Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006994.1 Corchorus capsularis cultivar CVL-1 contig07015, 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: 17784
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:321 original size:41 final size:41
Alignment explanation
Indices: 264--414 Score: 180
Period size: 41 Copynumber: 3.7 Consensus size: 41
254 AATAATATTG
*
264 AAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTACTTTTGACACCAGAAGTTGTCATTTTGGTAAATT
*
305 AAAATTACTTTTGACACTAGAAGTTGTCATTTTGGTAAATT
1 AAAATTACTTTTGACACCAGAAGTTGTCATTTTGGTAAATT
* * *** *
346 AAAATTA-TCTTTGACACCAGAAG-TGTTACTCCAGTAAATC
1 AAAATTACT-TTTGACACCAGAAGTTGTCATTTTGGTAAATT
* * *
386 ATAATTACTGTTGACACCAGAAATTGTCA
1 AAAATTACTTTTGACACCAGAAGTTGTCA
415 CCTTTGAATT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 30 0.32
41 64 0.68
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (41 bp):
AAAATTACTTTTGACACCAGAAGTTGTCATTTTGGTAAATT
Found at i:413 original size:81 final size:82
Alignment explanation
Indices: 264--414 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 82
254 AATAATATTG
* *** * * * *
264 AAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTACTTTTGACACTAGAAGT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTCCAGTAAATCAAAATTACTGTTGACACCAGAAAT
329 TGTCATTTTGGTAAATT
66 TGTCATTTTGGTAAATT
* * *
346 AAAATTATCTTTGACACCAGAAG-TGTTACTCCAGTAAATCATAATTACTGTTGACACCAGAAAT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTCCAGTAAATCAAAATTACTGTTGACACCAGAAAT
410 TGTCA
66 TGTCA
415 CCTTTGAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 36 0.62
82 22 0.38
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (82 bp):
AAAATTACCTTTGACACCAGAAGTTGTCACTCCAGTAAATCAAAATTACTGTTGACACCAGAAAT
TGTCATTTTGGTAAATT
Found at i:9726 original size:19 final size:21
Alignment explanation
Indices: 9694--9736 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
9684 TTCTTTACTA
9694 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
9715 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
9734 TTA
1 TTA
9737 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:10159 original size:22 final size:22
Alignment explanation
Indices: 10130--10218 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
10120 TTCTTGTCTC
10130 TAAG-TGGTTATCAAAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
10151 TAAGATGGTTATTATAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
10173 TGAGGA-GGTTATCAAAATTCCA
1 T-AAGATGGTTATCAAAATTTCA
* * *
10195 T-AGTGTGGTTACCAAAATATCA
1 TAAG-ATGGTTATCAAAATTTCA
10217 TA
1 TA
10219 GTGTGGTTAG
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
20 1 0.02
21 4 0.08
22 44 0.85
23 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TAAGATGGTTATCAAAATTTCA
Found at i:10219 original size:22 final size:22
Alignment explanation
Indices: 10179--10227 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
10169 TTCATGAGGA
*
10179 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
10201 GGTTACCAAAATAT-CATAGTGT
1 GGTTACCAAAAT-TCCATAGTGT
10223 GGTTA
1 GGTTA
10228 GGATCAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTCCATAGTGT
Found at i:10260 original size:22 final size:22
Alignment explanation
Indices: 10234--10282 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
