Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005732.1 Corchorus capsularis cultivar CVL-1 contig05750, 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: 5175
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Found at i:455 original size:30 final size:30
Alignment explanation
Indices: 421--477 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
411 GTGATGAAAT
*
421 AAGTCAACTGTGTATTTACAGCAGGATTCA
1 AAGTCAACAGTGTATTTACAGCAGGATTCA
* *
451 AAGTCAACAGTTTGTTTACAGCAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
478 CAATTCATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATTCA
Found at i:1430 original size:2 final size:2
Alignment explanation
Indices: 1423--1466 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
1413 GTAAATCACA
* *
1423 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
1466 A
1 A
1467 AAAGTACGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1549 original size:30 final size:32
Alignment explanation
Indices: 1495--1560 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
1485 AACTTTATGT
* *
1495 TTTCCGATTGTACCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCCCTATTTTTAAAAACATA
1526 TTTCCAATTGTACCCCT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCCTATTTTTAAAAACATA
1557 TTTC
1 TTTC
1561 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTCCAATTGTACCCCTATTTTTAAAAACATA
Found at i:1567 original size:32 final size:31
Alignment explanation
Indices: 1501--1568 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1491 ATGTTTTCCG
* *
1501 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
1532 ATTGTACCCCTT-TTTTAAAAACATATTTCTAA
1 ATTGTA-CCCTTATTTTAAAAACATATTTC-AA
1564 ATTGT
1 ATTGT
1569 CATTACTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:1989 original size:22 final size:22
Alignment explanation
Indices: 1961--2144 Score: 160
Period size: 22 Copynumber: 8.3 Consensus size: 22
1951 TGTCTCTATG
*
1961 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
1983 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
2006 -GGTTATCAAAATTCCATAGCG-
1 TGGTTATCAAAATTTCATAG-GA
*
2027 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
**
2050 -ACTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
2071 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
2093 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
2117 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
2139 TGGTTA
1 TGGTTA
2145 ATTTTCACAA
Statistics
Matches: 131, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.03
22 105 0.80
23 4 0.03
24 18 0.14
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:2205 original size:22 final size:22
Alignment explanation
Indices: 2180--2571 Score: 115
Period size: 22 Copynumber: 17.6 Consensus size: 22
2170 ATCAAAGAGA
*
2180 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
2202 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
* *
2224 TCAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGCGAGG
* * *
2246 TTAGT-AATATTTCATGGGGAGG
1 TTA-TCAAAATTTCATAGCGAGG
* *
2268 TTATCAAAATTTTATAGCGTGG
1 TTATCAAAATTTCATAGCGAGG
*
2290 TTATCAAAATTTCATATG-AAGG
1 TTATCAAAATTTCATA-GCGAGG
* **
2312 TTATAAAAGTCTCAGTTTCATAAGGA-G
1 TTATCAAA-----A-TTTCATAGCGAGG
* * *
2339 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGCGAGG
* * * *
2359 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGCGAGG
* * * *
2380 TTATCGAAATTCCATAGAGATCAGA
1 TTATCAAAATTTCATAGCG---AGG
*
2405 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGCG-AGG
** **
2426 TTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAGCGAGG
* *
2448 TTATCAAAA-TTCGAAAGCGATG
1 TTATCAAAATTTC-ATAGCGAGG
* ** * *
2470 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGCGAGG
* * **
2492 TTATCAGAATCTCATAAAG-GG
1 TTATCAAAATTTCATAGCGAGG
* * * **
2513 ATCAACAAAATTTTATAAAGAGG
1 -TTATCAAAATTTCATAGCGAGG
**
2536 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
*
2558 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2572 GAATGTTATT
Statistics
Matches: 276, Mismatches: 67, Indels: 54
0.70 0.17 0.14
Matches are distributed among these distances:
19 1 0.00
20 16 0.06
21 34 0.12
