Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019844.1 Corchorus olitorius cultivar O-4 contig19877, 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: 42818
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:514 original size:96 final size:96
Alignment explanation
Indices: 342--523 Score: 301
Period size: 96 Copynumber: 1.9 Consensus size: 96
332 GAAAATATTA
*
342 ATTTAGTTAGATTATATTAGAATTAAATTAAATTTACCCACAACCAATTAACTTTGGACAAATGT
1 ATTTAATTAGATTATATTAGAATTAAATTAAATTTACCCACAACCAATTAACTTTGGACAAATGT
**
407 TTGAAGGAGAAAAACCAAATACTGAGCATAC
66 CAGAAGGAGAAAAACCAAATACTGAGCATAC
* *
438 ATTTAATTAGATTATATTAGAATTAAATTAAATTTACTCTCAACCAATTAACTTTGGACAAATGT
1 ATTTAATTAGATTATATTAGAATTAAATTAAATTTACCCACAACCAATTAACTTTGGACAAATGT
* *
503 CAGAAGTAGAAAAACTAAATA
66 CAGAAGGAGAAAAACCAAATA
524 GTAAACATAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (96 bp):
ATTTAATTAGATTATATTAGAATTAAATTAAATTTACCCACAACCAATTAACTTTGGACAAATGT
CAGAAGGAGAAAAACCAAATACTGAGCATAC
Found at i:2567 original size:36 final size:37
Alignment explanation
Indices: 2490--2575 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 37
2480 AAGCCGAACA
* **
2490 GATCCTCGAATAGGAAAAAGAAATTTAAATTAAAGAT
1 GATCCTCGAATAGGAAAAAGAAATGTAAAGCAAAGAT
* *
2527 -ATCCTTGAATAGGAAAACGAAATGTAAAGCAAAG-T
1 GATCCTCGAATAGGAAAAAGAAATGTAAAGCAAAGAT
2562 GATCCTCGAATAGG
1 GATCCTCGAATAGG
2576 GTTTTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.02
36 41 0.98
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.22
Consensus pattern (37 bp):
GATCCTCGAATAGGAAAAAGAAATGTAAAGCAAAGAT
Found at i:2646 original size:39 final size:39
Alignment explanation
Indices: 2600--2932 Score: 441
Period size: 39 Copynumber: 8.5 Consensus size: 39
2590 ACTCTAAGAT
*
2600 AGGATTTTGAAACGAAACTCTCGAACAGAGATCTAAAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
* * * * * **
2639 AGGATTTTGGAACGAAACACTCGTACAGAAACCTCAAGT
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
* *
2678 AGGATTTTGAAACGAAACTCTCGAACAGAGCCCTCAAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
* * *
2717 AGGATTTTAAAAACAAAACTCTCGAACAGAGACCTAAAAT
1 AGGATTTT-GAAACGAAACTCTCGAACAGAGACCTAAAAC
*
2757 AGGATTTTGAAACGAAACTCTCGAACAGAAACCTAAAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
** *
2796 AGGATTTTGAATTGAAACTCTCGAACAGAGACCTCAAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
*
2835 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTCAAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
* * * *
2874 AGGATTTTGAAATGAAACTCTCGGACAGAGAACTACAAC
1 AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
*
2913 AGGATTTTTAAACGGAAACT
1 AGGATTTTGAAAC-GAAACT
2933 AAAGCAATAA
Statistics
Matches: 255, Mismatches: 37, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
39 215 0.84
40 40 0.16
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (39 bp):
AGGATTTTGAAACGAAACTCTCGAACAGAGACCTAAAAC
Found at i:2813 original size:157 final size:156
Alignment explanation
Indices: 2593--2932 Score: 484
Period size: 157 Copynumber: 2.2 Consensus size: 156
2583 AAACGTAACT
* * *
2593 CTAAGATAGGATTTTGAAACGAAACTCTCGAACAGAGATCTAAAACAGGATTTTGGAACGAAACA
1 CTAAAATAGGATTTTGAAACGAAACTCTCGAACAGAAACCTAAAACAGGATTTTGGAACGAAACA
* ** *
2658 CTCGTACAGAAACCTCAAGTAGGATTTTGAAACGAAACTCTCGAACAGAGCCCTCAAACAGGATT
66 CTCGAACAGAAACCTCAAACAGGATTTTGAAACGAAACTCTCGAACAGAGACCTCAAACAGGATT
*
2723 TTAAAAACAAAACTCTCGAACAGAGAC
131 TT-AAAACAAAACTCTCGAACAGAGAA
*
2750 CTAAAATAGGATTTTGAAACGAAACTCTCGAACAGAAACCTAAAACAGGATTTT-GAATTGAAAC
