Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013041.1 Corchorus capsularis cultivar CVL-1 contig13062, 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: 48684
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3375 original size:45 final size:44
Alignment explanation
Indices: 3324--3408 Score: 152
Period size: 45 Copynumber: 1.9 Consensus size: 44
3314 TAATAGAGTT
3324 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTA-CCCAAATTAATGATGAGCTGG
*
3369 GTGGAATTACTAAAAGATCCCTACCCGAATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCAAATTAATGATGAG
3409 TTGGAGAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (44 bp):
GTGGAATTACTAAAAGATCCCTACCCAAATTAATGATGAGCTGG
Found at i:3883 original size:2 final size:2
Alignment explanation
Indices: 3876--3902 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3866 TTTTAATTGA
3876 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 A
3903 AATGAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4285 original size:166 final size:163
Alignment explanation
Indices: 4010--4434 Score: 488
Period size: 168 Copynumber: 2.6 Consensus size: 163
4000 GAACTATTTT
* *
4010 TTTTTTTGTCTTTTCCCACTTGGCAGATTACTTAAATGTCCTAA----GATTCTTGAGGGGATTA
1 TTTTTTTGTCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTGATTCTTGA-GGGATTA
* * * *
4071 AAT-AGCTAGACTTTTTGGTCATTTCTCAATTGACTTTAATACAGTAGTGGAATTACT-AAAAGA
65 AATAAG-TA-ACTTTTTGGTCATTTCTCAATGGACTTGAATACAGTAGTGGAATTAATAAAAAAA
* * ** * *
4134 T-TCCTAACAAGGCTTGCTTTTGGAG-TAGAGAACTTA
128 TCTCC-AACAAGGATTGATGAT-GAGCTAAAGAACTAA
4170 TTTTTTTGATCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTCTGATTCTTGAGTGGAT
1 TTTTTTTG-TCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTT-TGATTCTTGAG-GGAT
* *
4235 TAAATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAATATAGTAGTGTAATTAATAAAAAA
63 TAAATAAGTAA-CTTTTTGGTCATTTCTCAATGGACTTGAATACAGTAGTGGAATTAAT-AAAAA
*
4300 AATCTCCATCAAGGATTGATGATGAGCTAAAGAACTAA
126 AATCTCCAACAAGGATTGATGATGAGCTAAAGAACTAA
* * * *
4338 TCTTTTTCGTCTTTACCTATTTGGCAAATTACTTAAATGTCATAACTTTTGATTCTTGAGGGAAT
1 T-TTTTTTGTCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAAC-TTTGATTCTTGAGGG-AT
*
4403 TAAATAACTAAACTTTTTGGTCATTTCTCAAT
63 TAAATAAGT-AACTTTTTGGTCATTTCTCAAT
4435 TGACAAATAT
Statistics
Matches: 228, Mismatches: 20, Indels: 26
0.83 0.07 0.09
Matches are distributed among these distances:
160 8 0.04
161 34 0.15
165 2 0.01
166 62 0.27
167 7 0.03
168 102 0.45
169 13 0.06
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (163 bp):
TTTTTTTGTCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTGATTCTTGAGGGATTAA
ATAAGTAACTTTTTGGTCATTTCTCAATGGACTTGAATACAGTAGTGGAATTAATAAAAAAATCT
CCAACAAGGATTGATGATGAGCTAAAGAACTAA
Found at i:5231 original size:15 final size:16
Alignment explanation
Indices: 5210--5245 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
5200 GATTATACTA
*
5210 ACTTTTGTAATATATT
1 ACTTTTGTAACATATT
5226 -CTTTTGTAACATATT
1 ACTTTTGTAACATATT
5241 ACTTT
1 ACTTT
5246 CTTTCTCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
ACTTTTGTAACATATT
Found at i:5848 original size:119 final size:119
Alignment explanation
Indices: 5632--5868 Score: 377
Period size: 119 Copynumber: 2.0 Consensus size: 119
5622 ATTGAGATAG
* *
5632 AAATTGACAAATTTATTGATAATTTTGGAGCAAATCGGCCAAAGCTTGTTAACTAAGATTCGGTC
1 AAATTGACAAATTTATTGATAATTTTGGAGCAAATCGACCAAAACTTGTTAACTAAGATTCGGTC
* * *
5697 CGTTAAGGCCTTTTTTTTTTAACGATTCGTTAAGGCATTATTAATCAACCAATA
66 CATTAAGGCCTTTTTTTTTGAACAATTCGTTAAGGCATTATTAATCAACCAATA
* * *
5751 AAATTTACAAATTTATTGATAATTTTGGAGCAAATCGACCAAAACTTGTTAATTAAGGTTCGGTC
1 AAATTGACAAATTTATTGATAATTTTGGAGCAAATCGACCAAAACTTGTTAACTAAGATTCGGTC
*
5816 CATTAAGGCCTTTTTTTTTGAACAA-TCTGTTAAGGCCTTATTAATCAACCAAT
66 CATTAAGGCCTTTTTTTTTGAACAATTC-GTTAAGGCATTATTAATCAACCAAT
5869 TTATTGATTG
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
118 2 0.02
119 106 0.98
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (119 bp):
AAATTGACAAATTTATTGATAATTTTGGAGCAAATCGACCAAAACTTGTTAACTAAGATTCGGTC
CATTAAGGCCTTTTTTTTTGAACAATTCGTTAAGGCATTATTAATCAACCAATA
Found at i:13011 original size:1 final size:1
Alignment explanation
Indices: 13005--13031 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
12995 GTAGGTTAGG
13005 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
13032 GCGCTGAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13522 original size:26 final size:23
Alignment explanation
Indices: 13459--13523 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 23
13449 AAAAAGTTAA
13459 AAAGAGAGAGAAAAAAATAAAAG
1 AAAGAGAGAGAAAAAAATAAAAG
* *
13482 AAAGAAAGTAGAAAAGTTAAA-GAAAG
1 AAAGAGAG-AGAAAA---AAATAAAAG
13508 AAAGAGAGAGAAAAAA