10224 GTTAGGATCA
* *
10234 GGTTATTAAAATCTCTTAGGTT
1 GGTTATTAAAATCTCATAGGGT
* *
10256 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATCTCATAGGGT
10278 GGTTA
1 GGTTA
10283 ATTATCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (22 bp):
GGTTATTAAAATCTCATAGGGT
Found at i:10409 original size:22 final size:22
Alignment explanation
Indices: 10384--10449 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
10374 TTCATTAAAT
*
10384 ATTTAATGGGGAGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
10406 ATTTTATAGTGTGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
10428 ATTTCATATGAAGGTTAT-AAA
1 ATTTAATAGGGAGGTTATCAAA
10449 A
1 A
10450 GTCTCAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTAATAGGGAGGTTATCAAA
Found at i:10411 original size:23 final size:22
Alignment explanation
Indices: 10392--10696 Score: 67
Period size: 22 Copynumber: 13.9 Consensus size: 22
10382 ATATTTAATG
10392 GGGAGGTTATCAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
* * *
10414 GTGTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
10436 TGAAGGTTAT-AAAAGTCTCAATTTCATA
1 GGGAGGTTATCAAAA---T---TTT-ATA
* *
10464 GGGA-G-TACCAAAATTTGATA
1 GGGAGGTTATCAAAATTTTATA
* *
10484 -GAAGGTTATC-AAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* * * * *
10504 GAGTGATTATCGAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
*
10526 GAGATCGGATTATCAAAA-TTTATA
1 GGGA--GG-TTATCAAAATTTTATA
** * *
10550 GAAAGATTATCAAAA-TTCATA
1 GGGAGGTTATCAAAATTTTATA
** * *
10571 --GTTGTTATCAAAATTTCAAA
1 GGGAGGTTATCAAAATTTTATA
* **
10591 GCGAGGTTATCAAAATTACATA
1 GGGAGGTTATCAAAATTTTATA
** * * * *
10613 ATGTGATTATCAGAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
*
10635 --GAGGTGTCAACAAAATTTTATA
1 GGGAGGT-T-ATCAAAATTTTATA
** * *
10657 AAGAGGTTATCAAAAATTCATA
1 GGGAGGTTATCAAAATTTTATA
**
10679 AAGAGGTTATC-AAATTTT
1 GGGAGGTTATCAAAATTTT
10697 CAAAATTTGA
Statistics
Matches: 210, Mismatches: 51, Indels: 45
0.69 0.17 0.15
Matches are distributed among these distances:
19 11 0.05
20 21 0.10
21 35 0.17
22 104 0.50
23 1 0.00
24 16 0.08
25 8 0.04
26 2 0.01
27 7 0.03
28 5 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTATA
Found at i:10670 original size:22 final size:22
Alignment explanation
Indices: 10472--10698 Score: 141
Period size: 22 Copynumber: 10.5 Consensus size: 22
10462 TAGGGAGTAC
* *
10472 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* * *
10493 C-AAATTTCATAGAGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
10514 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAGA--GG-TTAT
*
10539 CAAAATTT-ATAGAA-AGATTAT
1 CAAAATTTCATA-AAGAGGTTAT
**
10560 CAAAA-TTCAT--AGTTGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
10579 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-AGAGGTTAT
* * * *
10601 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
10623 CAGAATTTCAT--AGAGGTGTCAA
1 CAAAATTTCATAAAGAGGT-T-AT
*
10645 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
10667 CAAAAATTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
10689 CAAATTTTCA
1 CAAAATTTCA
10699 AAATTTGATT
Statistics
Matches: 158, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
18 1 0.01
19 9 0.06
20 20 0.13
21 19 0.12
22 83 0.53
23 3 0.02