1 CTAAAATAGGATTTTGAAACGAAACTCTCGAACAGAAACCTAAAACAGGATTTTGGAA-CGAAAC
* *
2814 TCTCGAACAGAGACCTCAAACAGGATTTTGAAACGAAACTCTCGAACAGAGACCTCAAACAGGAT
65 ACTCGAACAGAAACCTCAAACAGGATTTTGAAACGAAACTCTCGAACAGAGACCTCAAACAGGAT
* ** *
2879 TTTGAAATGAAACTCTCGGACAGAGAA
130 TTTAAAACAAAACTCTCGAACAGAGAA
* * *
2906 CTACAACAGGATTTTTAAACGGAAACT
1 CTAAAATAGGATTTTGAAAC-GAAACT
2933 AAAGCAATAA
Statistics
Matches: 163, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
156 39 0.24
157 124 0.76
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.21
Consensus pattern (156 bp):
CTAAAATAGGATTTTGAAACGAAACTCTCGAACAGAAACCTAAAACAGGATTTTGGAACGAAACA
CTCGAACAGAAACCTCAAACAGGATTTTGAAACGAAACTCTCGAACAGAGACCTCAAACAGGATT
TTAAAACAAAACTCTCGAACAGAGAA
Found at i:3088 original size:42 final size:44
Alignment explanation
Indices: 3029--3167 Score: 143
Period size: 39 Copynumber: 3.3 Consensus size: 44
3019 GCAATGATAC
* *
3029 TTCAAACAGAAATTAACTGAT-AAGCAATGCTCCTGAA-CAGGA
1 TTCAAACAGAAATTAACTGATAAAGCAATGATCCTAAATCAGGA
* * *
3071 TTCAAACATAGATTAACTGATAAAGCTATGATCCTAAATCAGGA
1 TTCAAACAGAAATTAACTGATAAAGCAATGATCCTAAATCAGGA
*
3115 TT------GAAAATAACATGATAAAGCAATGATCCTAAATCAGGA
1 TTCAAACAGAAATTAAC-TGATAAAGCAATGATCCTAAATCAGGA
3154 TTCACAA-AGAAATT
1 TTCA-AACAGAAATT
3168 GATAGAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 15
0.76 0.10 0.15
Matches are distributed among these distances:
38 6 0.08
39 28 0.36
42 19 0.24
43 13 0.17
44 7 0.09
45 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (44 bp):
TTCAAACAGAAATTAACTGATAAAGCAATGATCCTAAATCAGGA
Found at i:3218 original size:20 final size:20
Alignment explanation
Indices: 3195--3235 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3185 AGAAGATATG
*
3195 AAATGCCCGAAGGTCTTATC
1 AAATGCCCGAAGGACTTATC
3215 AAATGCCCGAAGGACTTATC
1 AAATGCCCGAAGGACTTATC
3235 A
1 A
3236 GAATTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
AAATGCCCGAAGGACTTATC
Found at i:5325 original size:18 final size:18
Alignment explanation
Indices: 5302--5336 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5292 CCCTTTATTT
5302 AGCCACGTGGATTTTATC
1 AGCCACGTGGATTTTATC
*
5320 AGCCACGTGTATTTTAT
1 AGCCACGTGGATTTTAT
5337 TTACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (18 bp):
AGCCACGTGGATTTTATC
Found at i:5626 original size:101 final size:101
Alignment explanation
Indices: 5486--5688 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
5476 TCTTCTCTCT
5486 AAGAAATTCACTTCTTCTCCTTAAAAAAATTCTTTGTTTCTCTCGTTGAAAATTTTTCTCTCGTT
1 AAGAAATTCACTTCTTCTCCTTAAAAAAATTCTTTGTTTCTCTCGTTGAAAATTTTTCTCTCGTT
5551 GAAAAATAAATGAAATCGTTAAAACTTTAGATTTGG
66 GAAAAATAAATGAAATCGTTAAAACTTTAGATTTGG
5587 AAGAAATTCACTTCTTCTCCTTAAAAAAATTCTTTGTTTCTCTCGTTGAAAATTTTTCTCTCGTT
1 AAGAAATTCACTTCTTCTCCTTAAAAAAATTCTTTGTTTCTCTCGTTGAAAATTTTTCTCTCGTT
5652 GAAAAATAAATGAAATCGTTAAAACTTTAGATTTGG
66 GAAAAATAAATGAAATCGTTAAAACTTTAGATTTGG
5688 A
1 A
5689 TTTAGGGTTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (101 bp):
AAGAAATTCACTTCTTCTCCTTAAAAAAATTCTTTGTTTCTCTCGTTGAAAATTTTTCTCTCGTT
GAAAAATAAATGAAATCGTTAAAACTTTAGATTTGG
Found at i:5855 original size:18 final size:18
Alignment explanation
Indices: 5801--5857 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
5791 GTTTAATTTC
5801 GAATTGATTTGGGGCTTT
1 GAATTGATTTGGGGCTTT
* ** **
5819 G-GTTCGATTTAAGTATTT
1 GAATT-GATTTGGGGCTTT
5837 GAATTGATTTGGGGCTTT
1 GAATTGATTTGGGGCTTT
5855 GAA
1 GAA
5858 AGGGTGAAAC
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (18 bp):
GAATTGATTTGGGGCTTT
