Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013486.1 Corchorus capsularis cultivar CVL-1 contig13507, 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: 30049
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:731 original size:20 final size:20
Alignment explanation
Indices: 706--743 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
696 ATACCCTTAC
706 TTAAACTATTGTAGTTTTTT
1 TTAAACTATTGTAGTTTTTT
726 TTAAACTATTGTAGTTTT
1 TTAAACTATTGTAGTTTT
744 ATTCTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (20 bp):
TTAAACTATTGTAGTTTTTT
Found at i:752 original size:19 final size:19
Alignment explanation
Indices: 709--749 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
699 CCCTTACTTA
*
709 AACTATTGTAGTTTTTTTT
1 AACTATTGTAGTTTTTTCT
728 AAACTATTGTAGTTTTATTCT
1 -AACTATTGTAGTTTT-TTCT
749 A
1 A
750 CTAAAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (19 bp):
AACTATTGTAGTTTTTTCT
Found at i:890 original size:22 final size:21
Alignment explanation
Indices: 865--915 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
855 TAATATACAG
865 TTTTATTCTAATAAAAATTC-TA
1 TTTTATT-TAAT-AAAATTCATA
*
887 TTTTCATTTAATTAAATTCAATA
1 TTTT-ATTTAATAAAATTC-ATA
910 TTTTAT
1 TTTTAT
916 AATTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTTAATAAAATTCATA
Found at i:2199 original size:22 final size:22
Alignment explanation
Indices: 2171--2793 Score: 144
Period size: 22 Copynumber: 27.9 Consensus size: 22
2161 TATCTCTATG
2171 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
2193 TGGTTATTATGATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
2216 -GGTTATCAAAA-TTCA-ATAGTG
1 TGGTTATCAAAATTTCATA-AG-A
* *
2237 TGGTTA-CCAAATTCTCATATGGA
1 TGGTTATCAAAATT-TCATA-AGA
*
2260 -AGTTATCAAAATTTCATACAG-
1 TGGTTATCAAAATTTCATA-AGA
* * *
2281 TGGTTACCAAAATTTCTTAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
2303 TCATGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
2327 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
* *
2349 TGGTTAATTATCACAATTTTAT-AGAA
1 TGG----TTATCAAAATTTCATAAG-A
* * *
2375 AGGTTATCAAAATGTCATAGCGA
1 TGGTTATCAAAATTTCATA-AGA
*
2398 -GG-TACTAAAAATTTCAT-AGTA
1 TGGTTA-TCAAAATTTCATAAG-A
* *
2419 TGGTTAACAAAATTTCATCAGGA
1 TGGTTATCAAAATTTCAT-AAGA
**
2442 -GGTTA-CAAATATTTCATGGGGA
1 TGGTTATCAAA-ATTTCAT-AAGA
*
2464 -GGTTATCAAAATTTTAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
2483 TGTGATTATCAAAATTTCATATGA
1 TG-G-TTATCAAAATTTCATAAGA
* *
2507 AGGTTATAAAAGTCTCATTTTCATAAG-
1 TGGTTATCAAA-----A-TTTCATAAGA
* *
2534 -GAG-TACCAAAATTTGAT-AGA
1 TG-GTTATCAAAATTTCATAAGA
* *
2554 AGGTTATC-AAATCTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* *
2574 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCATA-AGA
2598 TCGGATTATCAAAATTT-AT-AGAA
1 T-GG-TTATCAAAATTTCATAAG-A
* * *
2621 AGATGATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
2641 TGTTGTTATCAAAATTTCA-AAGCGA
1 TG--GTTATCAAAATTTCATAA--GA
*
2666 -GGTTATCAAAATTACATAATG-
1 TGGTTATCAAAATTTCATAA-GA
*
2687 TGATTATCAGAAA-TTCAT-AGA
1 TGGTTATCA-AAATTTCATAAGA
* * * * *
2708 GGGGTCAACAAAATTTTATAAAA
1 -TGGTTATCAAAATTTCATAAGA
*
2731 AGGTTATCAAAATTTCATAAAGA
1 TGGTTATCAAAATTTCAT-AAGA
*
2754 -GGTTATCAAATTTTCA-AA-A
1 TGGTTATCAAAATTTCATAAGA
2773 TGTGATTA-CAAAAATTTCATA
1 TG-G-TTATC-AAAATTTCATA
2794 GTGGTATTTC
Statistics
Matches: 444, Mismatches: 88, Indels: 137
0.66 0.13 0.20
Matches are distributed among these distances:
19 4 0.01
20 25 0.06
21 45 0.10
22 262 0.59
23 35 0.08
24 32 0.07
