Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010865.1 Corchorus olitorius cultivar O-4 contig10897, 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: 12340
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2422 original size:56 final size:56
Alignment explanation
Indices: 2298--2506 Score: 375
Period size: 56 Copynumber: 3.8 Consensus size: 56
2288 GTGCGGTCTT
* *
2298 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAG-TTTTTTAAGGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
2353 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
2409 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
* *
2465 TTGATCCTCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTT
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTT
2507 CGATGATCAG
Statistics
Matches: 149, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
55 37 0.25
56 112 0.75
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (56 bp):
TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTTAATGATTAGAG
Found at i:2531 original size:35 final size:35
Alignment explanation
Indices: 2493--2882 Score: 489
Period size: 35 Copynumber: 10.9 Consensus size: 35
2483 AGTGCGGTCG
*
2493 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
2528 TTTCAAGAAGTTTTCGGTGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
2563 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
2598 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATC-T--CA
* *
2636 TTTCAGGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
2671 TTTCAAGAAGTTTTCAATGATCAGAGTTGGTCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
2706 TTTCAAGAAGTTTT-TACGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
2740 TTTTAAGAAGTTTTTG-TCGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGAT-GATCAGAGTTGATCTCA
** * *
2775 TTTCAAGTAAGTTTT-TTTGGTCAGAGTTGATCTCC
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
** *
2810 TTTCAAGAAGTTTTTTTTTATGTATCAGAGTTGATCTTA
1 TTTCAAGAAG---TTTTCGATG-ATCAGAGTTGATCTCA
2849 TTTCAAGTAAGTTTTCGATGATCAGAGTTGATCT
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCT
2883 TCACATTGAT
Statistics
Matches: 312, Mismatches: 30, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
34 32 0.10
35 187 0.60
36 22 0.07
37 12 0.04
38 36 0.12
39 20 0.06
40 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:2653 original size:143 final size:140
Alignment explanation
Indices: 2493--2881 Score: 496
Period size: 143 Copynumber: 2.7 Consensus size: 140
2483 AGTGCGGTCG
* **
2493 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGA
1 TTTCAGGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGATCAGAGTTGA
*
2558 TCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGAT-GATCAG
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCG-TCGATCAG
2622 AGTTGATCATCGCA
130 AGTTGATC-T--CA
*
2636 TTTCAGGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGATCAGAGTTGG
1 TTTCAGGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGATCAGAGTTGA
* * * * * *
2701 TCTCATTTCAAGAAGTTTT-TACGATCAGAGTTGATCTCCTTTTAAGAAGTTTTTGTCGATCAGA
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGTCGATCAGA
2765 GTTGATCTCA
131 GTTGATCTCA
* ** * * **
2775 TTTCAAGTAAGTTTT-TTTGGTCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTTATGTATCAGA
1 TTTC-AGGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAG---TTTTCAATG-ATCAGA
*
2839 GTTGATCTTATTTCAAGTAAGTTTTCGATGATCAGAGTTGATC
61 GTTGATCTCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATC
2882 TTCACATTGA
Statistics
Matches: 216, Mismatches: 22, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
139 32 0.15
140 9 0.04
141 2 0.01
142 51 0.24
143 100 0.46
144 7 0.03
145 15 0.07
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (140 bp):
TTTCAGGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGTCGATCAGA
GTTGATCTCA
Found at i:5301 original size:19 final size:20
Alignment explanation
Indices: 5274--5311 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5264 TACTATTATT
5274 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5294 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5312 AATGTCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:5577 original size:24 final size:22
Alignment explanation
Indices: 5484--5638 Score: 73
Period size: 22 Copynumber: 7.0 Consensus size: 22
5474 TGTGGCAATC
* * *
5484 AAAATTTTATAAGATGGTTATT
1 AAAATTTCATAGGAAGGTTATT
* * *
5506 ATAATTTCA-AGAGGAGGTTATC
1 AAAATTTCATAG-GAAGGTTATT
* ** **
5528 AAAATTCCAT-GGTGCGGTTACC
1 AAAATTTCATAGG-AAGGTTATT
5550 AAAATTTCATAGGATTAGGTTATT
1 AAAATTTCATAGGA--AGGTTATT
**
5574 AAAATTTTTTAGGAAGGTTATT
1 AAAATTTCATAGGAAGGTTATT
* * *
5596 GAAATTTCATAGTG-TGGTTATC
1 AAAATTTCATAG-GAAGGTTATT
* * *
5618 ACAATTTTATAGAAAGGTTAT
1 AAAATTTCATAGGAAGGTTAT
5639 CAAAGAGATT
Statistics
Matches: 98, Mismatches: 27, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
21 2 0.02
22 76 0.78
23 3 0.03
24 17 0.17
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATT
Found at i:5791 original size:66 final size:66
Alignment explanation
Indices: 5647--5794 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 66
5637 ATCAAAGAGA
*
