAGGGA
1 GAGAGAGAAGGA
43298378 GAGAGA
1 GAGAGA
43298384 AATGTCCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 12 0.43
13 15 0.54
14 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.50, T:0.07
Consensus pattern (12 bp):
GAGAGAGAAGGA
Found at i:43299210 original size:23 final size:24
Alignment explanation
Indices: 43299166--43299210 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
43299156 CATTTAGAAG
*
43299166 CTCGTTTATCGGCTCGTGTATTAA
1 CTCGTTTATCAGCTCGTGTATTAA
*
43299190 CTCGTTTAT-AGCTCGTTTATT
1 CTCGTTTATCAGCTCGTGTATT
43299211 TATTAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (24 bp):
CTCGTTTATCAGCTCGTGTATTAA
Found at i:43299377 original size:22 final size:22
Alignment explanation
Indices: 43299334--43299377 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43299324 TATATGTTCG
*
43299334 TGAACATGTCCGATTAAGTTAA
1 TGAACATGTCCGATTAAATTAA
*
43299356 TGAACATGTTCG-TTAACATTAA
1 TGAACATGTCCGATTAA-ATTAA
43299378 ACAAACGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
TGAACATGTCCGATTAAATTAA
Found at i:43316807 original size:16 final size:16
Alignment explanation
Indices: 43316786--43316822 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43316776 AATTATGATT
*
43316786 AAAATTTTAAAAATCA
1 AAAATTGTAAAAATCA
*
43316802 AAAATTGTAAAAATTA
1 AAAATTGTAAAAATCA
43316818 AAAAT
1 AAAAT
43316823 AATCAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATTGTAAAAATCA
Found at i:43317585 original size:14 final size:13
Alignment explanation
Indices: 43317538--43317591 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 13
43317528 AATTAATGAC
43317538 TTAAATAATTTTT
1 TTAAATAATTTTT
43317551 TT-AATAATTTAATAAT
1 TTAAATAATTT--T--T
43317567 TTAAATGAATTTTT
1 TTAAAT-AATTTTT
43317581 TTAAATAATTT
1 TTAAATAATTT
43317592 AATAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 8 0.23
13 7 0.20
14 8 0.23
16 4 0.11
17 3 0.09
18 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTT
Found at i:43317612 original size:31 final size:30
Alignment explanation
Indices: 43317522--43317598 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
43317512 ACAAAAAAAA
* * *
43317522 TTAATAAATTAATGACTTAAAT-AATTTTT
1 TTAATAATTTAATAATTTAAATGAATTTTT
43317551 TTAATAATTTAATAATTTAAATGAATTTTT
1 TTAATAATTTAATAATTTAAATGAATTTTT
43317581 TTAAATAATTTAATAATT
1 TT-AATAATTTAATAATT
43317599 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 19 0.44
30 9 0.21
31 15 0.35
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TTAATAATTTAATAATTTAAATGAATTTTT
Found at i:43321496 original size:31 final size:31
Alignment explanation
Indices: 43321443--43321505 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
43321433 AAGGGTTCAA
* * * *
43321443 GCCCAAATGTGGGAATAGTTGCCTAGTTTAG
1 GCCCAAATGTGGGAACAATTGCCAAATTTAG
*
43321474 GCCCCAATGTGGGAACAATTGCCAAATTTAG
1 GCCCAAATGTGGGAACAATTGCCAAATTTAG
43321505 G
1 G
43321506 GCTTAACTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
GCCCAAATGTGGGAACAATTGCCAAATTTAG
Found at i:43326562 original size:31 final size:32
Alignment explanation
Indices: 43326521--43326585 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
43326511 TAAATTCACA
43326521 TTTTGATTATTACACTATTCAAAAGCTTTCAT
1 TTTTGATTATTACACTATTCAAAAGCTTTCAT
** * * *
43326553 TTTTG-TTATTGGACTATTCGAAAGTTTTTAT
1 TTTTGATTATTACACTATTCAAAAGCTTTCAT
43326584 TT
1 TT
43326586 AAGTCCTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (32 bp):
TTTTGATTATTACACTATTCAAAAGCTTTCAT
Found at i:43334640 original size:3 final size:3
Alignment explanation
Indices: 43334632--43334661 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
43334622 GATGTTTTCT
43334632 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43334662 AAGCATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:43339747 original size:10 final size:11
Alignment explanation
Indices: 43339727--43339818 Score: 53
Period size: 11 Copynumber: 8.2 Consensus size: 11
43339717 GTTGCTTTGG
43339727 TGCTGTTTTTT
1 TGCTGTTTTTT
*
43339738 TGCTTTTTTTT
1 TGCTGTTTTTT
* *
43339749 TACTGTTTTGGT
1 TGCTGTTTT-TT
* *
43339761 TGCTGTTTATG
1 TGCTGTTTTTT
*
43339772 TGCTATTTTTT
1 TGCTGTTTTTT
**
43339783 AT--TGTTTTGA
1 -TGCTGTTTTTT
43339793 TGCTGTTATTTT
1 TGCTGTT-TTTT
*
43339805 TGTTGTTGTTTT
1 TGCTGTT-TTTT
43339817 TG
1 TG
43339819 TTGTGTTGTT
Statistics
Matches: 58, Mismatches: 18, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
9 1 0.02
10 5 0.09
11 29 0.50
12 23 0.40
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (11 bp):
TGCTGTTTTTT
Found at i:43339766 original size:34 final size:32
Alignment explanation
Indices: 43339722--43339806 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
43339712 ATATTGTTGC
*
43339722 TTTGGTGCTGTTTTTTTGCTTTTTTTTTACTGT
1 TTTGGTGCTGTTTTTTTGC-TATTTTTTACTGT
* * *
43339755 TTTGGTTGCTGTTTATGTGCTATTTTTTATTGT
1 TTTGG-TGCTGTTTTTTTGCTATTTTTTACTGT
*
43339788 TTTGATGCTGTTATTTTTG
1 TTTGGTGCTGTT-TTTTTG
43339807 TTGTTGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 7 0.16
33 24 0.56
34 12 0.28
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (32 bp):
TTTGGTGCTGTTTTTTTGCTATTTTTTACTGT
Found at i:43339847 original size:44 final size:44
Alignment explanation
Indices: 43339799--43339891 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
43339789 TTGATGCTGT
* * *
43339799 TATTTTTG-TTGTTGTTTTTGTTGTGTT-GTTGTTATTTTTACTGC
1 TATTTTTGATTGTTATTTTAGTTGT-TTGGATGTTATTTTTA-TGC
43339843 TA-TTTTGATTGTTATTTTAGTTGTTTGGATGTTATTTTTATGC
1 TATTTTTGATTGTTATTTTAGTTGTTTGGATGTTATTTTTATGC
43339886 -ATTTTT
1 TATTTTT
43339892 ACTATTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
42 1 0.02
43 14 0.33
44 28 0.65
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (44 bp):
TATTTTTGATTGTTATTTTAGTTGTTTGGATGTTATTTTTATGC
Found at i:43340078 original size:38 final size:37
Alignment explanation
Indices: 43339997--43340079 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
43339987 ATATAAAGAA
* *
43339997 TTTTTAATGTATTTTAAATTTATTTATTTTTAATGTT
1 TTTTTAATGTATTTTAAATTTATTTATTATTAATGAT
*
43340034 TGTTTTAATGT-TTTTAAGTTTATTTGATATATTATAT-AT
1 T-TTTTAATGTATTTTAAATTTATTT-AT-TATTA-ATGAT
43340073 TTTTTAA
1 TTTTTAA
43340080 ATTTATTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 14 0.36
38 17 0.44
39 6 0.15
40 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (37 bp):
TTTTTAATGTATTTTAAATTTATTTATTATTAATGAT
Found at i:43350069 original size:28 final size:27
Alignment explanation
Indices: 43350031--43350085 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
43350021 TTTGACTTTA
*
43350031 ATGTTCAATTTGATACTTGAGTGTTTTTT
1 ATGTTCAATTTGAAACTTG-G-GTTTTTT
43350060 ATGTT-AATTTGAAACTTGGGTTTTTT
1 ATGTTCAATTTGAAACTTGGGTTTTTT
43350086 CAATATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 1 0.04
28 12 0.48
29 5 0.20
ACGTcount: A:0.22, C:0.05, G:0.18, T:0.55
Consensus pattern (27 bp):
ATGTTCAATTTGAAACTTGGGTTTTTT
Found at i:43359362 original size:2 final size:2
Alignment explanation
Indices: 43359355--43359383 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43359345 TGTTATATTT
43359355 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
43359384 TATCTAAACT
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:43377418 original size:2 final size:2
Alignment explanation
Indices: 43377413--43377446 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43377403 TATCACACAC
*
43377413 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43377447 CTCAATGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43378146 original size:23 final size:23
Alignment explanation
Indices: 43378120--43378195 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
43378110 CTTAGTTCAA
*
43378120 TTAGGTTATTGGGTCAAATGGGT
1 TTAGGTTATTGAGTCAAATGGGT
* * *
43378143 TTAGGTTATTGCGTCAATTAGGT
1 TTAGGTTATTGAGTCAAATGGGT
*
43378166 TTAAAGGGTTATTGAATCAAAATGGGT
1 TT--A-GGTTATTGAGTC-AAATGGGT
43378193 TTA
1 TTA
43378196 AAGGTTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 22 0.52
25 2 0.05
26 10 0.24
27 8 0.19
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.39
Consensus pattern (23 bp):
TTAGGTTATTGAGTCAAATGGGT
Found at i:43378233 original size:21 final size:22
Alignment explanation
Indices: 43378204--43378244 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
43378194 TAAAGGTTTA
43378204 TTGGATTTAA-TTTTAAAAGAT
1 TTGGATTTAAGTTTTAAAAGAT
*
43378225 TTGGGTTTAAGTTTTAAAAG
1 TTGGATTTAAGTTTTAAAAG
43378245 GGTTTGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (22 bp):
TTGGATTTAAGTTTTAAAAGAT
Found at i:43380359 original size:59 final size:59
Alignment explanation
Indices: 43380228--43380361 Score: 137
Period size: 59 Copynumber: 2.3 Consensus size: 59
43380218 ATTTGGGGTT
* * *
43380228 AAAAT-GATATTTTAGATATCCGAGGGTAAAATAATAATTTTTAGAAAAATCGAGACCA
1 AAAATGGAAATTTTGGATATCCGAGGGTAAAATAATAATTTTTAGAAAAATCAAGACCA
** * * *** **
43380286 AAAATGGAGTTTTTGGATGTCCGAGGGTAAAATGATAATTTTTA-AAGTTTCAAGGTCA
1 AAAATGGAAATTTTGGATATCCGAGGGTAAAATAATAATTTTTAGAAAAATCAAGACCA
43380344 AAAATGGTAAATTTTGGA
1 AAAATGG-AAATTTTGGA
43380362 ATTTTTACGG
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
58 20 0.33
59 41 0.67
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATGGAAATTTTGGATATCCGAGGGTAAAATAATAATTTTTAGAAAAATCAAGACCA
Found at i:43380380 original size:89 final size:89