24 11 0.07
25 12 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:10694 original size:109 final size:108
Alignment explanation
Indices: 10486--10700 Score: 237
Period size: 109 Copynumber: 2.0 Consensus size: 108
10476 ATTTGATAGA
* * *
10486 AGGTTATCAAATTTCATAGAGTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTTATAG
1 AGGTTATCAAATTACATAGAGTGATTATCGAAATTTCATAGAGATC-GATCAACAAAATTTATAG
**
10551 AAAGATTATCAAAATTCATAGTTGTTATCAAAA-TTTCAAAGCG
65 AAAGATTATCAAAATTCATAGAGGTTATCAAAATTTTCAAAGCG
*
10594 AGGTTATCAAAATTACATA-ATGTGATTATC-AGAATTTCATAGAGGT-G-TCAACAAAATTTTA
1 AGGTTATC-AAATTACATAGA-GTGATTATCGA-AATTTCATAGAGATCGATCAACAAAA-TTTA
*
10655 TA-AAGAGGTTATCAAAAATTCATAAAGAGGTTATC-AAATTTTCAAA
62 TAGAA-AGATTATC-AAAATTCAT--AGAGGTTATCAAAATTTTCAAA
10701 ATTTGATTAC
Statistics
Matches: 91, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
106 9 0.10
107 14 0.15
108 19 0.21
109 34 0.37
110 15 0.16
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (108 bp):
AGGTTATCAAATTACATAGAGTGATTATCGAAATTTCATAGAGATCGATCAACAAAATTTATAGA
AAGATTATCAAAATTCATAGAGGTTATCAAAATTTTCAAAGCG
Found at i:10834 original size:19 final size:19
Alignment explanation
Indices: 10804--10851 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
10794 TTATGGAGTA
10804 ATCAAAATTTCAAGGAGAAT
1 ATCAAAA-TTCAAGGAGAAT
* *
10824 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGAAT
10843 ATCAAAATT
1 ATCAAAATT
10852 TCATATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGAAT
Found at i:10870 original size:22 final size:22
Alignment explanation
Indices: 10842--11338 Score: 152
Period size: 22 Copynumber: 22.7 Consensus size: 22
10832 TCAGGGAGGA
10842 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
10864 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
* *
10886 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
10908 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
10930 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* ** *
10946 TATCAAGATTTCATAAAAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
10968 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
10991 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
11014 TATCAAAATTTCATA-GCGAGGTT
1 TATCAAAATTTCATATG-AAGG-T
* * *
11037 ATATCACAATTTCATAGTG-TGAT
1 -TATCAAAATTTCATA-TGAAGGT
* * *
11060 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
11082 TA-CTAACAA-TTCATATGGAGCT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
11104 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
11126 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
11148 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
**
11171 CGTCAAAATTTCAT-TG--GGAAT
1 TATCAAAATTTCATATGAAGG--T
*
11192 TAATCAAATTTTCATATTG-AGGT
1 T-ATCAAAATTTCATA-TGAAGGT
* * * *
11215 CT-TCAAAATTCCTTAGGAAAGT
1 -TATCAAAATTTCATATGAAGGT
* * *
11237 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
11259 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
11280 TATCAAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
11302 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
11324 TATCAAAATTTCATA
1 TATCAAAATTTCATA
11339 ATGGGATCAT
Statistics
Matches: 356, Mismatches: 84, Indels: 70
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