1 AAAGAGAGAGAAAAAA
13524 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
22 2 0.06
23 7 0.20
24 6 0.17
25 6 0.17
26 11 0.31
27 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (23 bp):
AAAGAGAGAGAAAAAAATAAAAG
Found at i:13526 original size:13 final size:14
Alignment explanation
Indices: 13502--13531 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
13492 GAAAAGTTAA
13502 AGAAAGAAAGAGAG
1 AGAAAGAAAGAGAG
13516 AGAAA-AAAGAGAG
1 AGAAAGAAAGAGAG
13529 AGA
1 AGA
13532 GAGAGGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAGAG
Found at i:16077 original size:10 final size:10
Alignment explanation
Indices: 16062--16087 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16052 AATTTAATAT
16062 GGATATTTAC
1 GGATATTTAC
16072 GGATATTTAC
1 GGATATTTAC
16082 GGATAT
1 GGATAT
16088 ATTGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:17764 original size:2 final size:2
Alignment explanation
Indices: 17759--17805 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
17749 ACACACACAC
* *
17759 AT AT AT AA AT AT AT AT AT AT AT AT GT 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 AT AT AT AT AT
17801 -T AT AT
1 AT AT AT
17806 GGAAATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18259 original size:2 final size:2
Alignment explanation
Indices: 18252--18290 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18242 TTTAAAATTG
18252 AT AT 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 AT AT A
18291 CACTGCCTAG
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21181 original size:14 final size:14
Alignment explanation
Indices: 21162--21188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21152 TAGGTGACAA
21162 TATATTATTTTTAC
1 TATATTATTTTTAC
21176 TATATTATTTTTA
1 TATATTATTTTTA
21189 AGGATAATTT
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:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTATTTTTAC
Found at i:27360 original size:31 final size:31
Alignment explanation
Indices: 27319--27393 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
27309 TCTTTTGCGT
* *
27319 ACATGGCATGCCACGTCAGCTGAAAATTGCC
1 ACATGGCATGCCACATCAGCCGAAAATTGCC
* *
27350 ACGTGGCATGCCACATCATCCGAAAATTGCC
1 ACATGGCATGCCACATCAGCCGAAAATTGCC
*
27381 ACATGACATGCCA
1 ACATGGCATGCCA
27394 TGGGGCTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (31 bp):
ACATGGCATGCCACATCAGCCGAAAATTGCC
Found at i:27694 original size:2 final size:2
Alignment explanation
Indices: 27687--27714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27677 CGACACATGA
27687 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
27715 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31246 original size:72 final size:72
Alignment explanation
Indices: 31170--31314 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
31160 TAAAAAGCTA
31170 TCACAGCTTTTTCTCTCTCTCAATCTGACAGATTCTCTCTCACACACAAAAAACTAAACAGAAAC
1 TCACAGCTTTTTCTCTCTCTCAATCTGACAGATTCTCTCTCACACACAAAAAACTAAACAGAAAC
31235 TGCTTAT
66 TGCTTAT
31242 TCACAGCTTTTTCTCTCTCTCAATCTGACAGATTCTCTCTCACACACAAAAAACTAAACAGAAAC
1 TCACAGCTTTTTCTCTCTCTCAATCTGACAGATTCTCTCTCACACACAAAAAACTAAACAGAAAC
31307 TGCTTAT
66 TGCTTAT
31314 T
1 T
31315 TATACTAATA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (72 bp):
TCACAGCTTTTTCTCTCTCTCAATCTGACAGATTCTCTCTCACACACAAAAAACTAAACAGAAAC
TGCTTAT
Found at i:35279 original size:7 final size:7
Alignment explanation
Indices: 35267--35296 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
35257 AAGGTAGAAA
35267 ATTAAAC
1 ATTAAAC
35274 ATTAAAC
1 ATTAAAC
35281 ATTAAAC
1 ATTAAAC
35288 ATTAAAC
1 ATTAAAC
35295 AT
1 AT
35297 ACTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAC
Found at i:35495 original size:11 final size:11
Alignment explanation
Indices: 35452--35489 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
35442 TTCCTATATA
*
35452 AAATAAATTAT
1 AAATTAATTAT
35463 CAAA-TAATTAT
1 -AAATTAATTAT
35474 AAATTAATTAT
1 AAATTAATTAT
35485 AAATT
1 AAATT
35490 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:39980 original size:38 final size:38
Alignment explanation
Indices: 39929--40003 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
39919 TATAAGTTCG
39929 TGGGCCTTTTTGAGCAATAAACCAATAAGATTAACACA
1 TGGGCCTTTTTGAGCAATAAACCAATAAGATTAACACA
39967 TGGGCCTTTTTGAGCAATAAACCAATAAGATTAACAC
1 TGGGCCTTTTTGAGCAATAAACCAATAAGATTAACAC
40004 TGCATTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (38 bp):
TGGGCCTTTTTGAGCAATAAACCAATAAGATTAACACA
Found at i:48662 original size:2 final size:2
Alignment explanation
Indices: 48655--48684 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
48645 TTTATGATCT
48655 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.