5647 TTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGATTAACAAATTTTTATATAAAG
1 TTATCAAAATTTCATAGCGAGGTTATAAGAATTTCATAGTGTGATTAACAAATTTTTATATAAAG
5712 G
66 G
* * * * *
5713 TTA-CTAATATTTCATGGGGAGGTTATCAA-AATTTCATAGTGTGGTTATCAAAATTTTT-TAGT
1 TTATC-AAAATTTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGATTAAC-AAATTTTTATA-T
**
5775 -GTGG
62 AAAGG
5779 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
5795 TGAAGGTTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
65 1 0.01
66 54 0.81
67 12 0.18
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (66 bp):
TTATCAAAATTTCATAGCGAGGTTATAAGAATTTCATAGTGTGATTAACAAATTTTTATATAAAG
G
Found at i:5802 original size:22 final size:22
Alignment explanation
Indices: 5647--5808 Score: 118
Period size: 22 Copynumber: 7.4 Consensus size: 22
5637 ATCAAAGAGA
* *
5647 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
5669 TTAT-AAGAATTTCATAGTGTGA
1 TTATCAA-AATTTCATAGTGAGG
* * * *
5691 TTAACAAATTTTTATA-TAAAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
5713 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
5735 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** *
5757 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
5779 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
5801 TTAT-AAAA
1 TTATCAAAA
5809 GTCTCAATTT
Statistics
Matches: 108, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
21 10 0.09
22 95 0.88
23 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:5933 original size:22 final size:23
Alignment explanation
Indices: 5905--5965 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
5895 TATCAGTGTT
5905 GTTATCAAAATTTCA-AA-GCGA
1 GTTATCAAAATTTCATAATGCGA
* *
5926 GGTTATCAAAATTACATAATGTGA
1 -GTTATCAAAATTTCATAATGCGA
5950 -TTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
5966 GAGGTGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 29 0.85
23 2 0.06
24 3 0.09
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (23 bp):
GTTATCAAAATTTCATAATGCGA
Found at i:6002 original size:22 final size:22
Alignment explanation
Indices: 5905--6029 Score: 67
Period size: 22 Copynumber: 5.7 Consensus size: 22
5895 TATCAGTGTT
* *
5905 GTTATCAAAATTTCA-AAGCGAG
1 GTTATCAAAATTTTATAA-AGAG
** * *
5927 GTTATCAAAATTACATAATGTG
1 GTTATCAAAATTTTATAAAGAG
* *
5949 ATTATCAAAATTTCAT--AGAG
1 GTTATCAAAATTTTATAAAGAG
* *
5969 GTGTCAACAAAATTTTATAGAGAG
1 GT-T-ATCAAAATTTTATAAAGAG
* * *
5993 GTTATTAAAACTTCATAAAGAG
1 GTTATCAAAATTTTATAAAGAG
* *
6015 TTTATCAAATTTTTA
1 GTTATCAAAATTTTA
6030 AAATGTGATT
Statistics
Matches: 78, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
20 3 0.04
21 1 0.01
22 65 0.83
23 3 0.04
24 6 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTTATAAAGAG
Found at i:6196 original size:23 final size:21
Alignment explanation
Indices: 6156--6281 Score: 69
Period size: 22 Copynumber: 5.7 Consensus size: 21
6146 TATCTTATGG
* *
6156 AGGTTATCAACATCTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
6177 ATTGGTTATCAAAATTTCATTGGG
1 A--GGTTATCAAAATTTCA-TAGT
*
6201 AAGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
*
6222 GAGGTCTA-CAAAATTTC-TCAGGG
1 -AGGT-TATCAAAATTTCAT-A-GT
*
6245 AGGTTAAT-AAAATTTCATAAGA
1 AGGTT-ATCAAAATTTCAT-AGT
**
6267 AGGTTAAAAAAATTT
1 AGGTTATCAAAATTT
6282 ATAAAAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 21
0.71 0.10 0.18
Matches are distributed among these distances:
21 6 0.07
22 54 0.66
23 19 0.23
24 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:6233 original size:22 final size:21
Alignment explanation
Indices: 6180--6277 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 21
6170 TCATAGTATT
*
6180 GGTTATCAAAATTTCATTGGGA
1 GGTTA-CAAAATTTCATAGGGA
* *
6202 AGTTATCAAAATTTCATAGTGA
1 GGTTA-CAAAATTTCATAGGGA
6224 GGTCTACAAAATTTC-TCAGGGA
1 GGT-TACAAAATTTCAT-AGGGA
* * *
6246 GGTTAATAAAATTTCATAAGAA
1 GGTT-ACAAAATTTCATAGGGA
*
6268 GGTTAAAAAA
1 GGTTACAAAA
6278 ATTTATAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.11
22 53 0.84
23 3 0.05
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (21 bp):
GGTTACAAAATTTCATAGGGA
Found at i:6338 original size:22 final size:22
Alignment explanation
Indices: 6252--6346 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 22
6242 GGGAGGTTAA
* *
6252 TAAAATTTCATAAGAAGGTTAA
1 TAAAATTTCATAAGAAGATTAT
* * * *
6274 AAAAATTT-ATAAAAATATTGT
1 TAAAATTTCATAAGAAGATTAT
* * *
6295 TGAAATTCCAT-AGTATCG-TTAT
1 TAAAATTTCATAAG-A-AGATTAT
6317 TAAAATTTCATAAGAAGATTAT
1 TAAAATTTCATAAGAAGATTAT
*
6339 CAAAATTT
1 TAAAATTT
6347 TAGAAGGAGG
Statistics
Matches: 51, Mismatches: 17, Indels: 10
0.65 0.22 0.13
Matches are distributed among these distances:
21 15 0.29
22 34 0.67
23 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAAATTTCATAAGAAGATTAT
Found at i:10672 original size:34 final size:34
Alignment explanation
Indices: 10627--10692 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
10617 ATACAAATAG
10627 AATTCAAGTTTTCCAAGTACAAACAACAATATCA
1 AATTCAAGTTTTCCAAGTACAAACAACAATATCA
* ** *
10661 AATTCATGTTTTTGAAGTACAAACGACAATAT
1 AATTCAAGTTTTCCAAGTACAAACAACAATAT
10693 GAAGAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (34 bp):
AATTCAAGTTTTCCAAGTACAAACAACAATATCA
Done.