Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017250.1 Corchorus olitorius cultivar O-4 contig17283, 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: 57653
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6475 original size:41 final size:41
Alignment explanation
Indices: 6430--6524 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
6420 GTTTTCACCT
* *
6430 TAGTCCCTGATTTAGTATCTCATTTACT-TTATGATGCAATC
1 TAGTCCCTGATTTAGGATCTCAGTTACTATT-TGATGCAATC
* * * *
6471 TAGTCCCTGATTTAGGATTTTAGTTACTATTTGATTCAATT
1 TAGTCCCTGATTTAGGATCTCAGTTACTATTTGATGCAATC
6512 TAGTCCCTGATTT
1 TAGTCCCTGATTT
6525 TAGAAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (41 bp):
TAGTCCCTGATTTAGGATCTCAGTTACTATTTGATGCAATC
Found at i:11297 original size:11 final size:11
Alignment explanation
Indices: 11281--11306 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11271 AGATAATTTC
11281 TTTTCTTCTAG
1 TTTTCTTCTAG
11292 TTTTCTTCTAG
1 TTTTCTTCTAG
11303 TTTT
1 TTTT
11307 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:12096 original size:15 final size:15
Alignment explanation
Indices: 12066--12107 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
12056 TTACTCTGCT
12066 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
12082 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
12097 TTGCTTTCTGT
1 TTGTTTTCTGT
12108 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:12421 original size:26 final size:25
Alignment explanation
Indices: 12392--12445 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
12382 TTTTTAATCT
12392 AAAAAAAATT-TTT-TGCGTCATATA
1 AAAAAAAATTGTTTCTGCGTCATA-A
12416 AAAAAAAATTGTTTCTGCGTCATAA
1 AAAAAAAATTGTTTCTGCGTCATAA
12441 AAAAA
1 AAAAA
12446 GTTTTTGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 10 0.36
25 9 0.32
26 9 0.32
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (25 bp):
AAAAAAAATTGTTTCTGCGTCATAA
Found at i:12491 original size:26 final size:24
Alignment explanation
Indices: 12392--12495 Score: 81
Period size: 26 Copynumber: 4.3 Consensus size: 24
12382 TTTTTAATCT
*
12392 AAAAAAAATTTTTTGCGTCATATAA
1 AAAAAAAAGTTTTTGCGTCATA-AA
* *
12417 AAAAAAATTGTTTCTGCGTCAT---
1 AAAAAAA-AGTTTTTGCGTCATAAA
** *
12439 -AAAAAAAGTTTTTGCGTTTTTCTAA
1 AAAAAAAAGTTTTTGCG-TCAT-AAA
*
12464 AAAAAAGAGTTTTTGCGTCATAAA
1 AAAAAAAAGTTTTTGCGTCATAAA
12488 AAAAAAAA
1 AAAAAAAA
12496 AATTTTGTGT
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
20 8 0.13
21 8 0.13
24 9 0.15
25 9 0.15
26 26 0.43
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.34
Consensus pattern (24 bp):
AAAAAAAAGTTTTTGCGTCATAAA
Found at i:15724 original size:21 final size:21
Alignment explanation
Indices: 15681--15735 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
15671 CGCCTATTCA
***
15681 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGACCAAGC
*
15702 CCGTGCCACCACCGACCATGC
1 CCGTGCCACCACCGACCAAGC
*
15723 CCGTGCCATCACC
1 CCGTGCCACCACC
15736 ATTCCAAGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGACCAAGC
Found at i:18243 original size:11 final size:11
Alignment explanation
Indices: 18227--18252 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18217 AGATAATTTC
18227 TTTTCTTCTAG
1 TTTTCTTCTAG
18238 TTTTCTTCTAG
1 TTTTCTTCTAG
18249 TTTT
1 TTTT
18253 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:19033 original size:16 final size:16
Alignment explanation
Indices: 19012--19052 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
19002 TTACTCTGCT
19012 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
19028 TTGTTTTAT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
19043 TTGCTTTCTA
1 TTGTTTTCTA
19053 TCAATCTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.63
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:24858 original size:5 final size:6
