Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013130.1 Corchorus capsularis cultivar CVL-1 contig13151, 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: 44973
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:106 original size:30 final size:30
Alignment explanation
Indices: 70--132 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
60 AAGGGGTCAA
*
70 ATGGCCGGTTGTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
*
100 ATGGCCGGTTGTGGCCGGTTGCCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
130 ATG
1 ATG
133 TTCCATGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGCCCCATGCG
Found at i:145 original size:42 final size:42
Alignment explanation
Indices: 93--174 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
83 GCCGGATGGC
**
93 CCATGCGATGGCCGGTTGTGGCCGGTTGCCCCATGCGATGTT
1 CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATGTT
* *
135 CCATGTGATGGCCGGTCATGGCCGGTTGCTCCATGCGATG
1 CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATG
175 GTGGCCGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.11, C:0.28, G:0.35, T:0.26
Consensus pattern (42 bp):
CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATGTT
Found at i:4642 original size:30 final size:30
Alignment explanation
Indices: 4606--4668 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
4596 AAGGGGTCAA
*
4606 ATGGCCGGTTGTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
*
4636 ATGGCCGGTTGTGGCCGGTTGCCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
4666 ATG
1 ATG
4669 TTCCATGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGCCCCATGCG
Found at i:4680 original size:42 final size:42
Alignment explanation
Indices: 4629--4710 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
4619 GCCGGATGGC
**
4629 CCATGCGATGGCCGGTTGTGGCCGGTTGCCCCATGCGATGTT
1 CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATGTT
* *
4671 CCATGCGATGGTCGGTCATGGCCGGTTGCTCCATGCGATG
1 CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATG
4711 GTGGTCGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.11, C:0.28, G:0.35, T:0.26
Consensus pattern (42 bp):
CCATGCGATGGCCGGTCATGGCCGGTTGCCCCATGCGATGTT
Found at i:7221 original size:6 final size:6
Alignment explanation
Indices: 7212--7251 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
7202 AACATTTTAA
**
7212 TTTTCT TTTTAG TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
7252 AAGATTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:7227 original size:12 final size:12
Alignment explanation
Indices: 7206--7245 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
7196 GTTACTAACA
7206 TTTTAATTTTCT
1 TTTTAATTTTCT
*
7218 TTTTAGTTTTCT
1 TTTTAATTTTCT
**
7230 TTTTCTTTTTCT
1 TTTTAATTTTCT
7242 TTTT
1 TTTT
7246 CTTTTTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTAATTTTCT
Found at i:7591 original size:20 final size:19
Alignment explanation
Indices: 7550--7591 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
7540 ATTTTCTTGC
*
7550 ATTGTTTTGTTGATTGATT
1 ATTGTTTTGTTGATTGACT
*
7569 ATTGTTTTGATTGATTGCCT
1 ATTGTTTTG-TTGATTGACT
7589 ATT
1 ATT
7592 CCTTGATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.60
Consensus pattern (19 bp):
ATTGTTTTGTTGATTGACT
Found at i:11788 original size:55 final size:55
Alignment explanation
Indices: 11683--11854 Score: 256
Period size: 55 Copynumber: 3.1 Consensus size: 55
11673 TTGTGCATTA
* **
11683 ATAGCTCAATTGCTTCAATTACATAA-CCTTTTACTTGCAATTATATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAATTATATCTGCATCT
*
11737 ATAGCTCAATTGCTTCAATTAGAGAACCCTTTTACAAGCAATTATATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAATTATATCTGCATCT
* * * * *
11792 ATAGCTCATTTGCTTCAATTATAGAACCCTTTTATAAGCAACTATATCTGCATTT