19 2 0.01
20 2 0.01
21 31 0.09
22 225 0.63
23 62 0.17
24 18 0.05
25 2 0.01
26 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:10995 original size:23 final size:23
Alignment explanation
Indices: 10967--11072 Score: 115
Period size: 23 Copynumber: 4.6 Consensus size: 23
10957 CATAAAAAAG
*
10967 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
10990 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
11013 TTATCAAAATTTCATAGCGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * * *
11036 TATATCACAATTTCATAGTG-TGA
1 T-TATCAAAATTTCATAGGGAGGT
11059 TTATCAAAATTTCA
1 TTATCAAAATTTCA
11073 GAGTGTGATT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
22 12 0.17
23 43 0.61
24 16 0.23
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:11019 original size:46 final size:46
Alignment explanation
Indices: 10967--11072 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
10957 CATAAAAAAG
* * *
10967 TTATCAAAATTTTATAGGGAGGTT-TATCAAAATTTTATAG-GAAGA
1 TTATCAAAATTTCATAGCGAGGTTATATCAAAATTTCATAGTG-AGA
* *
11012 TTTATCAAAATTTCATAGCGAGGTTATATCACAATTTCATAGTGTGA
1 -TTATCAAAATTTCATAGCGAGGTTATATCAAAATTTCATAGTGAGA
11059 TTATCAAAATTTCA
1 TTATCAAAATTTCA
11073 GAGTGTGATT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
46 36 0.68
47 16 0.30
48 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (46 bp):
TTATCAAAATTTCATAGCGAGGTTATATCAAAATTTCATAGTGAGA
Found at i:11047 original size:24 final size:22
Alignment explanation
Indices: 10804--11072 Score: 131
Period size: 22 Copynumber: 12.5 Consensus size: 22
10794 TTATGGAGTA
**
10804 ATCAAAATTTCA-AGGA-GAAT
1 ATCAAAATTTCATAGGAGGTTT
* *
10824 ATCAAAA-TTCA-GGGAGG-AT
1 ATCAAAATTTCATAGGAGGTTT
*
10843 ATCAAAATTTCATATGAAGG-TT
1 ATCAAAATTTCATA-GGAGGTTT
*
10865 ATCAAAATTTCATAGG-GAGATT
1 ATCAAAATTTCATAGGAG-GTTT
* * *
10887 AACAAAATTTCATAATGA-GATT
1 ATCAAAATTTCAT-AGGAGGTTT
**
10909 ATCAAAAAATCATAGGGAGG-TT
1 ATCAAAATTTCATA-GGAGGTTT
*
10931 ATCAAAA-TT--T-GTA-G-TT
1 ATCAAAATTTCATAGGAGGTTT
* ** *
10947 ATCAAGATTTCATAAAAAAG-TT
1 ATCAAAATTTCAT-AGGAGGTTT
*
10969 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GGAGGTTT
* *
10992 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGG-AGGTTT
11015 ATCAAAATTTCATAGCGAGGTTAT
1 ATCAAAATTTCATAG-GAGGTT-T
* * *
11039 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATAG-GAGGTTT
11061 ATCAAAATTTCA
1 ATCAAAATTTCA
11073 GAGTGTGATT
Statistics
Matches: 199, Mismatches: 29, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.05
17 4 0.02
19 18 0.09
20 13 0.07
21 6 0.03
22 88 0.44
23 44 0.22
24 17 0.09
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAGGTTT
Found at i:11942 original size:70 final size:69
Alignment explanation
Indices: 11860--12006 Score: 242
Period size: 70 Copynumber: 2.1 Consensus size: 69
11850 ATTTTTATTT
* *
11860 TATTA-AATCTAATATCTTTATAACTATTTTATTTTTACCAGTTTACTATTTTAATTAAAATCTT
1 TATTAGAATCTAATATCTTTATAACTATTTTATTTTTACCAGTTTACTATTTT-ATAAAAAACTT
*
11924 AGATA
65 AAATA
*
11929 TATTAGAATCTAATATCTTTATAACTATTTTATTTTTACCATTTTACTATTTTATAAAAAACTTA
1 TATTAGAATCTAATATCTTTATAACTATTTTATTTTTACCAGTTTACTATTTTATAAAAAACTTA
11994 AATA
66 AATA
11998 TATTAGAAT
1 TATTAGAAT
12007 TTTTCTAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 27 0.37
70 46 0.63
