Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007398.1 Corchorus capsularis cultivar CVL-1 contig07419, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 49287
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:5441 original size:24 final size:24
Alignment explanation
Indices: 5395--5441 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5385 TTATTCGGGT
* * * *
5395 TTCGGTTCATCTTGGTTTGGGTTA
1 TTCGGGTCATCTGGGTCTCGGTTA
5419 TTCGGGTCATCTGGGTCTCGGTT
1 TTCGGGTCATCTGGGTCTCGGTT
5442 CATACGAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.32, T:0.45
Consensus pattern (24 bp):
TTCGGGTCATCTGGGTCTCGGTTA
Found at i:5747 original size:42 final size:42
Alignment explanation
Indices: 5700--5781 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
5690 TAGATATTAA
*
5700 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
5742 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
5782 TGTATCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:6316 original size:16 final size:16
Alignment explanation
Indices: 6273--6377 Score: 99
Period size: 16 Copynumber: 6.5 Consensus size: 16
6263 CCGGTCACAA
*
6273 GTCATTCGGGTTTCGG
1 GTCATTCGGGTTACGG
*
6289 GTTCACTCGGGTTACGG
1 G-TCATTCGGGTTACGG
*
6306 GTCATTCGGGTTTCGG
1 GTCATTCGGGTTACGG
*
6322 GTCA-TCTGGGTTACGA
1 GTCATTC-GGGTTACGG
6338 GTCATTCGGGTCT-CGG
1 GTCATTCGGGT-TACGG
* *
6354 GTCA-TCTGGGTTGCAG
1 GTCATTC-GGGTTACGG
6370 GTCATTCG
1 GTCATTCG
6378 AGTCTCGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.07
16 50 0.68
17 19 0.26
ACGTcount: A:0.10, C:0.21, G:0.35, T:0.33
Consensus pattern (16 bp):
GTCATTCGGGTTACGG
Found at i:6342 original size:32 final size:32
Alignment explanation
Indices: 6272--6387 Score: 146
Period size: 32 Copynumber: 3.6 Consensus size: 32
6262 TCCGGTCACA
*
6272 AGTCATTCGGGTTTCGGGTTCA-CTCGGGTTACG
1 AGTCATTCGGGTCTCGGG-TCATCT-GGGTTACG
* *
6305 GGTCATTCGGGTTTCGGGTCATCTGGGTTACG
1 AGTCATTCGGGTCTCGGGTCATCTGGGTTACG
*
6337 AGTCATTCGGGTCTCGGGTCATCTGGGTTGC-
1 AGTCATTCGGGTCTCGGGTCATCTGGGTTACG
*
6368 AGGTCATTCGAGTCTCGGGT
1 A-GTCATTCGGGTCTCGGGT
6388 TCGTTGGGTC
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.01
32 56 0.74
33 19 0.25
ACGTcount: A:0.11, C:0.21, G:0.35, T:0.33
Consensus pattern (32 bp):
AGTCATTCGGGTCTCGGGTCATCTGGGTTACG
Found at i:6400 original size:16 final size:16
Alignment explanation
Indices: 6379--6417 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6369 GGTCATTCGA
*
6379 GTCTCGGGTTC-GTTGG
1 GTCTCGGG-TCGGGTGG
6395 GTCTCGGGTCGGGTGG
1 GTCTCGGGTCGGGTGG
6411 GTCTCGG
1 GTCTCGG
6418 ATTGGGCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.00, C:0.21, G:0.49, T:0.31
Consensus pattern (16 bp):
GTCTCGGGTCGGGTGG
Found at i:7566 original size:6 final size:6
Alignment explanation
Indices: 7555--7591 Score: 53
Period size: 5 Copynumber: 6.7 Consensus size: 6
7545 GTTACTAACC
7555 TTTTGT TTTTGT TTTTG- TTTTG- TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
7592 AGAGTGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.50
6 15 0.50
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:8519 original size:18 final size:18
Alignment explanation
Indices: 8492--8531 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
8482 TATGAAATCC
*
8492 TAAAAGGAAAAAGAAAAA
1 TAAAAAGAAAAAGAAAAA
*
8510 TAAAAAGAAAAAGAAAAT
1 TAAAAAGAAAAAGAAAAA
8528 TAAA
1 TAAA
8532 TGTTAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
TAAAAAGAAAAAGAAAAA
Found at i:8520 original size:5 final size:6
Alignment explanation
Indices: 8493--8526 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
8483 ATGAAATCCT
* *
8493 AAAAGG AAAAAG AAAAAT AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
8527 TTAAATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:17132 original size:30 final size:30
Alignment explanation
Indices: 17092--17154 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
17082 TGTCTTCAAG
*
17092 TCCATAATAAGTCCTT-GGCGCATCATTCCC
1 TCCATAATAAG-CCTTGGGCGCATCAGTCCC
*
17122 TCCATGATAAGCCTTGGGCGCATCAGTCCC
1 TCCATAATAAGCCTTGGGCGCATCAGTCCC
17152 TCC
1 TCC
17155 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCAGTCCC
Found at i:18646 original size:30 final size:30
Alignment explanation
Indices: 18606--18668 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
18596 TGTCTTCAAG
*
18606 TCCATAATAAGTCCTT-GGCTCATCATTCCC
1 TCCATAATAAG-CCTTGGGCACATCATTCCC
*
18636 TCCATGATAAGCCTTGGGCACATCATTCCC
1 TCCATAATAAGCCTTGGGCACATCATTCCC
18666 TCC
1 TCC
18669 CCTTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCC
Found at i:20249 original size:36 final size:36
Alignment explanation
Indices: 20207--20358 Score: 216
Period size: 36 Copynumber: 4.2 Consensus size: 36
20197 CTCTTTTTAG
* *
20207 ATTAAGTTCTTTATTGACTCCACCTATTTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
*
20243 ATTAAGTTCTTTATTAAC-CCGACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCC-ACTTAATTACCCTGA
20279 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
* * * *
20315 ATTAAGCTCACTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTTC-TTTATTGACTCCACTTAATTACCCTGA
20352 ATTAAGT
1 ATTAAGT
20359 CCCTGACTCG
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
35 2 0.02
36 70 0.67
37 32 0.31
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.39
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
Found at i:20381 original size:32 final size:32
Alignment explanation
Indices: 20340--20412 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
20330 TGACGCTACT
*
20340 TAATTACCCTGAATTAAGTCCCTGACTCGACA
1 TAATTACCCTGAACTAAGTCCCTGACTCGACA
* *
20372 TAATTACCCTGAACTAAGTCCCTGACTCTACT
1 TAATTACCCTGAACTAAGTCCCTGACTCGACA
20404 TAATT-CCCT
1 TAATTACCCT
20413 TCCTTGGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (32 bp):
TAATTACCCTGAACTAAGTCCCTGACTCGACA