1 ATAGCTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAATTATATCTGCATCT
11847 ATAGCTCA
1 ATAGCTCA
11855 CATGCATATG
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
54 24 0.22
55 84 0.78
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (55 bp):
ATAGCTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAATTATATCTGCATCT
Found at i:19291 original size:36 final size:36
Alignment explanation
Indices: 19209--19292 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
19199 ATAATTAATA
* **
19209 CTTTCCCCATCATCATCACTAACCAAAGGTGAAGAC
1 CTTTCCCCATGATCAAAACTAACCAAAGGTGAAGAC
* * *
19245 CTTTCCCCATGATCAAAACTCACCGAAGGTGACGAC
1 CTTTCCCCATGATCAAAACTAACCAAAGGTGAAGAC
19281 CTTTCCCCATGA
1 CTTTCCCCATGA
19293 AATTTCCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.23
Consensus pattern (36 bp):
CTTTCCCCATGATCAAAACTAACCAAAGGTGAAGAC
Found at i:20135 original size:2 final size:2
Alignment explanation
Indices: 20128--20166 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20118 AGAAGTAAAT
20128 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20167 TATATATACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20440 original size:15 final size:15
Alignment explanation
Indices: 20420--20450 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20410 TTATAAAGAA
20420 ACCTTGCCAATAATT
1 ACCTTGCCAATAATT
*
20435 ACCTTGCCAGTAATT
1 ACCTTGCCAATAATT
20450 A
1 A
20451 TGCTTTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (15 bp):
ACCTTGCCAATAATT
Found at i:21982 original size:23 final size:23
Alignment explanation
Indices: 21940--21983 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21930 CATGAATCGA
* *
21940 TGAATGCGCAGCAAATAAAAATG
1 TGAATGCGAAGCAAAGAAAAATG
*
21963 TGAATGCGAAGCAGAGAAAAA
1 TGAATGCGAAGCAAAGAAAAA
21984 GGAAAGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.25, T:0.14
Consensus pattern (23 bp):
TGAATGCGAAGCAAAGAAAAATG
Found at i:22145 original size:19 final size:20
Alignment explanation
Indices: 22099--22145 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
22089 CAAACAGATG
*
22099 CTTACCAAATTGAAGAGAAA
1 CTTACAAAATTGAAGAGAAA
22119 CTTACAAAATTGAAGAGAAA
1 CTTACAAAATTGAAGAGAAA
22139 CTT-CAAA
1 CTTACAAA
22146 TCGCTAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (20 bp):
CTTACAAAATTGAAGAGAAA
Found at i:22475 original size:14 final size:14
Alignment explanation
Indices: 22456--22506 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
22446 AGATTTTAGA
22456 GGGTTTCAATTTTG
1 GGGTTTCAATTTTG
22470 GGGTTTCAGAAATTTTG
1 GGGTTTC---AATTTTG
* *
22487 GGGTTTTAACTTTG
1 GGGTTTCAATTTTG
22501 GGGTTT
1 GGGTTT
22507 AAAAATGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 19 0.59
17 13 0.41
ACGTcount: A:0.16, C:0.06, G:0.31, T:0.47
Consensus pattern (14 bp):
GGGTTTCAATTTTG
Found at i:23970 original size:165 final size:163
Alignment explanation
Indices: 23702--24182 Score: 531
Period size: 166 Copynumber: 2.9 Consensus size: 163
23692 TAAACATGTG
* ** * * *
23702 GAATTACTAAAAGATCCCCACCCTGGATTAATGAAGAGTGAGAGAACTAATTTTTTCGTCTTTTC
1 GAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTCGTC-TTTC
* * *
23767 C--CATTTGACAGATTGCTTAAATTTCCCAACTTTTGATTCTTGAGGGATTAAATAACTAGACTT
65 CTACA-TTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGATTAAATAACTA-ACTT
* * *
23830 TTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTG
128 TTTGGTCATTTCTCAATTGACTTAAATAAAGTAGTA
* * * * * ** *
23866 GAATTACCT-AAAGATCTCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTCCGTCTT
1 GAATTA-ATAAAAGATCCCCACCAAGGATTGATGAT-GAGTTAGAGAACTAATTTTTT-CGTCTT
* *
23930 TCCTACATTG-CAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGTGGATTAAATAAGTAATC
63 TCCTACATTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAG-GGATTAAATAACTAA-C
* *
23994 TTTTTGGTCATTTCTTAATGGACTTAAATAAAGTAGTA
126 TTTTTGGTCATTTCTCAATTGACTTAAATAAAGTAGTA
* **
24032 GAATTAATAAAAGATCCCCATCAAGGATTGATGATGAACTAGAGAACTAATCTTTTTCGTCTTTA
1 GAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAAT-TTTTTCGTCTTT-
* * * * *
24097 CCTAC-TTGTCAAATTAGTTAAATGTCCTAGCTTTTGATTCTTGAGGAGATTAAATAACAAAACT
64 CCTACATTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGG-GATTAAATAAC-TAACT
24161 TTTTGGTCATTTCTCAATTGAC
127 TTTTGGTCATTTCTCAATTGAC
24183 AAATGACTCA
Statistics
Matches: 263, Mismatches: 41, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
164 22 0.08
165 84 0.32
166 153 0.58
167 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (163 bp):
GAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTCGTCTTTCC
TACATTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGATTAAATAACTAACTTTTT
GGTCATTTCTCAATTGACTTAAATAAAGTAGTA
Found at i:25355 original size:198 final size:199
Alignment explanation
Indices: 24993--25395 Score: 605
Period size: 198 Copynumber: 2.0 Consensus size: 199
24983 CTGGAGCAAC
* * * *
24993 CTTC-CTTCGCGGAGCTGTCGTATAAGCTATAGCCTCCCTGATTTGAGCCGATTTTGCAACGTTA
1 CTTCTCTTCGCGGAGCTGTCATATAAGCGATAGCCTCCCTAATTTGAGCCGATTTTGCAACATTA
* * * * * *
25057 ATAACTAATTTAAGCAGGTTTTGCAACGTTTGAGACTTAATTAACCAAATTAGAAGGTTAGACCT
66 AGAACTAATTTAAGCAGGTTTTCCAACATTTAAAACTTAATTAACCAAATTAGAAGGTTAGACCC
* *
25122 TTATTTGAGTATTTTCACAAAAATTGGGTACCAATTTGAGCAATTAGCCCATCTTTTCTTAGTTA
131 TTATTTGAGTATTTTAACAAAAATAGGGTACCAATTTGAGCAATTAGCCCATCTTTTCTTAGTTA
25187 CTTT
196 CTTT
* *
25191 CTTCTCTT-GCGGAGTTGTCATATAAGCGGTAGCCTCCCTAATTTGAGCCGATTTTGCAACATTA
1 CTTCTCTTCGCGGAGCTGTCATATAAGCGATAGCCTCCCTAATTTGAGCCGATTTTGCAACATTA
* * *
25255 GGGATTAATTTAAGCAGGTTTTCCAACATTTAAAACTTAATTAACCAAATTAGAAGGTTAGACCC
66 AGAACTAATTTAAGCAGGTTTTCCAACATTTAAAACTTAATTAACCAAATTAGAAGGTTAGACCC
*
25320 TTATTTGAGTATTTTAATAAAAATCAGGG-ACCAATTTGAGCAATTAGCCCATCTTTTCTTAGTT
131 TTATTTGAGTATTTTAACAAAAAT-AGGGTACCAATTTGAGCAATTAGCCCATCTTTTCTTAGTT
25384 ACTTT
195 ACTTT
*
25389 TTTCTCT
1 CTTCTCT
25396 CTCTTTCTTC
Statistics
Matches: 184, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
198 178 0.97
199 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (199 bp):
CTTCTCTTCGCGGAGCTGTCATATAAGCGATAGCCTCCCTAATTTGAGCCGATTTTGCAACATTA
AGAACTAATTTAAGCAGGTTTTCCAACATTTAAAACTTAATTAACCAAATTAGAAGGTTAGACCC
TTATTTGAGTATTTTAACAAAAATAGGGTACCAATTTGAGCAATTAGCCCATCTTTTCTTAGTTA
CTTT
Found at i:34962 original size:135 final size:134
Alignment explanation
Indices: 34787--35054 Score: 410
Period size: 135 Copynumber: 2.0 Consensus size: 134
34777 GTTGTTGGTT
* *
34787 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTGAGCCATGACTTGTTGGTTGTTCACCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTAAGCCATGACTTGTTGGTTGTTCACCTGAT
* ** * * *
34852 GGTTGACTTGTTGAAGAGGTAGAGCACTGGGCTGGGCACCAAGCAGTTGTTGGTTTTGCCCCCTG
66 GGTTAACTTGTTGAAGAGACAGAGCACCGGGCTGGGCACCAAACAATTGTTGGTTTTGCCCCC-G
34917 AGTCC
130 AGTCC
*
34922 TTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTAAGCCATGAGTTGTTGGTTGTTCACCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTAAGCCATGACTTGTTGGTTGTTCACCTGAT
* * **
34987 GGTTAACTTGTTGAAGATACAGAGCACCGGGTTGGGCGTCAAACAATTGTTGGTTTTGCCCCCGA
66 GGTTAACTTGTTGAAGAGACAGAGCACCGGGCTGGGCACCAAACAATTGTTGGTTTTGCCCCCGA
35052 GTC
131 GTC
35055 TTTCTTCGAT
Statistics
Matches: 120, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
134 5 0.04
135 115 0.96
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.30
Consensus pattern (134 bp):
TTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTAAGCCATGACTTGTTGGTTGTTCACCTGAT
GGTTAACTTGTTGAAGAGACAGAGCACCGGGCTGGGCACCAAACAATTGTTGGTTTTGCCCCCGA
GTCC
Done.