22 182 0.66
23 12 0.04
24 4 0.01
25 12 0.04
26 5 0.02
27 2 0.01
28 8 0.03
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:2414 original size:25 final size:21
Alignment explanation
Indices: 2378--2441 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 21
2368 CTCATAGAGT
*
2378 GATTATCGAAATTCCATAGAGATCA
1 GATTATCAAAATT-CATAG-GA--A
*
2403 GATTATCAAAATTTATAGGAA
1 GATTATCAAAATTCATAGGAA
2424 GATTATCAAAATTTCATA
1 GATTATCAAAA-TTCATA
2442 ATGTTGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 5 0.14
23 2 0.06
24 4 0.11
25 12 0.34
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (21 bp):
GATTATCAAAATTCATAGGAA
Found at i:2899 original size:104 final size:105
Alignment explanation
Indices: 2715--2923 Score: 239
Period size: 104 Copynumber: 2.0 Consensus size: 105
2705 TTTTATAGTT
* ** *
2715 TAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAA
2780 GAGGTTATCAAAAAATC-C-TATG-GAGGTTATCAAAATTTG
66 GAGGTTATC-AAAAATCTCATA-GCGAGGTTATCAAAATTTG
* * * * *
2819 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGATGTTTATCAAAATTTTATAG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGA-GATTAACAAAATTTCATA-
* *
2884 GAAGA-TTTATC-AAAATTTCATAGCGAGGTTATCAAAATTT
64 -AAGAGGTTATCAAAAATCTCATAGCGAGGTTATCAAAATTT
2924 CATAGTGTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
104 45 0.51
105 17 0.19
106 23 0.26
107 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (105 bp):
TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAA
GAGGTTATCAAAAATCTCATAGCGAGGTTATCAAAATTTG
Found at i:3230 original size:44 final size:44
Alignment explanation
Indices: 2608--3236 Score: 274
Period size: 44 Copynumber: 14.5 Consensus size: 44
2598 GGTATTTCTG
* * *
2608 GGAAGGTTATCAAAATTTCATAGTATGGTTA-CCAAA--T--TA
1 GGAAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * *
2647 GGAAGGTTATTAAACTTTTATTATGGAA-GATATCAAAATTTC--A
1 GGAAGGTTATCAAAATTTCA-TA-GGAAGGTTATCAAAATTTCATA
* * * ** *
2690 GGGAGGATATCAAAATTTTATAGTTTA-GTTTTCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATA
* * * * *
2734 AGAGGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAA
1 GGAAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-A
* ** *
2779 TG-AGGTTATCAAAAAATCCTATGG-AGGTTATCAAAA-TT--T-
1 GGAAGGTTATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATA
* * * * *
2818 -GTA-GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATA
1 GGAAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * *
2860 GGGATGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATA
1 -GGAAGGTTATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATA
*
2906 GCG-AGGTTATCAAAATTTCATAGTGTAA--TTATCAAAATTTCAGA
1 G-GAAGGTTATCAAAATTTCATAG-G-AAGGTTATCAAAATTTCATA
* * * * * *
2950 GTATGATTA-CTAACAA-TTCATATGG-AGGTTTTTAAATTTTCATAA
1 GGAAGGTTATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCAT-A
* * * * * *
2995 CG-TGGTTATCAATATATCATATGG-AGGTTATCAACATCTCATA
1 GGAAGGTTATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATA
* *
3038 GTGTTA-GTTATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA
1 G-G-AAGGTTATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATA
* * * * *
3083 CTG-AGGTCT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 -GGAAGGT-TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * ** * ** * *
3127 AGAAGCTTAAAAAAAAATT-ATAAAAAGGTTCTCAAAATTCCATA
1 GGAAGGTT-ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* *** *
3171 GTATCATTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
3215 GGAAGGTTATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
3237 ATGGAATTAT
Statistics
Matches: 432, Mismatches: 111, Indels: 89
0.68 0.18 0.14
Matches are distributed among these distances:
37 1 0.00
38 25 0.06
39 20 0.05
40 5 0.01
41 9 0.02
42 16 0.04
43 38 0.09
44 216 0.50
45 81 0.19
46 19 0.04
47 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (44 bp):
GGAAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:3246 original size:66 final size:67
Alignment explanation
Indices: 2677--3241 Score: 263
Period size: 66 Copynumber: 8.6 Consensus size: 67
2667 TTATGGAAGA
* * * * ** * * *
2677 TATCAAAATTTC--AGGGAGGATATCAAAATTTTATAGTTTA-GTTTTCAAAATTTCATAAGAGG