Alignment explanation
Indices: 43380284--43380451 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 89
43380274 AAATCGAGAC
* * * *
43380284 CAAAAATGGAGTTTTTGGATGTCCGAGGG-TAAAATGATAATTTTT-AAAGTTTCAAGGTCAAAA
1 CAAAAATGGAGTTTTTAGAAGTCCGAGGGCAAAAATG-TAATTTTTGAAAATTTCAAGGTCAAAA
43380347 ATGGTAAATTTTGGAATTTTTACGGT
65 AT-GTAAATTTTGGAATTTTTACGGT
* ***
43380373 CAAAAATGGAGTTTTTAGAAGTTCGAGGGCAAAAATGTAATTTTTGAAAATTTTGGGGTCAAAAA
1 CAAAAATGGAGTTTTTAGAAGTCCGAGGGCAAAAATGTAATTTTTGAAAATTTCAAGGTCAAAAA
*
43380438 TGTAATTTTTGGAA
66 TGTAAATTTTGGAA
43380452 GTTTGGGGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 46 0.68
90 22 0.32
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (89 bp):
CAAAAATGGAGTTTTTAGAAGTCCGAGGGCAAAAATGTAATTTTTGAAAATTTCAAGGTCAAAAA
TGTAAATTTTGGAATTTTTACGGT
Found at i:43380416 original size:29 final size:29
Alignment explanation
Indices: 43380314--43380476 Score: 107
Period size: 30 Copynumber: 5.5 Consensus size: 29
43380304 GTCCGAGGGT
* *
43380314 AAAATGATAATTTTTA-AAGTTTCAAGGTCA
1 AAAATG-TAATTTTTAGAAGTTT-GAGGGCA
* * * * *
43380344 AAAATGGTAAATTTTGGAATTTTTACGGTCA
1 AAAAT-GTAATTTTTAGAAGTTTGA-GGGCA
* * *
43380375 AAAATGGAGTTTTTAGAAGTTCGAGGGCA
1 AAAATGTAATTTTTAGAAGTTTGAGGGCA
* *
43380404 AAAATGTAATTTTTGAAAATTTTG-GGGTCA
1 AAAATGTAATTTTT-AGAAGTTTGAGGG-CA
* *
43380434 AAAATGTAATTTTTGGAAGTTTGGGGGTC-
1 AAAATGTAATTTTTAGAAGTTTGAGGG-CA
*
43380463 AAAATATAATTTTT
1 AAAATGTAATTTTT
43380477 GGATAATTTA
Statistics
Matches: 106, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
29 38 0.36
30 52 0.49
31 16 0.15
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTGAGGGCA
Found at i:43380447 original size:59 final size:59
Alignment explanation
Indices: 43380314--43380477 Score: 161
Period size: 59 Copynumber: 2.7 Consensus size: 59
43380304 GTCCGAGGGT
* * * * *
43380314 AAAATGATAATTTTTA-AAGTTTCAAGGTCAAAAATGGTAAATTTTGGAATTTTTACGGTCA
1 AAAATG-TAATTTTTAGAAG-TTCGAGGGCAAAAAT-GTAATTTTTGAAAATTTTACGGTCA
* * **
43380375 AAAATGGAGTTTTTAGAAGTTCGAGGGCAAAAATGTAATTTTTGAAAATTTTGGGGTCA
1 AAAATGTAATTTTTAGAAGTTCGAGGGCAAAAATGTAATTTTTGAAAATTTTACGGTCA
* * * *
43380434 AAAATGTAATTTTTGGAAGTTTGGGGGTC-AAAATATAATTTTTG
1 AAAATGTAATTTTTAGAAGTTCGAGGG-CAAAAATGTAATTTTTG
43380478 GATAATTTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 56 0.65
60 21 0.24
61 9 0.10
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTAGAAGTTCGAGGGCAAAAATGTAATTTTTGAAAATTTTACGGTCA
Found at i:43380477 original size:29 final size:30
Alignment explanation
Indices: 43380339--43380485 Score: 127
Period size: 30 Copynumber: 4.9 Consensus size: 30
43380329 AAAGTTTCAA
* * ***
43380339 GGTCAAAAATGGTAAATTTTGGAATTTTTAC
1 GGTCAAAAAT-GTAATTTTTGGAAATTTGGG
* * * * * *
43380370 GGTCAAAAATGGAGTTTTTAGAAGTTCGAG
1 GGTCAAAAATGTAATTTTTGGAAATTTGGG
* *
43380400 GG-CAAAAATGTAATTTTTGAAAATTTTGG
1 GGTCAAAAATGTAATTTTTGGAAATTTGGG
*
43380429 GGTCAAAAATGTAATTTTTGGAAGTTTGGG
1 GGTCAAAAATGTAATTTTTGGAAATTTGGG
*
43380459 GGTC-AAAATATAATTTTTGGATAATTT
1 GGTCAAAAATGTAATTTTTGGA-AATTT
43380486 AAGGACCTCC
Statistics
Matches: 93, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
29 37 0.40
30 46 0.49
31 10 0.11
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (30 bp):
GGTCAAAAATGTAATTTTTGGAAATTTGGG
Found at i:43381356 original size:22 final size:21
Alignment explanation
Indices: 43381293--43381354 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
43381283 TCTTCCTTTT
43381293 TTTTTCTTTC-TTTAAAACCA
1 TTTTTCTTTCTTTTAAAACCA
* *
43381313 TTTTGATTTTTCTTTTGAAAACCC
1 TTTT--TCTTTCTTTT-AAAACCA
43381337 TTTTTCTTTCTTTTAAAA
1 TTTTTCTTTCTTTTAAAA
43381355 ACTTCTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 14 0.40
23 3 0.09
24 10 0.29
ACGTcount: A:0.23, C:0.16, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTTTCTTTCTTTTAAAACCA
Found at i:43382147 original size:25 final size:25
Alignment explanation
Indices: 43382119--43382174 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
43382109 GGCAGTGGCT
* *
43382119 GTGGCAGAGTAGGTTGAAGCGGGTG
1 GTGGCAGAGCAAGTTGAAGCGGGTG
*
43382144 GTGGCAGAGCAAGTTGAAGCTGGTG
1 GTGGCAGAGCAAGTTGAAGCGGGTG
*
43382169 ATGGCA
1 GTGGCA
43382175 CTATTGATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.46, T:0.20
Consensus pattern (25 bp):
GTGGCAGAGCAAGTTGAAGCGGGTG
Found at i:43382457 original size:17 final size:17
Alignment explanation
Indices: 43382435--43382503 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
43382425 CTTTTTATTC
43382435 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
43382452 AATTTAAATTTAAACTTT
1 AATTTAAATTTAAAC-TT
**
43382470 AATAGAAAAGTTTAAACTT
1 AAT-TTAAA-TTTAAACTT
* *
43382489 AAATCAAATTTAAAC
1 AATTTAAATTTAAAC
43382504 CCAAAATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 22 0.50
18 8 0.18
19 7 0.16
20 7 0.16
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAACTT
Found at i:43389684 original size:12 final size:12
Alignment explanation
Indices: 43389667--43389771 Score: 71
Period size: 12 Copynumber: 9.3 Consensus size: 12
43389657 TGTTTTGGTT
43389667 TTTTTGCTGTTA
1 TTTTTGCTGTTA
* *
43389679 TTTTTGTTGTTG
1 TTTTTGCTGTTA
* * *
43389691 TTATTGTTGCTA
1 TTTTTGCTGTTA
*
43389703 TTTTTGCTGCTA
1 TTTTTGCTGTTA
43389715 -TTTTGC---TA
1 TTTTTGCTGTTA
*
43389723 -TTTT--TGTTG
1 TTTTTGCTGTTA
*
43389732 TTTTTGTTGTTA
1 TTTTTGCTGTTA
43389744 TTTTTGCTGTTA
1 TTTTTGCTGTTA
* *
43389756 TTTTGGTTGTTA
1 TTTTTGCTGTTA
43389768 TTTT
1 TTTT
43389772 GGTTGTTTGG
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
10 4 0.05
11 6 0.08
12 58 0.77
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
TTTTTGCTGTTA
Found at i:43389772 original size:12 final size:12
Alignment explanation
Indices: 43389726--43389778 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
43389716 TTTGCTATTT
* *
43389726 TTGTTGTTTTTG
1 TTGTTATTTTGG
*
43389738 TTGTTATTTTTG
1 TTGTTATTTTGG
*
43389750 CTGTTATTTTGG
1 TTGTTATTTTGG
43389762 TTGTTATTTTGG
1 TTGTTATTTTGG
43389774 TTGTT
1 TTGTT
43389779 TGGATGTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.06, C:0.02, G:0.23, T:0.70
Consensus pattern (12 bp):
TTGTTATTTTGG
Found at i:43400909 original size:16 final size:17
Alignment explanation
Indices: 43400890--43400935 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
43400880 ATCATAAAAG
43400890 GTTCAAATCAATTCA-A
1 GTTCAAATCAATTCATA
* *
43400906 GTTCTAATCACTTCATA
1 GTTCAAATCAATTCATA
*
43400923 CTT-AAATCAATTC
1 GTTCAAATCAATTC
43400936 GGATTCAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (17 bp):
GTTCAAATCAATTCATA
Found at i:43402465 original size:4 final size:4
Alignment explanation
Indices: 43402451--43402487 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
43402441 AACTCCCAAG
*
43402451 GTAT TTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
43402488 AGTAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
GTAT
Found at i:43408548 original size:11 final size:12
Alignment explanation
Indices: 43408515--43408582 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 12
43408505 ATATTAGTTA
43408515 ATAATAATAA-T
1 ATAATAATAATT
*
43408526 ATAATACTAATT
1 ATAATAATAATT
43408538 A-AATAATAATTT
1 ATAATAATAA-TT
* *
43408550 ATATTATTATATT
1 ATAATAATA-ATT
* *
43408563 ATATTATTAATT
1 ATAATAATAATT
43408575 AATAATAA
1 -ATAATAA
43408583 ATTAAAAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 16 0.35
12 8 0.17
13 21 0.46
14 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:43412896 original size:26 final size:25
Alignment explanation
Indices: 43412829--43412900 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
43412819 CAATCTACAG
* *
43412829 TTTCATGGCTTTTTTTTTTTCTATAT
1 TTTCATGG-TTTTGTTTTGTCTATAT
***
43412855 TTTCGCAGTTTTGTTTTGTCTATAT
1 TTTCATGGTTTTGTTTTGTCTATAT
43412880 TTTCATGGTTTTCGTTTTGTC
1 TTTCATGGTTTT-GTTTTGTC
43412901 CACTTTATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 24 0.65
26 13 0.35
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (25 bp):
TTTCATGGTTTTGTTTTGTCTATAT
Found at i:43415311 original size:11 final size:11
Alignment explanation
Indices: 43415295--43415330 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
43415285 ATACTTTGAG
43415295 TTTTAAAATTA
1 TTTTAAAATTA
43415306 TTTTAAAATT-
1 TTTTAAAATTA
*
43415316 TTTGAAAATTA
1 TTTTAAAATTA
43415327 TTTT
1 TTTT
43415331 GATTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:43419719 original size:31 final size:31
Alignment explanation
Indices: 43419656--43419719 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
43419646 ATACTTTAAT
* *
43419656 TTGATCAATTTTCATTCTTGTACTTTTTGAA
1 TTGATCAATTTTCATTCTTGTACTATTCGAA
43419687 TTGATCAATTTT-ATTCATTGTA-TGATTCGAA
1 TTGATCAATTTTCATTC-TTGTACT-ATTCGAA
43419718 TT
1 TT
43419720 TTGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (31 bp):
TTGATCAATTTTCATTCTTGTACTATTCGAA
Found at i:43422158 original size:15 final size:16
Alignment explanation
Indices: 43422140--43422175 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
43422130 TATTTATTAT
43422140 TTTTTGATTTTTA-AA
1 TTTTTGATTTTTATAA
*
43422155 TTTTTTATTTTTATAA
1 TTTTTGATTTTTATAA
43422171 TTTTT
1 TTTTT
43422176 AAATTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTGATTTTTATAA
Found at i:43422159 original size:16 final size:16
Alignment explanation
Indices: 43422132--43422175 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
