Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011478.1 Corchorus capsularis cultivar CVL-1 contig11499, 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: 64797
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:890 original size:41 final size:42
Alignment explanation
Indices: 825--908 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
815 AACTAAAAAT
*
825 GAAGGTTTTAAATCTAATTTCCACCTCTTCTTTTATAATGTA
1 GAAGGTTTTAAATCTAATTCCCACCTCTTCTTTTATAATGTA
*
867 GAAGGTTTT-TATCTAATTCCCACCTCTTCTTTTATAATGTA
1 GAAGGTTTTAAATCTAATTCCCACCTCTTCTTTTATAATGTA
908 G
1 G
909 TGGTTGCAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 31 0.77
42 9 0.22
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (42 bp):
GAAGGTTTTAAATCTAATTCCCACCTCTTCTTTTATAATGTA
Found at i:5565 original size:63 final size:64
Alignment explanation
Indices: 5483--5607 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 64
5473 TCTTCGGATC
* * *
5483 AGTGTAAGAAAAGATCTTGTCCTTAGGAGAATCACATAGTTCACTCCTGTCTTTACATATATTT
1 AGTGTAAGAAAAGACCTTGTCCTTAAGAGAATCACATAGTTCACTCCAGTCTTTACATATATTT
*
5547 AGTGTAA-AAAAGACCTTGTCCTTAAGAGAATCACATATTTCACTCCAGTCTTTACATATAT
1 AGTGTAAGAAAAGACCTTGTCCTTAAGAGAATCACATAGTTCACTCCAGTCTTTACATATAT
5608 GTAATGTGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 50 0.88
64 7 0.12
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (64 bp):
AGTGTAAGAAAAGACCTTGTCCTTAAGAGAATCACATAGTTCACTCCAGTCTTTACATATATTT
Found at i:5637 original size:7 final size:7
Alignment explanation
Indices: 5625--5649 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5615 GATAATACTG
5625 AATTCTT
1 AATTCTT
5632 AATTCTT
1 AATTCTT
5639 AATTCTT
1 AATTCTT
5646 AATT
1 AATT
5650 GCAGATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTCTT
Found at i:10306 original size:21 final size:21
Alignment explanation
Indices: 10280--10323 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10270 AATTACTGGA
10280 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
10301 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
10322 TT
1 TT
10324 TACGCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:20542 original size:13 final size:13
Alignment explanation
Indices: 20526--20550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20516 GCCTCAACTT
20526 TTAGGCTCACATG
1 TTAGGCTCACATG
20539 TTAGGCTCACAT
1 TTAGGCTCACAT
20551 TGACTTTAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (13 bp):
TTAGGCTCACATG
Found at i:35472 original size:51 final size:51
Alignment explanation
Indices: 35393--35646 Score: 287
Period size: 51 Copynumber: 5.0 Consensus size: 51
35383 GGCTGGAGCA
* *
35393 GGCTGCTGAATCAAGAA-AGGAAGTTGGAAT-GTCAGGGAGAAGTTTGGAACG
1 GGCTGCTGAATCAAGAAGA-GAAGTTGGAATAG-CTGGGAGAAGTTTGGAACC
* * * * * *
35444 GGCTGCTGAATCCAGAAGAGAAGCTGGAATATCTGTGAGAAGCTTGGAACA
1 GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGGAGAAGTTTGGAACC
* * *
35495 GGCTGCTGAATCGAGAAGAGAAGTTGGAATAGCTGGGAGGAGTTTGGAGCC
1 GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGGAGAAGTTTGGAACC
* *
35546 GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGAAGGAGTTTGGAACC
1 GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGGAGAAGTTTGGAACC
* * * * * * * *
35597 GGCTGCTGAATCTAGAAAAGAAGCTGGCATTGTTGGAAGAAATTTGGAAC
1 GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGGAGAAGTTTGGAAC
35647 AGGGAACTGA
Statistics
Matches: 175, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
51 174 0.99
52 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.20
Consensus pattern (51 bp):
GGCTGCTGAATCAAGAAGAGAAGTTGGAATAGCTGGGAGAAGTTTGGAACC
Found at i:36507 original size:30 final size:30
Alignment explanation
Indices: 36471--36529 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
36461 CACATACTCA
*
36471 TTGGAACCATTTCAACCAAAGAATTATACG
1 TTGGAACCATGTCAACCAAAGAATTATACG
* *
36501 TTGGAACCATGTCAACCGAAGATTTATAC
1 TTGGAACCATGTCAACCAAAGAATTATAC
36530 TTCTATGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (30 bp):
TTGGAACCATGTCAACCAAAGAATTATACG
Found at i:43818 original size:124 final size:124
Alignment explanation
Indices: 43594--43892 Score: 404
Period size: 113 Copynumber: 2.5 Consensus size: 124
43584 CTCGAAAATC
* *
43594 AATTTAGATAAATGAAAGTTATGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTTTG
1 AATTTAGATAAACGAAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTTTG
*
43659 TCTTATTTTCAATCTTAAAAATCAATTTAGATTTCCCTCAAAACAAAGAAATAAAAAAA
66 TCTTATTTTCAATCTTAAAAATCAAGTTAGATTTCCCTCAAAACAAAGAAATAAAAAAA
* * *
43718 AATTTAGATAAACGAAAGTTACGAGACATAGTACTAGCAACGTAATAAGTCTTCCCAAA-TTTTG
1 AATTTAGATAAACGAAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTTTG
* * **
43782 TTTTATTTTCAATCTTAAAAATCAAGTTAGATTT---TC----C--CGAAA-AAAAATC
66 TCTTATTTTCAATCTTAAAAATCAAGTTAGATTTCCCTCAAAACAAAGAAATAAAAAAA
* * *
43831 AATTTAGATAAACGAAAGTTACGAGACATAGCATTAGTAACATAATAATCCTTCCCAAATTT
1 AATTTAGATAAACGAAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTT
43893 GCTAGAGTAT
Statistics
Matches: 158, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
113 58 0.37
114 6 0.04
116 1 0.01
120 2 0.01
123 37 0.23
124 54 0.34
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (124 bp):
AATTTAGATAAACGAAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTTTG
TCTTATTTTCAATCTTAAAAATCAAGTTAGATTTCCCTCAAAACAAAGAAATAAAAAAA
Found at i:43972 original size:64 final size:64
Alignment explanation
Indices: 43845--43973 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
43835 TAGATAAACG
* * * * * *
43845 AAAGTTACGAGACATAGCATTAGTAACATAATAATCCTTCCCAAATTTGCTAGAGTATCAGTCA
1 AAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTGCCAGAGCATAAGTCA
**
43909 AAAGTTACGAGACATAGCACTAGCAATGTAATAAGCCTTCCCAAATTTGCCAGTA-CATAAGTCA
1 AAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTGCCAG-AGCATAAGTCA
43973 A
1 A
43974 TCTATTAGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 55 0.98
65 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (64 bp):
AAAGTTACGAGACATAGCACTAGCAACATAATAAGCCTTCCCAAATTTGCCAGAGCATAAGTCA
Found at i:47029 original size:2 final size:2
Alignment explanation
Indices: 47022--47047 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47012 CCAACTTTTG
47022 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