Found at i:13916 original size:19 final size:18
Alignment explanation
Indices: 13879--13923 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
13869 CGAAATTTAC
13879 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
13897 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
13916 TTATTATT
1 TAATTATT
13924 AATTTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:24432 original size:12 final size:12
Alignment explanation
Indices: 24415--24459 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
24405 AACTAGGAAA
24415 AAAATAAATAAC
1 AAAATAAATAAC
24427 AAAATAAACTTAA-
1 AAAATAAA--TAAC
24440 AAAATAAATAAC
1 AAAATAAATAAC
24452 AAAATAAA
1 AAAATAAA
24460 CTTAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.10
12 16 0.53
13 8 0.27
14 3 0.10
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATAAATAAC
Found at i:24442 original size:25 final size:25
Alignment explanation
Indices: 24413--24467 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
24403 CCAACTAGGA
24413 AAAAAATAAATAACAAAATAAACTT
1 AAAAAATAAATAACAAAATAAACTT
24438 AAAAAATAAATAACAAAATAAACTT
1 AAAAAATAAATAACAAAATAAACTT
24463 AAAAA
1 AAAAA
24468 TAAGGTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (25 bp):
AAAAAATAAATAACAAAATAAACTT
Found at i:24467 original size:12 final size:11
Alignment explanation
Indices: 24413--24470 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 11
24403 CCAACTAGGA
24413 AAAAAATAAAT
1 AAAAAATAAAT
24424 AACAAAATAAACTT
1 AA-AAAATAAA--T
24438 AAAAAATAAAT
1 AAAAAATAAAT
24449 AACAAAATAAACT
1 AA-AAAATAAA-T
*
24462 TAAAAATAA
1 AAAAAATAA
24471 GGTTTTCCCG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 5 0.12
12 23 0.56
13 10 0.24
14 3 0.07
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:24513 original size:22 final size:22
Alignment explanation
Indices: 24482--24524 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24472 GTTTTCCCGC
*
24482 AACAACTTCTGTCCCGAAGTTA
1 AACAACTTCTGGCCCGAAGTTA
* *
24504 AACAAGTTCTGGGCCGAAGTT
1 AACAACTTCTGGCCCGAAGTT
24525 GTCCTGCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTA
Found at i:34696 original size:2 final size:2
Alignment explanation
Indices: 34644--34677 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
34634 GAGGGAGGGA
34644 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
34678 GTCTTTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36875 original size:78 final size:78
Alignment explanation
Indices: 36774--36942 Score: 259
Period size: 78 Copynumber: 2.2 Consensus size: 78
36764 TTATTTAAAC
* * **
36774 TTTTA-TAGTTTTTCTCAACTAAAAACTCTATATTTATTTAATTAAATCTATTATTTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACT
*
36838 ATCTTATTTTACCA
65 ATCTTAGTTTACCA
*
36852 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTA
*
36917 TTTTAGTTTACCA
66 TCTTAGTTTACCA
36930 TTTTACTATTTTA
1 TTTTACTATTTTA
36943 ATTAAAAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 81 0.98
79 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.01, T:0.52
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTA
TCTTAGTTTACCA
Found at i:40744 original size:32 final size:32
Alignment explanation
Indices: 40708--40773 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40698 TTGCACTTTC
40708 GAGTCTTCACCATTGTCTTTGAAATCGGACTA
1 GAGTCTTCACCATTGTCTTTGAAATCGGACTA
40740 GAGTCTTCACCATTGTCTTTGAAATCGGACTA
1 GAGTCTTCACCATTGTCTTTGAAATCGGACTA
40772 GA
1 GA
40774 TCAGTCGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (32 bp):
GAGTCTTCACCATTGTCTTTGAAATCGGACTA
Done.