43422122 GTGTAATTTA
*
43422132 TTTATTATTTTTTGATT
1 TTTATAATTTTTT-ATT
43422149 TTTA-AATTTTTTATT
1 TTTATAATTTTTTATT
43422164 TTTATAATTTTT
1 TTTATAATTTTT
43422176 AAATTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTATAATTTTTTATT
Found at i:43422176 original size:15 final size:15
Alignment explanation
Indices: 43422128--43422176 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
43422118 ACACGTGTAA
43422128 TTTATTTATTAT--TT
1 TTTATTT-TTATAATT
43422142 TTTGATTTTTA-AATTT
1 TTT-ATTTTTATAA-TT
43422158 TTTATTTTTATAATT
1 TTTATTTTTATAATT
43422173 TTTA
1 TTTA
43422177 AATTATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.20
15 17 0.57
16 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATAATT
Found at i:43427155 original size:12 final size:12
Alignment explanation
Indices: 43427138--43427168 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43427128 AAATTACAGA
*
43427138 ATTCATCGTAGG
1 ATTCATCATAGG
43427150 ATTCATCATAGG
1 ATTCATCATAGG
43427162 ATTCATC
1 ATTCATC
43427169 TCCCCTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (12 bp):
ATTCATCATAGG
Found at i:43431171 original size:14 final size:14
Alignment explanation
Indices: 43431152--43431186 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
43431142 CAACCGAAAG
43431152 CTCTTTTTCTCTTT
1 CTCTTTTTCTCTTT
43431166 CTCTTTTTCTCTTT
1 CTCTTTTTCTCTTT
43431180 CTCTTTT
1 CTCTTTT
43431187 ACAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
CTCTTTTTCTCTTT
Found at i:43433115 original size:12 final size:12
Alignment explanation
Indices: 43433098--43433122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43433088 TCCCAATCTG
43433098 CTTACATACATA
1 CTTACATACATA
43433110 CTTACATACATA
1 CTTACATACATA
43433122 C
1 C
43433123 ATATATTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (12 bp):
CTTACATACATA
Found at i:43445483 original size:16 final size:15
Alignment explanation
Indices: 43445462--43445518 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 15
43445452 AAATTTCACC
43445462 AAAAAAACAAAAAAGG
1 AAAAAAA-AAAAAAGG
*
43445478 AAAAAAAAGAAAAGG
1 AAAAAAAAAAAAAGG
*
43445493 AAAAAAAAGAAGAAAAG
1 AAAAAAAA-AA-AAAGG
43445510 AAAAAAAAA
1 AAAAAAAAA
43445519 GAGGTCGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 15 0.42
16 9 0.25
17 12 0.33
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:43445485 original size:18 final size:17
Alignment explanation
Indices: 43445462--43445518 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
43445452 AAATTTCACC
*
43445462 AAAAAAACAA-AAAAGG
1 AAAAAAAAAAGAAAAGG
43445478 --AAAAAAAAGAAAAGG
1 AAAAAAAAAAGAAAAGG
43445493 AAAAAAAAGAAGAAAA-G
1 AAAAAAAA-AAGAAAAGG
43445510 AAAAAAAAA
1 AAAAAAAAA
43445519 GAGGTCGAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 7 0.19
15 6 0.17
16 1 0.03
17 15 0.42
18 7 0.19
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGG
Found at i:43445519 original size:18 final size:18
Alignment explanation
Indices: 43445478--43445520 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
43445468 ACAAAAAAGG
*
43445478 AAAAAA-AAGAAAAGGAA
1 AAAAAAGAAGAAAAGAAA
43445495 AAAAAAGAAGAAAAGAAA
1 AAAAAAGAAGAAAAGAAA
43445513 AAAAAAGA
1 AAAAAAGA
43445521 GGTCGAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAGAAAAGAAA
Found at i:43446505 original size:49 final size:49
Alignment explanation
Indices: 43446397--43446623 Score: 202
Period size: 49 Copynumber: 4.6 Consensus size: 49
43446387 TCTACAGGTT
* * * ** * *
43446397 TGAAGGGAAAGATTGAAGCCGCAACGGCAAATCTAATACCCTATAGATA
1 TGAAGGGAAAGATTAAAGCCGCAACGGCGAACCTTGTACCCTAGAGATG
* * * * * *
43446446 TAAAGAGAAAGGTTAAAGCCGCAACGGCGAACCTTGTACCTTAGGGACG
1 TGAAGGGAAAGATTAAAGCCGCAACGGCGAACCTTGTACCCTAGAGATG
* * * * * * ** * *
43446495 TGATGGGAAAGATTGAAGTCGCGACAGTGAATTTTGTACCCTAGAGTTA
1 TGAAGGGAAAGATTAAAGCCGCAACGGCGAACCTTGTACCCTAGAGATG
* * *
43446544 TGAAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTGTACCCTAGAGATG
1 TGAAGGGAAAGATTAAAGCCGCAACGGCGAACCTTGTACCCTAGAGATG
* *
43446593 TGAAGGGAAAGATTAGAGCCGCAACGACGAA
1 TGAAGGGAAAGATTAAAGCCGCAACGGCGAA
43446624 TCTTACACCG
Statistics
Matches: 133, Mismatches: 45, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
49 133 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGATTAAAGCCGCAACGGCGAACCTTGTACCCTAGAGATG
Found at i:43446960 original size:40 final size:39
Alignment explanation
Indices: 43446905--43446993 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 39
43446895 TACAATCATC
*
43446905 CAATCTTTTACCCTAATCAGAGGACAGATTGAAGACCATT
1 CAATCTTTTACCCTAATCAAAGGACAGATTGAAGACCA-T
* *
43446945 CAATCTTTTACCCTAATCAAAGGGCAGATTGAAGACTAT
1 CAATCTTTTACCCTAATCAAAGGACAGATTGAAGACCAT
43446984 CAGATCTTTT
1 CA-ATCTTTT
43446994 TGAAGACCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (39 bp):
CAATCTTTTACCCTAATCAAAGGACAGATTGAAGACCAT
Found at i:43446998 original size:20 final size:20
Alignment explanation
Indices: 43446973--43447013 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
43446963 AAAGGGCAGA
*
43446973 TTGAAGACTAT-CAGATCTTT
1 TTGAAGACCATCCA-ATCTTT
43446993 TTGAAGACCATCCAATCTTT
1 TTGAAGACCATCCAATCTTT
43447013 T
1 T
43447014 ACCCTAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
TTGAAGACCATCCAATCTTT
Found at i:43447056 original size:40 final size:40
Alignment explanation
Indices: 43446993--43448521 Score: 965
Period size: 40 Copynumber: 39.1 Consensus size: 40
43446983 TCAGATCTTT
*
43446993 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * **
43447033 TTGAAGACCATCTAACCTCTTACCCCGACCATG-GGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* *
43447073 TTGAAGTA--GTCCAATCTTTTTCCCTAACCAGAGGGCAGA
1 TTGAAG-ACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
** * * * * *
43447112 TTGAAG-TGATCCAATCTCTTA-CCTCGACCATAGAGCATA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCAGAGGGCAGA
* * *
43447151 TTGAAG-CAATTCAATCTTTTACCCTAACTAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * *
43447190 TTGAAGACCAT-CAGATCTTTTACCCTAATCAAAGGAG-AAA
1 TTGAAGACCATCCA-ATCTTTTACCCTAACCAGAGG-GCAGA
* * *
43447230 TTGAAGACCAT-TAATTCTTTTACCCTAATCAAAGGGCAGA
1 TTGAAGACCATCCAA-TCTTTTACCCTAACCAGAGGGCAGA
* *
43447270 TTAAAGACCATCCAATCTTTTACCCTAATCAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * *
43447310 TT-AAAATCATCCAATCTCTTA-CCTCGACCATG-GGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGA
* * *
43447349 TTGAAG--CAGTCTAATCTTTTACCTTAACCAGAGGGGAGA
1 TTGAAGACCA-TCCAATCTTTTACCCTAACCAGAGGGCAGA
** *
43447388 TT---GA--A--C--TC--TTACCCCGACCATG-GGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* * * * *
43447417 TTAAAG-CAATCTAATCTTTTACCCTAACTAGAGGGAAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * **
43447456 TTGAAAATCATACAATCTTTTACCTTAACCAGAGGATAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * *
43447496 TTGAAGACCAT-CAGATCTTTTACCTTAACCAGAAGACAGA
1 TTGAAGACCATCCA-ATCTTTTACCCTAACCAGAGGGCAGA
* * * *
43447536 TTGAAGACCATCCAATCTCTTACCC-GATCATG-GGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* **
43447575 TTGAAGA-AATCCAATCTTTTACCCTAATTAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* ** * * *
43447614 TTGAAGACCATCTAATCTTTTACCCCGATC-GTGGGGTAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAG-AGGGCAGA
* * *
43447654 TTGAA-ACAATCCAATATTTTACCCAAACCAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * * *
43447693 TTGAAAACCATTCGATCTCTTACCCCAACCATG-GGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* *
43447733 TTGAAG--CAGTCCAATCTTTTACCCTAACTAGAGGGAAGA
1 TTGAAGACCA-TCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * *
43447772 TTGAAG-TCATCCAATCTCTTACTCC-GATCATGA-AGCAGA
1 TTGAAGACCATCCAATCTTTTAC-CCTAACCA-GAGGGCAGA
* * *
43447811 TTGAA-ACAATCCAATCTTTTACCCTAACCAGAGAGTAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * *
43447850 TTGAAGACCATCAAATCTTTTACCCTAACTAGAGGTCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* ** * *
43447890 TTGAAGACCATCTAAT-TTCTTACCCCGATCATG-GGGCAAA
1 TTGAAGACCATCCAATCTT-TTACCCTAACCA-GAGGGCAGA
* *
43447930 TTGAAG-CAATCCAATCTTTTACCCCAACCATG-GGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
*
43447969 TTGAAGTA--ATTCAGATCTTTTACCCTAACCAGAGGGCAGA
1 TTGAAG-ACCATCCA-ATCTTTTACCCTAACCAGAGGGCAGA
*
43448009 TTGAAGTA--ATCCAATCTTTTACCCTAACCAGAGGGCAAA
1 TTGAAG-ACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* *
43448048 TTGAAG-CCATCCAATCTCTTA-CCTCGACCATGA-GGCAGA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGA
* * *
43448087 TTGAAG-CAATCCAATCTTTTACCCTAATC--A--G-ATA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * *
43448121 TTGAAG-CCATCCAATCTCTTA-CCTCGACTATG-GGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGA
* * * *
43448160 TTGAAG-CAATCTAATCTTTTACCCTAACCAGAGAGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * *
43448199 TTGAAGACCATCCGATCTCTTACCCCAACCATG-GGGTAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* ** *
43448239 TTAAAGACCATCTGATCTTTTACCCTAACTAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * *
43448279 TTGAAG-CCATCTAATCTCTT-GCCTCGACCATG-GGGTAGA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGA
* * *
43448318 TTGAAG-CAATCCAATCTTTTACCTTAATCAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * ** ** *
43448357 TTGAAGACCATCCGATCTCTTACCCCGACCA-TCGGCAGG
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * *
43448396 TTGAAAACC-TGTCGATCTTTTA-CCTCGACCAGAGGGCAGA
1 TTGAAGACCAT-CCAATCTTTTACCCT-AACCAGAGGGCAGA
* * *
43448436 TTGAAGACCATCCGATCTCTTA-CCTCAATCATG-GGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCT-AACCA-GAGGGCAGA
* *
43448476 TTGAAGTA--ATTCAGATCTTTTACCTTAACCA-AGAGGCAGA
1 TTGAAG-ACCATCCA-ATCTTTTACCCTAACCAGAG-GGCAGA
43448516 TTGAAG
1 TTGAAG
43448522 TAATCCAGAT
Statistics
Matches: 1168, Mismatches: 229, Indels: 184
0.74 0.14 0.12
Matches are distributed among these distances:
29 16 0.01
30 1 0.00
31 2 0.00
32 1 0.00
33 4 0.00
34 22 0.02
35 1 0.00
36 3 0.00
37 2 0.00
38 46 0.04
39 520 0.45
40 535 0.46
41 15 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
Found at i:43447176 original size:78 final size:79
Alignment explanation
Indices: 43446993--43448562 Score: 597
Period size: 79 Copynumber: 20.1 Consensus size: 79
43446983 TCAGATCTTT
* * *
43446993 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCTAACCTCTTACCC
1 TTGAAG-CAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCC
* *
43447058 CGACCATGGGGCAGA
65 CGACCATAGAGCAGA
* * * ** * *
43447073 TTGAAGTAGTCCAATCTTTTTCCCTAACCAGAGGGCAGATTGAAG-TGATCCAATCTCTTACCTC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
*
43447137 GACCATAGAGCATA
66 GACCATAGAGCAGA
* * * *
43447151 TTGAAGCAATTCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCAT-CAGATCTTTTACCC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCA-ACCTCTTACCC
** * * *
43447215 TAATCAAAGGAG-AAA
65 CGACCATA-GAGCAGA
* * * * * * *
43447230 TTGAAGACCAT-TAATTCTTTTACCCTAATCAAAGGGCAGATTAAAGACCATCCAATCTTTTACC
1 TTGAAG-CAATCCAA-TCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACC
** * * *
43447294 CTAATCAGAGGGCAGA
64 CCGACCATAGAGCAGA
* * * * * * *
43447310 TTAAAATC-ATCCAATCTCTTA-CCTCGACCATG-GGGCAGATTGAAG--CAGTCTAATCTTTTA
1 TT-GAAGCAATCCAATCTTTTACCCT-AACCA-GAGGGCAGATTGAAGACCA-TCCAACCTCTTA
*** * * *
43447370 CCTTAACCAGAGGGGAGA
62 CCCCGACCATAGAGCAGA
** * * * * * *
43447388 TT---G-AA--C--TC--TTACCCCGACCATG-GGGCAAATTAAAG-CAATCTAATCTTTTACCC
1 TTGAAGCAATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACCATCCAACCTCTTACCC
** * * * *
43447441 TAACTAGAGGGAAGA
65 CGACCATAGAGCAGA
* ** * *
43447456 TTGAA--AATCATACAATCTTTTACCTTAACCAGAGGATAGATTGAAGACCAT-CAGATCTTTTA
1 TTGAAGCAATC---CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCA-ACCTCTTA
*** *
43447518 CCTTAACCAGA-AGACAGA
62 CCCCGACCATAGAG-CAGA
* * * * * * * *
43447536 TTGAAGACCATCCAATCTCTTACCC-GATCATG-GGGCAAATTGAAGA-AATCCAATCTTTTACC
1 TTGAAG-CAATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACCATCCAACCTCTTACC
** ** * *
43447598 CTAATTAGAGGGCAGA
64 CCGACCATAGAGCAGA
* * ** * * * * ** *
43447614 TTGAAGACCATCTAATCTTTTACCCCGATC-GTGGGGTAGATTGAA-ACAATCCAATATTTTACC
1 TTGAAG-CAATCCAATCTTTTACCCTAACCAG-AGGGCAGATTGAAGACCATCCAACCTCTTACC
** * *
43447677 CAAACCAGAGGGCAGA
64 CCGACCATAGAGCAGA
* * * * * * * * *
43447693 TTGAAAACCATTCGATCTCTTACCCCAACCATG-GGGCAAATTGAAG--CAGTCCAATCTTTTAC
1 TTG-AAGCAATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACCA-TCCAACCTCTTAC
** * * * *
43447755 CCTAACTAGAGGGAAGA
63 CCCGACCATAGAGCAGA
* * * * * * *
43447772 TTGAAGTC-ATCCAATCTCTTACTCC-GATCATGA-AGCAGATTGAA-ACAATCCAATCTTTTAC
1 TTGAAG-CAATCCAATCTTTTAC-CCTAACCA-GAGGGCAGATTGAAGACCATCCAACCTCTTAC
** * *
43447833 CCTAACCAGAGAGTAGA
63 CCCGACCATAGAGCAGA
* * * * * **
43447850 TTGAAGACCATCAAATCTTTTACCCTAACTAGAGGTCAGATTGAAGACCATCTAATTTCTTACCC
1 TTGAAG-CAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCC
* * * *
43447915 CGATCATGGGGCAAA
65 CGACCATAGAGCAGA
* * * *
43447930 TTGAAGCAATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAGTA--ATTCAGATCTTTTAC
1 TTGAAGCAATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-ACCATCCA-ACCTCTTAC
** * *
43447992 CCTAACCAGAGGGCAGA
63 CCCGACCATAGAGCAGA
* * * *
43448009 TTGAAGTAATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAG-CCATCCAATCTCTTACCTC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
43448073 GACCAT-GAGGCAGA
66 GACCATAGA-GCAGA
* * * *
43448087 TTGAAGCAATCCAATCTTTTACCCTAATC--A--G-ATATTGAAG-CCATCCAATCTCTTACCTC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
* * *
43448146 GACTATGGGGCAGA
66 GACCATAGAGCAGA
* * * * *
43448160 TTGAAGCAATCTAATCTTTTACCCTAACCAGAGAGCAAATTGAAGACCATCCGATCTCTTACCCC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
* * * *
43448225 AACCATGGGGTAGA
66 GACCATAGAGCAGA
* * ** * * * * *
43448239 TTAAAGACCATCTGATCTTTTACCCTAACTAGAGGGCAGATTGAAG-CCATCTAATCTCTTGCCT
1 TTGAAG-CAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCC
* * *
43448303 CGACCATGGGGTAGA
65 CGACCATAGAGCAGA
* * * *
43448318 TTGAAGCAATCCAATCTTTTACCTTAATCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCC
1 TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
* *
43448383 GACCATCG-GCAGG
66 GACCATAGAGCAGA
* * * * *
43448396 TTGAA--AACCTGTCGATCTTTTA-CCTCGACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
1 TTGAAGCAA--T-CCAATCTTTTACCCT-AACCAGAGGGCAGATTGAAGACCATCCAACCTCTTA
* * * * *
43448458 CCTCAATCATGGGGCAGA
62 CCCCGACCATAGAGCAGA
* * * *
43448476 TTGAAGTAATTCAGATCTTTTACCTTAACCA-AGAGGCAGATTGAAGTA--ATCCAGATCTCTTA
1 TTGAAGCAATCCA-ATCTTTTACCCTAACCAGAG-GGCAGATTGAAG-ACCATCCA-ACCTCTTA
* * * *
43448538 CCTCGACCATGGGGTAGA
62 CCCCGACCATAGAGCAGA
43448556 TTGAAGC
1 TTGAAGC
43448563 TATCAAATTA
Statistics
Matches: 1191, Mismatches: 216, Indels: 166
0.76 0.14 0.11
Matches are distributed among these distances:
68 50 0.04
69 3 0.00
70 4 0.00
72 1 0.00
73 64 0.05
74 3 0.00
75 2 0.00
76 3 0.00
77 7 0.01
78 313 0.26
79 490 0.41
80 238 0.20
81 8 0.01
82 2 0.00
83 3 0.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
TTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAACCTCTTACCCC
GACCATAGAGCAGA
Found at i:43447410 original size:68 final size:68
Alignment explanation
Indices: 43447325--43447460 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 68
43447315 ATCATCCAAT
* * * * * *
43447325 CTCTTACCTCGACCATGGGGCAGATTGAAGCAGTCTAATCTTTTACCTTAACCAGAGGGGAGATT
1 CTCTTACCCCGACCATGGGGCAAATTAAAGCAATCTAATCTTTTACCCTAACCAGAGGGAAGATT
43447390 GAA
66 GAA
*
43447393 CTCTTACCCCGACCATGGGGCAAATTAAAGCAATCTAATCTTTTACCCTAACTAGAGGGAAGATT
1 CTCTTACCCCGACCATGGGGCAAATTAAAGCAATCTAATCTTTTACCCTAACCAGAGGGAAGATT
43447458 GAA
66 GAA
43447461 AATCATACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (68 bp):
CTCTTACCCCGACCATGGGGCAAATTAAAGCAATCTAATCTTTTACCCTAACCAGAGGGAAGATT
GAA
Found at i:43447869 original size:276 final size:271
Alignment explanation
Indices: 43447468--43448539 Score: 802
Period size: 276 Copynumber: 3.9 Consensus size: 271
43447458 GAAAATCATA
* ** * * **
43447468 CAATCTTTTACCTTAACCAGAGGATAGATTGAAGACCAT-CAGATCTTTTACCTTAACCA-GAAG
1 CAATCTTTTACCCTAACCAGAGGGCAAATTGAAG-CCATCCA-ATCTCTTACCTCGACCATGAAG
* * * * * *
43447531 ACAGATTGAAGACCATCCAATCTCTTACCC-GATCATGGGGCAAATTGAAGA-AATCCAATCTTT
64 -CAGATTGAA-ACAATCCAATCTTTTACCCTAACCA----G-ATATTGAAGACCATCCAATCTTT
* * * *
43447594 TACCCTAATTAGAGGGCAGATTGAAGACCATCTAATCTTTTACCCCGATCGTGGGGTAGATTGAA
122 TACCCTAACTAGAGGGCAGATTGAAGACCATCTAATCTTTTACCCCGATCATGGGGCAAATTGAA
43447659 ACAATCCAATATTTTACCCAAACCA-GAGGGCAGATTGAA-AACCATTC-GATCTCTTACCCCAA
187 ACAATCCAATATTTTACCCAAACCATG-GGGCAGATTGAAGAA--ATTCAGATCTCTTACCCCAA
*
43447721 CCATG-GGGCAAATTGAAGCAGTC
249 CCA-GAGGGCAAATTGAAGCAATC
* * *
43447744 CAATCTTTTACCCTAACTAGAGGG-AAGATTGAAGTCATCCAATCTCTTA-CTCCGATCATGAAG
1 CAATCTTTTACCCTAACCAGAGGGCAA-ATTGAAGCCATCCAATCTCTTACCT-CGACCATGAAG
*
43447807 CAGATTGAAACAATCCAATCTTTTACCCTAACCAGAGAGTAGATTGAAGACCATCAAATCTTTTA
64 CAGATTGAAACAATCCAATCTTTTACCCTAACC--AGA-T--ATTGAAGACCATCCAATCTTTTA
* *
43447872 CCCTAACTAGAGGTCAGATTGAAGACCATCTAAT-TTCTTACCCCGATCATGGGGCAAATTGAAG
124 CCCTAACTAGAGGGCAGATTGAAGACCATCTAATCTT-TTACCCCGATCATGGGGCAAATTGAAA
* * * * *
43447936 CAATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGTAATTCAGATCTTTTACCCTAACCAG
188 CAATCCAATATTTTACCCAAACCATGGGGCAGATTGAAGAAATTCAGATCTCTTACCCCAACCAG
* *
43448001 AGGGCAGATTGAAGTAATC
253 AGGGCAAATTGAAGCAATC
*
43448020 CAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCCATCCAATCTCTTACCTCGACCATGAGGCA
1 CAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCCATCCAATCTCTTACCTCGACCATGAAGCA
* * * *
43448085 GATTGAAGCAATCCAATCTTTTACCCTAATCAGATATTGAAG-CCATCCAATCTCTTA-CCTCGA
66 GATTGAAACAATCCAATCTTTTACCCTAACCAGATATTGAAGACCATCCAATCTTTTACCCT-AA
* ** * * *
43448148 CTATG-GGGCAGATTGAAG-CAATCTAATCTTTTACCCTAACCA-GAGAGCAAATTGAAGACCAT
130 CTA-GAGGGCAGATTGAAGACCATCTAATCTTTTACCCCGATCATG-GGGCAAATTGAA-ACAAT
* * * * * * * * * * *
43448210 CCGATCTCTTACCCCAACCATGGGGTAGATTAAAGACCA-TCTGATCTTTTACCCTAACTAGAGG
192 CCAATATTTTACCCAAACCATGGGGCAGATTGAAGA-AATTCAGATCTCTTACCCCAACCAGAGG
* *
43448274 GCAGATTGAAGCCATC
256 GCAAATTGAAGCAATC
* * * * * * * * ** * *
43448290 TAATCTCTT-GCCTCGACCATG-GGGTAGATTGAAGCAATCCAATCTTTTACCTTAATCA-GAGG
1 CAATCTTTTACCCT-AACCA-GAGGGCAAATTGAAGCCATCCAATCTCTTACCTCGACCATGA-A
* * * ** ** * * *
43448352 GCAGATTGAAGACCATCCGATCTCTTACCCCGACCATCGGCAGGTTGAAAACC-TGTCGATCTTT
63 GCAGATTGAA-ACAATCCAATCTTTTACCCTAACCA---G-ATATTGAAGACCAT-CCAATCTTT
* * ** * * * *
43448416 TA-CCTCGACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCTCAATCATGGGGCAGATTGA
122 TACCCT-AACTAGAGGGCAGATTGAAGACCATCTAATCTTTTACCCCGATCATGGGGCAAATTGA
** * * ** * * * *
43448480 AGTAATTCAGATCTTTTACCTTAACCAAGAGGCAGATTGAAGTAATCCAGATCTCTTACC