47048 ACAAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:49467 original size:3 final size:3
Alignment explanation
Indices: 49459--49507 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
49449 GTCTCCTTCT
49459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49507 T
1 T
49508 AATGAGACCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49738 original size:3 final size:3
Alignment explanation
Indices: 49730--49779 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
49720 TCTCATTCTT
49730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49778 TT
1 TT
49780 GTTAGAATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50350 original size:188 final size:188
Alignment explanation
Indices: 49819--50369 Score: 930
Period size: 188 Copynumber: 2.9 Consensus size: 188
49809 CTGATCGAAT
*
49819 CGATTTGATTATATTTTAGGGTAAGTTTTAGATATAAGTTTTATGAATGATTAAAGTAAGATATA
1 CGATTTGATTATATTTTAGGGTAAGTTTTAGATATAAGTTTTATGAATGATTAAGGTAAGATATA
*
49884 TGTAAGTACCAAATAAAGAAAAGG-GGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTAG
66 TATAAGTACCAAATAAAGAAAAGGAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTAG
*
49948 GAAGTTCATAAAAGGAATGGGTTCGATCCCAGGCTCTCCCTTCCCCGATTCATAGAAC
131 GAAGTTCATAAAAGGAATGGGTTCGATCCCAGGCTCTCCCCTCCCCGATTCATAGAAC
*
50006 CGATTTGATTTATATTTTAGGGTAAGTTTTAGATATACGTTTTATGAATGATTAAGGTAAGATAT
1 CGATTTGA-TTATATTTTAGGGTAAGTTTTAGATATAAGTTTTATGAATGATTAAGGTAAGATAT
* *
50071 ATACAAGTACCAAA-AAA-AGAA-GAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTA
65 ATATAAGTACCAAATAAAGAAAAGGAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTA
*
50133 GGAAGTTCATAAAAGGAACGGGTTCGATCCCAGGCTCTCCCCTCCCCGATTCATAGAAC
130 GGAAGTTCATAAAAGGAATGGGTTCGATCCCAGGCTCTCCCCTCCCCGATTCATAGAAC
* * *
50192 CGATTTGATTATTTTTTCGGGTAAGTTTTAGATAAAAGTTTTATGAATGATTAAGGTAAGATATA
1 CGATTTGATTATATTTTAGGGTAAGTTTTAGATATAAGTTTTATGAATGATTAAGGTAAGATATA
*
50257 TATAAGTACCAAATAAAGAAAAGGAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGACTTAG
66 TATAAGTACCAAATAAAGAAAAGGAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTAG
* * **
50322 GGAGTTCATAAAAGGAATGGGGTCGATCCTGGGCTCTCCCCTCCCCGA
131 GAAGTTCATAAAAGGAATGGGTTCGATCCCAGGCTCTCCCCTCCCCGA
50370 CAATGTAAAC
Statistics
Matches: 340, Mismatches: 19, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
185 66 0.19
186 110 0.32
187 14 0.04
188 150 0.44
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (188 bp):
CGATTTGATTATATTTTAGGGTAAGTTTTAGATATAAGTTTTATGAATGATTAAGGTAAGATATA
TATAAGTACCAAATAAAGAAAAGGAGGGAACTCAACCTCTTGGCCGAGTGGCCAAAGAGGCTTAG
GAAGTTCATAAAAGGAATGGGTTCGATCCCAGGCTCTCCCCTCCCCGATTCATAGAAC
Found at i:50714 original size:82 final size:82
Alignment explanation
Indices: 50560--50723 Score: 217
Period size: 82 Copynumber: 2.0 Consensus size: 82
50550 TGTTCTATAC
** * * * *
50560 ACATATGATGATATTTCCATGTTACTTAGTTATGGATATAGTACATGTAATATTTTCATAGAAGG
1 ACATATGATGATAGATCAATGTTACTTAGTTATGAATATAATACATGTAATATATTCATAGAAGG
50625 TATGATCATTTTCATTT
66 TATGATCATTTTCATTT
50642 ACATATGATGATAGATCAATGTTACTTAGTTATGAATATAATACATGTAATA-ATTCAATAGTAA
1 ACATATGATGATAGATCAATGTTACTTAGTTATGAATATAATACATGTAATATATTC-ATAG-AA
*
50706 -TTCA-GATCATTTTCATTT
