Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014036.1 Corchorus capsularis cultivar CVL-1 contig14057, 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: 68556
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:11547 original size:41 final size:41
Alignment explanation
Indices: 11511--11593 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
11501 TATTTATTCT
11511 TAAACATTTCGATTTC-AATGGAATAAAAAGGAATTTAACTC
1 TAAACATTTCGATTTCGAAT-GAATAAAAAGGAATTTAACTC
*
11552 TAAACATTTTGATTTCGAATGAATAAAAAGGAATTTAACTC
1 TAAACATTTCGATTTCGAATGAATAAAAAGGAATTTAACTC
11593 T
1 T
11594 TTAAATTCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 37 0.93
42 3 0.08
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (41 bp):
TAAACATTTCGATTTCGAATGAATAAAAAGGAATTTAACTC
Found at i:22594 original size:14 final size:14
Alignment explanation
Indices: 22572--22604 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22562 AACTAGAACT
*
22572 AGAGAGAGAAGGGG
1 AGAGGGAGAAGGGG
22586 AGAGGGAGAAGGGG
1 AGAGGGAGAAGGGG
22600 AGAGG
1 AGAGG
22605 AGCGGCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (14 bp):
AGAGGGAGAAGGGG
Found at i:22635 original size:3 final size:3
Alignment explanation
Indices: 22627--22658 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
22617 TACCTTATAT
*
22627 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22659 GTATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27797 original size:11 final size:11
Alignment explanation
Indices: 27781--27805 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27771 GTTTTGATTA
27781 TTAGGTGTTAG
1 TTAGGTGTTAG
27792 TTAGGTGTTAG
1 TTAGGTGTTAG
27803 TTA
1 TTA
27806 TGAGCTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (11 bp):
TTAGGTGTTAG
Found at i:28675 original size:18 final size:18
Alignment explanation
Indices: 28652--28689 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28642 ATGACACCTT
*
28652 TTTTTGTATGGTGTGGCA
1 TTTTTGTATGATGTGGCA
*
28670 TTTTTGTCTGATGTGGCA
1 TTTTTGTATGATGTGGCA
28688 TT
1 TT
28690 ATCACGTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.08, G:0.29, T:0.53
Consensus pattern (18 bp):
TTTTTGTATGATGTGGCA
Found at i:44740 original size:30 final size:31
Alignment explanation
Indices: 44686--44750 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
44676 AACTTTATGT
*
44686 TTTCCGATTGTACCCATATTTTTAAAACATA
1 TTTCCAATTGTACCCATATTTTTAAAACATA
* *
44717 TTTCCAATTGTACCC-TTTTTTTAATACATA
1 TTTCCAATTGTACCCATATTTTTAAAACATA
44747 TTTC
1 TTTC
44751 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCATATTTTTAAAACATA
Found at i:44757 original size:31 final size:31
Alignment explanation
Indices: 44692--44758 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
44682 ATGTTTTCCG
*
44692 ATTGTACCCATATTTTTAAAACATATTTCCA
1 ATTGTACCCATATTTTTAAAACATATTTCAA
* *
44723 ATTGTACCC-TTTTTTTAATACATATTTCTAA
1 ATTGTACCCATATTTTTAAAACATATTTC-AA
44754 ATTGT
1 ATTGT
44759 CATTACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTGTACCCATATTTTTAAAACATATTTCAA
Found at i:44910 original size:38 final size:36
Alignment explanation
Indices: 44849--44925 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
44839 CAATTTGCCT
*
44849 TTTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTTGTTTCCAACGTCATATTTAATTTTG-C-TTTGTC
*
44887 TTTT-TTTCCAATCGTTATATTTAATTTTGCTTTGTC
1 TTTTGTTTCCAA-CGTCATATTTAATTTTGCTTTGTC
44923 TTT
1 TTT
44926 GGTCCTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 9 0.25
37 8 0.22
38 19 0.53
ACGTcount: A:0.14, C:0.17, G:0.09, T:0.60
Consensus pattern (36 bp):
TTTTGTTTCCAACGTCATATTTAATTTTGCTTTGTC
Found at i:45091 original size:19 final size:21
Alignment explanation
Indices: 45059--45101 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
45049 TTCTTTACTA