Alignment explanation
Indices: 24835--24864 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
24825 GTTCCCATTC
24835 GAAAGAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAA-AA GAAAAA GAAAAA GAAAAA GAAAA
24865 CTTGGCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:34989 original size:16 final size:15
Alignment explanation
Indices: 34968--35009 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
34958 TTACTCTGCT
*
34968 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTGAA
34984 TTGTTTTCTGTTGAA
1 TTGTTTTCTGTTGAA
*
34999 TTGCTTTCTGT
1 TTGTTTTCTGT
35010 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTGAA
Found at i:35431 original size:30 final size:30
Alignment explanation
Indices: 35388--35484 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 30
35378 TTGCGTTTTT
*
35388 AATTTATTAGTTTTGCGTTTTTTGAAAAAAA
1 AATTTCTT-GTTTTGCGTTTTTTGAAAAAAA
* * *
35419 AGTTTTTTGTTTTGCGTTTTCTGAAAAAAAAA
1 AATTTCTTGTTTTGCGTTTTTTG--AAAAAAA
* *
35451 AATTTCTTGTTCTCGCGTTTTTAGAAAAAAA
1 AATTTCTTGTT-TTGCGTTTTTTGAAAAAAA
35482 AAT
1 AAT
35485 ATTTTCTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
30 14 0.25
31 16 0.29
32 16 0.29
33 9 0.16
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (30 bp):
AATTTCTTGTTTTGCGTTTTTTGAAAAAAA
Found at i:35469 original size:33 final size:32
Alignment explanation
Indices: 35412--35488 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
35402 GCGTTTTTTG
* * *
35412 AAAAAAAAGTTTTTTGTTTTGCGTTTTCT-GAA
1 AAAAAAAAATTTCTTGTTTCGCGTTTT-TAGAA
35444 AAAAAAAAATTTCTTGTTCTCGCGTTTTTAGAA
1 AAAAAAAAATTTCTTGTT-TCGCGTTTTTAGAA
*
35477 AAAAAAATATTT
1 AAAAAAAAATTT
35489 TCTTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 17 0.44
33 22 0.56
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.42
Consensus pattern (32 bp):
AAAAAAAAATTTCTTGTTTCGCGTTTTTAGAA
Found at i:37999 original size:21 final size:21
Alignment explanation
Indices: 37973--38022 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
37963 CGGCCATTCA
**
37973 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
37994 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
38015 CCGTGCCA
1 CCGTGCCA
38023 TCGCCTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:38399 original size:15 final size:14
Alignment explanation
Indices: 38379--38408 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
38369 ATCTTTTTAA
38379 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
38394 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
38408 T
1 T
38409 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:41322 original size:16 final size:15
Alignment explanation
Indices: 41301--41342 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
41291 TTACTCTACT
*
41301 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTGAA
41317 TTGTTTTCTGTTGAA
1 TTGTTTTCTGTTGAA
*
41332 TTGCTTTCTGT
1 TTGTTTTCTGT
41343 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTGAA
Found at i:41728 original size:35 final size:35
Alignment explanation
Indices: 41632--41923 Score: 300
Period size: 35 Copynumber: 8.3 Consensus size: 35
41622 GATTTTCGAA
* * *
41632 ATTTTAATCGACCCAGGGCGGTCTTTCTTCAGTTGT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTT-T
* * ** *
41668 TTTTCAGTTGATTCATGGCGATCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
* *
41703 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
* * * * * *
41738 ATTTCAGTTGGCCTAGGGCGGTCTTTATTAAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
* *
41773 ATTTCAGTTGATCCA-GG-GATCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
* *
41806 ATTTCAAGTTGATCCAGGGCGATCTTTCGTCAGTTT
1 ATTTCAA-TTGACCCAGGGCGATCTTTCTTCAGTTT
* *
41842 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
* * * * *
41877 ATTTGAGTTGATCCAAGGCGATCTTTATTCAGTTT