25 12 0.03
26 19 0.04
27 2 0.00
28 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:2836 original size:22 final size:22
Alignment explanation
Indices: 2810--3142 Score: 127
Period size: 22 Copynumber: 15.7 Consensus size: 22
2800 TTTCTGGGGA
2810 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
2832 GGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGTAT
* * *
2849 GGTTATTAAACTTT--TATTAT
1 GGTTATCAAAATTTCATAGTAT
* *
2869 GGAGTAATCAAAATTTCA-AGGA-
1 GG-TTA-TCAAAATTTCATAGTAT
* *
2891 GGATATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
*
2913 GGTTATCAAAATTTCATAGTTT
1 GGTTATCAAAATTTCATAGTAT
* * * *
2935 AGTTTTCAAAATGTCATAAG-AG
1 GGTTATCAAAATTTCAT-AGTAT
2957 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* **
2979 -GTAGATCAAAATTTCATAGGGT
1 GGT-TATCAAAATTTCATAGTAT
* *
3001 GATTAACAAAATTTCATA--AT
1 GGTTATCAAAATTTCATAGTAT
* *
3021 GAGATTATCAAAA-ATCATAGGGA-
1 G-G-TTATCAAAATTTCATA-GTAT
3044 GGTTATCAAAA-TT--T-GTA-
1 GGTTATCAAAATTTCATAGTAT
* *
3061 -GTTATCAAGATTTCATAAG-AA
1 GGTTATCAAAATTTCAT-AGTAT
* * * *
3082 AGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGTAT
* *
3104 GATTTATCAAAATTTCATAGTGT
1 G-GTTATCAAAATTTCATAGTAT
* *
3127 GATAATCAAAATTTCA
1 GGTTATCAAAATTTCA
3143 GAGTGTGTGA
Statistics
Matches: 231, Mismatches: 51, Indels: 58
0.68 0.15 0.17
Matches are distributed among these distances:
16 9 0.04
17 13 0.06
18 2 0.01
19 3 0.01
20 20 0.09
21 32 0.14
22 127 0.55
23 24 0.10
24 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:3039 original size:21 final size:21
Alignment explanation
Indices: 3014--3054 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3004 TAACAAAATT
*
3014 TCATAATGAGATTATCAAAAA
1 TCATAAGGAGATTATCAAAAA
* *
3035 TCATAGGGAGGTTATCAAAA
1 TCATAAGGAGATTATCAAAA
3055 TTTGTAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATAAGGAGATTATCAAAAA
Found at i:3583 original size:6 final size:6
Alignment explanation
Indices: 3572--3672 Score: 74
Period size: 6 Copynumber: 17.2 Consensus size: 6
3562 TAGTTTATAG
*
3572 ATAGAT ATAGATAT ATAGAT ATA-A- ATAGA- ATAGAT ATTATAGT ATAGAT
1 ATAGAT ATAG--AT ATAGAT ATAGAT ATAGAT ATAGAT A-TAGA-T ATAGAT
*
3621 ATAGAT AT--AT ATAGAT ATA-A- ATAGA- ATAGAT ATTATAGT ATAGAT
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT A-TAGA-T ATAGAT
3666 ATAGAT A
1 ATAGAT A
3673 GATTATATAG
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
4 10 0.13
5 14 0.18
6 33 0.42
7 12 0.15
8 10 0.13
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (6 bp):
ATAGAT
Found at i:3591 original size:14 final size:15
Alignment explanation
Indices: 3568--3673 Score: 112
Period size: 14 Copynumber: 7.3 Consensus size: 15
3558 TATATAGTTT
3568 ATAG-ATAGATATAG
1 ATAGTATAGATATAG
*
3582 ATA-TATAGATATAA
1 ATAGTATAGATATAG
* *
3596 ATAGAATAGATAT-T
1 ATAGTATAGATATAG
3610 ATAGTATAGATATAG
1 ATAGTATAGATATAG
* *
3625 ATATATATAGATATAA
1 ATA-GTATAGATATAG
* *
3641 ATAGAATAGATAT-T
1 ATAGTATAGATATAG
3655 ATAGTATAGATATAG
1 ATAGTATAGATATAG
3670 ATAG
1 ATAG
3674 ATTATATAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
14 39 0.52
15 23 0.31
16 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (15 bp):
ATAGTATAGATATAG
Found at i:3643 original size:45 final size:45
Alignment explanation
Indices: 3566--3672 Score: 193
Period size: 45 Copynumber: 2.4 Consensus size: 45
3556 TATATATAGT
3566 TTATAG-ATAGATATAG--ATATATAGATATAAATAGAATAGATA
1 TTATAGTATAGATATAGATATATATAGATATAAATAGAATAGATA
3608 TTATAGTATAGATATAGATATATATAGATATAAATAGAATAGATA