45059 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
45080 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
45099 TTA
1 TTA
45102 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:45295 original size:22 final size:22
Alignment explanation
Indices: 45267--45369 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
45257 TGTCTCTATG
45267 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
45289 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
45312 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
45333 TGGTTACCGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
45355 TCAGGTTATTAAAAT
1 T--GGTTATCAAAAT
45370 CTCTTAGGTT
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.02
22 45 0.76
23 4 0.07
24 9 0.15
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:45403 original size:26 final size:26
Alignment explanation
Indices: 45341--45408 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
45331 TGTGGTTACC
*
45341 GAAATTTCATAGGAT--CAGGTTATT
1 GAAATTTCATAGGATGGTAGGTTATT
* * * *
45365 AAAATCTCTTAGGTTGGTAGGTTATT
1 GAAATTTCATAGGATGGTAGGTTATT
*
45391 GAAATTTCATAGGGTGGT
1 GAAATTTCATAGGATGGT
45409 TAATTATCAC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.33
26 22 0.67
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
GAAATTTCATAGGATGGTAGGTTATT
Found at i:45555 original size:22 final size:22
Alignment explanation
Indices: 45507--45791 Score: 68
Period size: 22 Copynumber: 12.8 Consensus size: 22
45497 TTTCATGGGG
* *
45507 AGGTTATCAAAATTTTATAGT-G
1 AGGTTATCAAAATTTCATA-TAA
*
45529 TGGTTATCAAAATTTCATATAA
1 AGGTTATCAAAATTTCATATAA
* *
45551 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-ATAT-A-A
* ** * *
45576 AGGAGTGCCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATAA
* * *
45598 AGGTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATATAA
* * * *
45619 TGATTATCGAAATTTCATAGAGA
1 AGGTTATCAAAATTTCATATA-A
* *
45642 TCGGATTATCAAAATTT-ATAGAA
1 -AGG-TTATCAAAATTTCATATAA
* * *
45665 AGATTATCAAAATTCCATAGT-G
1 AGGTTATCAAAATTTCATA-TAA
** *
45687 TTGTTATCAAAA-TT-ACATAA
1 AGGTTATCAAAATTTCATATAA
* * * *
45707 TGTGATTATCAGAATTTCATAGAG
1 AG-G-TTATCAAAATTTCATATAA
* * * *
45731 GGGTCAACAAAATTTTATA-AA
1 AGGTTATCAAAATTTCATATAA
45752 GAGGTTATCAAAATTTCATA-AA
1 -AGGTTATCAAAATTTCATATAA
*
45774 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
45792 AAATGTGATT
Statistics
Matches: 189, Mismatches: 54, Indels: 40
0.67 0.19 0.14
Matches are distributed among these distances:
19 1 0.01
20 11 0.06
21 27 0.14
22 108 0.57
23 7 0.04
24 11 0.06
25 17 0.09
26 3 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATAA
Found at i:45742 original size:44 final size:44
Alignment explanation
Indices: 45584--45816 Score: 127
Period size: 44 Copynumber: 5.3 Consensus size: 44
45574 TAAGGAGTGC
* * * *
45584 CAAAATTTGATAGA-AGGTTATC-AAATCTCATAGA-GTGATTAT
1 CAAAATTTCATAGAGAGGTCAACAAAATTTCATA-ATGTGATTAT
* * * **
45626 CGAAATTTCATAGAGATCGGATTATCAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGA--GG-TCAACAAAATTTCATA-ATGTGATTAT
* * ** * * *
45672 CAAAATTCCATAGTGTTGTTATCAAAATTACATAATGTGATTAT
1 CAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTGATTAT
* * * * * *
45716 CAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTGATTAT
* * * * *
45760 CAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA-
1 CAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTGATTAT
45803 CAAAAATTTCATAG
1 C-AAAATTTCATAG
45817 TGGTATTTCT
Statistics
Matches: 146, Mismatches: 37, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
42 12 0.08
43 14 0.10
44 85 0.58
45 2 0.01
46 28 0.19
47 5 0.03
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (44 bp):
CAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTGATTAT
Found at i:45763 original size:88 final size:87