1 ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
41912 ATTTCAAGTTGA
1 ATTTCAA-TTGA
41924 TTCCTAGTGA
Statistics
Matches: 210, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
33 19 0.09
34 10 0.05
35 129 0.61
36 52 0.25
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (35 bp):
ATTTCAATTGACCCAGGGCGATCTTTCTTCAGTTT
Found at i:41777 original size:70 final size:70
Alignment explanation
Indices: 41632--41923 Score: 356
Period size: 70 Copynumber: 4.2 Consensus size: 70
41622 GATTTTCGAA
* * * * ** * *
41632 ATTTTAATCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTTCAGTTGATTCATGGCGATCTTTCTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTT-TATTTCAGTTGAGCCAGGGCGATCTTTATT
41697 CAGTTT
65 CAGTTT
*
41703 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTG-GCCTAGGGCGGTCTTTATT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGAGCC-AGGGCGATCTTTATT
*
41767 AAGTTT
65 CAGTTT
* * * * **
41773 ATTTCAGTTGATCCA-GG-GATCTTTCTTCAGTTTATTTCAAGTTGATCCAGGGCGATCTTTCGT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTC-AGTTGAGCCAGGGCGATCTTTATT
41836 CAGTTT
65 CAGTTT
* * *
41842 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTGAGTTGATCCAAGGCGATCTTTATTC
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGAGCCAGGGCGATCTTTATTC
41907 AGTTT
66 AGTTT
41912 ATTTCAAGTTGA
1 ATTTCAA-TTGA
41924 TTCCTAGTGA
Statistics
Matches: 190, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
68 20 0.11
69 38 0.20
70 78 0.41
71 54 0.28
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (70 bp):
ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGAGCCAGGGCGATCTTTATTC
AGTTT
Found at i:41903 original size:139 final size:140
Alignment explanation
Indices: 41653--41924 Score: 424
Period size: 139 Copynumber: 1.9 Consensus size: 140
41643 CCCAGGGCGG
* * * *
41653 TCTTTCTTCAGTTGTTTTTCAGTTGATTCATGGCGATCTTTCTTCAGTTTATTTCAATTGACCCA
1 TCTTTCTTCAGTTGTATTTCAGTTGATCCAGGGCGATCTTTCGTCAGTTTATTTCAATTGACCCA
* *
41718 GGGTGGTCTTTCTTCAGTTTATTTCAGTTGGCCTAGGGCGGTCTTTATTAAGTTTATTTC-AGTT
66 GGGTGGTCTTTCTTCAGTTTATTTCAGTTGGCCTAAGGCGATCTTTATTAAGTTTATTTCAAGTT
41782 GATCCAGGGA
131 GATCCAGGGA
41792 TCTTTCTTCAGTT-TATTTCAAGTTGATCCAGGGCGATCTTTCGTCAGTTTATTTCAATTGACCC
1 TCTTTCTTCAGTTGTATTTC-AGTTGATCCAGGGCGATCTTTCGTCAGTTTATTTCAATTGACCC
* * *
41856 AGGGTGGTCTTTCTTCAGTTTATTTGAGTTGATCC-AAGGCGATCTTTATTCAGTTTATTTCAAG
65 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTG-GCCTAAGGCGATCTTTATTAAGTTTATTTCAAG
41920 TTGAT
129 TTGAT
41925 TCCTAGTGAA
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
138 5 0.04
139 107 0.88
140 9 0.07
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (140 bp):
TCTTTCTTCAGTTGTATTTCAGTTGATCCAGGGCGATCTTTCGTCAGTTTATTTCAATTGACCCA
GGGTGGTCTTTCTTCAGTTTATTTCAGTTGGCCTAAGGCGATCTTTATTAAGTTTATTTCAAGTT
GATCCAGGGA
Found at i:43065 original size:25 final size:24
Alignment explanation
Indices: 43029--43075 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
43019 TCCTTCTATT
43029 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
43052 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
43076 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:43546 original size:21 final size:21
Alignment explanation
Indices: 43520--43560 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43510 TTTAAACCCT
43520 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
43541 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
43561 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:48773 original size:29 final size:28
Alignment explanation
Indices: 48707--48780 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
48697 GTGAACTTAA
*
48707 AATGACCAAAATGCCCC-TGAATGTGCG
1 AATGACCAAAATGCCCCTTGAATGTGAG
* * *
48734 AATGACTAAAATGCCCCTTGATTCTTGAG
1 AATGACCAAAATGCCCCTTGAAT-GTGAG
