Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006945.1 Corchorus capsularis cultivar CVL-1 contig06966, 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: 6620
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:61 original size:31 final size:31
Alignment explanation
Indices: 26--91 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
16 AACTTTATGT
*
26 TTTCCGATTGTACCATTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
*
57 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
88 TTTC
1 TTTC
92 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:261 original size:36 final size:36
Alignment explanation
Indices: 191--266 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
181 AATTTGACCT
*
191 TTTGTTTCCAACGTCCTATTTAATTTGACTTTTGTC
1 TTTGTTTCCAACGTCATATTTAATTTGACTTTTGTC
*
227 TTTGTTTCCAATCGTTATATTTAATTTTG-C-TTTGTC
1 TTTGTTTCCAA-CGTCATATTTAA-TTTGACTTTTGTC
263 TTTG
1 TTTG
267 GTCTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 21 0.58
37 11 0.31
38 4 0.11
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.57
Consensus pattern (36 bp):
TTTGTTTCCAACGTCATATTTAATTTGACTTTTGTC
Found at i:430 original size:19 final size:20
Alignment explanation
Indices: 403--440 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
393 TACTATTATT
403 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
423 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
441 AATGTCAATA
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:663 original size:22 final size:21
Alignment explanation
Indices: 609--767 Score: 111
Period size: 22 Copynumber: 7.1 Consensus size: 21
599 CTCTATGTGA
*
609 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
* *
631 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
653 TTATCAAAATTCCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
675 TTACCAAAATTTCATAGCGTGG
1 TTATCAAAATTTCATAG-GAGG
*
697 TTACCAAAATTTCATAGGATTGGG
1 TTATCAAAATTTCATAGGA---GG
* * * *
721 TTATTAAAATCTCTTAGGTTGG
1 TTATCAAAATTTCATAGG-AGG
**
743 TTATTGAAATTTCATAGGATGG
1 TTATCAAAATTTCATAGGA-GG
765 TTA
1 TTA
768 ATTATCACAA
Statistics
Matches: 110, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 88 0.80
23 3 0.03
24 16 0.15
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:824 original size:22 final size:22
Alignment explanation
Indices: 799--841 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
789 AGTTATCAAA
799 GAGATTATCAA-AATGTCATAGC
1 GAGATTAT-AAGAATGTCATAGC
*
821 GAGATTATAAGAATTTCATAG
1 GAGATTATAAGAATGTCATAG
842 TGTGCTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGC
Found at i:926 original size:22 final size:22
Alignment explanation
Indices: 877--934 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
867 ATTTCATGGG
* *
877 GAGGTTATCAAAATTTTATAGT
1 GAGGTTATCAAAAGTTCATAGT
*
899 GTGGTTATCAAAAGTTCATA-T
1 GAGGTTATCAAAAGTTCATAGT
920 GAAGGTTAT-AAAAGT
1 G-AGGTTATCAAAAGT
935 CTCAATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAAGTTCATAGT
Found at i:1007 original size:22 final size:22
Alignment explanation
Indices: 938--1534 Score: 139
Period size: 22 Copynumber: 27.8 Consensus size: 22
928 TAAAAGTCTC
* *
938 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
958 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
*
978 AATCTCATAGAGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
1000 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
** *
1025 AATTT-ATAGAAAGATTATTAA
1 AATTTCATAGAGTGATTATCAA
*
1046 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
*
1068 AATTTCAAAGCAAG-G-TTATCAA
1 AATTTCATAG--AGTGATTATCAA
*
1090 AATTAT-ATA-ATGTGATTATCAG
1 AATT-TCATAGA-GTGATTATCAA
* * * *
1112 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
1134 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
1156 AATTTCATAGTA-TGGTTA-CCA
1 AATTTCATAG-AGTGATTATCAA
* *
1177 AA-TT-A-GGAAG-G-TTATTAA
1 AATTTCATAG-AGTGATTATCAA
* * *
1195 ATTTTTATTATGGAGT-A--ATTAA
1 AATTTCA-TA--GAGTGATTATCAA
1217 AATTTCA-AGGAG-GA-TATCAA
1 AATTTCATA-GAGTGATTATCAA
1237 AATTTCATATGAAG-G-TTATCAA
1 AATTTCATA-G-AGTGATTATCAA
* * *
1259 AATTTCATAG-TTTAGTTTTCAA
1 AATTTCATAGAGTGA-TTATCAA
* *
1281 AATTTCACAAGAG-GTTTATCAA
1 AATTTCA-TAGAGTGATTATCAA
*
1303 AATTTCATAGTA-TG-TAGATC--
1 AATTTCATAG-AGTGAT-TATCAA
* * * *
1323 AATTTAATAGGGAGATTAACAA
1 AATTTCATAGAGTGATTATCAA