186 AACAATCCA-ATATTTTACCCAAACCATGGGGCAGATTGAAGAAATTCAGATCTCTTACC
43448540 TCGACCATGG
Statistics
Matches: 649, Mismatches: 108, Indels: 77
0.78 0.13 0.09
Matches are distributed among these distances:
268 1 0.00
269 36 0.06
270 154 0.24
271 28 0.04
272 1 0.00
273 2 0.00
274 23 0.04
275 48 0.07
276 285 0.44
277 70 0.11
278 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (271 bp):
CAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCCATCCAATCTCTTACCTCGACCATGAAGCA
GATTGAAACAATCCAATCTTTTACCCTAACCAGATATTGAAGACCATCCAATCTTTTACCCTAAC
TAGAGGGCAGATTGAAGACCATCTAATCTTTTACCCCGATCATGGGGCAAATTGAAACAATCCAA
TATTTTACCCAAACCATGGGGCAGATTGAAGAAATTCAGATCTCTTACCCCAACCAGAGGGCAAA
TTGAAGCAATC
Found at i:43448289 original size:79 final size:79
Alignment explanation
Indices: 43447468--43448561 Score: 693
Period size: 79 Copynumber: 13.9 Consensus size: 79
43447458 GAAAATCATA
* ** * *** *
43447468 CAATCTTTTACCTTAACCAGAGGATAGATTGAAGACCAT-CAGATCTTTTACCTTAACCA-GAAG
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CCATCCA-ATCTCTTACCCCGACCATG-GG
* *
43447531 ACAGATTGAAGACCATC
63 GCAGATTGAAGACAATC
* * * * ** * ** **
43447548 CAATCTCTTACCC-GATCATG-GGGCAAATTGAAGAAATCCAATCTTTTACCCTAATTA-GAGGG
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATG-GGG
*
43447610 CAGATTGAAGACCATC
64 CAGATTGAAGACAATC
* ** * * * * * * * **
43447626 TAATCTTTTACCCCGATC-GTGGGGTAGATTGAAACAATCCAATATTTTACCCAAACCA-GAGGG
1 CAATCTTTTACCCTAACCAG-AGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATG-GGG
* * *
43447689 CAGATTGAAAACCATT
64 CAGATTGAAGACAATC
* * * * * ** *
43447705 CGATCTCTTACCCCAACCATG-GGGCAAATTGAAG-CAGTCCAATCTTTTACCCTAACTA-GAGG
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCCA-TCCAATCTCTTACCCCGACCATG-GG
* *
43447767 GAAGATTGAAGTC-ATC
63 GCAGATTGAAGACAATC
* * * * * * * ** *
43447783 CAATCTCTTACTCC-GATCATGA-AGCAGATTGAAACAATCCAATCTTTTACCCTAACCA-GAGA
1 CAATCTTTTAC-CCTAACCA-GAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATG-GG
* *
43447845 GTAGATTGAAGACCATC
63 GCAGATTGAAGACAATC
* * * * * *
43447862 AAATCTTTTACCCTAACTAGAGGTCAGATTGAAGACCATCTAATTTCTTACCCCGATCATGGGGC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCCGACCATGGGGC
*
43447927 AAATTGAAG-CAATC
65 AGATTGAAGACAATC
* ** * * **
43447941 CAATCTTTTACCCCAACCATG-GGGCAGATTGAAGTAATTCAGATCTTTTACCCTAACCA-GAGG
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCCATCCA-ATCTCTTACCCCGACCATG-GG
*
43448004 GCAGATTGAAG-TAATC
63 GCAGATTGAAGACAATC
* * *
43448020 CAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCCATCCAATCTCTTACCTCGACCATGAGGCA
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGGGGCA
43448085 GATTGAAG-CAATC
66 GATTGAAGACAATC
* * * *
43448098 CAATCTTTTACCCTAATC--A--G-ATATTGAAGCCATCCAATCTCTTACCTCGACTATGGGGCA
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGGGGCA
43448158 GATTGAAG-CAATC
66 GATTGAAGACAATC
* * * * * *
43448171 TAATCTTTTACCCTAACCAGAGAGCAAATTGAAGACCATCCGATCTCTTACCCCAACCATGGGGT
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCCGACCATGGGGC
* *
43448236 AGATTAAAGACCATC
65 AGATTGAAGACAATC
** * * * * *
43448251 TGATCTTTTACCCTAACTAGAGGGCAGATTGAAGCCATCTAATCTCTTGCCTCGACCATGGGGTA
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGGGGCA
43448316 GATTGAAG-CAATC
66 GATTGAAGACAATC
* * * *
43448329 CAATCTTTTACCTTAATCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAT-CGGC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCCGACCATGGGGC
* * * *
43448393 AGGTTGAAAAC-CTGT
65 AGATTGAAGACAAT-C
* * * * * *
43448408 CGATCTTTTA-CCTCGACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCTCAATCATGGGG
1 CAATCTTTTACCCT-AACCAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCCGACCATGGGG
* *
43448472 CAGATTGAAG-TAATT
64 CAGATTGAAGACAATC
* ** *
43448487 CAGATCTTTTACCTTAACCA-AGAGGCAGATTGAAGTAATCCAGATCTCTTACCTCGACCATGGG
1 CA-ATCTTTTACCCTAACCAGAG-GGCAGATTGAAGCCATCCA-ATCTCTTACCCCGACCATGGG
*
43448551 GTAGATTGAAG
63 GCAGATTGAAG
43448562 CTATCAAATT
Statistics
Matches: 817, Mismatches: 159, Indels: 76
0.78 0.15 0.07
Matches are distributed among these distances:
73 66 0.08
74 1 0.00
75 1 0.00
76 1 0.00
77 2 0.00
78 215 0.26
79 389 0.48
80 138 0.17
81 4 0.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGGGGCA
GATTGAAGACAATC
Found at i:43448522 original size:40 final size:40
Alignment explanation
Indices: 43447924--43448561 Score: 155
Period size: 39 Copynumber: 16.3 Consensus size: 40
43447914 CCGATCATGG
* * * * * * *
43447924 GGCAAATTGAAGCAATCCA-ATCTTTTACCCCAACCATGG
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
*
43447963 GGCAGATTGAAGTAATTCAGATCTTTTACC-CTAACC-AGA
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTC-AACCAAGA
* *
43448002 GGGCAGATTGAAGTAATCCA-ATCTTTTACC-CTAACC-AGA
1 -GGCAGATTGAAGTAATTCAGATCTCTTACCTC-AACCAAGA
* ** * * *
43448041 GGGCAAATTGAAGCCATCCA-ATCTCTTACCTCGACCATGA
1 -GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
* * * *
43448081 GGCAGATTGAAGCAATCCA-ATCTTTTACC-CTAATC---A
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTC-AACCAAGA
* ** * * * * *
43448117 -G-ATATTGAAGCCATCCA-ATCTCTTACCTCGACTATGG
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
* *
43448154 GGCAGATTGAAGCAA-TCTA-ATCTTTTACC-CTAACC-AGA
1 GGCAGATTGAAGTAATTC-AGATCTCTTACCTC-AACCAAGA
* * * * *
43448192 GAGCAAATTGAAG-ACCA-TCCGATCTCTTACCCCAACCATGG
1 G-GCAGATTGAAGTA--ATTCAGATCTCTTACCTCAACCAAGA
* * * * *
43448233 GGTAGATTAAAG-ACCA-TCTGATCTTTTACC-CTAA-CTAGA
1 GGCAGATTGAAGTA--ATTCAGATCTCTTACCTC-AACCAAGA
** * * * *
43448272 GGGCAGATTGAAGCCA-TCTA-ATCTCTTGCCTCGACCATGG
1 -GGCAGATTGAAGTAATTC-AGATCTCTTACCTCAACCAAGA
* * * * * *
43448312 GGTAGATTGAAGCAATCCA-ATCTTTTACCTTAATC-AGA
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
* * * **
43448350 GGGCAGATTGAAG-ACCA-TCCGATCTCTTACCCCGACC-ATC
1 -GGCAGATTGAAGTA--ATTCAGATCTCTTACCTCAACCAAGA
* * *
43448390 GGCAGGTTGAA--AACCTGTC-GATCTTTTACCTCGACC-AGA
1 GGCAGATTGAAGTAA--T-TCAGATCTCTTACCTCAACCAAGA
* * * *
43448429 GGGCAGATTGAAG-ACCA-TCCGATCTCTTACCTCAATCATGG
1 -GGCAGATTGAAGTA--ATTCAGATCTCTTACCTCAACCAAGA
* *
43448470 GGCAGATTGAAGTAATTCAGATCTTTTACCTTAACCAAGA
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
* * * *
43448510 GGCAGATTGAAGTAATCCAGATCTCTTACCTCGACCATGG
1 GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
*
43448550 GGTAGATTGAAG
1 GGCAGATTGAAG
43448562 CTATCAAATT
Statistics
Matches: 457, Mismatches: 99, Indels: 85
0.71 0.15 0.13
Matches are distributed among these distances:
34 24 0.05
35 2 0.00
36 2 0.00
38 10 0.02
39 207 0.45
40 205 0.45
41 6 0.01
43 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (40 bp):
GGCAGATTGAAGTAATTCAGATCTCTTACCTCAACCAAGA
Found at i:43448681 original size:132 final size:133
Alignment explanation
Indices: 43448439--43448693 Score: 308
Period size: 132 Copynumber: 1.9 Consensus size: 133
43448429 GGGCAGATTG
* * ** * * *
43448439 AAGACCATCCGATCTCTTACCTCAATCATGGGGCAGATTGAAGTAATTCAGATCTTTTACCTTAA
1 AAGACCATCCAATCTCTTACCCCAATCATGAAGCAAATTGAAGCAATCCAGATCTTTTACCTTAA
*
43448504 CCAAGAGGCAGATTGAAGTAATCCAGATCTCTTACCTCGACCATGGGGTAGATTGAAGCTATCAA
66 CCAAGAGGCAGATTGAAGTAATCCAGATCTCTTACCCCGACCAT-GGGTAGATTGAAGCTATCAA
43448569 ATTA
130 ATTA
*
43448573 AAGACCATCCAATCTCTTACCCCGA-CATGAAGCAAATTGAAGCAATCCA-ATCTTTTACAC-TA
1 AAGACCATCCAATCTCTTACCCCAATCATGAAGCAAATTGAAGCAATCCAGATCTTTTAC-CTTA
* *
43448635 A-CTAGAGGGCAGATTGAAG-ACCATCC-GAT-TCTTTACCCCGATCATGGGTAGATTGAAGC
65 ACCAAGA-GGCAGATTGAAGTA--ATCCAGATCTC-TTACCCCGACCATGGGTAGATTGAAGC
43448694 AATCCAATCT
Statistics
Matches: 105, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
131 21 0.20
132 38 0.36
133 24 0.23
134 22 0.21
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (133 bp):
AAGACCATCCAATCTCTTACCCCAATCATGAAGCAAATTGAAGCAATCCAGATCTTTTACCTTAA
CCAAGAGGCAGATTGAAGTAATCCAGATCTCTTACCCCGACCATGGGTAGATTGAAGCTATCAAA
TTA
Found at i:43450809 original size:21 final size:21
Alignment explanation
Indices: 43450779--43450835 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
43450769 AAACTATAAT
*
43450779 ATTTTATATTTTTATCCCAAA
1 ATTTTTTATTTTTATCCCAAA
*
43450800 CTTTTTTATTTTT-T-CCAAA
1 ATTTTTTATTTTTATCCCAAA
*
43450819 ATCTTTTATTTCTTATC
1 ATTTTTTATTT-TTATC
43450836 ACTTTTCCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTTATTTTTATCCCAAA
Found at i:43451745 original size:23 final size:20
Alignment explanation
Indices: 43451719--43451774 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 20
43451709 GAAGTTAAAT
43451719 TGTAATTTTTACGATAATAAAAG
1 TGTAATTTTTA--A-AATAAAAG
43451742 TGTAATTTTT-AAATAAAAG
1 TGTAATTTTTAAAATAAAAG
*
43451761 TGCAATTTTTAAAA
1 TGTAATTTTTAAAA
43451775 GATTAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 17 0.55
20 4 0.13
23 10 0.32
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTAATTTTTAAAATAAAAG
Found at i:43451758 original size:19 final size:19
Alignment explanation
Indices: 43451734--43451773 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
43451724 TTTTTACGAT
*
43451734 AATAAAAGTGTAATTTTTA
1 AATAAAAGTGCAATTTTTA
43451753 AATAAAAGTGCAATTTTTA
1 AATAAAAGTGCAATTTTTA
43451772 AA
1 AA
43451774 AGATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (19 bp):
AATAAAAGTGCAATTTTTA
Found at i:43452331 original size:15 final size:15
Alignment explanation
Indices: 43452308--43452346 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43452298 TTGTTTAATT