Found at i:20437 original size:37 final size:37
Alignment explanation
Indices: 20387--20703 Score: 553
Period size: 37 Copynumber: 8.6 Consensus size: 37
20377 ACCCTGAACT
* *
20387 AAGTCCCTGACTCTACTTAATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
* *
20424 AAGTCCATAACTCTACTTGATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
*
20461 AAGTCCTTAAATCTACTTAATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
*
20498 AAGTCCTTAACTCTACTTAATTCTCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
20535 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
* * *
20572 AAGTCCTTTACTATACTTAACTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
20609 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
20646 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
1 AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
20683 AAGTCCTTAACTCTACTTAAT
1 AAGTCCTTAACTCTACTTAAT
20704 CATTTTTGGA
Statistics
Matches: 265, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 265 1.00
ACGTcount: A:0.25, C:0.29, G:0.09, T:0.38
Consensus pattern (37 bp):
AAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATC
Found at i:20853 original size:76 final size:76
Alignment explanation
Indices: 20745--21017 Score: 440
Period size: 76 Copynumber: 3.6 Consensus size: 76
20735 TTAATTCTTG
* *
20745 TGAAATTAAGTCTTTGC-TAATTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
1 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
* *
20809 ACTTCTTTCCT
66 ATTTCCTTCCT
* * *
20820 TGAAATTAAGTCTATGCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTA
1 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
20885 ATTTCCTTCCT
66 ATTTCCTTCCT
* * *
20896 TGAAATTAAGTATGTGCTTACTTTACTTAATTACCCTGGATTAAGTATGTGTTTGTCTTTACCTA
1 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
20961 ATTTCCTTCCT
66 ATTTCCTTCCT
*
20972 TGAAATTAAGTCTGTGCTTACCTTACTTAATTACCCTGAATTAAGT
1 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGT
21018 TCTTTACTGT
Statistics
Matches: 182, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
75 16 0.09
76 166 0.91
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (76 bp):
TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
ATTTCCTTCCT
Found at i:21033 original size:76 final size:76
Alignment explanation
Indices: 20713--21022 Score: 416
Period size: 76 Copynumber: 4.1 Consensus size: 76
20703 TCATTTTTGG
* * * * *
20713 ATTAAGTCTTTGC-TGACTTTACTTAA-TT-CTT--GTGAAATTAAGTCTTTGC-TAATTTACTT
1 ATTAAGTCTTTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTT
20772 AATTACCCTGA
66 AATTACCCTGA
* * * * *
20783 ATTAAGTATGTGCTTGTCTTTACCTAACTTCTTTCCTTGAAATTAAGTCTATGCTTACTTTACTT
1 ATTAAGTCTTTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTT
20848 AATTACCCTGA
66 AATTACCCTGA
* *
20859 ATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTACTTTACTT
1 ATTAAGTCTTTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTT
*
20924 AATTACCCTGG
66 AATTACCCTGA
* * * *
20935 ATTAAGTATGTGTTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACCTTACTT
1 ATTAAGTCTTTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTT
21000 AATTACCCTGA
66 AATTACCCTGA
21011 ATTAAGTTCTTT
1 ATTAAG-TCTTT
21023 ACTGTTTTTA
Statistics
Matches: 210, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
70 11 0.05
71 11 0.05
72 2 0.01
73 2 0.01
75 16 0.08
76 165 0.79
77 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (76 bp):
ATTAAGTCTTTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTT
AATTACCCTGA
Found at i:21128 original size:75 final size:73
Alignment explanation
Indices: 20994--21176 Score: 226
Period size: 75 Copynumber: 2.5 Consensus size: 73
20984 TGTGCTTACC
* *
20994 TTACTTAATTACCCTGAATTAAGTTCTTTACTGTTTTTACTTAATCACCCTGAATTAAGTAT-TT
1 TTACTTAATTACCCTGAATTAAGTTCTTTACTGTCTTTACTTAATCACCCTGAATTAAGT-TCTC
* *
21058 TAACTGTTT
65 TAACTATGT
*
21067 TTACTTAATTACCCTGAATTAAGTAT-TTTAACTGCTCTTTACTTAATTACCCTGAATTAAGTTC
1 TTACTTAATTACCCTGAATTAAGT-TCTTT-ACTG-TCTTTACTTAATCACCCTGAATTAAGTTC
*
21131 TCTGACTATGT
63 TCTAACTATGT
* *
21142 TTACTTTATTTCCCTGAATTAAGTTCCTTTGACTG
1 TTACTTAATTACCCTGAATTAAGTT-CTTT-ACTG
21177 ACTTATGGAC
Statistics
Matches: 95, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
73 27 0.28
74 7 0.07
75 54 0.57
76 7 0.07
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.46
Consensus pattern (73 bp):
TTACTTAATTACCCTGAATTAAGTTCTTTACTGTCTTTACTTAATCACCCTGAATTAAGTTCTCT
AACTATGT
Found at i:21166 original size:37 final size:37
Alignment explanation
Indices: 20994--21176 Score: 228
Period size: 37 Copynumber: 4.9 Consensus size: 37
20984 TGTGCTTACC
20994 TTACTTAATTACCCTGAATTAAGTTCTTT-ACTGTTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGTTT
*
21030 TTACTTAATCACCCTGAATTAAGTAT-TTTAACTGTTT
1 TTACTTAATTACCCTGAATTAAGT-TCTTTAACTGTTT
*
21067 TTACTTAATTACCCTGAATTAAGTAT-TTTAACTGCTCT
1 TTACTTAATTACCCTGAATTAAGT-TCTTTAACTG-TTT
* * * *
21105 TTACTTAATTACCCTGAATTAAGTTCTCTGACTATGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGTTT
* * *
21142 TTACTTTATTTCCCTGAATTAAGTTCCTTTGACTG
1 TTACTTAATTACCCTGAATTAAGTT-CTTTAACTG
21177 ACTTATGGAC
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
36 26 0.20
37 67 0.51
38 38 0.29
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.46
Consensus pattern (37 bp):
TTACTTAATTACCCTGAATTAAGTTCTTTAACTGTTT
Found at i:21251 original size:45 final size:45
Alignment explanation
Indices: 21202--21299 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
21192 TCAATTTTCT
*
21202 TGAATTAAGATTTTGATTGACTAT-GTTT-ACTTTTCTTAATTACCC
1 TGAATTAAGATTTTGACTGA-T-TGGTTTGACTTTTCTTAATTACCC
21247 TGAATTAAGATTTTGACTGATTGGTTTGACTTTTCTTAATTACCC
1 TGAATTAAGATTTTGACTGATTGGTTTGACTTTTCTTAATTACCC
21292 TGAATTAA
1 TGAATTAA
21300 ATCCTCTAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
43 1 0.02
