Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014541.1 Corchorus capsularis cultivar CVL-1 contig14562, 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: 42343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:61 original size:40 final size:40
Alignment explanation
Indices: 4--128 Score: 162
Period size: 39 Copynumber: 3.1 Consensus size: 40
1 ACA
* *
4 AACGCAGACGCGACTCTCGGCAGTGATGCTCCCCAAATAC
1 AACGCAGACGCAACTCTCGGCAGTGATGCTCCCCAAACAC
* * ** *
44 ATCGCAGACACAACTCTC-AAAGTGATGCTCCCCACACAC
1 AACGCAGACGCAACTCTCGGCAGTGATGCTCCCCAAACAC
83 AACGCAGACGCAACTCTCGGCAGTGATGCTCCCCACACACAC
1 AACGCAGACGCAACTCTCGGCAGTGATGCTCCCCA-A-ACAC
125 AACG
1 AACG
129 GAAGATTATC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 33 0.47
40 29 0.41
42 8 0.11
ACGTcount: A:0.30, C:0.38, G:0.18, T:0.14
Consensus pattern (40 bp):
AACGCAGACGCAACTCTCGGCAGTGATGCTCCCCAAACAC
Found at i:2255 original size:160 final size:159
Alignment explanation
Indices: 1992--2312 Score: 633
Period size: 160 Copynumber: 2.0 Consensus size: 159
1982 AATTCCTTGT
1992 TATCTTTTGGACTTAACAGGCTAGCATATGCTGGCTTAGGCTTACCATGTATTGAATTTTTCTTG
1 TATCTTTTGGACTTAACAGGCTAGCATATGCTGGCTTAGGCTTACCATGTATTGAATTTTTCTTG
2057 CAAGATGCTTAAGCAACATTAGATAGCTGGTTTTCATCCACTTGAGTTTCTGAAAGCATTTGAAC
66 CAAGATGCTTAAGCAACATTAGATAGCTGGTTTTCATCCACTTGAGTTTCTGAAAGCATTTGAAC
2122 TCCTTAAATTTGAGGAGACAAACTACCAA
131 TCCTTAAATTTGAGGAGACAAACTACCAA
2151 TATCTTTTGGACTTAACAGAGCTAGCATATGCTGGCTTAGGCTTACCATGTATTGAATTTTTCTT
1 TATCTTTTGGACTTAACAG-GCTAGCATATGCTGGCTTAGGCTTACCATGTATTGAATTTTTCTT
2216 GCAAGATGCTTAAGCAACATTAGATAGCTGGTTTTCATCCACTTGAGTTTCTGAAAGCATTTGAA
65 GCAAGATGCTTAAGCAACATTAGATAGCTGGTTTTCATCCACTTGAGTTTCTGAAAGCATTTGAA
2281 CTCCTTAAATTTGAGGAGACAAACTACCAA
130 CTCCTTAAATTTGAGGAGACAAACTACCAA
2311 TA
1 TA
2313 ATAAGGGTCC
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 19 0.12
160 142 0.88
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (159 bp):
TATCTTTTGGACTTAACAGGCTAGCATATGCTGGCTTAGGCTTACCATGTATTGAATTTTTCTTG
CAAGATGCTTAAGCAACATTAGATAGCTGGTTTTCATCCACTTGAGTTTCTGAAAGCATTTGAAC
TCCTTAAATTTGAGGAGACAAACTACCAA
Found at i:6428 original size:23 final size:23
Alignment explanation
Indices: 6398--6443 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6388 CCGTTCGTAG
6398 ATTCGACGTGCAACTCCAACTTC
1 ATTCGACGTGCAACTCCAACTTC
6421 ATTCGACGTGCAACTCCAACTTC
1 ATTCGACGTGCAACTCCAACTTC
6444 GTGAACTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (23 bp):
ATTCGACGTGCAACTCCAACTTC
Found at i:7630 original size:1 final size:1
Alignment explanation
Indices: 7624--7661 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
7614 GTTTGTAAGT
7624 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7662 CTGAAAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10324 original size:52 final size:52
Alignment explanation
Indices: 10245--10349 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
10235 TGTCAATGAA
* *
10245 CTAATTCATCAAAATGTCCTACGAAATTAGGAATTGACCTAAAAAAATCAAG
1 CTAATTCATCAAAATATCCTACGAAATTAAGAATTGACCTAAAAAAATCAAG
*
10297 CTAATTCATCAAAATATCTTA-GAAAATTAAGAATTGACCTAAAAAAATCAAG
1 CTAATTCATCAAAATATCCTACG-AAATTAAGAATTGACCTAAAAAAATCAAG
10349 C
1 C
10350 CAAAAAATGG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 48 0.98
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.26
Consensus pattern (52 bp):
CTAATTCATCAAAATATCCTACGAAATTAAGAATTGACCTAAAAAAATCAAG
Found at i:18410 original size:10 final size:10
Alignment explanation
Indices: 18395--18428 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
18385 ATAGAACTAA
18395 TTCCTCTGCT
1 TTCCTCTGCT
18405 TTCCTCTGC-
1 TTCCTCTGCT
18414 TTCCTCTGCT
1 TTCCTCTGCT
18424 TTCCT
1 TTCCT
18429 TTTGATGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.00, C:0.41, G:0.09, T:0.50
Consensus pattern (10 bp):
TTCCTCTGCT
Found at i:18419 original size:9 final size:9
Alignment explanation
Indices: 18395--18424 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
18385 ATAGAACTAA
18395 TTCCTCTGC
1 TTCCTCTGC
18404 TTTCCTCTGC
1 -TTCCTCTGC
18414 TTCCTCTGC
1 TTCCTCTGC
18423 TT
1 TT
18425 TCCTTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.40, G:0.10, T:0.50
Consensus pattern (9 bp):
TTCCTCTGC
Found at i:20373 original size:31 final size:32
Alignment explanation
Indices: 20303--20380 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
20293 ATTGCTGAAT
*
20303 GCCACGTCGTACCAAAAATGCCACGTGGCAAC
1 GCCACGTCGGACCAAAAATGCCACGTGGCAAC
* * * *
20335 ACTACGTCGGA-CTAAAATGCCACGTGGCAAG
1 GCCACGTCGGACCAAAAATGCCACGTGGCAAC
*
20366 GCCACGTCAGACCAA