*
43452308 TTATTAAATAAAATA
1 TTATAAAATAAAATA
* *
43452323 TTATAAAATTATATA
1 TTATAAAATAAAATA
43452338 TTATAAAAT
1 TTATAAAAT
43452347 TTTTGATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAAAATAAAATA
Found at i:43452982 original size:26 final size:30
Alignment explanation
Indices: 43452892--43452972 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
43452882 TTCGTGAACA
* * *
43452892 TTAAACAAATGAATATGAACACACATAATT
1 TTAAATAAACGAACATGAACACACATAATT
43452922 TTAAATAAACGAACATGAACACACATAATT
1 TTAAATAAACGAACATGAACACACATAATT
*
43452952 TTAAATAAACTAACATGAACA
1 TTAAATAAACGAACATGAACA
43452973 AATATTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (30 bp):
TTAAATAAACGAACATGAACACACATAATT
Found at i:43455140 original size:22 final size:22
Alignment explanation
Indices: 43455096--43455141 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
43455086 ATCATAAATT
* * *
43455096 TTTTTTTATTATTTTCTTGTTA
1 TTTTTTTACTATTATCTTATTA
*
43455118 TTTTTTTACTATTATGTTATTA
1 TTTTTTTACTATTATCTTATTA
43455140 TT
1 TT
43455142 ATTATTTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTTTACTATTATCTTATTA
Found at i:43455143 original size:25 final size:24
Alignment explanation
Indices: 43455093--43455149 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
43455083 AAAATCATAA
* * * *
43455093 ATTTTTTTTTATTATTTTCTTGTT
1 ATTTTTTTCTATTATGTTATTATT
43455117 ATTTTTTTACTATTATGTTATTATT
1 ATTTTTTT-CTATTATGTTATTATT
*
43455142 ATTATTTT
1 ATTTTTTT
43455150 GTTGTTATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (24 bp):
ATTTTTTTCTATTATGTTATTATT
Found at i:43456852 original size:26 final size:26
Alignment explanation
Indices: 43456823--43456886 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
43456813 TATAAAAATT
43456823 AAATATAATTATAA-TATTAATATTAA
1 AAATATAATTA-AATTATTAATATTAA
* * *
43456849 AAATAT-ATTAAATTATTTATGTTTA
1 AAATATAATTAAATTATTAATATTAA
*
43456874 AAATATAAATAAA
1 AAATATAATTAAA
43456887 AGAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 19 0.59
26 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
AAATATAATTAAATTATTAATATTAA
Found at i:43465116 original size:23 final size:25
Alignment explanation
Indices: 43465090--43465136 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43465080 TCCAATTAGG
43465090 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
43465113 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
43465137 TGGATCCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:43473474 original size:23 final size:24
Alignment explanation
Indices: 43473448--43473495 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43473438 TACAAAGATG
* *
43473448 AAATTGT-AATTTTATCTCTTTAA
1 AAATTGTCAATTTAATCCCTTTAA
*
43473471 AAATTTTCAATTTAATCCCTTTAA
1 AAATTGTCAATTTAATCCCTTTAA
43473495 A
1 A
43473496 CTTCTAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTGTCAATTTAATCCCTTTAA
Found at i:43492717 original size:3 final size:3
Alignment explanation
Indices: 43492709--43492744 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
43492699 TAATTAAGTC
*
43492709 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43492745 ACGGATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:43496515 original size:26 final size:27
Alignment explanation
Indices: 43496482--43496539 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
43496472 TATTAAAACT
*
43496482 AAAT-TTAAATATCAAATTGAATA-AA
1 AAATATTAAATATCAAATTAAATATAA
* *
43496507 AAATATTAAGTGTCAAATTAAATATTAA
1 AAATATTAAATATCAAATTAAATA-TAA
43496535 AAATA
1 AAATA
43496540 AATTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 16 0.59
28 7 0.26
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
AAATATTAAATATCAAATTAAATATAA
Found at i:43496546 original size:19 final size:19
Alignment explanation
Indices: 43496466--43496559 Score: 61
Period size: 19 Copynumber: 4.9 Consensus size: 19
43496456 ATATCTCCAT
*
43496466 TTTAAATATTAAAACTAAA
1 TTTAAATATTAAAAATAAA
*
43496485 TTTAAATATCAAATTGAATAAA
1 TTTAAATATTAAA---AATAAA
***
43496507 ---AAATATTAAGTGTCAAA
1 TTTAAATATTAAAAAT-AAA
43496524 -TTAAATATTAAAAATAAA
1 TTTAAATATTAAAAATAAA
*
43496542 TTTAAATACTAAATAATA
1 TTTAAATATTAAA-AATA
43496560 TATTAGCCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
16 1 0.02
17 3 0.05
18 3 0.05
19 41 0.72
20 4 0.07
22 5 0.09
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTAAATATTAAAAATAAA
Found at i:43513506 original size:27 final size:27
Alignment explanation
Indices: 43513476--43513528 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43513466 ATTTGTTTTA
* *
43513476 TTTTATTTTTTTAATAA-TTTTATATAT
1 TTTTATTTATTGAA-AATTTTTATATAT
43513503 TTTTATTTATTGAAAATTTTTATATA
1 TTTTATTTATTGAAAATTTTTATATA
43513529 GTCATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTATTTATTGAAAATTTTTATATAT
Found at i:43514594 original size:145 final size:145
Alignment explanation
Indices: 43514395--43514688 Score: 552
Period size: 145 Copynumber: 2.0 Consensus size: 145
43514385 TAACTTTTAA
*
43514395 AAAGGGGTAAACTACAAAAATAGTCATTTTTGTTTGACTCAGATTACATTTTAGTCACTTATATT
1 AAAGAGGTAAACTACAAAAATAGTCATTTTTGTTTGACTCAGATTACATTTTAGTCACTTATATT
43514460 TGAAATATTACGTTTTAGTCACTTATGTTATTATTTTGTTATGAAGTGATCACTCTGCCGTTAAG
66 TGAAATATTACGTTTTAGTCACTTATGTTATTATTTTGTTATGAAGTGATCACTCTGCCGTTAAG
43514525 TTCCGTTATCTCCCT
131 TTCCGTTATCTCCCT
* *
43514540 AAAGAGGTAAACTACAAAAATAGTCATTTTTGTTTGACTCAGGTTACATTTTAGTCACTTTTATT
1 AAAGAGGTAAACTACAAAAATAGTCATTTTTGTTTGACTCAGATTACATTTTAGTCACTTATATT
43514605 TGAAATATTACGTTTTAGTCACTTATGTTATTATTTTGTTATGAAGTGATCACTCTGCCGTTAAG
66 TGAAATATTACGTTTTAGTCACTTATGTTATTATTTTGTTATGAAGTGATCACTCTGCCGTTAAG
*
43514670 TTCTGTTATCTCCCT
131 TTCCGTTATCTCCCT
43514685 AAAG
1 AAAG
43514689 GTAATCTTAC
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (145 bp):
AAAGAGGTAAACTACAAAAATAGTCATTTTTGTTTGACTCAGATTACATTTTAGTCACTTATATT
TGAAATATTACGTTTTAGTCACTTATGTTATTATTTTGTTATGAAGTGATCACTCTGCCGTTAAG
TTCCGTTATCTCCCT
Found at i:43518185 original size:16 final size:16
Alignment explanation
Indices: 43518164--43518206 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
43518154 ACTTCTCTTG
43518164 TTATTTTCCTTTTTTA
1 TTATTTTCCTTTTTTA
*
43518180 TTATTTTCCCTTTTTA
1 TTATTTTCCTTTTTTA
43518196 -TATTTT-CTTTT
1 TTATTTTCCTTTT
43518207 AAAAACTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 15 0.60
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTCCTTTTTTA
Found at i:43519199 original size:40 final size:39
Alignment explanation
Indices: 43519155--43519378 Score: 128
Period size: 40 Copynumber: 5.8 Consensus size: 39
43519145 TAATAGCTTT
*
43519155 AATCTACCCCATGATCGGGGTAAGAGATTGGTATGTCTTC
1 AATCTGCCCCATGATCGGGGTAAGAGATTGGTATGT-TTC
* ** * *
43519195 AATCTGCTCTC-TGATTAGGGTAA-AGACTGG-ATGCTTC
1 AATCTGC-CCCATGATCGGGGTAAGAGATTGGTATGTTTC
* * * *
43519232 GATC-GCCCCATGGTCGTGGTAAGAGA-TCG-ATGGTTGT-
1 AATCTGCCCCATGATCGGGGTAAGAGATTGGTAT-GTT-TC
* *
43519269 GATCTGCCCCATGATTC-GGGTAAGAGATCGGGTA-GTTGT-
1 AATCTGCCCCATGA-TCGGGGTAAGAGAT-TGGTATGTT-TC
* * * * *
43519308 GATCTACCTCATGATCAGGGTAAGAGATTGAGT-GGTTTTC
1 AATCTGCCCCATGATCGGGGTAAGAGATTG-GTATG-TTTC
*
43519348 AACCTGCCCCATGATCGGGGTAAGAGATTGG
1 AATCTGCCCCATGATCGGGGTAAGAGATTGG
43519379 GTGGTGATAT
Statistics
Matches: 143, Mismatches: 26, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
35 2 0.01
36 14 0.10
37 15 0.10
38 24 0.17
39 41 0.29
40 44 0.31
41 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (39 bp):
AATCTGCCCCATGATCGGGGTAAGAGATTGGTATGTTTC
Found at i:43519278 original size:38 final size:37
Alignment explanation
Indices: 43519232--43519375 Score: 137
Period size: 39 Copynumber: 3.7 Consensus size: 37
43519222 TGGATGCTTC
*
43519232 GATC-GCCCCATGGTCGTGGTAAGAGATCGATGGTTGT
1 GATCTGCCCCATGATCG-GGTAAGAGATCGATGGTTGT
* *
43519269 GATCTGCCCCATGATTCGGGTAAGAGATCGGGTAGTTGT
1 GATCTGCCCCATGA-TCGGGTAAGAGATC-GATGGTTGT
* * * *
43519308 GATCTACCTCATGATCAGGGTAAGAGATTGAGTGGTTTT
1 GATCTGCCCCATGATC-GGGTAAGAGATCGA-TGGTTGT
* *
43519347 CAACCTGCCCCATGATCGGGGTAAGAGAT
1 -GATCTGCCCCATGATC-GGGTAAGAGAT
43519376 TGGGTGGTGA
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
37 4 0.05
38 22 0.25
39 38 0.44
40 23 0.26
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
GATCTGCCCCATGATCGGGTAAGAGATCGATGGTTGT
Found at i:43519797 original size:98 final size:98
Alignment explanation
Indices: 43519627--43520441 Score: 1076
Period size: 98 Copynumber: 8.3 Consensus size: 98
43519617 TTAGGGCATA
* * * ** * *
43519627 AGATTCACCGTTGCGGCTTTAATCTTTCCTTGTCAAATTTCTAAGGTACAAGGTTCGCCGTTGCG
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCT-TCATGTTTCTGAGGTACAAGGTTCACCGTTGCG
* * * *
43519692 ACTTAAACATTTTCCTTCATATCTTCGTGGTATC
65 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
43519726 AGATTCGCTGTTGCGGCTTCAATCTTTCCCAGT-ATGTTTCTGAGGTACAAGATTTACCGTTGCA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCC-TTCATGTTTCTGAGGTACAAGGTTCACCGTTGCG
* *
43519790 ACTTAAACCTTTCCTTCCATATCTTCATGGTACC
65 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
43519824 AGATTCGCCGTTGTGGCTTCAATCTTTCCCTTCATGTTTCTGAAGTGCAAGGTTCACCGTTGTGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
* **
43519889 CTTAAACCTTTCTCTCCATATCTTTATGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * ** * *