44 5 0.10
45 44 0.88
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (45 bp):
TGAATTAAGATTTTGACTGATTGGTTTGACTTTTCTTAATTACCC
Found at i:21322 original size:37 final size:36
Alignment explanation
Indices: 21276--21372 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 36
21266 ATTGGTTTGA
21276 CTTTT-CTTAATTACCCTGAATTAAATCCTCTAACTG
1 CTTTTACTTAATTACCCTGAATTAAAT-CTCTAACTG
* * *
21312 CTTTTACTTAATCACCCTGAATTAAGTTTCTAACTG
1 CTTTTACTTAATTACCCTGAATTAAATCTCTAACTG
*
21348 CTCTTTACTTGATT-CCCTGAATTAA
1 CT-TTTACTTAATTACCCTGAATTAA
21373 GTCCCTGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 26 0.48
37 28 0.52
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (36 bp):
CTTTTACTTAATTACCCTGAATTAAATCTCTAACTG
Found at i:21373 original size:36 final size:37
Alignment explanation
Indices: 21276--21376 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 37
21266 ATTGGTTTGA
* *
21276 CTTTT-CTTAATTACCCTGAATTAAATCCTCTAACTG
1 CTTTTACTTAATCACCCTGAATTAAGTCCTCTAACTG
*
21312 CTTTTACTTAATCACCCTGAATTAAGT-TTCTAACTG
1 CTTTTACTTAATCACCCTGAATTAAGTCCTCTAACTG
* *
21348 CTCTTTACTTGAT-TCCCTGAATTAAGTCC
1 CT-TTTACTTAATCACCCTGAATTAAGTCC
21377 CTGGCTTGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 28 0.50
37 28 0.50
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.42
Consensus pattern (37 bp):
CTTTTACTTAATCACCCTGAATTAAGTCCTCTAACTG
Found at i:21486 original size:40 final size:40
Alignment explanation
Indices: 21427--21535 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
21417 CCCAAACTTG
* *
21427 GACCTTGACTGTACTTTCTTTCCTTAATTACTCAGATTAT
1 GACCTTGACTGTACATTCTTTTCTTAATTACTCAGATTAT
*
21467 GACTTTGACTGTACATTCTTTTCTTAATTACTCAGATTAT
1 GACCTTGACTGTACATTCTTTTCTTAATTACTCAGATTAT
*
21507 GACCTTGACTATACATTCTTTTCTTAATT
1 GACCTTGACTGTACATTCTTTTCTTAATT
21536 CACAGTAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (40 bp):
GACCTTGACTGTACATTCTTTTCTTAATTACTCAGATTAT
Found at i:25604 original size:30 final size:30
Alignment explanation
Indices: 25563--25635 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
25553 CTTGATTCCT
*
25563 CTTGTGCGCATCCCTCCTTGCTCAAATCAA
1 CTTGTGCGCATCCCTCCCTGCTCAAATCAA
*
25593 CTTGTGTGCATCCCTCCCTGCTCAAATCAA
1 CTTGTGCGCATCCCTCCCTGCTCAAATCAA
25623 CTTGTGCGCATCC
1 CTTGTGCGCATCC
25636 TAGCTCTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.37, G:0.15, T:0.30
Consensus pattern (30 bp):
CTTGTGCGCATCCCTCCCTGCTCAAATCAA
Found at i:28413 original size:663 final size:655
Alignment explanation
Indices: 27127--28441 Score: 2450
Period size: 663 Copynumber: 2.0 Consensus size: 655
27117 CATTCTCTTA
* *
27127 TTATTAGGATAAAATAGGGCGTGAAAATACATTATCATTAAAATACAAAATTTATATATATTTAC
1 TTATTAGGATAAAATAGGACGTGAAAATACATTATCATTAAAATACAAAATTTATATATATTAAC
*
27192 CACGTTTAAAAAAGTGTAAAAAAAACATGAAAATGGTAATGGTAGCACTCGAACTCATGAAAAAC
66 CACGTTTAAAAAAGTGTAAAAAAAACATGAAAATGGTAATGGTAGCACTCAAACTCATGAAAAAC
27257 ATTTCTACATTACCTACTCCTACCAAACCATCTAATGTTAACCTTATGAAAACAAATGGTAAGAT
131 ATTTCTACATTACCTACTCCTACCAAACCATCTAATGTTAACCTTATGAAAACAAATGGTAAGAT
*
27322 ATTTTTATTGTAGCTTAAGGCTAGAGTCTAATATGATAGCTTTCACTAAGTGTCTCCTATCATGA
196 ATTTTTATTGTAGCTTAAGGCTAGAGTCTAATATGATAGCTTTCACTAAGTGTCTCCCATCATGA
27387 TAGTCTACATTGAAATAACAATGTGTTTAGAGAATGAAAATTGATTTTTACATAGACTATTACAG
261 TAGTCTACATTGAAATAACAATGTGTTTAGAGAATGAAAATTGATTTTTACATAGACTATTACAG
27452 GTAACGAGTGGATCGAAAATTCCAAATCTCCTTAAAAAGGTAAAAAATCAGAAATTAAGTATGAA
326 GTAACGAGTGGATCGAAAATTCCAAATCTCCTTAAAAAGGTAAAAAATCAGAAATTAAGTATGAA
*
27517 AACGGCCTTTTTTTGATGCGTTCGTCAATATTTTGGGAAATATATTTACAATAGCGGCGTTTGTT
391 AACGGCCTTTTTTTGATGCGTTCGTCAATATTTTGGGAAATATATTTACAATAGCGGCATTTGTT
27582 GTTATAAACGCCTTTATTTAGTGGTGTTTTGGTTTCGAAACGCCGCTATTGGATAATTAGAATTA
456 GTTATAAACGCCTTTATTTAGTGGTGTTTTGGTTTCGAAACGCCGCTATTGGATAATTAGAATTA
27647 CAAAACGATGTCGTTGTGTCTATTACAACCAGCAGATAGATAAAATTCTACCAAGTCTCCTTTTT
521 CAAAACGATGTCGTTGTGTCTATTACAACCAGCAGATAGATAAAATTCTACCAAGTCTCCTTTTT
*
27712 TGTCCTTTCATTCGAAAATTTTCTAGAAGTCTTCCTCTTCCTTTCTCCTTCTCCTTTCCTTCTCT
586 TGTCCTTTCATTCGAAAATTTTCTACAAGTCTTCCTCTTCCTTTCTCCTTCTCCTTTCCTTCTCT
27777 TCCCT
651 TCCCT
27782 TTATTAGGATAAAATAGGACGTGAAAATACATTATCATTAAAATACAAAATTTATATATATTAAC
1 TTATTAGGATAAAATAGGACGTGAAAATACATTATCATTAAAATACAAAATTTATATATATTAAC
27847 CACGTTTAAAAAAGTGTAAAAAGAAAAAAAAACATGAAAATGGTAATGGTAGCACTCAAACTCAT
66 CACGTTTAAAAAAGTGT-------AAAAAAAACATGAAAATGGTAATGGTAGCACTCAAACTCAT
* *
27912 GAAAAACATTTCTACATTACCTTCTCCTACCAAACCATCTAATGTTAACCTTATGAAAACCAATG
124 GAAAAACATTTCTACATTACCTACTCCTACCAAACCATCTAATGTTAACCTTATGAAAACAAATG
* *
27977 TTAAGATATTTTTATTGTAGCTTAAGGTTAGAGTCTAATATGATAGCTTTCACTAAGTGTCTCCC
189 GTAAGATATTTTTATTGTAGCTTAAGGCTAGAGTCTAATATGATAGCTTTCACTAAGTGTCTCCC
*
28042 ATCATGATAGTCTACATTGAAATAACAATGTGTTTAGAGAATGAAAATTGATTTTTACATAGATT
254 ATCATGATAGTCTACATTGAAATAACAATGTGTTTAGAGAATGAAAATTGATTTTTACATAGACT
28107 ATTACAGGTAACGAGTGGATCGAAAATTCCAAATCTCCTTAAAAAAGGTAAAAAATCAGAAATTA
319 ATTACAGGTAACGAGTGGATCGAAAATTCCAAATCTCCTT-AAAAAGGTAAAAAATCAGAAATTA
28172 AGTATGAAAACGGCCTTTTTTTGATGCGTTCGTCAATATTTTGGGAAATATATTTACAATAGCGG
383 AGTATGAAAACGGCCTTTTTTTGATGCGTTCGTCAATATTTTGGGAAATATATTTACAATAGCGG
28237 CATTTGTTGTTATAAACGCCTTTATTTAGTGGTGTTTTGGTTTCGAAACGCCGCTATTGGATAAT
448 CATTTGTTGTTATAAACGCCTTTATTTAGTGGTGTTTTGGTTTCGAAACGCCGCTATTGGATAAT
*
28302 TAGAATTACAAAACGATGTCGTTGTGTCTATTACAACCAGCAGATAGATAAAATTCTGCCAAGTC
513 TAGAATTACAAAACGATGTCGTTGTGTCTATTACAACCAGCAGATAGATAAAATTCTACCAAGTC
28367 TCCTTTTTTGTCCTTTCATTCGAAAATTTTCTACAAGTCTTCCTCTTCCTTTCTCCTTCTCCTTT
578 TCCTTTTTTGTCCTTTCATTCGAAAATTTTCTACAAGTCTTCCTCTTCCTTTCTCCTTCTCCTTT
28432 CCTTCTCTTC
643 CCTTCTCTTC
28442 GCTTCGCTTC
Statistics
Matches: 640, Mismatches: 12, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
655 80 0.12
662 269 0.42
663 291 0.45
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (655 bp):