64 GGT-ATGATCATTTTCATTT
50724 TTCAAGTCAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
81 3 0.04
82 66 0.92
83 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (82 bp):
ACATATGATGATAGATCAATGTTACTTAGTTATGAATATAATACATGTAATATATTCATAGAAGG
TATGATCATTTTCATTT
Found at i:58237 original size:16 final size:15
Alignment explanation
Indices: 58212--58338 Score: 116
Period size: 16 Copynumber: 8.0 Consensus size: 15
58202 GAACCCGCCG
58212 ACCCGAATGACCCGCA
1 ACCCGAATGACCCG-A
58228 ACCC-AGATGACCCGA
1 ACCCGA-ATGACCCGA
58243 GACCCGAATGACCCGTA
1 -ACCCGAATGACCCG-A
*
58260 ACTC-AGATGACCCGAA
1 ACCCGA-ATGACCCG-A
58276 ACCCGAATGACCCGTA
1 ACCCGAATGACCCG-A
58292 ACCC-AGATGACCCGA
1 ACCCGA-ATGACCCGA
*
58307 GACCCGTATGACCCGAA
1 -ACCCGAATGACCCG-A
*
58324 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
58339 GAAGTTAACC
Statistics
Matches: 94, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.06
16 84 0.89
17 4 0.04
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.09
Consensus pattern (15 bp):
ACCCGAATGACCCGA
Found at i:58247 original size:32 final size:32
Alignment explanation
Indices: 58211--58340 Score: 190
Period size: 32 Copynumber: 4.1 Consensus size: 32
58201 CGAACCCGCC
*
58211 GACCCGAATGACCCGCAACCCAGATGACCCGA
1 GACCCGAATGACCCGTAACCCAGATGACCCGA
*
58243 GACCCGAATGACCCGTAACTCAGATGACCCGA
1 GACCCGAATGACCCGTAACCCAGATGACCCGA
*
58275 AACCCGAATGACCCGTAACCCAGATGACCCGA
1 GACCCGAATGACCCGTAACCCAGATGACCCGA
* * *
58307 GACCCGTATGACCCGAAACCC-GAATAACCCGA
1 GACCCGAATGACCCGTAACCCAG-ATGACCCGA
58339 GA
1 GA
58341 AGTTAACCCG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 1 0.01
32 88 0.99
ACGTcount: A:0.33, C:0.37, G:0.21, T:0.09
Consensus pattern (32 bp):
GACCCGAATGACCCGTAACCCAGATGACCCGA
Found at i:58318 original size:48 final size:48
Alignment explanation
Indices: 58211--58340 Score: 144
Period size: 48 Copynumber: 2.7 Consensus size: 48
58201 CGAACCCGCC
*
58211 GACCCGAATGACCCGCAACCC-AGATGACCCGAGACCCGAATGACCCGTA
1 GACCCG-ATGACCCGAAACCCGA-ATGACCCGAGACCCGAATGACCCGTA
*
58260 -ACTCAGATGACCCGAAACCCGAATGACCCGTA-ACCC-AGATGACCCG-A
1 GAC-CCGATGACCCGAAACCCGAATGACCCG-AGACCCGA-ATGACCCGTA
*
58307 GACCCGTATGACCCGAAACCCGAATAACCCGAGA
1 GACCCG-ATGACCCGAAACCCGAATGACCCGAGA
58341 AGTTAACCCG
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
47 5 0.07
48 61 0.87
49 4 0.06
ACGTcount: A:0.33, C:0.37, G:0.21, T:0.09
Consensus pattern (48 bp):
GACCCGATGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCGTA
Found at i:58350 original size:22 final size:23
Alignment explanation
Indices: 58323--58368 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
58313 TATGACCCGA
*
58323 AACCCGAATAACCCGAGAA-GTT
1 AACCCGAATAACCCAAGAATGTT
*
58345 AACCCGAATGACCCAAGAATGTT
1 AACCCGAATAACCCAAGAATGTT
58368 A
1 A
58369 TAAACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.15
Consensus pattern (23 bp):
AACCCGAATAACCCAAGAATGTT
Found at i:60705 original size:16 final size:16
Alignment explanation
Indices: 60640--60719 Score: 88
Period size: 16 Copynumber: 5.0 Consensus size: 16
60630 AGACCCGGTA
60640 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