1 TTATAGTATAGATATAGATATATATAGATATAAATAGAATAGATA
3653 TTATAGTATAGATATAGATA
1 TTATAGTATAGATATAGATA
3673 GATTATATAG
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
42 6 0.10
43 10 0.16
45 46 0.74
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (45 bp):
TTATAGTATAGATATAGATATATATAGATATAAATAGAATAGATA
Found at i:3695 original size:39 final size:40
Alignment explanation
Indices: 3572--3684 Score: 135
Period size: 45 Copynumber: 2.8 Consensus size: 40
3562 TAGTTTATAG
3572 ATAGATATAGATAT--ATAGATATAAATAGAATAGATATTATAGT
1 ATAGATATAGATATAGATAGATATAAATAGAATAG--A-TAT--T
*
3615 ATAGATATAGATATATATAGATATAAATAGAATAGATATT
1 ATAGATATAGATATAGATAGATATAAATAGAATAGATATT
*
3655 ATAG-TATAGATATAGATAGAT-TATATAGAA
1 ATAGATATAGATATAGATAGATATAAATAGAA
3685 AATTGCATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
38 8 0.12
39 16 0.24
40 5 0.08
42 3 0.05
43 15 0.23
45 19 0.29
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (40 bp):
ATAGATATAGATATAGATAGATATAAATAGAATAGATATT
Found at i:10578 original size:27 final size:27
Alignment explanation
Indices: 10545--10615 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
10535 CCAATAACAT
10545 AGCCAACAAGGTTAGCACCCTGCATAA
1 AGCCAACAAGGTTAGCACCCTGCATAA
10572 AGCCAACAAGGTTAGCACCCTGCATAA
1 AGCCAACAAGGTTAGCACCCTGCATAA
10599 AGCCAACAAGGTTAGCA
1 AGCCAACAAGGTTAGCA
10616 AAAAATAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (27 bp):
AGCCAACAAGGTTAGCACCCTGCATAA
Found at i:12822 original size:1 final size:1
Alignment explanation
Indices: 12816--12847 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
12806 CATTAACATT
12816 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12848 GCTGCCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22106 original size:172 final size:173
Alignment explanation
Indices: 21801--22140 Score: 499
Period size: 172 Copynumber: 2.0 Consensus size: 173
21791 GACCTGCGCA
* ** * * *
21801 AAATCCAATGTTTTCAAACTCGGACCGGCTCGGTCGGTTCAACCGGGACCCTAGGGTCTTGCCGG
1 AAATCCAATGTTTTCAAACCCGGACCGGCTCGACCGGTTCAACCGAGACCCGAGGGCCTTGCCGG
* *
21866 CCCGGAAGACCCCCTTCTACGGTGCCTTTGGGAACCGGTCAAAACCTGTAAAACTCGGATCAGCT
66 CCCGGAAGACCCCCTTCTACGGTGCCTTTGGGAACCGGTCAAAACCTGAAAAACCCGGATCAGCT
* *
21931 CGGACCGCCTAAACCGGAAAAAAACGGCTTTTATAAATACAAT
131 CGGACCACCTAAACCGGAAAAAAACAGCTTTTATAAATACAAT
21974 AAAT-CAATGTTTTCAAACCCGGACCGGCTCGACCGGTTCAACCGAGACCCG-GAGGCCTTGCCG
1 AAATCCAATGTTTTCAAACCCGGACCGGCTCGACCGGTTCAACCGAGACCCGAG-GGCCTTGCCG
* * *
22037 GTCCGGAAGACCCCCTTGCT-CGGTGCCTTTGGGAACCGGTCAAAA-ATCGAAAAACCCGGATCG
65 GCCCGGAAGACCCCCTT-CTACGGTGCCTTTGGGAACCGGTCAAAACCT-GAAAAACCCGGATCA
*
22100 GCTCGGACCACCTAAACCGGAAAAAACCAGCTTTTATAAAT
128 GCTCGGACCACCTAAACCGGAAAAAAACAGCTTTTATAAAT
22141 TCAAAAGGTT
Statistics
Matches: 150, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
171 2 0.01
172 142 0.95
173 6 0.04
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (173 bp):
AAATCCAATGTTTTCAAACCCGGACCGGCTCGACCGGTTCAACCGAGACCCGAGGGCCTTGCCGG
CCCGGAAGACCCCCTTCTACGGTGCCTTTGGGAACCGGTCAAAACCTGAAAAACCCGGATCAGCT
CGGACCACCTAAACCGGAAAAAAACAGCTTTTATAAATACAAT
Found at i:26979 original size:17 final size:17
Alignment explanation
Indices: 26954--26993 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
26944 AACTAAGTAG
26954 ACTAAGATAACTAACAT
1 ACTAAGATAACTAACAT
*
26971 ACTAGGATAACTAACAT
1 ACTAAGATAACTAACAT
*
26988 ATTAAG
1 ACTAAG
26994 CATTGACCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (17 bp):
ACTAAGATAACTAACAT
Done.