TTATTAGGATAAAATAGGACGTGAAAATACATTATCATTAAAATACAAAATTTATATATATTAAC
CACGTTTAAAAAAGTGTAAAAAAAACATGAAAATGGTAATGGTAGCACTCAAACTCATGAAAAAC
ATTTCTACATTACCTACTCCTACCAAACCATCTAATGTTAACCTTATGAAAACAAATGGTAAGAT
ATTTTTATTGTAGCTTAAGGCTAGAGTCTAATATGATAGCTTTCACTAAGTGTCTCCCATCATGA
TAGTCTACATTGAAATAACAATGTGTTTAGAGAATGAAAATTGATTTTTACATAGACTATTACAG
GTAACGAGTGGATCGAAAATTCCAAATCTCCTTAAAAAGGTAAAAAATCAGAAATTAAGTATGAA
AACGGCCTTTTTTTGATGCGTTCGTCAATATTTTGGGAAATATATTTACAATAGCGGCATTTGTT
GTTATAAACGCCTTTATTTAGTGGTGTTTTGGTTTCGAAACGCCGCTATTGGATAATTAGAATTA
CAAAACGATGTCGTTGTGTCTATTACAACCAGCAGATAGATAAAATTCTACCAAGTCTCCTTTTT
TGTCCTTTCATTCGAAAATTTTCTACAAGTCTTCCTCTTCCTTTCTCCTTCTCCTTTCCTTCTCT
TCCCT
Found at i:31132 original size:2 final size:2
Alignment explanation
Indices: 31125--31151 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31115 AATACAATGT
31125 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 T
31152 TCAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31339 original size:62 final size:62
Alignment explanation
Indices: 31222--31373 Score: 214
Period size: 62 Copynumber: 2.4 Consensus size: 62
31212 AGCCATAATA
** * * *
31222 GCTATATTTAATTTGAGATTTTTTAAAAAAAAAAAAACCCTTAAATATAGTGGCGTCTAGAGGCC
1 GCTATATTTAATTTGAGATTTTTT---TTATAAAAAACCCTTAAATATAGCGGCGTCTAGACGCC
* *
31287 GTTATTTTTAATTTGAGATTTTTTTTATAAAAAACCCTTAAATATAGCGGCGTCTAGACGCC
1 GCTATATTTAATTTGAGATTTTTTTTATAAAAAACCCTTAAATATAGCGGCGTCTAGACGCC
31349 GCTATATTTAATTTGAGATTTTTTT
1 GCTATATTTAATTTGAGATTTTTTT
31374 AAAACATTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
62 56 0.72
65 22 0.28
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (62 bp):
GCTATATTTAATTTGAGATTTTTTTTATAAAAAACCCTTAAATATAGCGGCGTCTAGACGCC
Found at i:31397 original size:56 final size:60
Alignment explanation
Indices: 31222--31402 Score: 190
Period size: 62 Copynumber: 3.0 Consensus size: 60
31212 AGCCATAATA
* * * * *
31222 GCTATATTTAATTTGAGATTTTTTAAAAAAAAAAAAACCCTTAAATATAGTGGCGTCTAGAGGCC
1 GCTATATTTAATTTGAGATTTTTT-----TATAAAAACCATTAAATATAGCGGCGTCTAGACGCC
* * *
31287 GTTATTTTTAATTTGAGATTTTTTTTATAAAAAACCCTTAAATATAGCGGCGTCTAGACGCC
1 GCTATATTTAATTTGAGA-TTTTTTTAT-AAAAACCATTAAATATAGCGGCGTCTAGACGCC
*
31349 GCTATATTTAATTTGAGA-TTTTTT-T-AAAA-CATTTAATATAGCGGCGTCTAGACG
1 GCTATATTTAATTTGAGATTTTTTTATAAAAACCATTAAATATAGCGGCGTCTAGACG
31403 TGTCGCAACG
Statistics
Matches: 104, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
56 23 0.22
57 4 0.04
59 1 0.01
60 6 0.06
61 1 0.01
62 47 0.45
65 16 0.15
66 6 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (60 bp):
GCTATATTTAATTTGAGATTTTTTTATAAAAACCATTAAATATAGCGGCGTCTAGACGCC
Found at i:31840 original size:35 final size:35
Alignment explanation
Indices: 31799--31970 Score: 220
Period size: 35 Copynumber: 4.9 Consensus size: 35
31789 TAAGCCCTTT
* ** * *
31799 ATTTACTTAATTATACCGAATTAAGCCAACTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG
* * *
31834 ATTTACTTAATTATACTGAATTAAGTTGATTACCG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG
*
31869 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG
* *
31904 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG
* *
31939 ATTTATTTAATTACACCGAATT-ACTTAATTAC
1 ATTTACTTAATTACACCGAATTAAGTTAATTAC
31971 ACCGAATTAA
Statistics
Matches: 121, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
34 8 0.07
35 113 0.93
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACCG
Found at i:31913 original size:16 final size:16
Alignment explanation
Indices: 31862--31917 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
31852 AATTAAGTTG
*
31862 ATTACCGATTTACTTA
1 ATTACCAATTTACTTA
* *
31878 ATTACACCGAATTAAGTTA
1 ATT--ACC-AATTTACTTA
31897 ATTACCAATTTACTTA
1 ATTACCAATTTACTTA
31913 ATTAC
1 ATTAC
31918 ACCGAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 16 0.50
17 3 0.09
18 3 0.09
19 10 0.31
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTACCAATTTACTTA
Found at i:31966 original size:53 final size:54
Alignment explanation
Indices: 31900--32165 Score: 237
Period size: 61 Copynumber: 4.5 Consensus size: 54
31890 TAAGTTAATT
* ** *
31900 ACCAATTTACTTAATTACACCGAATTAAGTTG-ATTACTGATTTATTTAATTAC
1 ACCAAATTACTTAATTACACCGAATTAAGTTGAATTACCAATTTACTTAATTAC
*
31953 ACCGAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTAC
1 ACCAAATTACTTAATTACACCGAATTAAGTTG-------AATTACCAATTTACTTAATTAC
*
32014 ACCAAATTACTTAATTACACCGAATTAAGTTATTTACCAAATTACCAATTTACTTAATTAC
1 ACCAAATTACTTAATTACACCGAATTAAG----TT---GAATTACCAATTTACTTAATTAC
*
32075 ACCAAATTACTTAATTACACCGAATTAAATTGTTTACCAAATTACCAATTTACTTAATTTAATC
1 ACCAAATTACTTAATTACACCGAATT-AA--G-TT---GAATTACCAATTTACTTAA-TT-A-C
*
32139 ACCAATTTACTTAATTACACCGAATTA
1 ACCAAATTACTTAATTACACCGAATTA
32166 CTTAATTACA
Statistics
Matches: 184, Mismatches: 8, Indels: 32
0.82 0.04 0.14
Matches are distributed among these distances:
53 30 0.16
61 119 0.65
62 4 0.02
63 2 0.01
64 27 0.15
65 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (54 bp):
ACCAAATTACTTAATTACACCGAATTAAGTTGAATTACCAATTTACTTAATTAC
Found at i:31968 original size:18 final size:18
Alignment explanation
Indices: 31865--32183 Score: 143
Period size: 18 Copynumber: 16.5 Consensus size: 18
31855 TAAGTTGATT
*
31865 ACCGATTTACTTAATTAC
1 ACCGAATTACTTAATTAC
*
31883 ACCGAATTAAGTTAATT--
1 ACCGAATT-ACTTAATTAC
31900 ACC-AATTTACTTAATTAC
1 ACCGAA-TTACTTAATTAC
* *
31918 ACCGAATTAAGTTGATT--
1 ACCGAATT-ACTTAATTAC
* * *
31935 ACTGATTTATTTAATTAC
1 ACCGAATTACTTAATTAC
31953 ACCGAATTACTTAATTAC
1 ACCGAATTACTTAATTAC
* **
31971 ACCGAATTAAGTTGTTTACC
1 ACCGAATT-ACTTAATTA-C
31991 AAATTACC-AATTTACTTAATTAC
1 -----ACCGAA-TTACTTAATTAC
*
32014 ACCAAATTACTTAATTAC
1 ACCGAATTACTTAATTAC
* *
32032 ACCGAATTAAGTTATTTACC
1 ACCGAATT-ACTTAATTA-C
32052 AAATTACC-AATTTACTTAATTAC
1 -----ACCGAA-TTACTTAATTAC
*
32075 ACCAAATTACTTAATTAC
1 ACCGAATTACTTAATTAC
* **