43519922 AGATTCGCCATTGCGACTTTAATCTTTCCCAGCATGTTTCTGAGGTACAAGTTTCGCCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
43519987 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
43520020 AAATTCGCCGTTGTGGCTTCAATCTTTCCCTTTATGTTTCTAAGGTATAAGGTT-AGCCGTTGCG
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCA-CCGTTGCG
43520084 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
65 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
43520118 AGATTCACCGTTGCGTCTTCAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCTCCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
* *
43520183 CTTAAACCTTTCCTTCCATATTTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* ** * *
43520216 AGATTTGCCGTTGCATCTTCAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACTGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
*
43520281 CTTAAACCTTTCCCTCCATATCTTCGTGATACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
43520314 AGATTTGCTGTTGCGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
* *
43520379 CTTAAACCTATCCCTCCATATCTTCGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
*
43520412 AGATTCGCCGTTGCGGCTTAAATCTTTCCC
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCC
43520442 ATCTCATCTC
Statistics
Matches: 622, Mismatches: 90, Indels: 9
0.86 0.12 0.01
Matches are distributed among these distances:
97 1 0.00
98 594 0.95
99 27 0.04
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (98 bp):
AGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
Found at i:43522495 original size:8 final size:8
Alignment explanation
Indices: 43522484--43522524 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
43522474 TTTTCTTCCA
43522484 TTCTTTTC
1 TTCTTTTC
43522492 TTCTTCTT-
1 TTCTT-TTC
43522500 TTCTTTTC
1 TTCTTTTC
43522508 TT-TTTTC
1 TTCTTTTC
*
43522515 TTTTTTTC
1 TTCTTTTC
43522523 TT
1 TT
43522525 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 9 0.30
8 19 0.63
9 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTCTTTTC
Found at i:43522497 original size:16 final size:16
Alignment explanation
Indices: 43522476--43522509 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43522466 AACTTTCTTT
43522476 TTCTTCCATTCTTTTC
1 TTCTTCCATTCTTTTC
**
43522492 TTCTTCTTTTCTTTTC
1 TTCTTCCATTCTTTTC
43522508 TT
1 TT
43522510 TTTTCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTCCATTCTTTTC
Found at i:43522503 original size:5 final size:5
Alignment explanation
Indices: 43522484--43522526 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
43522474 TTTTCTTCCA
*
43522484 TTCTT TTCTT CTTCTT TTCTT TTCTT TT-TT CTTTTT TTCTT TT
1 TTCTT TTCTT -TTCTT TTCTT TTCTT TTCTT -TTCTT TTCTT TT
43522527 TAAAAAATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
4 2 0.06
5 25 0.74
6 7 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:43522515 original size:12 final size:13
Alignment explanation
Indices: 43522484--43522526 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
43522474 TTTTCTTCCA
43522484 TTCTTTTC--TTC
1 TTCTTTTCTTTTC
43522495 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
*
43522508 TT-TTTTCTTTTT
1 TTCTTTTCTTTTC
43522520 TTCTTTT
1 TTCTTTT
43522527 TAAAAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.29
12 11 0.39
13 9 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:43526659 original size:21 final size:19
Alignment explanation
Indices: 43526628--43526683 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
43526618 TAAATGAATA
*
43526628 ATAGTATACAATACATGTAC
1 ATAGTATACAAAACATG-AC
43526648 ATAGTAATACAAAACATGAC
1 ATAGT-ATACAAAACATGAC
*
43526668 ATGAGTATACATAACA
1 AT-AGTATACAAAACA
43526684 GTAAATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (19 bp):
ATAGTATACAAAACATGAC
Found at i:43527583 original size:16 final size:16
Alignment explanation
Indices: 43527562--43527604 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
43527552 ACTTCTCTTG
43527562 TTATTTTCCTTTTTTA
1 TTATTTTCCTTTTTTA
*
43527578 TTATTTTCCCTTTTTA
1 TTATTTTCCTTTTTTA
43527594 -TATTTT-CTTTT
1 TTATTTTCCTTTT
43527605 AAAAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 15 0.60
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTCCTTTTTTA
Found at i:43528640 original size:18 final size:18
Alignment explanation
Indices: 43528617--43528657 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43528607 TTTTCAATTG
43528617 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
43528635 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
43528653 TAATT
1 TAATT
43528658 TATAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:43535388 original size:21 final size:21
Alignment explanation
Indices: 43535362--43535407 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
43535352 CAACATCGCA
*
43535362 ACGTGGTGACGATAGTGAGTG
1 ACGTGGTGACGACAGTGAGTG
43535383 ACGTGGTGACGACAGTGAGTG
1 ACGTGGTGACGACAGTGAGTG
43535404 ACGT
1 ACGT
43535408 TGCGACGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.41, T:0.22
Consensus pattern (21 bp):
ACGTGGTGACGACAGTGAGTG
Found at i:43535414 original size:21 final size:21
Alignment explanation
Indices: 43535362--43535414 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43535352 CAACATCGCA
* *
43535362 ACGTGGTGACGATAGTGAGTG
1 ACGTGGCGACGACAGTGAGTG
*
43535383 ACGTGGTGACGACAGTGAGTG
1 ACGTGGCGACGACAGTGAGTG
*
43535404 ACGTTGCGACG
1 ACGTGGCGACG
43535415 TCGGCATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (21 bp):
ACGTGGCGACGACAGTGAGTG
Found at i:43536281 original size:15 final size:16
Alignment explanation
Indices: 43536255--43536284 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43536245 AACAAAATTG
43536255 TAAAATTGACTCGAAC
1 TAAAATTGACTCGAAC
43536271 TAAAA-TGACTCGAA
1 TAAAATTGACTCGAA
43536285 ATGATCCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (16 bp):
TAAAATTGACTCGAAC
Found at i:43538704 original size:6 final size:6
Alignment explanation
Indices: 43538693--43538726 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
43538683 GGGACGTAGC
43538693 ACACAT ACACAT ACACAT ACACAT ACACAT ACAC
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACAC
43538727 CTATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACACAT
Found at i:43538745 original size:10 final size:10
Alignment explanation
Indices: 43538730--43538754 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43538720 CATACACCTA
43538730 TATATATAGG
1 TATATATAGG
43538740 TATATATAGG
1 TATATATAGG
43538750 TATAT
1 TATAT
43538755 GGCAGTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (10 bp):
TATATATAGG
Found at i:43557308 original size:22 final size:23
Alignment explanation
Indices: 43557274--43557325 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
43557264 AGGTTTGAAA
*
43557274 ATAACATTATTAAGAGAGA-TAATT
1 ATAA-ATTATTAAAAGA-ATTAATT
43557298 ATAAATT-TTAAAAGAATTAATT
1 ATAAATTATTAAAAGAATTAATT
*
43557320 AAAAAT
1 ATAAAT
43557326 AAATTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 3 0.12
24 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (23 bp):
ATAAATTATTAAAAGAATTAATT
Found at i:43557975 original size:19 final size:19
Alignment explanation
Indices: 43557947--43557983 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43557937 GCCTTATATT
43557947 ATATTCAAATTGACATTTA
1 ATATTCAAATTGACATTTA
* *
43557966 ATATTTAAATTGATATTT
1 ATATTCAAATTGACATTT
43557984 TTAATAAATA
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:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATTCAAATTGACATTTA
Found at i:43559690 original size:21 final size:19
Alignment explanation
Indices: 43559665--43559707 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
43559655 ACATCAACAA
43559665 TTTTATTCTAAATTTTAATAT
1 TTTTATT-TAAA-TTTAATAT
*
43559686 TTTTATTTTAATTTAAT-T
1 TTTTATTTAAATTTAATAT
43559704 TTTT
1 TTTT
43559708 TTTCAAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 3 0.14
21 7 0.33
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTTAAATTTAATAT
Found at i:43559980 original size:22 final size:22
Alignment explanation
Indices: 43559903--43559981 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
43559893 TTAAGAAATT
*
43559903 TATAAGTATAATTACAATAATAGAAA
1 TATAA-TATAATTA-AA-ATTA-AAA
43559929 TATAATATAATTAAAATTAAAA
1 TATAATATAATTAAAATTAAAA
* * *
43559951 T-TAAAATATATTCAAATTTAAA
1 TATAATATA-ATTAAAATTAAAA
43559973 TCATAATAT
1 T-ATAATAT
43559982 GCTGAACAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 6 0.13
22 16 0.36
23 3 0.07
24 7 0.16
25 8 0.18
26 5 0.11
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (22 bp):
TATAATATAATTAAAATTAAAA
Found at i:43563418 original size:63 final size:59
Alignment explanation
Indices: 43563346--43563498 Score: 157
Period size: 63 Copynumber: 2.5 Consensus size: 59
43563336 TAAATCTGAT
43563346 AAAGTTGGTGCCAACCATCTATAAGGAAAAAAAACCAGCAAAAAAATATTTCAAGTACTGAAA
1 AAAG-TGGTGCCAACCATCTATAAGG-AAAAAAACCAGCAAAAAAA-ATTT-AAGTACTGAAA
* * * ** *
43563409 ATAAGTGGTGCCGACCATTTATAAGG-TAAAAACCAGCAAAAAAAATTTTGGTTCTGAAA
1 A-AAGTGGTGCCAACCATCTATAAGGAAAAAAACCAGCAAAAAAAATTTAAGTACTGAAA
* * *
43563468 AAGGTGGTGTCAACCA-CTAATAAGGCAAAAA
1 AAAGTGGTGCCAACCATCT-ATAAGGAAAAAA
43563499 CCATTGAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
57 1 0.01
58 18 0.24
59 13 0.17
60 4 0.05
61 17 0.22
63 20 0.26
64 3 0.04
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (59 bp):