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (69 bp):
TATTAGAATCTAATATCTTTATAACTATTTTATTTTTACCAGTTTACTATTTTATAAAAAACTTA
AATA
Found at i:12277 original size:22 final size:22
Alignment explanation
Indices: 12249--12466 Score: 154
Period size: 22 Copynumber: 9.7 Consensus size: 22
12239 TTAACTTTGC
* *
12249 AATTTTGTTAACTTCACTATGA
1 AATTTTGGTAACCTCACTATGA
* * *
12271 AATTTTGGTAACCACGCAATGA
1 AATTTTGGTAACCTCACTATGA
* *
12293 AATTTTGGTAACCTCATTTTGA
1 AATTTTGGTAACCTCACTATGA
**
12315 AATTTTGGTAATGGTAACCTTGCTATGA
1 AA--TT--T--TGGTAACCTCACTATGA
* *
12343 AATTTTGGTAACCCCA-AATGA
1 AATTTTGGTAACCTCACTATGA
* **
12364 AATTTTGGTAACGTCGTTATGA
1 AATTTTGGTAACCTCACTATGA
* * *
12386 AATTTCGATAACAT--CTAATGA
1 AATTTTGGTAACCTCACT-ATGA
12407 AATTTTGGTAACCTCACTATGA
1 AATTTTGGTAACCTCACTATGA
** *
12429 AATTTTGGTAACCTTGCTATCAA
1 AATTTTGGTAACCTCACTAT-GA
*
12452 AATTCTGGTAACCTC
1 AATTTTGGTAACCTC
12467 CTTATGTAAT
Statistics
Matches: 151, Mismatches: 34, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 32 0.21
22 81 0.54
23 16 0.11
24 3 0.02
26 3 0.02
28 15 0.10
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (22 bp):
AATTTTGGTAACCTCACTATGA
Found at i:12365 original size:21 final size:21
Alignment explanation
Indices: 12339--12441 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 21
12329 TAACCTTGCT
12339 ATGAAATTTTGGTAACCCCAA
1 ATGAAATTTTGGTAACCCCAA
* ***
12360 ATGAAATTTTGGTAACGTCGTT
1 ATGAAATTTTGGTAAC-CCCAA
* * ** *
12382 ATGAAATTTCGATAACATCTA
1 ATGAAATTTTGGTAACCCCAA
* *
12403 ATGAAATTTTGGTAACCTCACT
1 ATGAAATTTTGGTAACCCCA-A
12425 ATGAAATTTTGGTAACC
1 ATGAAATTTTGGTAACC
12442 TTGCTATCAA
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 33 0.51
22 32 0.49
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGAAATTTTGGTAACCCCAA
Found at i:12387 original size:43 final size:43
Alignment explanation
Indices: 12267--12441 Score: 143
Period size: 43 Copynumber: 3.9 Consensus size: 43
12257 TAACTTCACT
* * * * *
12267 ATGAAATTTTGGTAACCACGCAATGAAATTTTGGTAACCTCATT
1 ATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACCCCA-A
* **
12311 TTGAAATTTTGGTAATGGTAACCTTGCTATGAAATTTTGGTAACCCCAA
1 ATGAAA--TT--T--TGGTAACCTCACTATGAAATTTTGGTAACCCCAA
* ** * * ** *
12360 ATGAAATTTTGGTAACGTCGTTATGAAATTTCGATAACATCTA
1 ATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACCCCAA
12403 ATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACC
1 ATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACC
12442 TTGCTATCAA
Statistics
Matches: 104, Mismatches: 21, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
43 59 0.57
44 5 0.05
45 1 0.01
46 2 0.02
47 2 0.02
48 1 0.01
49 5 0.05
50 29 0.28
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (43 bp):
ATGAAATTTTGGTAACCTCACTATGAAATTTTGGTAACCCCAA
Found at i:13423 original size:35 final size:34
Alignment explanation
Indices: 13330--13536 Score: 182
Period size: 35 Copynumber: 5.8 Consensus size: 34
13320 AATATTTTAC
* *
13330 TCTTTACTGGATTACTCTTTACTCTTCACCATTCT
1 TCTTTACT-GATTACTCTTTACTCTTTACCATTTT
* *
13365 TCTTTACTGACTT-CCCTTCACTCTTTACCATTTTT
1 TCTTTACTGA-TTACTCTTTACTCTTTACCA-TTTT
* *
13400 TCTTTACCGATTACTCTTTACTCTACTCTTTACCCTTTT
1 TCTTTACTGATTACTC--T--T-TACTCTTTACCATTTT
* *
13439 TCTTTACTGATTACTCTTTTACTTTTTATCATTTT