32093 ACCGAATTAAATTGTTTACC
1 ACCGAATT-ACTTAATTA-C
32113 AAATTACC-AATTTACTTAATTTAATC
1 -----ACCGAA-TTACTTAA-TT-A-C
32139 ACC-AATTTACTTAATTAC
1 ACCGAA-TTACTTAATTAC
32157 ACCGAATTACTTAATTAC
1 ACCGAATTACTTAATTAC
32175 ACCGAATTA
1 ACCGAATTA
32184 AGTTGTTTAC
Statistics
Matches: 233, Mismatches: 31, Indels: 74
0.69 0.09 0.22
Matches are distributed among these distances:
16 15 0.06
17 11 0.05
18 104 0.45
19 41 0.18
20 5 0.02
21 14 0.06
23 2 0.01
24 22 0.09
25 17 0.07
26 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (18 bp):
ACCGAATTACTTAATTAC
Found at i:31997 original size:61 final size:61
Alignment explanation
Indices: 31939--32269 Score: 434
Period size: 61 Copynumber: 5.4 Consensus size: 61
31929 TTGATTACTG
* *
31939 ATTTATTTAATTACACCGAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
1 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
*
32000 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTATTTACCAAATTACCA
1 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
*
32061 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAATTGTTTACCAAATTACCA
1 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
* * * * * *
32122 ATTTACTTAATTTAATCACCAATTTACTTAATTACACCGAATT-ACTTAATTACACCGAATTAAG
1 ATTTACTTAA-TT-A-CACCAAATTACTTAATTACACCGAATTAAGTT-GTT-TACCAAATT-AC
**
32186 TT
60 CA
* ** *
32188 GTTTACCAAATT--ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
1 ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
*
32247 ATTCACTTAATTACACCAAATTA
1 ATTTACTTAATTACACCAAATTA
32270 AGTTGTTTAC
Statistics
Matches: 233, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
59 9 0.04
60 7 0.03
61 163 0.70
62 5 0.02
63 4 0.02
64 28 0.12
65 9 0.04
66 8 0.03
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (61 bp):
ATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
Found at i:32007 original size:43 final size:43
Alignment explanation
Indices: 31959--32646 Score: 613
Period size: 43 Copynumber: 15.9 Consensus size: 43
31949 TTACACCGAA
31959 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* * **
32002 TTACTTAATTACACCAAATT-ACTTAATTA-C-----ACCGAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACC-AAT
* * * * **** ** *
32039 TAAGTT-ATT-TACCAAATT-ACCAATTTACTTAATTACACCAAA
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATT--ACCAAT
*
32081 TTACTTAATTACACCGAATTAAATTGTTTACCAAATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* * **
32124 TTACTTAATTTAATCACC-AATTTACTTAATTA-C-----ACCGAA-
1 TTACTTAA-TT-A-CACCGAATTAAGTTGTTTACCAAATTACC-AAT
32163 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
32206 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* *
32249 TCACTTAATTACACCAAATTAAGTTGTTTACCAAATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* *
32292 TTACTTAATTACACCGAATTAAGTTGATTACCAACTTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* * *
32335 TTACTTAATTGCACCGAATTAAGTTGTCTACCAGATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
*
32378 TTACTTAATTACACCAAATTAAGTTGTTTACC-AATTGACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATT-ACCAAT
* * ** **
32421 TTACTTAATTACACTGAATTAAGTTGATTACCATCTTACTTGAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC-CAAT
* *
32465 TTACTCAATTACACCGAATTAAGTCGTTTACCAAATTACTTAATTTAATCACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAAT
* * *
32521 TTACTTAATTACACCGAATTAAGTTGATTACCAACTGACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* ** **
32564 TTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTGAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC-CAAT
* **
32608 TTACTCAATTACACCGAATTAAGTCATTTACCAAATTAC
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
32647 TTAATTTAAT
Statistics
Matches: 528, Mismatches: 76, Indels: 81
0.77 0.11 0.12
Matches are distributed among these distances:
35 14 0.03
36 10 0.02
37 18 0.03
38 3 0.01
39 11 0.02
40 2 0.00
41 1 0.00
42 17 0.03
43 311 0.59
44 77 0.15
45 21 0.04
46 5 0.01
48 1 0.00
49 1 0.00
51 1 0.00
54 1 0.00
56 32 0.06
57 2 0.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (43 bp):
TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
Found at i:32265 original size:143 final size:142
Alignment explanation
Indices: 31991--32312 Score: 375
Period size: 143 Copynumber: 2.2 Consensus size: 142
31981 GTTGTTTACC
* *
31991 AAATTACCAATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAGTTATTTACCAAAT
1 AAATCACCAATTTACTTAATTACACCGAATTACTTAATTACACCGAATTAAGTTATTTACCAAAT
* *
32056 TACCAATTTACTTAATTACACCAAATTACTTAATTACACCGAATTAAATTGTTTACCAAATTACC
66 TACCAATTTACTTAATTACACCAAATTACTTAATTACACCAAATTAAA-T-TTCACCAAATTACC
*
32121 -AATTTACTTAATTT
129 AAATTAACTT-ATTT
*
32135 -AATCACCAATTTACTTAATTACACCGAATTACTTAATTACACCGAATTAAGTTGTTTACCAAAT
1 AAATCACCAATTTACTTAATTACACCGAATTACTTAATTACACCGAATTAAGTTATTTACCAAAT
* * * * **
32199 TACCAATTTACTTAATTACACCGAATTAAGTT-GTT-TACCAAATTACCAA-TTCACTTAATTAC
66 TACCAATTTACTTAATTACACCAAATT-ACTTAATTACACCAAATTA--AATTTCACCAAATT--
* *
32261 ACCAAATTAAGTTGTTT
126 ACCAAATTAACTTATTT
*
32278 ACCAAATTACCAATTTACTTAATTACACCGAATTA
1 ---AAATCACCAATTTACTTAATTACACCGAATTA
32313 AGTTGATTAC
Statistics
Matches: 153, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
141 8 0.05
142 8 0.05
143 95 0.62
144 12 0.08
147 30 0.20
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (142 bp):
AAATCACCAATTTACTTAATTACACCGAATTACTTAATTACACCGAATTAAGTTATTTACCAAAT
TACCAATTTACTTAATTACACCAAATTACTTAATTACACCAAATTAAATTTCACCAAATTACCAA
ATTAACTTATTT
Found at i:32534 original size:143 final size:143
Alignment explanation
Indices: 32372--32699 Score: 611
Period size: 143 Copynumber: 2.3 Consensus size: 143
32362 CTACCAGATT
* * *
32372 ACCAATTTACTTAATTACACCAAATTAAGTTGTTTACCAATTGACCAATTTACTTAATTACACTG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATTGACCAATTTACTTAATTACACCG
*