AAAGTGGTGCCAACCATCTATAAGGAAAAAAACCAGCAAAAAAAATTTAAGTACTGAAA
Found at i:43563498 original size:58 final size:59
Alignment explanation
Indices: 43563340--43563501 Score: 157
Period size: 58 Copynumber: 2.7 Consensus size: 59
43563330 AAAAATTAAA
* *
43563340 TCTGATAAAGTTGGTGCCAACCATCTATAAGGAAAAAAAACCAGCAAAAAAATATTTCAAGT
1 TCTGAAAAAGGTGGTGCCAACCA-CTATAAGG--AAAAAACCAGCAAAAAAATATTTCAAGT
* * * * * **
43563402 ACTGAAAATAAGTGGTGCCGACCATTTATAAGGTAAAAACCAGCAAAAAAA-ATTT-TGGT
1 TCTGAAAA-AGGTGGTGCCAACCA-CTATAAGGAAAAAACCAGCAAAAAAATATTTCAAGT
* *
43563461 TCTGAAAAAGGTGGTGTCAACCACTAATAAGGCAAAAACCA
1 TCTGAAAAAGGTGGTGCCAACCACT-ATAAGGAAAAAACCA
43563502 TTGAAAACAT
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.01
58 26 0.31
59 9 0.11
60 4 0.05
61 17 0.20
62 6 0.07
63 20 0.24
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (59 bp):
TCTGAAAAAGGTGGTGCCAACCACTATAAGGAAAAAACCAGCAAAAAAATATTTCAAGT
Found at i:43564333 original size:243 final size:246
Alignment explanation
Indices: 43563875--43564343 Score: 586
Period size: 243 Copynumber: 1.9 Consensus size: 246
43563865 TAATACTATA
* * *
43563875 TGATTTAATATACTTTTAAAAAAATGATGGTGTTGAGTTGTTGGTTAGTTGTATAGTGAGTTACT
1 TGATTTAATATACTTTTAAAAAAATGAT-GTGTTGAGTTGTCGATCAGTTGTATAGTGAGTTACT
* * * * *
43563940 ACTAATAATAGAACTGAATCTAGAAAAGAAAAACAACGAATACACGAGTTACACAATTTAAAACC
65 ACTAACAATACAACTGAAACTAGAAAAGAAAAACAACAAATACACGAGTTACACAATTCAAAACC
*
43564005 TTTTCCTACGCTTGTAGAGGCCTCACTGAGAGAATAATTCACTATAATTCAACAATACAAGGCAT
130 TTTTCCTACACTTGTAGAGGCCTCACTGAGAGAATAATTCACTATAATTCAACAATACAAGGCAT
* *
43564070 AATTTAAGCTCCAGTCACTCACCATGTTGCAACCCACAATACTAATGCTTTG
195 AATTTAAGCTCAAGTCACTCACCAAGTTGCAACCCACAATACTAATGCTTTG
** * *
43564122 TGATTTAATATA-TTTTTTAAAAATG-T-TGTTGAGTTGTCGATCAGTTGTATTGTGAGTTGCTA
1 TGATTTAATATACTTTTAAAAAAATGATGTGTTGAGTTGTCGATCAGTTGTATAGTGAGTTACTA
* * * *
43564184 CTAACAATACAACTGAAACTGGAAAAGTAAAACAACAAATGCACGAGTTACATAATTCAAAACCT
66 CTAACAATACAACTGAAACTAGAAAAGAAAAACAACAAATACACGAGTTACACAATTCAAAACCT
* * * * * ** ** * **
43564249 CTTT-TTTCATTTGTGGGGGGTTCGTTGAGAGAATAATTCACTATATTTCAACAATACAAGGTGT
131 -TTTCCTACACTTGTAGAGGCCTCACTGAGAGAATAATTCACTATAATTCAACAATACAAGGCAT
** *
43564313 AATTTAATTTTAAGTCACTCACCAAGTTGCA
195 AATTTAAGCTCAAGTCACTCACCAAGTTGCA
43564344 GCCTCAGCTT
Statistics
Matches: 187, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
243 160 0.86
244 3 0.02
245 1 0.01
246 11 0.06
247 12 0.06
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (246 bp):
TGATTTAATATACTTTTAAAAAAATGATGTGTTGAGTTGTCGATCAGTTGTATAGTGAGTTACTA
CTAACAATACAACTGAAACTAGAAAAGAAAAACAACAAATACACGAGTTACACAATTCAAAACCT
TTTCCTACACTTGTAGAGGCCTCACTGAGAGAATAATTCACTATAATTCAACAATACAAGGCATA
ATTTAAGCTCAAGTCACTCACCAAGTTGCAACCCACAATACTAATGCTTTG
Found at i:43571827 original size:18 final size:18
Alignment explanation
Indices: 43571792--43571827 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43571782 ATTAAATAGT
* *
43571792 TCGAGTTATTTGAGTCAA
1 TCGAGTTATTCGAATCAA
43571810 TCGAGTTATTCGAATCAA
1 TCGAGTTATTCGAATCAA
43571828 CTCAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (18 bp):
TCGAGTTATTCGAATCAA
Found at i:43592547 original size:32 final size:32
Alignment explanation
Indices: 43592498--43592624 Score: 143
Period size: 32 Copynumber: 4.0 Consensus size: 32
43592488 ATTGATGATT
* *
43592498 ACAGATTGACAGCTCTTACGAGCATACTATTC
1 ACAGATTGAAAGCTCTTACGAGCATACTGTTC
*
43592530 ACAGATTGATAAG-TCTTACAAGCATACTGTTC
1 ACAGATTGA-AAGCTCTTACGAGCATACTGTTC
*
43592562 ACAGATTGACAA-CTCTTATGAGCATA-TCGTTC
1 ACAGATTGA-AAGCTCTTACGAGCATACT-GTTC
* * *
43592594 ACAGATTGACAGCTCTTACGAGTATAATGTT
1 ACAGATTGAAAGCTCTTACGAGCATACTGTT
43592625 TACTGAGTGA
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
31 2 0.02
32 76 0.94
33 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (32 bp):
ACAGATTGAAAGCTCTTACGAGCATACTGTTC
Found at i:43601265 original size:20 final size:21
Alignment explanation
Indices: 43601240--43601281 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
43601230 TTTAACCTCA
43601240 TTTATAA-T-TTATATTAATTT
1 TTTATAATTGTTATA-TAATTT
43601260 TTTATAATTGTTATATAATTT
1 TTTATAATTGTTATATAATTT
43601281 T
1 T
43601282 ATTTTTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATAATTGTTATATAATTT
Found at i:43601283 original size:10 final size:10
Alignment explanation
Indices: 43601242--43601283 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
43601232 TAACCTCATT
43601242 TATAA-TTTA
1 TATAATTTTA
*
43601251 TATTAATTTTT
1 TA-TAATTTTA
43601262 TATAATTGTTA
1 TATAATT-TTA
43601273 TATAATTTTA
1 TATAATTTTA
43601283 T
1 T
43601284 TTTTCTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 12 0.43
11 14 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TATAATTTTA
Found at i:43601962 original size:16 final size:17
Alignment explanation
Indices: 43601936--43601971 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43601926 TTAAAAATTC
*
43601936 ATAATTTTTATATAAAA
1 ATAATTTTTATAAAAAA
43601953 ATAA-TTTTATAAAAAA
1 ATAATTTTTATAAAAAA
43601969 ATA
1 ATA
43601972 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATTTTTATAAAAAA
Found at i:43608030 original size:52 final size:52
Alignment explanation
Indices: 43607949--43608054 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
43607939 TCTTCGATGA
43607949 CTCTTTAAACTACCCACAATGTAAATTCAATATTTTTCTTTAAATACCTCAT
1 CTCTTTAAACTACCCACAATGTAAATTCAATATTTTTCTTTAAATACCTCAT
*
43608001 CTCTTTAAACTACCCACAATGTAATTTCAATATTTTTCTTTAAATACCTCAT
1 CTCTTTAAACTACCCACAATGTAAATTCAATATTTTTCTTTAAATACCTCAT
43608053 CT
1 CT
43608055 TAACATCAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.42
Consensus pattern (52 bp):
CTCTTTAAACTACCCACAATGTAAATTCAATATTTTTCTTTAAATACCTCAT
Found at i:43611561 original size:60 final size:58
Alignment explanation
Indices: 43611395--43611561 Score: 151
Period size: 60 Copynumber: 2.8 Consensus size: 58
43611385 TTGGTACCAG
* * * * ** *
43611395 AGTTTGGCTTCAATGTTCAATTTGATACTTGATTTTTTT-GTCCCAATTTAGTGCATG
1 AGTTTGGCTTTAATATTCAATTTGGTACTTGATTTTTTTAGTCCCAATTAAGCACATA
* * *
43611452 AGTTTGG-TTTCAATATTCAAATTGGTATTTGACTTTTCTTTTA-TCCCAATTAAGCATATA
1 AGTTTGGCTTT-AATATTCAATTTGGTACTTGA--TTT-TTTTAGTCCCAATTAAGCACATA
* *
43611512 AGTTTGGCTTTGATATTCAATTTGGTACTTGAGTTTTTTCTAGTTCCAAT
1 AGTTTGGCTTTAATATTCAATTTGGTACTTGA-TTTTTT-TAGTCCCAAT
43611562 CAAAGTACTT
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
56 2 0.02
57 24 0.28
58 3 0.03
59 8 0.09
60 47 0.54
61 3 0.03
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (58 bp):
AGTTTGGCTTTAATATTCAATTTGGTACTTGATTTTTTTAGTCCCAATTAAGCACATA
Found at i:43629021 original size:24 final size:23
Alignment explanation
Indices: 43628976--43629023 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43628966 AAGGCAGAAG
* *
43628976 CGTGCCACAAGACAGAGGAAAAA
1 CGTGCCACAAAACAGAGAAAAAA
*
43628999 CGTGCCACAAAAGCAGATAAAAAA
1 CGTGCCACAAAA-CAGAGAAAAAA
43629023 C
1 C
43629024 TATAAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.50, C:0.23, G:0.21, T:0.06
Consensus pattern (23 bp):
CGTGCCACAAAACAGAGAAAAAA
Found at i:43632577 original size:21 final size:20
Alignment explanation
Indices: 43632531--43632577 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
43632521 CTTAAATAAA
**
43632531 AACTTTCCTTTTAATTTTAT
1 AACTTTCCTTTTAATAATAT
43632551 AACTTTCCTTTTAATGAATAT
1 AACTTTCCTTTTAAT-AATAT
*
43632572 AGCTTT
1 AACTTT
43632578 ATTAATTGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (20 bp):
AACTTTCCTTTTAATAATAT
Found at i:43641952 original size:23 final size:24
Alignment explanation
Indices: 43641910--43641954 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
43641900 AAATAGCTAA
*
43641910 CTAACAACTAACACCATAAAAACT
1 CTAACAACTAAAACCATAAAAACT
*
43641934 CTAA-AACTAAAACCCTAAAAA
1 CTAACAACTAAAACCATAAAAA
43641955 TTTGAAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.16
Consensus pattern (24 bp):
CTAACAACTAAAACCATAAAAACT
Found at i:43650670 original size:28 final size:28
Alignment explanation
Indices: 43650638--43650703 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
43650628 CAAATTTTAT
*
43650638 ATTTTAAAAAAAT-TATAAAAATTCTAAA
1 ATTTTAAAAAAATATATAAAAAGT-TAAA
* * * *
43650666 ATTTTCAATATATATATAAAAAGTTACA
1 ATTTTAAAAAAATATATAAAAAGTTAAA
43650694 ATTTTAAAAA
1 ATTTTAAAAA
43650704 TGTTCTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (28 bp):
ATTTTAAAAAAATATATAAAAAGTTAAA
Found at i:43653333 original size:22 final size:23
Alignment explanation
Indices: 43653289--43653333 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
43653279 TACTTGAAAA
43653289 GAAATAATTTTTAGAAATATTAT
1 GAAATAATTTTTAGAAATATTAT
*
43653312 GAAA-AATATTTTA-AAATTTTAT
1 GAAATAAT-TTTTAGAAATATTAT
43653334 TTAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
GAAATAATTTTTAGAAATATTAT
Found at i:43665636 original size:15 final size:15
Alignment explanation
Indices: 43665591--43665644 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
43665581 AAAATTTTGT
*
43665591 AATAAATAAATAAATA
1 AATAAA-AAACAAATA
*
43665607 AATAACAAACAAATA
1 AATAAAAAACAAATA
43665622 AATAAAAGAAC-AATA
1 AATAAAA-AACAAATA
*
43665637 AGTAAAAA
1 AATAAAAA
43665645 TTAAACACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.03
15 24 0.73
16 8 0.24
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (15 bp):
AATAAAAAACAAATA
Done.