60656 GATCCGGAACCCGAAT
1 GACCCGAAACCCGAAT
* * **
60672 GTCCCGAGACCAAAAT
1 GACCCGAAACCCGAAT
*
60688 GACCCGAAACCCGTAT
1 GACCCGAAACCCGAAT
*
60704 GACCCGATACCCGAAT
1 GACCCGAAACCCGAAT
60720 AACTCGAACC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.34, C:0.35, G:0.20, T:0.11
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:63163 original size:3 final size:3
Alignment explanation
Indices: 63155--63192 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
63145 TTATATATAT
63155 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63193 CTATTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:63178 original size:20 final size:20
Alignment explanation
Indices: 63153--63192 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
63143 TATTATATAT
63153 ATATAATAATAATAATAATA
1 ATATAATAATAATAATAATA
63173 ATATAATAATAATAATAATA
1 ATATAATAATAATAATAATA
63193 CTATTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAATAATAATAATAATA
Found at i:63180 original size:17 final size:17
Alignment explanation
Indices: 63158--63192 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
63148 TATATATATA
63158 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
63175 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
63192 A
1 A
63193 CTATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:63565 original size:13 final size:14
Alignment explanation
Indices: 63532--63575 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
63522 AATTGCAATT
*
63532 ATTATATGATGATTA
1 ATTAAATGAT-ATTA
*
63547 AATAAAT-ATATTA
1 ATTAAATGATATTA
63560 ATTAAATGATATTA
1 ATTAAATGATATTA
63574 AT
1 AT
63576 ACAACTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTAAATGATATTA
Found at i:64343 original size:33 final size:32
Alignment explanation
Indices: 64274--64411 Score: 152
Period size: 32 Copynumber: 4.2 Consensus size: 32
64264 CCGTGGTATT
* * *
64274 TGCCGCCCCAAGAGGGCGGCTGTGCCCCGGCA
1 TGCCGCCCCAGGAGGGCGGCTGAGCCACGGCA
*
64306 TGCCGCCCCAGGAGGGCTGCATGAGCCACGGCA
1 TGCCGCCCCAGGAGGGCGGC-TGAGCCACGGCA
* *
64339 TGCCGCCCTAGGAGGGCAGCTGTA-CCACGGCA
1 TGCCGCCCCAGGAGGGCGGCTG-AGCCACGGCA
* * * *
64371 TGTCGCCCTAGGAGGGCGGCATGAGCCATGGTA
1 TGCCGCCCCAGGAGGGCGGC-TGAGCCACGGCA
64404 TGCCGCCC
1 TGCCGCCC
64412 TCCTGGGGCG
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
32 47 0.52
33 44 0.48
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.12
Consensus pattern (32 bp):
TGCCGCCCCAGGAGGGCGGCTGAGCCACGGCA
Found at i:64412 original size:65 final size:65
Alignment explanation
Indices: 64274--64412 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 65
64264 CCGTGGTATT
* * * * *
64274 TGCCGCCCCAAGAGGGCGGCTGTGCCCCGGCATGCCGCCCCAGGAGGGCTGCATGAGCCACGGCA
1 TGCCGCCCTAAGAGGGCAGCTGTACCACGGCATGCCGCCCCAGGAGGGCGGCATGAGCCACGGCA
* * * * *
64339 TGCCGCCCTAGGAGGGCAGCTGTACCACGGCATGTCGCCCTAGGAGGGCGGCATGAGCCATGGTA
1 TGCCGCCCTAAGAGGGCAGCTGTACCACGGCATGCCGCCCCAGGAGGGCGGCATGAGCCACGGCA
64404 TGCCGCCCT
1 TGCCGCCCT
64413 CCTGGGGCGG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.16, C:0.35, G:0.36, T:0.13
Consensus pattern (65 bp):
TGCCGCCCTAAGAGGGCAGCTGTACCACGGCATGCCGCCCCAGGAGGGCGGCATGAGCCACGGCA
Done.