32437 AATTAAGTTGATTACCATCTTACTTGATTTACTCAATTACACCGAATTAAGTCGTTTACCAAATT
66 AATTAAGTTGATTACCATCTTACTTGATTTACTCAATTACACCGAATTAAGTCATTTACCAAATT
32502 ACTTAATTTAATC
131 ACTTAATTTAATC
*
32515 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAACTGACCAATTTACTTAATTACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATTGACCAATTTACTTAATTACACCG
32580 AATTAAGTTGATTACCATCTTACTTGATTTACTCAATTACACCGAATTAAGTCATTTACCAAATT
66 AATTAAGTTGATTACCATCTTACTTGATTTACTCAATTACACCGAATTAAGTCATTTACCAAATT
32645 ACTTAATTTAATC
131 ACTTAATTTAATC
32658 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATT
32700 TACTTAATCA
Statistics
Matches: 179, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 179 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (143 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAATTGACCAATTTACTTAATTACACCG
AATTAAGTTGATTACCATCTTACTTGATTTACTCAATTACACCGAATTAAGTCATTTACCAAATT
ACTTAATTTAATC
Found at i:32550 original size:19 final size:19
Alignment explanation
Indices: 32528--32594 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
32518 AATTTACTTA
32528 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
* * * *
32547 ATTACCAACTGACCAATTTACTTA
1 ATTA-C-AC---CGAATTAAGTTG
32571 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
32590 ATTAC
1 ATTAC
32595 CATCTTACTT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 17 0.49
20 1 0.03
21 2 0.06
22 2 0.06
23 1 0.03
24 12 0.34
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (19 bp):
ATTACACCGAATTAAGTTG
Found at i:32693 original size:19 final size:19
Alignment explanation
Indices: 32671--32729 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
32661 AATTTACTTA
32671 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
* * *
32690 ATT--ACC-AATTTACTTA
1 ATTACACCGAATTAAGTTG
*
32706 ATCACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
32725 ATTAC
1 ATTAC
32730 CAACTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 9 0.31
17 3 0.10
18 3 0.10
19 14 0.48
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (19 bp):
ATTACACCGAATTAAGTTG
Found at i:32697 original size:35 final size:35
Alignment explanation
Indices: 32658--32732 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
32648 TAATTTAATC
*
32658 ACCAATTTACTTAATTACACCGAATTAAGTTGATT
1 ACCAATTTACTTAATCACACCGAATTAAGTTGATT
32693 ACCAATTTACTTAATCACACCGAATTAAGTTGATT
1 ACCAATTTACTTAATCACACCGAATTAAGTTGATT
32728 ACCAA
1 ACCAA
32733 CTGATTTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (35 bp):
ACCAATTTACTTAATCACACCGAATTAAGTTGATT
Found at i:33707 original size:54 final size:50
Alignment explanation
Indices: 33511--33943 Score: 252
Period size: 50 Copynumber: 8.4 Consensus size: 50
33501 AACTAATCAA
* ** * * * * *
33511 TTTATTTACTAATGGCTTAAAAGTTCAAACTTTAATTCAAAGGTGACA-T
1 TTTACTTACTAATTACTAAAAAATTCAATCTTTTAGTCAAAGGTGACATT
* * * * *
33560 TTTATTTACCAATTACTAAAAAAAAATTCAATCTTTTATTCAAAGG-GTATATC
1 TTTACTTACTAATTACT---AAAAAATTCAATCTTTTAGTCAAAGGTG-ACATT
* * *
33613 CTTATTTACTAATTACTTAAAAATTCAATCTTTT-GCTCAAAGGTGACATT
1 TTTACTTACTAATTACTAAAAAATTCAATCTTTTAG-TCAAAGGTGACATT
* * *
33663 TTTACTTACTCATTACTAAAAAAAAAATTCAATCTTTTAGTCAAAAGGTTACATC
1 TTTACTTACTAATTACT----AAAAAATTCAATCTTTTAGTC-AAAGGTGACATT
* * * *
33718 TTTATTTACTAATTACTTAAAAAAAAAATCAATCTTTT-GCTCCAAGGTGACATC
1 TTTACTTACTAATTAC-T---AAAAAATTCAATCTTTTAG-TCAAAGGTGACATT
* * ** ** * *
33772 TTTACTTATTAATCACTAAAAGTTTCAATCTTTTACCCAAAGATAACATT
1 TTTACTTACTAATTACTAAAAAATTCAATCTTTTAGTCAAAGGTGACATT
* ** * *
33822 TTGACTTACTAATTACT-AAAAATTCAATCTTTTACCCAAAGATGGCATT
1 TTTACTTACTAATTACTAAAAAATTCAATCTTTTAGTCAAAGGTGACATT
* *** *
33871 TTTACTTACTAACTCACTTGGAAA-TCTAAT-TTTTTGCTCAAAGGTGACATT
1 TTTACTTACTAA-TTACTAAAAAATTC-AATCTTTTAG-TCAAAGGTGACATT
* *
33922 TTTATTTAC-AACATACTAAAAA
1 TTTACTTACTAA-TTACTAAAAA
33944 TTTCTCCTTC
Statistics
Matches: 304, Mismatches: 60, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
49 53 0.17
50 95 0.31
51 27 0.09
52 24 0.08
53 16 0.05
54 42 0.14
55 46 0.15
56 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (50 bp):
TTTACTTACTAATTACTAAAAAATTCAATCTTTTAGTCAAAGGTGACATT
Found at i:33740 original size:55 final size:54
Alignment explanation
Indices: 33529--33792 Score: 260
Period size: 55 Copynumber: 5.0 Consensus size: 54
33519 CTAATGGCTT
* * * * *
33529 AAAAGTTCAAACTTTAATTCAAAGGTGACAT-TTTATTTACCAATTAC-TAAAA
1 AAAAATTCAATCTTTTAGTCAAAGGTGACATCTTTATTTACTAATTACTTAAAA
* * *
33581 AAAAATTCAATCTTTTATTCAAAGG-GTATATCCTTATTTACTAATTACTT----
1 AAAAATTCAATCTTTTAGTCAAAGGTG-ACATCTTTATTTACTAATTACTTAAAA
* * * *
33631 AAAAATTCAATCTTTT-GCTCAAAGGTGACATTTTTACTTACTCATTACTAAAAA
1 AAAAATTCAATCTTTTAG-TCAAAGGTGACATCTTTATTTACTAATTACTTAAAA
*
33685 AAAAATTCAATCTTTTAGTCAAAAGGTTACATCTTTATTTACTAATTACTTAAAA
1 AAAAATTCAATCTTTTAGTC-AAAGGTGACATCTTTATTTACTAATTACTTAAAA
* * * * *
33740 AAAAAATCAATCTTTT-GCTCCAAGGTGACATCTTTACTTATTAATCAC-TAAAA
1 AAAAATTCAATCTTTTAG-TCAAAGGTGACATCTTTATTTACTAATTACTTAAAA
33793 GTTTCAATCT
Statistics
Matches: 176, Mismatches: 24, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
50 40 0.23
51 2 0.01
52 25 0.14
53 19 0.11
54 43 0.24
55 47 0.27
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (54 bp):
AAAAATTCAATCTTTTAGTCAAAGGTGACATCTTTATTTACTAATTACTTAAAA
Found at i:33790 original size:109 final size:103
Alignment explanation
Indices: 33547--33792 Score: 323
Period size: 109 Copynumber: 2.3 Consensus size: 103
33537 AAACTTTAAT
* * * *
33547 TCAAAGGTGACATTTTATTTACCAATTACT-AAAAAAAAATTCAATCTTTTATTCAAAGGGTATA
1 TCAAAGGTGACATTTTACTTACTAATTACTAAAAAAAAAATTCAATCTTTTAGTCAAAGGGTACA
*
33611 TCCTTATTTACTAATTACTTAAAAATTCAATCTTTTGC
66 TCCTTATTTACTAATTACTTAAAAAATCAATCTTTTGC
* *
33649 TCAAAGGTGACATTTTTACTTACTCATTACTAAAAAAAAAATTCAATCTTTTAGTCAAAAGGTTA
1 TCAAAGGTGACA-TTTTACTTACTAATTACTAAAAAAAAAATTCAATCTTTTAGTC-AAAGGGTA
*
