Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009252.1 Corchorus capsularis cultivar CVL-1 contig09273, 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: 49313
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:13742 original size:4 final size:4
Alignment explanation
Indices: 13733--13778 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
13723 ACATATACAA
* *
13733 TATC TATC TATC TATC TATC TATC TCTC TGTC TATC TATC TA-C TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
13779 ACATTTAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.22, C:0.26, G:0.02, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:13743 original size:171 final size:174
Alignment explanation
Indices: 13406--13754 Score: 490
Period size: 171 Copynumber: 2.0 Consensus size: 174
13396 AAGACTACGA
13406 TACTTCTTTATTAATTTTTACTTTTAAAAAAAATTAAGTATACTTTTCTTTTTCTCTATATATTC
1 TACTTCTTTATTAATTTTTACTTTTAAAAAAAATTAAGTATACTTTTCTTTTTCTCTATATATTC
* * *
13471 ATGTTTCTTGCAAACATTAAGTTAGCAAGAACATTAAAAGCAAAACTTTATGCCAAAAACACCCC
66 ATGTTTCTTGCAAACATT-AG-TAACAAGAACAATAAAAACAAAACTTTATGCCAAAAACACCCC
* * *
13536 ATTTGGATAAGTCATAACATATATAACATTTATCTATCTATCTATC
129 ATTTGAATAAGTCATAACATATACAACATCTATCTATCTATCTATC
* * * * *
13582 TACTTCTTTATTAA-TTTTATTTTTTTAAAGAAATTAATTATACTTTTCTTTTTCTCTGTATATT
1 TACTTCTTTATTAATTTTTA-CTTTTAAAAAAAATTAAGTATACTTTTCTTTTTCTCTATATATT
* * * * *
13646 CGTGTTTTTTGCATACA-T-G-AACAAGAATAATAAAAACAAAACTTTATGCCAAAGACACCCCA
65 CATGTTTCTTGCAAACATTAGTAACAAGAACAATAAAAACAAAACTTTATGCCAAAAACACCCCA
*
13708 TTTGAATAAGTCATAACATATACAATATCTATCTATCTATCTATC
130 TTTGAATAAGTCATAACATATACAACATCTATCTATCTATCTATC
13753 TA
1 TA
13755 TCTCTCTGTC
Statistics
Matches: 155, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
171 81 0.52
173 1 0.01
175 6 0.04
176 67 0.43
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.41
Consensus pattern (174 bp):
TACTTCTTTATTAATTTTTACTTTTAAAAAAAATTAAGTATACTTTTCTTTTTCTCTATATATTC
ATGTTTCTTGCAAACATTAGTAACAAGAACAATAAAAACAAAACTTTATGCCAAAAACACCCCAT
TTGAATAAGTCATAACATATACAACATCTATCTATCTATCTATC
Found at i:22107 original size:39 final size:39
Alignment explanation
Indices: 22053--22141 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
22043 AAAATGACAA
* *
22053 GACTTCTTTATGTATGGTTTTGTTTTCTATTTTCTAACG
1 GACTTCTTTATGTATGGTTTTGTTTTCTATTTCCCAACG
*
22092 GACTTCTTTATGTATGGTTTTGTTTTCTATTTCCCAATG
1 GACTTCTTTATGTATGGTTTTGTTTTCTATTTCCCAACG
22131 GACTTCTTTAT
1 GACTTCTTTAT
22142 TCGTTGCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.16, C:0.15, G:0.15, T:0.55
Consensus pattern (39 bp):
GACTTCTTTATGTATGGTTTTGTTTTCTATTTCCCAACG
Found at i:24912 original size:23 final size:23
Alignment explanation
Indices: 24859--24904 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
24849 AACAAGCAAG
24859 CATATTCATTGAAGCATTATCAA
1 CATATTCATTGAAGCATTATCAA
*
24882 CATATTCATTGAAGTATTATCAA
1 CATATTCATTGAAGCATTATCAA
24905 TGTTTTCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
CATATTCATTGAAGCATTATCAA
Found at i:29772 original size:92 final size:94
Alignment explanation
Indices: 29667--29855 Score: 328
Period size: 94 Copynumber: 2.0 Consensus size: 94
29657 AACAAAAAAT
* *
29667 TGACAACAAAAAAACATAAACAAAAACAATGATAC-CTAG-TAGTAGTATTTTGGAATTCTTTCC
1 TGACAACAAAAAAACAGAAACAAAAACAATGATACGCTAGAAAGTAGTATTTTGGAATTCTTTCC
29730 AAGATCACTGTGGTAATCTAATAACATGG
66 AAGATCACTGTGGTAATCTAATAACATGG
*
29759 TGACAACAAAAAAACAGAAACAAAAACAATGATACGTTAGAAAGTAGTATTTTGGAATTCTTTCC
1 TGACAACAAAAAAACAGAAACAAAAACAATGATACGCTAGAAAGTAGTATTTTGGAATTCTTTCC