1 GCCACGTCGGACCAA
20381 GGTGCTGACG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 26 0.72
32 10 0.28
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.13
Consensus pattern (32 bp):
GCCACGTCGGACCAAAAATGCCACGTGGCAAC
Found at i:22659 original size:11 final size:11
Alignment explanation
Indices: 22616--22653 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22606 TTCCTATATA
*
22616 AAATAAATTAT
1 AAATTAATTAT
22627 CAAA-TAATTAT
1 -AAATTAATTAT
22638 AAATTAATTAT
1 AAATTAATTAT
22649 AAATT
1 AAATT
22654 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:23037 original size:41 final size:40
Alignment explanation
Indices: 22965--23046 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
22955 ACAAAATTTC
* *
22965 ATTTTTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTT-T-AAATAAA
23007 ATTTCTTAACT-AAATTTTCTTAAAAGAATTTTAAATAAA
1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTTTAAATAAA
23046 A
1 A
23047 CAGCCGCACG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 8 0.21
40 1 0.03
41 19 0.50
42 10 0.26
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (40 bp):
ATTTCTTAACTGAAATTTTCTTAAAAGAATTTTAAATAAA
Found at i:23988 original size:2 final size:2
Alignment explanation
Indices: 23983--24017 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23973 TAGCTCTCTC
23983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24018 CTATTCAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24734 original size:19 final size:19
Alignment explanation
Indices: 24710--24747 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24700 AGTAGATCCA
24710 TAGAACCAGAAACTTTGTC
1 TAGAACCAGAAACTTTGTC
24729 TAGAACCAGAAACTTTGTC
1 TAGAACCAGAAACTTTGTC
24748 GGCGGCCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
TAGAACCAGAAACTTTGTC
Found at i:25212 original size:15 final size:15
Alignment explanation
Indices: 25192--25256 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
25182 CACCGGAGAT
25192 TCCATCGATTCGGGC
1 TCCATCGATTCGGGC
* *
25207 TCCATCGGTTCAGGAGAT
1 TCCATCGATTC-GG-G-C
*
25225 TTCATCGATTCGGGC
1 TCCATCGATTCGGGC
* *
25240 TCTATCGATTCAGGC
1 TCCATCGATTCGGGC
25255 TC
1 TC
25257 TAAACCTGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 24 0.62
16 3 0.08
17 3 0.08
18 9 0.23
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.31
Consensus pattern (15 bp):
TCCATCGATTCGGGC
Found at i:25223 original size:33 final size:33
Alignment explanation
Indices: 25186--25253 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
25176 AAGATTCACC
*
25186 GGAGATTCCATCGATTCGGGCTCCATCGGTTCA
1 GGAGATTCCATCGATTCGGGCTCCATCGATTCA
* *
25219 GGAGATTTCATCGATTCGGGCTCTATCGATTCA
1 GGAGATTCCATCGATTCGGGCTCCATCGATTCA
25252 GG
1 GG
25254 CTCTAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (33 bp):
GGAGATTCCATCGATTCGGGCTCCATCGATTCA
Found at i:29285 original size:19 final size:19
Alignment explanation
Indices: 29261--29298 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29251 ACAACGATTA
29261 AGAGTATACTAATTATGAT
1 AGAGTATACTAATTATGAT
29280 AGAGTATACTAATTATGAT
1 AGAGTATACTAATTATGAT
29299 GTGAAGTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
AGAGTATACTAATTATGAT
Found at i:29521 original size:21 final size:21
Alignment explanation
Indices: 29474--29524 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
29464 AAAATTCAAA
*
29474 ATAAAATAAAAACTATCCATT
1 ATAAGATAAAAACTATCCATT
*
29495 -TTAGATAAAAACTA-CTCATT
1 ATAAGATAAAAACTATC-CATT
29515 ATAAGATAAA
1 ATAAGATAAA
29525 TATAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 8 0.32
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAAGATAAAAACTATCCATT
Found at i:37649 original size:27 final size:27
Alignment explanation
Indices: 37608--37668 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
37598 TGAAAAATAC
* *
37608 TCCCTCTGTTTCTTTTTAACTGTCTATT
1 TCCCT-TGTTCCTTTTTAACTGTCCATT
*
37636 TCCCTTGTTCCTTTTTAATTGTCCATT
1 TCCCTTGTTCCTTTTTAACTGTCCATT
37663 TCCCTT
1 TCCCTT
37669 ATTTTCCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.10, C:0.28, G:0.07, T:0.56
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAACTGTCCATT
Found at i:41026 original size:21 final size:21
Alignment explanation
Indices: 40983--41027 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40973 GAAGAGAGGC
* ***
40983 AAAAAAAAAACCCAAACCCAG
1 AAAAAAAAAACCAAAAAAAAG
41004 AAAAAAAAAACCAAAAAAAAG
1 AAAAAAAAAACCAAAAAAAAG
41025 AAA
1 AAA
41028 GAAGAAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.78, C:0.18, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACCAAAAAAAAG
Done.