1 TCTTTACTGATTACTC-TTTACTCTTTACCATTTT
* * * * * *
13474 ACTTTGCTGATTATTCTTTACTCTTCACTATTCT
1 TCTTTACTGATTACTCTTTACTCTTTACCATTTT
*
13508 TCTTTTACTGATTACTCTTTACTTTTTAC
1 TC-TTTACTGATTACTCTTTACTCTTTAC
13537 TGATTGCCTT
Statistics
Matches: 138, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
34 32 0.23
35 72 0.52
36 1 0.01
37 1 0.01
38 2 0.01
39 20 0.14
40 10 0.07
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (34 bp):
TCTTTACTGATTACTCTTTACTCTTTACCATTTT
Found at i:13452 original size:20 final size:20
Alignment explanation
Indices: 13396--13744 Score: 121
Period size: 21 Copynumber: 17.4 Consensus size: 20
13386 TCTTTACCAT
* *
13396 TTTTTCTTTACCGATTACTC
1 TTTTACTTTACTGATTACTC
* ** *
13416 -TTTACTCTACTCTTTACCC
1 TTTTACTTTACTGATTACTC
*
13435 TTTTTCTTTACTGATTACTC
1 TTTTACTTTACTGATTACTC
13455 TTTTAC-TT--T--TTA-TC
1 TTTTACTTTACTGATTACTC
* *
13469 ATTTTACTTTGCTGATTATTC
1 -TTTTACTTTACTGATTACTC
13490 -TTTACTCTTCACT-A-T--TC
1 TTTTACT-TT-ACTGATTACTC
*
13507 TTCT--TTTACTGATTACTC
1 TTTTACTTTACTGATTACTC
*
13525 -TTTACTTTTTACTGATTGC-C
1 TTTTAC--TTTACTGATTACTC
*
13545 TTTTGCTTTTTACTGATTAC-C
1 TTTTAC--TTTACTGATTACTC
*
13566 TTTTTACTTCTTGCTGATTAGCT-
1 -TTTTAC-T-TTACTGATTA-CTC
*
13589 TTTTACTCTTTACTGATCAC-C
1 TTTTA--CTTTACTGATTACTC
*
13610 TTTTTACTCTTACTGATTTC-C
1 -TTTTACT-TTACTGATTACTC
* *
13631 TTTTACTTCTTACTTATTACTT
1 TTTTAC-T-TTACTGATTACTC
13653 TTTTACTCTTACTGATTACT-
1 TTTTACT-TTACTGATTACTC
* * *
13673 ATTTACTTTTTACTGACTACTA
1 TTTTAC--TTTACTGATTACTC
**
13695 TTTTACTCTTGTTGATTAC-C
1 TTTTACT-TTACTGATTACTC
*
13715 TTCTTACTTTTTACTGATTACTA
1 TT-TTAC--TTTACTGATTACTC
13738 TTTTACT
1 TTTTACT
13745 CTTTACTAAT
Statistics
Matches: 252, Mismatches: 38, Indels: 78
0.68 0.10 0.21
Matches are distributed among these distances:
14 5 0.02
15 12 0.05
16 4 0.02
17 5 0.02
18 5 0.02
19 22 0.09
20 43 0.17
21 93 0.37
22 57 0.23
23 5 0.02
24 1 0.00
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTACTTTACTGATTACTC
Found at i:13534 original size:21 final size:21
Alignment explanation
Indices: 13510--13751 Score: 213
Period size: 21 Copynumber: 11.3 Consensus size: 21
13500 ACTATTCTTC
*
13510 TTTTACTGATTACTCTTTACT
1 TTTTACTGATTACTTTTTACT
* * *
13531 TTTTACTGATTGCCTTTTGCT
1 TTTTACTGATTACTTTTTACT
13552 TTTTACTGATTACCTTTTTACT
1 TTTTACTGATTA-CTTTTTACT
* *
13574 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTTTTTACT
* *
13596 CTTTACTGATCACCTTTTTAC-
1 TTTTACTGATTA-CTTTTTACT
* * *
13617 TCTTACTGATTTCCTTTTACT
1 TTTTACTGATTACTTTTTACT
* *
13638 TCTTACTTATTACTTTTTTAC-
1 TTTTACTGATTAC-TTTTTACT
* *
13659 TCTTACTGATTACTATTTACT
1 TTTTACTGATTACTTTTTACT
*
13680 TTTTACTGACTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
* *
13702 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTA-CTTTTTACT
13723 TTTTACTGATTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
*
13745 CTTTACT
1 TTTTACT
13752 AATTTCCATT
Statistics
Matches: 177, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
20 16 0.09
21 84 0.47
22 74 0.42
23 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTACTGATTACTTTTTACT
Found at i:13548 original size:35 final size:33
Alignment explanation
Indices: 13441--13548 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 33
13431 ACCCTTTTTC
* *