*
29824 AAGATCACTGTGGTGATCTAATAACATGG
66 AAGATCACTGTGGTAATCTAATAACATGG
29853 TGA
1 TGA
29856 TTTTATTACT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 34 0.37
93 3 0.03
94 54 0.59
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (94 bp):
TGACAACAAAAAAACAGAAACAAAAACAATGATACGCTAGAAAGTAGTATTTTGGAATTCTTTCC
AAGATCACTGTGGTAATCTAATAACATGG
Found at i:31586 original size:17 final size:16
Alignment explanation
Indices: 31546--31596 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
31536 CATGTAATCT
31546 TTGATCAAC-GGTGATC
1 TTGATC-ACTGGTGATC
31562 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
31579 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
31596 T
1 T
31597 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 5 0.16
17 25 0.81
18 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:32145 original size:27 final size:26
Alignment explanation
Indices: 32115--32211 Score: 124
Period size: 27 Copynumber: 3.7 Consensus size: 26
32105 AAACTTGGAT
*
32115 TGCTATTATTTTTTTTTTGAAATGGGC
1 TGCTACTATTTTTTTTTT-AAATGGGC
*
32142 TGCTACTA-TTTTTTGTTAAATGGGC
1 TGCTACTATTTTTTTTTTAAATGGGC
* *
32167 TGCTACTCTTTTTTTTTTTAAATGGAC
1 TGCTACT-ATTTTTTTTTTAAATGGGC
*
32194 TGCTACTCTTTTTTTTTT
1 TGCTACTATTTTTTTTTT
32212 CTTTGATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
25 15 0.24
26 18 0.29
27 29 0.47
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.57
Consensus pattern (26 bp):
TGCTACTATTTTTTTTTTAAATGGGC
Found at i:32255 original size:33 final size:34
Alignment explanation
Indices: 32186--32261 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
32176 TTTTTTTTTT
* * *
32186 AAATGGACTGCTACTCTTTTTTTTTTCTTTGATG
1 AAATGGGCTGCTACTCTTTTTTTTGTCTGTGATG
*
32220 AAATGGGCTG-TACTCTTTTTTATTGTGTGTG-TG
1 AAATGGGCTGCTACTCTTTTTT-TTGTCTGTGATG
32253 AAATGGGCT
1 AAATGGGCT
32262 TCTAGCCTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.18, C:0.12, G:0.22, T:0.47
Consensus pattern (34 bp):
AAATGGGCTGCTACTCTTTTTTTTGTCTGTGATG
Found at i:32566 original size:22 final size:22
Alignment explanation
Indices: 32541--32582 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
32531 GACAAACACA
32541 TAACCCAAATGACCCGAGAAGT
1 TAACCCAAATGACCCGAGAAGT
*
32563 TAACCCAAATGATCCGAGAA
1 TAACCCAAATGACCCGAGAA
32583 TATTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCGAGAAGT
Found at i:33611 original size:14 final size:14
Alignment explanation
Indices: 33589--33618 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33579 CTGAATAAAG
*
33589 AACCTAATCCAATA
1 AACCCAATCCAATA
33603 AACCCAATCCAATA
1 AACCCAATCCAATA
33617 AA
1 AA
33619 TTTTTGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (14 bp):
AACCCAATCCAATA
Found at i:34984 original size:24 final size:26
Alignment explanation
Indices: 34957--35014 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
34947 ATCCGTTTCT
*
34957 TTTCTTTTTCAAGCAA-TCTT-TTTA
1 TTTCTTTTTCAAACAAGTCTTATTTA
*
34981 TTTCTTTTTCAAACAAGTTTTATTTA
1 TTTCTTTTTCAAACAAGTCTTATTTA
35007 TTT-TTTTT
1 TTTCTTTTT
35015 AAAAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 15 0.50
25 8 0.27
26 7 0.23
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTCTTTTTCAAACAAGTCTTATTTA
Found at i:36020 original size:14 final size:14
Alignment explanation
Indices: 36001--36027 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35991 TTAATCATTT
36001 TTAATAATTACTAC
1 TTAATAATTACTAC
36015 TTAATAATTACTA
1 TTAATAATTACTA
36028 GTAATTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATAATTACTAC
Found at i:38549 original size:2 final size:2
Alignment explanation
Indices: 38542--38573 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38532 ACTGTAACTC
38542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38574 TATTATTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41392 original size:59 final size:59
Alignment explanation
Indices: 41290--41403 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
41280 TCTTCTTCCC
* * * *
41290 TATAGCTAATCATTATCTTTCCCGCAACCAAAATTTCCTAATGGTTCCTTAAGATCTAG
1 TATAACTAATCATTAACTTCCCCCCAACCAAAATTTCCTAATGGTTCCTTAAGATCTAG
*
41349 TATAACTAATCCTTAACTTCCCCCCAACCAAAATTT-CTGAATGGTTCCTTAAGAT
1 TATAACTAATCATTAACTTCCCCCCAACCAAAATTTCCT-AATGGTTCCTTAAGAT
41404 TATTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 2 0.04
59 47 0.96
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (59 bp):
TATAACTAATCATTAACTTCCCCCCAACCAAAATTTCCTAATGGTTCCTTAAGATCTAG
Found at i:41426 original size:15 final size:15
Alignment explanation
Indices: 41406--41436 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41396 CTTAAGATTA
41406 TTAAAAAATAAACCC
1 TTAAAAAATAAACCC
41421 TTAAAAAATAAACCC
1 TTAAAAAATAAACCC
41436 T
1 T
41437 GACAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (15 bp):
TTAAAAAATAAACCC
Found at i:42622 original size:25 final size:27
Alignment explanation
Indices: 42588--42643 Score: 98
Period size: 25 Copynumber: 2.1 Consensus size: 27
42578 AGCATGTTGG
42588 AATTTTCTTTATGTGT-ATTCATAAA-
1 AATTTTCTTTATGTGTAATTCATAAAT
42613 AATTTTCTTTATGTGTAATTCATAAAT
1 AATTTTCTTTATGTGTAATTCATAAAT
42640 AATT
1 AATT
42644 ATATACAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 16 0.55
26 9 0.31
27 4 0.14
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (27 bp):
AATTTTCTTTATGTGTAATTCATAAAT
Found at i:44981 original size:2 final size:2
Alignment explanation
Indices: 44976--45013 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44966 CAAGTGTGTC
44976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45014 GGATTTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45355 original size:52 final size:52
Alignment explanation
Indices: 45277--45386 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
45267 TGAACCTACT
45277 CATATATTCAAGTACTGCAATTTGATTATAATTAAGCCTAGTTAAGCCTTCC
1 CATATATTCAAGTACTGCAATTTGATTATAATTAAGCCTAGTTAAGCCTTCC
*
45329 CATATATTCAATTACTGCAATTTGATTATAATTAAGCCTAGTTAAGCCTTCC
1 CATATATTCAAGTACTGCAATTTGATTATAATTAAGCCTAGTTAAGCCTTCC
45381 CATATA
1 CATATA
45387 GTACTCATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (52 bp):
CATATATTCAAGTACTGCAATTTGATTATAATTAAGCCTAGTTAAGCCTTCC
Found at i:48550 original size:2 final size:2
Alignment explanation
Indices: 48543--48615 Score: 85
Period size: 2 Copynumber: 35.5 Consensus size: 2
48533 GTATAAAATA
* *
48543 AT AT AT AT AT AT AT CT AT AT CT AT ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
48586 ACT -T AT CT AT AT AT AT AT AT ACT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT A
48616 AAAGTACGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
1 1 0.02
2 55 0.90
3 5 0.08
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49243 original size:25 final size:26
Alignment explanation
Indices: 49192--49243 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
49182 TTACTCAACT
**
49192 AAAAACTCTATTTTATTTTTCTGTAA
1 AAAAACTCTATTTTATTTTAATGTAA
49218 AAAAACTCTATTTT-TATTTAAT-TAA
1 AAAAACTCTATTTTAT-TTTAATGTAA
49243 A
1 A
49244 TCTAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (26 bp):
AAAAACTCTATTTTATTTTAATGTAA
Done.