48763 AATGACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
48781 AGTTGATTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.40
28 4 0.10
29 20 0.50
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (28 bp):
AATGACCAAAATGCCCCTTGAATGTGAG
Found at i:50351 original size:71 final size:70
Alignment explanation
Indices: 50180--50905 Score: 852
Period size: 71 Copynumber: 10.3 Consensus size: 70
50170 CCACTCTGTG
* * *
50180 TCAACTGAAATAAACCGAAGAAAGACCACCCTAGATCAACTGAAATAAACTGAAGAACGATCGCC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGATCGCC
*
50245 CTAGA
66 CTGGA
*
50250 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAGGAAAAGATCGC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAG-AAAGATCGC
*
50315 TCTGGA
65 CCTGGA
* * * * * *
50321 TCAACTAAAATAAACTAAAGAAAGATCACCCT-GGATCAACTGCAATAAACTGAAGAAAGACCAC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGG-TCAACTGAAATAAACTGAAGAAAGATCGC
*
50385 TCTAGG-
65 CCT-GGA
* * * *** *
50391 TCAACTGAAATAAACTGAGGAAAAGATCGCCCTACACCAACTGAAATTAACTGAAGAAAGATCGC
1 TCAACTGAAATAAACTGAAG-AAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGATCGC
*
50456 CCTAGA
65 CCTGGA
* *
50462 TCAACT-ACAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAGGAAAAGATCG
1 TCAACTGA-AATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAG-AAAGATCG
50526 CCCTGGA
64 CCCTGGA
* * *
50533 TCAACTGAAATTAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAGGAAAAGATCGC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAG-AAAGATCGC
50598 CCTGGA
65 CCTGGA
* * * *
50604 TCAACTGAAATTAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAGGAAAAGATCAC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAG-AAAGATCGC
50669 CCTGGA
65 CCTGGA
* * * * * * * *
50675 TCAACTGAAATAAACTAAAGAAAGATCGCCCTAGATCAACTGCAATAAACTGAAGAAAGACCACT
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGATCGCC
50740 CTAGG-
66 CT-GGA
* * * * * *
50745 TCAACTGAAATAAACT-AACGAAAAGATCGCCCTAGATCAACTGAAATTAACTTAAGAAAGATTG
1 TCAACTGAAATAAACTGAA-G-AAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGATCG
50809 CCCTGGA
64 CCCTGGA
* * *
50816 TCAACT-ACAATAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAGGAAAAGATCG
1 TCAACTGA-AATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAG-AAAGATCG
50880 CCCTGGA
64 CCCTGGA
* *
50887 TCAATTAAAATAAACTGAA
1 TCAACTGAAATAAACTGAA
50906 AGATTGCCCT
Statistics
Matches: 573, Mismatches: 66, Indels: 33
0.85 0.10 0.05
Matches are distributed among these distances:
69 2 0.00
70 168 0.29
71 399 0.70
72 4 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (70 bp):
TCAACTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGATCGCC
CTGGA
Found at i:50358 original size:106 final size:104
Alignment explanation
Indices: 50163--50905 Score: 819
Period size: 106 Copynumber: 7.0 Consensus size: 104
50153 CATAAATTTG
* * *
50163 AGAAAGACCACTCTGTGTCAACTGAAATAAACCGAAGAAAGACCACCCTAGATCAACTGAAATAA
1 AGAAAGACCACCCTG-GTCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTGAAATAA
* *
50228 ACTGAAGAACGATCGCCCTAGATCAACTGAAATAAACTGA
65 ACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * * *
50268 AGAAAGACCACCCTAGGTCAACTGAAATAAACTGAGGAAAAGATCGCTCTGGATCAACTAAAATA
1 AGAAAGACCACCCT-GGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGATCAACTGAAATA
* * *
50333 AACTAAAGAAAGATCACCCTGGATCAACTGCAATAAACTGA
64 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * * ** * *
50374 AGAAAGACCACTCTAGGTCAACTGAAATAAACTGAGGAAAAGATCGCCCTACACCAACTGAAATT
1 AGAAAGACCACCCT-GGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGATCAACTGAAATA
*
50439 AACTGAAGAAAGATCGCCCTAGATCAACT-ACAATAAACTGA
64 AACTGAAGAAAGATCGCCCTGGATCAACTGA-AATAAACTGA
* * * *
50480 AGAAAGACCACCCTGGGTCAACTGAAATAAACTGAGGAAAAGATCGCCCTGGATCAACTGAAATT
1 AGAAAGACCACCCT-GGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGATCAACTGAAATA
* * *
50545 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGA
64 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * * *
50586 GGAAAAGATCGCCCTGGATCAACTGAAATTAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
1 AG-AAAGACCACCCTGG-TCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTGAAATA
* * *
50651 AACTGAGGAAAAGATCACCCTGGATCAACTGAAATAAACTAA
64 AACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * * *
50693 AGAAAGATCGCCCTAGATCAACTGCAATAAACTGAAGAAAGACCACTCTAGG-TCAACTGAAATA
1 AGAAAGACCACCCT-GGTCAACTGAAATAAACTGAAGAAAGACCACCCT-GGATCAACTGAAATA
* * *
50757 AACT-AACGAAAAGATCGCCCTAGATCAACTGAAATTAACTTA
64 AACTGAA-G-AAAGATCGCCCTGGATCAACTGAAATAAACTGA
*** * *
50799 AGAAAGATTGCCCTGGATCAACT-ACAATAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATA
1 AGAAAGACCACCCTGG-TCAACTGA-AATAAACTGAAGAAAGACCACCCTGGATCAACTGAAATA
* * *
50863 AACTGAGGAAAAGATCGCCCTGGATCAATTAAAATAAACTGA
64 AACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGA
50905 A
1 A
50906 AGATTGCCCT
Statistics
Matches: 557, Mismatches: 67, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
105 36 0.06
106 457 0.82
107 64 0.11
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (104 bp):
AGAAAGACCACCCTGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTGAAATAAA
CTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGA
Found at i:50954 original size:35 final size:35
Alignment explanation
Indices: 50180--50952 Score: 808
Period size: 35 Copynumber: 22.0 Consensus size: 35
50170 CCACTCTGTG
* * * *
50180 TCAACTGAAATAAACCGAAGAAAGACCACCCTAGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
50215 TCAACTGAAATAAACTGAAGAACGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
50250 TCAACTGAAATAAACTGAAGAAAGACCACCCTAGG-
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCT-GGA
* *
50285 TCAACTGAAATAAACTGAGGAAAAGATCGCTCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * *
50321 TCAACTAAAATAAACTAAAGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
50356 TCAACTGCAATAAACTGAAGAAAGACCACTCTAGG-
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCT-GGA
* **
50391 TCAACTGAAATAAACTGAGGAAAAGATCGCCCTACA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * *
50427 CCAACTGAAATTAACTGAAGAAAGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
50462 TCAACT-ACAATAAACTGAAGAAAGACCACCCTGGG
1 TCAACTGA-AATAAACTGAAGAAAGATCGCCCTGGA
*
50497 TCAACTGAAATAAACTGAGGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
50533 TCAACTGAAATTAACTGAAGAAAGACCACCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
50568 TCAACTGAAATAAACTGAGGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
50604 TCAACTGAAATTAACTGAAGAAAGACCACCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
50639 TCAACTGAAATAAACTGAGGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
50675 TCAACTGAAATAAACTAAAGAAAGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
50710 TCAACTGCAATAAACTGAAGAAAGACCACTCTAGG-
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCT-GGA
*
50745 TCAACTGAAATAAACT-AACGAAAAGATCGCCCTAGA
1 TCAACTGAAATAAACTGAA-G-AAAGATCGCCCTGGA
* * *
50781 TCAACTGAAATTAACTTAAGAAAGATTGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
50816 TCAACT-ACAATAAATTGAAGAAAGACCACCCTGGG
1 TCAACTGA-AATAAACTGAAGAAAGATCGCCCTGGA
*
50851 TCAACTGAAATAAACTGAGGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
50887 TCAATTAAAATAAACT---GAAAGATTGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
50919 TCAACCGGAATCAACTGAATAAAGACCGCCCTGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGG
50953 GTGATACGAA
Statistics
Matches: 612, Mismatches: 104, Indels: 44
0.81 0.14 0.06
Matches are distributed among these distances:
32 24 0.04
33 1 0.00
34 4 0.01
35 381 0.62
36 200 0.33
37 2 0.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Done.