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGAGGTTATCAAAATTTCATAGGAAG
2739 GT
66 GT
* * * ** *
2741 TATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT-GAGGTTATCAAAAAATCCTATGG-A
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGAGGTTATCAAAATTTCATA-GGAA
2804 GGT
65 GGT
* * * * * *
2807 TATCAAAA-TT--T--GTA-GTTATCAAGATTTCATAA-GAAAGTTATCAAAATTTTATAGGGAT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGAGGTTATCAAAATTTCATA-GGAA
*
2865 GTT
65 GGT
* *
2868 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCAT-A-GCGAGGTTATCAAAATTTCATAGTG
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAATG-GAGGTTATCAAAATTTCATAG-G
2931 TAA--T
63 -AAGGT
* * * * * * * *
2935 TATCAAAATTTCAGAGTATGATTA-CTAACAA-TTCAT-ATGGAGGTTTTTAAATTTTCATAACG
1 TATCAAAATTTCATAGGAAGGTTATC-AA-AATTTCATAATGGAGGTTATCAAAATTTCAT-AGG
*
2997 -TGGT
63 AAGGT
* * * * * * *
3001 TATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTA-GTTATCAAAATTTCATTGGG
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAATG-GAGGTTATCAAAATTTCA-TAGG
3064 AA-GT
63 AAGGT
* * * * * *
3068 TATCAAAATTTCATACTG-AGGTCT-TCAAAA-TTCCTTAGGGAGGTTAACAAAATTTCATAAGA
1 TATCAAAATTTCATA-GGAAGGT-TATCAAAATTTCATAATGGAGGTTATCAAAATTTCATAGGA
*
3130 AGCT
64 AGGT
** * ** * * * *
3134 TAAAAAAAAATT-ATAAAAAGGTTCTCAAAATTCCATAGTAT-CA--TTATTAAAATTTCATAGG
1 T-ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA--ATGGAGGTTATCAAAATTTCATAGG
3195 AAGGT
63 AAGGT
3200 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGA
3242 ATTATAAAAA
Statistics
Matches: 366, Mismatches: 95, Indels: 79
0.68 0.18 0.15
Matches are distributed among these distances:
60 31 0.08
61 12 0.03
62 2 0.01
63 1 0.00
64 15 0.04
65 19 0.05
66 171 0.47
67 77 0.21
68 36 0.10
69 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (67 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGGAGGTTATCAAAATTTCATAGGAAG
GT
Found at i:3251 original size:22 final size:21
Alignment explanation
Indices: 2671--3236 Score: 238
Period size: 22 Copynumber: 26.0 Consensus size: 21
2661 CTTTTATTAT
* *
2671 GGAAGATATCAAAATTTCA-G
1 GGAAGTTATCAAAATTTCATA
* * *
2691 GGAGGATATCAAAATTTTATA
1 GGAAGTTATCAAAATTTCATA
** *
2712 GTTTAGTTTTCAAAATTTCATA
1 G-GAAGTTATCAAAATTTCATA
* *
2734 AGAGGGTTATCAAAATTTCATA
1 GGA-AGTTATCAAAATTTCATA
* *
2756 GGGAGATTAACAAAATTTCATAA
1 GGAAG-TTATCAAAATTTCAT-A
* * ** *
2779 TGAGGTTATCAAAAAATCCTA
1 GGAAGTTATCAAAATTTCATA
*
2800 TGGAGGTTATCAAAA-TT--T-
1 -GGAAGTTATCAAAATTTCATA
* *
2818 -GTAGTTATCAAGATTTCATAA
1 GGAAGTTATCAAAATTTCAT-A
* *
2839 GAAAGTTATCAAAATTTTATA
1 GGAAGTTATCAAAATTTCATA
* *
2860 GGGATGTTTATCAAAATTTTATA
1 -GGAAG-TTATCAAAATTTCATA
2883 GGAAGATTTATCAAAATTTCATA
1 GGAAG--TTATCAAAATTTCATA
*
2906 GCGAGGTTATCAAAATTTCATA
1 G-GAAGTTATCAAAATTTCATA
*
2928 GTGTAA-TTATCAAAATTTCAGA
1 G-G-AAGTTATCAAAATTTCATA
* *
2950 GTATGATTA-CTAACAA-TTCATA
1 GGAAG-TTATC-AA-AATTTCATA
* * * *
2972 TGGAGGTTTTTAAATTTTCATAA
1 -GGAAGTTATCAAAATTTCAT-A
* ** * *
2995 CGTGGTTATCAATATATCATA
1 GGAAGTTATCAAAATTTCATA
* * *
3016 TGGAGGTTATCAACATCTCATA
1 -GGAAGTTATCAAAATTTCATA
* *
3038 GTGTTAGTTATCAAAATTTCATTG
1 G-G-AAGTTATCAAAATTTCA-TA
3062 GGAAGTTATCAAAATTTCATA
1 GGAAGTTATCAAAATTTCATA
* * * *
3083 CTGAGGTCT-TCAAAATTCCTTA
1 -GGAAGT-TATCAAAATTTCATA
* *
3105 GGGAGGTTAACAAAATTTCATA
1 -GGAAGTTATCAAAATTTCATA
* ** *
3127 AGAAGCTTAAAAAAAAATT-ATA
1 GGAAG-TT-ATCAAAATTTCATA
** * *
3149 AAAAGGTTCTCAAAATTCCATA
1 GGAA-GTTATCAAAATTTCATA
* *
3171 GTATCA-TTATTAAAATTTCATA
1 GGA--AGTTATCAAAATTTCATA
3193 GGAAGGTTATCAAAATTTCATA
1 GGAA-GTTATCAAAATTTCATA
3215 GGAAGGTTATCAAAATTTCATA
1 GGAA-GTTATCAAAATTTCATA
3237 ATGGAATTAT
Statistics
Matches: 412, Mismatches: 94, Indels: 78
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
19 2 0.00
20 19 0.05
21 19 0.05
22 287 0.70
23 67 0.16
24 6 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
GGAAGTTATCAAAATTTCATA
Found at i:5139 original size:2 final size:2
Alignment explanation
Indices: 5134--5162 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5124 TTCCAAAAAA
5134 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5163 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.