1345 AATTTCATA-A-TGAGGTTATCAA
1 AATTTCATAGAGTGA--TTATCAA
** * * *
1367 AAAATCATAGGGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
1389 AA--TC-T---GT-AGTTATCAA
1 AATTTCATAGAGTGA-TTATCAA
* **
1405 GATTTCATA-AGAAAGTTATCAA
1 AATTTCATAGAGTGA-TTATCAA
* *
1427 AATTTTATAGGGAG-GTTTATCAA
1 AATTTCATA--GAGTGATTATCAA
* *
1450 AATTTTATAG-GAAGATTTATCAA
1 AATTTCATAGAG-TGA-TTATCAA
* * * *
1473 AATTTCATAGCGAGGTTATCAC
1 AATTTCATAGAGTGATTATCAA
*
1495 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
1517 AATTTCAGAGTGTGATTA
1 AATTTCATAGAGTGATTA
1535 CTAACAATTC
Statistics
Matches: 431, Mismatches: 82, Indels: 126
0.67 0.13 0.20
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 7 0.02
19 13 0.03
20 51 0.12
21 36 0.08
22 244 0.57
23 43 0.10
24 9 0.02
25 16 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:1285 original size:44 final size:44
Alignment explanation
Indices: 1231--1786 Score: 230
Period size: 44 Copynumber: 12.8 Consensus size: 44
1221 TCAAGGAGGA
*
1231 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * *
1275 TTTCAAAATTTCACAAG-AGGTTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGT-T-TAGT
* * * * * *
1320 -ATC--AATTTAATAGGGAGATTAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-GT
** *
1361 TATCAAAAAATCATAGGGAGGTTATCAAAA--TC-T-G--TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * **
1399 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG-GGAGGTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-G-T
* * **
1444 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTTA-GT
* * * * *
1489 TATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTTTAG-T
* * * *** *
1533 TA-CTAACAA-TTCATATGGAA-GTTTTTAAATTTTCATAACGTAAT
1 TATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * *
1577 TATCAATATATCATATGG-AGGTTATCAACATCTCATAGTATTGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGT-TTAGT
* * *
1622 TATCGAAATTTCATTGGGAA-GTTATCAAAATTTCATA-TTGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTTTA-GT
* * * * *
1666 TTTCAAAATTTCTTAGGGAGGTTAACCAAATTTCATA----AGCT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAG-T
** ** * * * * *
1707 TAAAAAAATTT-ATAAAAAGGTTCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* *
1750 TATTAAAATTTCATAGGAAGATTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1787 ATGGGATCAT
Statistics
Matches: 376, Mismatches: 96, Indels: 80
0.68 0.17 0.14
Matches are distributed among these distances:
38 26 0.07
39 2 0.01
40 21 0.06
41 12 0.03
42 29 0.08
43 25 0.07
44 168 0.45
45 67 0.18
46 26 0.07
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:1450 original size:23 final size:23
Alignment explanation
Indices: 1398--1702 Score: 120
Period size: 22 Copynumber: 13.7 Consensus size: 23
1388 AAATCTGTAG
* * * *
1398 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
1420 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
1443 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
1466 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
1488 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* * * *
1510 TTATCAAAATTTCAGAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* *
1532 TTA-CTAACAA-TTCATATGGAAGT
1 TTATC-AA-AATTTCATAGGGAGGT
* * *
1555 TT-TTAAATTTTCATA---ACGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
1574 AATTATCAATATATCATATGGAGG-
1 --TTATCAAAATTTCATAGGGAGGT
* * *
1598 TTATCAACATCTCATA-GTATTGG-
1 TTATCAAAATTTCATAGGGA--GGT
* * *
1621 TTATCGAAATTTCATTGGGAAG-
1 TTATCAAAATTTCATAGGGAGGT
**
1643 TTATCAAAATTTCATATTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
*
1666 TT-TCAAAATTTCTTAGGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* *
1687 TTAACCAAATTTCATA
1 TTATCAAAATTTCATA
1703 AGCTTAAAAA
Statistics
Matches: 216, Mismatches: 49, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.01
21 9 0.04
22 140 0.65
23 60 0.28
24 2 0.01
25 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:3033 original size:25 final size:25
Alignment explanation
Indices: 3005--3054 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2995 TCACATGGTA
* *
3005 AAAACGAATTTATTGATTAAATTCC
1 AAAACGAATTTATTAAATAAATTCC
*
3030 AAAATGAATTTATTAAATAAATTCC
1 AAAACGAATTTATTAAATAAATTCC
3055 TATAGGCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (25 bp):
AAAACGAATTTATTAAATAAATTCC
Done.