13441 TTTACTGATTACTCTTTTACTTTTTATCATTTTAC-
1 TTTACTGATTACTC-TTTACTTTTTA-C-TATTCCT
* * * *
13476 TTTGCTGATTATTCTTTACTCTTCACTATTCTTCT
1 TTTACTGATTACTCTTTACTTTTTACTATTC--CT
13511 TTTACTGATTACTCTTTACTTTTTACTGATTGCCT
1 TTTACTGATTACTCTTTACTTTTTACT-ATT-CCT
13546 TTT
1 TTT
13549 GCTTTTTACT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
32 3 0.05
33 1 0.02
34 10 0.17
35 40 0.69
36 3 0.05
37 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTACTGATTACTCTTTACTTTTTACTATTCCT
Found at i:13556 original size:42 final size:42
Alignment explanation
Indices: 13510--13744 Score: 235
Period size: 42 Copynumber: 5.5 Consensus size: 42
13500 ACTATTCTTC
* * *
13510 TTTTACTGATTACTCTTTACTTTTTACTGATTGCCTTTTGCT
1 TTTTACTGATTACTTTTTACTTCTTACTGATTGCCTTTTACT
* *
13552 TTTTACTGATTACCTTTTTACTTCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTTTTTACTTCTTACTGATT-GCCTTTTACT
* * *
13596 CTTTACTGATCACCTTTTTAC-TCTTACTGATTTCCTTTTACT
1 TTTTACTGATTA-CTTTTTACTTCTTACTGATTGCCTTTTACT
* * *
13638 TCTTACTTATTACTTTTTTAC-TCTTACTGATT-ACTATTTACT
1 TTTTACTGATTAC-TTTTTACTTCTTACTGATTGCCT-TTTACT
* ** *
13680 TTTTACTGACTACTATTTTAC-TCTTGTTGATTACCTTCTTACT
1 TTTTACTGATTACT-TTTTACTTCTTACTGATTGCCTT-TTACT
13723 TTTTACTGATTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
13745 CTTTACTAAT
Statistics
Matches: 163, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
41 4 0.02
42 78 0.48
43 54 0.33
44 27 0.17
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (42 bp):
TTTTACTGATTACTTTTTACTTCTTACTGATTGCCTTTTACT
Found at i:13685 original size:14 final size:13
Alignment explanation
Indices: 13609--13686 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
13599 TACTGATCAC
*
13609 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
13622 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
13636 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
13650 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
13664 CTGATTACTATTTA
1 CTTTTTACT-TTTA
13678 CTTTTTACT
1 CTTTTTACT
13687 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:13779 original size:64 final size:64
Alignment explanation
Indices: 13661--13797 Score: 163
Period size: 64 Copynumber: 2.1 Consensus size: 64
13651 TTTTTTACTC
* * * * *
13661 TTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTT-ACTTT
1 TTACTGATTACTATTTACTCTTTACTAACTACCATTTTACCCTTGTAGATTACCTT-TTAACTTT
* *
13725 TTACTGATTACTATTTTACTCTTTACTAATTTCCATTTTACCCTT-TCAGA-TACCTTTTAACTT
1 TTACTGATTACTA-TTTACTCTTTACTAACTACCATTTTACCCTTGT-AGATTACCTTTTAACTT
13788 T
64 T
13789 TTACTGATT
1 TTACTGATT
13798 GCATGCTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 2 0.03
64 34 0.54
65 27 0.43
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (64 bp):
TTACTGATTACTATTTACTCTTTACTAACTACCATTTTACCCTTGTAGATTACCTTTTAACTTT
Found at i:13793 original size:149 final size:148
Alignment explanation
Indices: 13512--13793 Score: 336
Period size: 149 Copynumber: 1.9 Consensus size: 148
13502 TATTCTTCTT
* * * * * * *
13512 TTACTGATTACTCTTTACTTTTTACTGATTGCCTTTTGCTTTTTACTGATTACCTTTTTACTTCT
1 TTACTGATTACTATTTACTTTTTACTGACTACATTTTACTTTGTA-TGATTACCTTCTTACTTCT
* * * * * *
13577 TGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTTCCTTTTACTTCTT
65 TACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACAGATTACCTTTTACTTCTT
13642 ACTTATTACTTTTTTACTC
130 ACTTATTACTTTTTTACTC
*
13661 TTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGT-TGATTACCTTCTTACTTT
1 TTACTGATTACTATTTACTTTTTACTGACTAC-ATTTTACT-TTGTATGATTACCTTCTTACTTC
** *
13725 TTACTGATTA-CTATTTTACTCTTTACTAATTTCCATTTTACCCTTTCAGA-TACCTTTTAACTT
64 TTACTGATTAGCT-TTTTACTCTTTACTAATCACCATTTTACCCTTACAGATTACCTTTT-ACTT
*
13788 TTTACT
127 CTTACT
13794 GATTGCATGC
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
148 9 0.08
149 93 0.84
150 6 0.05
151 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (148 bp):
TTACTGATTACTATTTACTTTTTACTGACTACATTTTACTTTGTATGATTACCTTCTTACTTCTT
ACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACAGATTACCTTTTACTTCTTA
CTTATTACTTTTTTACTC
Found at i:14028 original size:26 final size:26
Alignment explanation
Indices: 13995--14059 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
13985 ATTTATCGAT
*
13995 TTACTGATTACTATCTTTTCACCTGA
1 TTACTGATTACTATCTTTTCACCTAA
* * *
14021 TTACTGATTACTCTCTTTTTACTTAA
1 TTACTGATTACTATCTTTTCACCTAA
14047 TTACTGACTTACT
1 TTACTGA-TTACT
14060 GATTACTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 29 0.85
27 5 0.15
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49
Consensus pattern (26 bp):
TTACTGATTACTATCTTTTCACCTAA
Found at i:14093 original size:55 final size:55
Alignment explanation
Indices: 14024--14292 Score: 430
Period size: 55 Copynumber: 4.9 Consensus size: 55
14014 CACCTGATTA
* *
14024 CTGATTACTCTCTTTTTACTTAATTACTGACTTACTGATTACTACTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
**
14079 CTGATTGGTCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
* *
14134 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTACTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
* *
14189 CTGATTAATCTCCTTTTACTTAACTACTGACTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
* * * *
14244 CTGATTAATCTCTTTTCACTTAATTATTGATTTACTGATTTCTATTACT
1 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACT
14293 CTTTACAGAT
Statistics
Matches: 197, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 197 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTACTATTACTTTGACT
Found at i:14192 original size:21 final size:21
Alignment explanation
Indices: 14168--14250 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
14158 TACTGATTTA
14168 CTGATTACTACTACTTTGACT
1 CTGATTACTACTACTTTGACT
* * *
14189 CTGATTAAT-CTCCTTTTACT
1 CTGATTACTACTACTTTGACT
14209 -T-A--ACTACTGAC-TT-A--
1 CTGATTACTACT-ACTTTGACT
*
14223 CTGATTACTATTACTTTGACT
1 CTGATTACTACTACTTTGACT
14244 CTGATTA
1 CTGATTA
14251 ATCTCTTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 6 0.13
18 9 0.20
19 2 0.04
20 9 0.20
21 15 0.33
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (21 bp):
CTGATTACTACTACTTTGACT
Found at i:17721 original size:26 final size:24
Alignment explanation
Indices: 17682--17730 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
17672 TATGATTAAA
17682 ATGCAACAATATTAAGCTAAATGAAG
1 ATGCAACAATATT-A-CTAAATGAAG
17708 ATGCAACTAA-ATTACTAAATGAA
1 ATGCAAC-AATATTACTAAATGAA
17731 AATATGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 10 0.45
27 2 0.09
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
ATGCAACAATATTACTAAATGAAG
Done.