Alignment explanation
Indices: 45651--45816 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 87
45641 ATCGGATTAT
** ** *
45651 CAAAATTTATAGAAAGATTATCAAAATTCCATAGTGTTGTTATCAAAATTACATAATGTGATTAT
1 CAAAATTTATAGAAAGATTATCAAAATTCCATAAAGAGGTTATCAAAATTACAAAATGTGATTA-
*
45716 C-AGAATTTCATAGAGGGGTCAA
65 CAAAAATTTCATAGAGGGGTCAA
* * * *
45738 CAAAATTTTATA-AAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATT
1 CAAAA-TTTATAGAA-AGATTATCAAAATTCCATAAAGAGGTTATCAAAATTACAAAATGTGATT
45802 ACAAAAATTTCATAG
64 ACAAAAATTTCATAG
45817 TGGTATTTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
87 8 0.12
88 58 0.88
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
CAAAATTTATAGAAAGATTATCAAAATTCCATAAAGAGGTTATCAAAATTACAAAATGTGATTAC
AAAAATTTCATAGAGGGGTCAA
Found at i:45963 original size:22 final size:22
Alignment explanation
Indices: 45935--46530 Score: 213
Period size: 22 Copynumber: 27.5 Consensus size: 22
45925 TCAGGGAGGA
*
45935 TATCAAAATTTCATACGAAGGT
1 TATCAAAATTTCATAGGAAGGT
**
45957 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-GAAGGT
* * * *
45979 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATAGGAAGGT
* *
46001 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAGGT
* * * *
46022 AGATCAAAATTTCATGGGGAGAT
1 -TATCAAAATTTCATAGGAAGGT
* *
46045 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
** *
46067 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGAAGGT
*
46089 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAAGGT
* *
46105 TATCAAGAA-ATCATAGGGAGGT
1 TATCAA-AATTTCATAGGAAGGT
*
46127 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAAGGT
* *
46143 TATCAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATAGGAAGGT
*
46165 TATCAAAATTTCATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGG-T
* *
46188 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGAAG-GT
*
46211 TATCAAAATTTCATAACG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
* * * *
46233 TATCATAATTTTATAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
* * * *
46255 TATCAAAATTTCAGAGTATGAT
1 TATCAAAATTTCATAGGAAGGT
*
46277 TA-CTAACAA-TTCATATGG-AGAT
1 TATC-AA-AATTTCATA-GGAAGGT
* * * * *
46299 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-AGGAAGGT
* *
46321 TATCAATATATCATATGG-AGGT
1 TATCAAAATTTCATA-GGAAGGT
* * **
46343 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GAAGGT
* *
46366 TATTAAAATTTCATTGGGAA-GT
1 TATCAAAATTTCA-TAGGAAGGT
*
46388 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-GGAAGGT
* * *
46410 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAGGAAGGT
* * * *
46432 TAACCAAATTTCATAAGAAGCT
1 TATCAAAATTTCATAGGAAGGT
* * **
46454 T-TAAAAAAATT-ATAAAAAGGT
1 TAT-CAAAATTTCATAGGAAGGT
* * * * **
46475 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGT
*
46497 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGAAGGT
46519 TATCAAAATTTC
1 TATCAAAATTTC
46531 CTAATGGAAT
Statistics
Matches: 420, Mismatches: 113, Indels: 82
0.68 0.18 0.13
Matches are distributed among these distances:
16 18 0.04
17 9 0.02
19 4 0.01
21 35 0.08
22 291 0.69
23 59 0.14
24 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:45990 original size:44 final size:43
Alignment explanation
Indices: 45935--46530 Score: 243
Period size: 44 Copynumber: 13.8 Consensus size: 43
45925 TCAGGGAGGA
*
45935 TATCAAAATTTCATACGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-TTAGT
* * * *
45979 TTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAG-TATGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-GT
* * * * * * *
46022 AGATCAAAATTTCATGGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-GT
** *
46067 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGT
* *
46105 TATCAAGAA-ATCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAA-AATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGT
* * **
46143 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-G-T
* * ***
46188 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAACGAGGT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTA-GT
* * * * *
46233 TATCATAATTTTATAGTG-TGATTATCAAAATTTCAGAG-TATGAT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTTA-G-T
* * * * *
46277 TA-CTAACAA-TTCATATGG-AGATTTTTAAATTTTCATAACG-TGGT
1 TATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCAT-A-GTTAGT
* * * * *
46321 TATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATA--GTTAGT
* *
46366 TATTAAAATTTCATTGGGAA-GTTATCAAAATTTCATA-TTGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTT-A-GT
* * * * * *
46410 CT-TCAAAATTCCTTAGGGAGGTTAACCAAATTTCATAAG-AAGCT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTTAG-T
* * ** * * * *
46454 T-TAAAAAAATT-ATAAAAAGGTTCTCGAAATTCCATAGTATCGT
1 TAT-CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT-TAGT
*
46497 TATTAAAATTTCATAGGAAGGTTATCAAAATTTC
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTC
46531 CTAATGGAAT
Statistics
Matches: 420, Mismatches: 94, Indels: 76
0.71 0.16 0.13
Matches are distributed among these distances:
37 2 0.00
38 60 0.14
39 5 0.01
41 2 0.00
42 7 0.02
43 41 0.10
44 201 0.48
45 77 0.18
46 25 0.06
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (43 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGT
Found at i:46108 original size:16 final size:16
Alignment explanation
Indices: 46087--46153 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 16
46077 TCATAGGGAG
46087 GTTATCAAAATTTGTA
1 GTTATCAAAATTTGTA
* *
46103 GTTATCAAGAAATCATAGGGA
1 GTTATC-A-AAAT--T-TGTA
46124 GGTTATCAAAATTTGTA
1 -GTTATCAAAATTTGTA
46141 GTTATCAAAATTT
1 GTTATCAAAATTT
46154 CATAAGAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 19 0.46
17 3 0.07
18 5 0.12
20 5 0.12
21 3 0.07
22 6 0.15
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (16 bp):
GTTATCAAAATTTGTA
Found at i:46116 original size:38 final size:37
Alignment explanation
Indices: 46065--46175 Score: 159
Period size: 38 Copynumber: 2.9 Consensus size: 37
46055 TCATAATGAG
46065 GTTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 GTTATC-AAAAATCATAGGGAGGTTATCAAAATTTGTA
46103 GTTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTA
1 GTTATCAA-AAATCATAGGGAGGTTATCAAAATTTGTA
* * * *
46141 GTTATCAAAATTTCATAAGAAAGTTATCAAAATTT
1 GTTATCAAAA-ATCATAGGGAGGTTATCAAAATTT
46176 CATAGGGAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
37 4 0.06
38 63 0.94
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.33
Consensus pattern (37 bp):
GTTATCAAAAATCATAGGGAGGTTATCAAAATTTGTA
Found at i:53174 original size:16 final size:15
Alignment explanation
Indices: 53153--53195 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
53143 TTACCTGGTA
53153 AATACTCACTTGATG
1 AATACTCACTTGATG
* *
53168 CAATACTCACATGTTG
1 -AATACTCACTTGATG
53184 AGATACTCACTT
1 A-ATACTCACTT
53196 ACAAAAGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (15 bp):
AATACTCACTTGATG
Found at i:59281 original size:20 final size:21
Alignment explanation
Indices: 59244--59282 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59234 CATATCTCCT
*
59244 CAACATAATTGTAAAAGATCA
1 CAACATAATTGCAAAAGATCA
59265 CAACATAATT-CAAAAGAT
1 CAACATAATTGCAAAAGAT
59283 TCATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (21 bp):
CAACATAATTGCAAAAGATCA
Found at i:63016 original size:8 final size:8
Alignment explanation
Indices: 62984--63008 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
62974 CTTGTAGTAC
62984 ATAAAAAA
1 ATAAAAAA
62992 ATAAAAAA
1 ATAAAAAA
63000 ATAAAAAA
1 ATAAAAAA
63008 A
1 A
63009 AATAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Done.