33714 CATCTTTATTTACTAATTACTTAAAAAAAAAATCAATCTTTTGC
64 CATCCTTATTTACTAATTACTT----AAAAAATCAATCTTTTGC
* * *
33758 TCCAAGGTGACATCTTTACTTATTAATCACTAAAA
1 TCAAAGGTGACAT-TTTACTTACTAATTACTAAAA
33793 GTTTCAATCT
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
102 12 0.10
103 15 0.12
104 23 0.19
105 27 0.22
108 1 0.01
109 46 0.37
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (103 bp):
TCAAAGGTGACATTTTACTTACTAATTACTAAAAAAAAAATTCAATCTTTTAGTCAAAGGGTACA
TCCTTATTTACTAATTACTTAAAAAATCAATCTTTTGC
Found at i:33805 original size:159 final size:157
Alignment explanation
Indices: 33549--33843 Score: 378
Period size: 159 Copynumber: 1.9 Consensus size: 157
33539 ACTTTAATTC
* * *
33549 AAAGGTGACATTTTATTTACCAATTACTAAAAAAAAATTCAATCTTTTATTCAAAGGGTATATCC
1 AAAGGTGACATTTTATTTACCAATTACTAAAAAAAAAATCAATCTTTTACTCAAAGGGTACATCC
* * * * * * * *
33614 TTATTTACTAATTACTTAAAAATTCAATCTTTTGCTCAAAGGTGACATTTTTACTTACTCATTAC
66 TTACTTACTAATCACTTAAAAATTCAATCTTTTACCCAAAGATAACATTTTGACTTACTAATTAC
33679 TAAAAAAAAAATTCAATCTTTTAGTCA
131 TAAAAAAAAAATTCAATCTTTTAGTCA
* * * *
33706 AAAGGTTACATCTTTATTTACTAATTACTTAAAAAAAAAATCAATCTTTTGCTCCAA-GGTGACA
1 AAAGGTGACAT-TTTATTTACCAATTAC-TAAAAAAAAAATCAATCTTTTACTCAAAGGGT-ACA
* * *
33770 TCTTTACTTATTAATCAC-TAAAAGTTTCAATCTTTTACCCAAAGATAACATTTTGACTTACTAA
63 TCCTTACTTACTAATCACTTAAAA-ATTCAATCTTTTACCCAAAGATAACATTTTGACTTACTAA
33834 TTACTAAAAA
127 TTACTAAAAA
33844 TTCAATCTTT
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
157 10 0.09
158 23 0.20
159 83 0.72
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (157 bp):
AAAGGTGACATTTTATTTACCAATTACTAAAAAAAAAATCAATCTTTTACTCAAAGGGTACATCC
TTACTTACTAATCACTTAAAAATTCAATCTTTTACCCAAAGATAACATTTTGACTTACTAATTAC
TAAAAAAAAAATTCAATCTTTTAGTCA
Found at i:39735 original size:15 final size:17
Alignment explanation
Indices: 39715--39755 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
39705 TCACTTCATA
39715 AAAAAAAACA-AAAC-C
1 AAAAAAAACACAAACTC
39730 AAAAAAAA-ACAAACTC
1 AAAAAAAACACAAACTC
39746 ATAAAAAAAC
1 A-AAAAAAAC
39756 CTCTACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 2 0.09
17 7 0.32
ACGTcount: A:0.78, C:0.17, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAACACAAACTC
Found at i:39735 original size:16 final size:16
Alignment explanation
Indices: 39714--39755 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
39704 CTCACTTCAT
39714 AAAAAAAAACAAAAC-C
1 AAAAAAAAAC-AAACTC
39730 AAAAAAAAACAAACTC
1 AAAAAAAAACAAACTC
*
39746 ATAAAAAAAC
1 AAAAAAAAAC
39756 CTCTACCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.79, C:0.17, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAAAAAACAAACTC
Found at i:40211 original size:11 final size:12
Alignment explanation
Indices: 40195--40237 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
40185 TTTGACCTTT
40195 AATTATA-AAAA
1 AATTATATAAAA
40206 AATTATATAAAA
1 AATTATATAAAA
** *
40218 AAAAATTTAAAA
1 AATTATATAAAA
40230 AATTATAT
1 AATTATAT
40238 TTTGATTAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTATATAAAA
Found at i:41210 original size:40 final size:39
Alignment explanation
Indices: 41132--41210 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
41122 ATTAATGACT
* *
41132 TTCTTTTCTTAATTAAATTTTCTTAAAAACACTTATAAA
1 TTCTTTTCTTAACTAAATTTTCTTAAAAACACTCATAAA
*
41171 TTCTATTTCTTAACTGAATTTTCTTAAAAGA-ACTCATAAA
1 TTCT-TTTCTTAACTAAATTTTCTTAAAA-ACACTCATAAA
41211 ATAAAACAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 4 0.11
40 30 0.86
41 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (39 bp):
TTCTTTTCTTAACTAAATTTTCTTAAAAACACTCATAAA
Found at i:47977 original size:165 final size:162
Alignment explanation
Indices: 47765--48228 Score: 660
Period size: 154 Copynumber: 2.9 Consensus size: 162
47755 AAACATAGCG
* *
47765 TTTTAGTAGAATAAAATTATAAAAGTTTAAACAATATCATTTAAGAAATATATTTAAACAATTCT
1 TTTTAGTAGAATAAAACTATAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAA-AATTCT
*
47830 AATATATCTAAGTTTTTTAATTAAAATAATAAAATGATATAAGTAAAATAGTTATAAAGATATTA
65 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATG-TATAA-TAAAATAGTTATAAAGATATTA
* *
47895 GATTTAATTAAATAAATATTAAATAGATCTGAAGT
128 GATTTAATTAAATAAATATTAAATAAATATGAAGT
* * *
47930 TTTTAGTAGAACAAAACTGTAAAAGTTTAAACAATGTCATGTAAGAAATATATTTAAAAATTCTA
1 TTTTAGTAGAATAAAACTATAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAAAATTCTA
47995 ATATATCTAAGTTTTTTTAATTAAAATAGTAAAATG-AT-AT---A-AG---TAAAGATATTAGA
66 ATATATCTAAG-TTTTTTAATTAAAATAGTAAAATGTATAATAAAATAGTTATAAAGATATTAGA
*
48051 TTTAATTAAATAAATATTAAATAAATATGGAGT
130 TTTAATTAAATAAATATTAAATAAATATGAAGT
*
48084 TTTTAGTAGAATAAAACTTTAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAGAAA-TCT
1 TTTTAGTAGAATAAAACTATAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAA-AAATTCT
* * *
48148 AATATATCTAAGTTTTTTTATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATGA
65 AATATATCTAAGTTTTTTAATTAAAATAGTAAAAT-GT-ATAATAAAATAGTTATAAAGATATTA
* *
48213 AATTTAATAAAATAAA
128 GATTTAATTAAATAAA
48229 AGTAGATCTT
Statistics
Matches: 269, Mismatches: 17, Indels: 27
0.86 0.05 0.09
Matches are distributed among these distances:
153 22 0.08
154 113 0.42
155 3 0.01
156 1 0.00
157 4 0.01
158 1 0.00
160 1 0.00
161 3 0.01
162 1 0.00
163 2 0.01
164 42 0.16
165 76 0.28
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (162 bp):
TTTTAGTAGAATAAAACTATAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAAAATTCTA
ATATATCTAAGTTTTTTAATTAAAATAGTAAAATGTATAATAAAATAGTTATAAAGATATTAGAT
TTAATTAAATAAATATTAAATAAATATGAAGT
Found at i:48162 original size:77 final size:77
Alignment explanation
Indices: 47916--48164 Score: 201
Period size: 77 Copynumber: 3.2 Consensus size: 77
47906 ATAAATATTA
* * *
47916 AATAGATCTGAAGTTTTTAGTAGAACAAAACTGTAAAAGTTTAAACAATGTCATGTAAGAAATAT
1 AATATATCTGAAGTTTTTAGTAGAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATAT
47981 ATTTAAAAATTCT
66 ATTTAAAAA-TCT
* * * ** * *
47994 AATATATCT-AAGTTTTT-TTA-ATTAAAA-TAGTAAAATGATATAAGTAAAG--ATATT-AGAT
1 AATATATCTGAAGTTTTTAGTAGAATAAAACT-GTAAAA-G-TTTAAACAATGTCAT-TTAAGAA
* * *
48052 TTA-ATTAAATAAATATT
62 ATATATTTAA-AAAT-CT
* * * *
48069 AAATAAATATGGAGTTTTTAGTAGAATAAAACTTTAAAAGTTTAAACAATGTCATTTAAGAAATA
1 -AATATATCTGAAGTTTTTAGTAGAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATA
48134 TATTTAAGAAATCT
65 TATTTAA-AAATCT
48148 AATATATCT-AAGTTTTT
1 AATATATCTGAAGTTTTT
48165 TTATTAAAAT
Statistics
Matches: 125, Mismatches: 31, Indels: 31
0.67 0.17 0.17
Matches are distributed among these distances:
74 7 0.06
75 22 0.18
76 11 0.09
77 36 0.29
78 20 0.16
79 19 0.15
80 10 0.08
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (77 bp):
AATATATCTGAAGTTTTTAGTAGAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATAT
ATTTAAAAATCT
Found at i:48279 original size:153 final size:153
Alignment explanation
Indices: 47883--48289 Score: 436
Period size: 154 Copynumber: 2.6 Consensus size: 153
47873 TAAAATAGTT
*** * * * *
47883 ATAAAGATATTAGATTTAATTAAATAAATATTAAATAGATCT-GAAGTTTTTAGTAGAACAAAAC
1 ATAAAGATATTAGAAAGAATGAAATAAATA-TAAATAAATATAG-AGTTTTTAGTAGAATAAAAC
** *
47947 TGTAAAAGTTTAAACAATGTCATGTAAGAAATATATTTAAAAATTCTAATATATCTAAGTTTTTT
64 TAAAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAAAATTCTAATATATCTAAGTTTTTT
*
48012 TAATTAAAATAGTAAAATGATATAA
129 TAATTAAAATAGTAAAATGATAAAA
* *** * *
48037 GTAAAGATATTAGATTTAATTAAATAAATATTAAATAAATATGGAGTTTTTAGTAGAATAAAACT
1 ATAAAGATATTAGAAAGAATGAAATAAATA-TAAATAAATATAGAGTTTTTAGTAGAATAAAACT
**
48102 TTAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAGAAA-TCTAATATATCTAAGTTTTTT
65 AAAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAA-AAATTCTAATATATCTAAGTTTTTT
*
48166 T-ATTAAAATAGTAAAATGGTAAAA
129 TAATTAAAATAGTAAAATGATAAAA
* * *
48190 ATAAA-ATAGTTATAAAGATATGAAATTTAATA-AAATAAA-AGTAGA-TCTTTTAGTTA-AGTA
1 ATAAAGATA-TTAGAAAGA-ATGAAA-TAAATATAAATAAATA-TAGAGT-TTTTAG-TAGAATA
*
48250 AAACTAAAAAAGATTAAACAATGGT-ATTTAAGAAATATAT
60 AAACTAAAAAAGTTTAAACAAT-GTCATTTAAGAAATATAT
48290 CTGAAAAAAT
Statistics
Matches: 224, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
152 5 0.02
153 83 0.37
154 127 0.57
155 9 0.04
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (153 bp):
ATAAAGATATTAGAAAGAATGAAATAAATATAAATAAATATAGAGTTTTTAGTAGAATAAAACTA
AAAAAGTTTAAACAATGTCATTTAAGAAATATATTTAAAAATTCTAATATATCTAAGTTTTTTTA
ATTAAAATAGTAAAATGATAAAA
Found at i:48816 original size:22 final size:22
Alignment explanation
Indices: 48790--48915 Score: 90
Period size: 22 Copynumber: 5.7 Consensus size: 22
48780 AACTACTTGT
**
48790 TTATCAAAATTTCATAGTGTTC
1 TTATCAAAATTTCATAGTGAAC
* * * * *
48812 TTATCAATATTCCACAGGGAAG
1 TTATCAAAATTTCATAGTGAAC
* * *
48834 TTATCAATATTTCGTAGTGTAC
1 TTATCAAAATTTCATAGTGAAC
* **
48856 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAAC
* * **
48878 TTATTAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAAC
*
48900 TTATGAAAATTTCATA
1 TTATCAAAATTTCATA
48916 TAAGAAGGCT
Statistics
Matches: 81, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 81 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAAC
Found at i:48840 original size:44 final size:44
Alignment explanation
Indices: 48790--48894 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
48780 AACTACTTGT
* * *
48790 TTATCAAAATTTCATAGTGTTCTTATCAATATTCCACAGGGAAG
1 TTATCAAAATTTCATAGTGTACTTATCAAAATTCCACAAGGAAG
* * * * * *
48834 TTATCAATATTTCGTAGTGTACTTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGTACTTATCAAAATTCCACAAGGAAG
*
48878 TTATTAAAATTTCATAG
1 TTATCAAAATTTCATAG
48895 GGAGGTTATG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGTACTTATCAAAATTCCACAAGGAAG
Found at i:48940 original size:24 final size:22
Alignment explanation
Indices: 48905--48963 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
48895 GGAGGTTATG
* *
48905 AAAATTTCATATAAGAAGGCTATC
1 AAAATTT-A-ATATGAAGGCTAAC
*
48929 AAAATTTAATATGGAGGCTAAC
1 AAAATTTAATATGAAGGCTAAC
*
48951 AAAATTTTATATG
1 AAAATTTAATATG
48964 GAGGTTCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 23 0.74
23 1 0.03
24 7 0.23
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (22 bp):
AAAATTTAATATGAAGGCTAAC
Found at i:48945 original size:46 final size:44
Alignment explanation
Indices: 48856--48957 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 44
48846 CGTAGTGTAC
* * * *
48856 TTATCAAAATTTCATAATGAGGTTATTAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAAAGAGGCTATCAAAATTTAATAGGGAGG
* *
48900 TTATGAAAATTTCATATAAGAAGGCTATCAAAATTTAATATGGAGG
1 TTATCAAAATTTCATA-AAG-AGGCTATCAAAATTTAATAGGGAGG
* *
48946 CTAACAAAATTT
1 TTATCAAAATTT
48958 TATATGGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 15 0.32
45 2 0.04
46 30 0.64
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCATAAAGAGGCTATCAAAATTTAATAGGGAGG
Found at i:48953 original size:22 final size:22
Alignment explanation
Indices: 48921--48967 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
48911 TCATATAAGA
*
48921 AGGCTATCAAAATTTAATATGG
1 AGGCTAACAAAATTTAATATGG
*
48943 AGGCTAACAAAATTTTATATGG
1 AGGCTAACAAAATTTAATATGG
48965 AGG
1 AGG
48968 TTCTCGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (22 bp):
AGGCTAACAAAATTTAATATGG
Found at i:49014 original size:22 final size:21
Alignment explanation
Indices: 48989--49057 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
48979 CTAAATATCA
48989 CATAGCATCATTATCAAAATTT
1 CATAGCAT-ATTATCAAAATTT
* * *
49011 CATAGCGATGTCATTAAAATTT
1 CATAGC-ATATTATCAAAATTT
**
49033 CATAGTTTGATTATCAAAATTT
1 CATAGCAT-ATTATCAAAATTT
49055 CAT
1 CAT
49058 GTACAGTGAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 34 0.92
23 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
CATAGCATATTATCAAAATTT
Done.