Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016095.1 Corchorus capsularis cultivar CVL-1 contig16116, 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: 22823
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2686 original size:18 final size:18
Alignment explanation
Indices: 2665--2719 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2655 TTGTAGATTT
2665 CTTATGACATTAATCATG
1 CTTATGACATTAATCATG
* *
2683 CTTAT-ACAATAGAT--TT
1 CTTATGACATTA-ATCATG
2699 CTTATGACATTAATCATG
1 CTTATGACATTAATCATG
2717 CTT
1 CTT
2720 GTACATGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 8 0.28
17 10 0.34
18 11 0.38
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (18 bp):
CTTATGACATTAATCATG
Found at i:2701 original size:34 final size:34
Alignment explanation
Indices: 2658--2724 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
2648 TTAATTATTG
2658 TAGATTTCTTATGACATTAATCATGCTTATACAA
1 TAGATTTCTTATGACATTAATCATGCTTATACAA
*
2692 TAGATTTCTTATGACATTAATCATGCTTGTACA
1 TAGATTTCTTATGACATTAATCATGCTTATACA
2725 TGGCAGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (34 bp):
TAGATTTCTTATGACATTAATCATGCTTATACAA
Found at i:3201 original size:46 final size:46
Alignment explanation
Indices: 3149--3284 Score: 200
Period size: 46 Copynumber: 3.0 Consensus size: 46
3139 AGCACTACAT
* **
3149 TTTAACCATTAGCAGTAGATTAATACACTGAATGAATGATAAAAAA
1 TTTAACCATTAGCAGCAGATTAATACACCAAATGAATGATAAAAAA
** *
3195 TTTAACCATTAGTGGCAGTTTAATACACCAAATGAATGATAAAAAA
1 TTTAACCATTAGCAGCAGATTAATACACCAAATGAATGATAAAAAA
* *
3241 TTTAACCATTAACAGCAGATTAATATACCAAATGAATGATAAAA
1 TTTAACCATTAGCAGCAGATTAATACACCAAATGAATGATAAAA
3285 TAAAAACAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (46 bp):
TTTAACCATTAGCAGCAGATTAATACACCAAATGAATGATAAAAAA
Found at i:4302 original size:32 final size:32
Alignment explanation
Indices: 4261--4343 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
4251 TCATTTCAGG
*
4261 TCAGGTTGATTCGGGTTCGGGTTGAATTT-AGA
1 TCAGGTTGATTCGGGTTCGGATTGAATTTGA-A
*
4293 TCAGGTTGATTCGAGTTCGGATTGAATTTGAA
1 TCAGGTTGATTCGGGTTCGGATTGAATTTGAA
*
4325 TCAGGTTAATTCGGGTTCG
1 TCAGGTTGATTCGGGTTCG
4344 AGTTTGGTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (32 bp):
TCAGGTTGATTCGGGTTCGGATTGAATTTGAA
Found at i:5145 original size:16 final size:16
Alignment explanation
Indices: 5126--5178 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
5116 GGGTTCGGGT
5126 TTTTTTGGGTTTGAGA
1 TTTTTTGGGTTTGAGA
* * *
5142 TTTTTCGGATTTGAGT
1 TTTTTTGGGTTTGAGA
*
5158 TTTTTTGAGTTTGAGA
1 TTTTTTGGGTTTGAGA
5174 TTTTT
1 TTTTT
5179 CGGGGTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.13, C:0.02, G:0.25, T:0.60
Consensus pattern (16 bp):
TTTTTTGGGTTTGAGA
Found at i:6709 original size:41 final size:40
Alignment explanation
Indices: 6647--6880 Score: 193
Period size: 41 Copynumber: 5.6 Consensus size: 40
6637 TTCTCTTTCT
* * *
6647 AAAGTCCTCAAGCACATTTATAACACAGAGGCACCCATATC
1 AAAGTCC-CAAACACAATTATAACACAGAGGCATCCATATC
* * *
6688 AAAGTCCCAAAGCACAATTATAACACAGGGGCACCTCTATTTC
1 AAAGTCCCAAA-CACAATTATAACACAGAGGCA--TCCATATC
* * ** *
6731 AAAGTCCTCAAACACATTTATAACAAAGAGAAATCTATATC
1 AAAGTCC-CAAACACAATTATAACACAGAGGCATCCATATC
* *
6772 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCC-TCTC
1 AAAGT-CCCAAACACAATTATAACACAGAGGC-ATCCATATC
* * * *
6813 TAGAAGTCATCAAACACATTTATAACAAAGAGACATCCATA-C
1 -A-AAGTC-CCAAACACAATTATAACACAGAGGCATCCATATC
6855 TAAAGTCCCTAAACACAATTATAACA
1 -AAAGTCCC-AAACACAATTATAACA
6881 GAAGGGCAAT
Statistics
Matches: 155, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
40 4 0.03
41 80 0.52
42 14 0.09
43 53 0.34
44 4 0.03
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (40 bp):
AAAGTCCCAAACACAATTATAACACAGAGGCATCCATATC
Found at i:6752 original size:43 final size:43
Alignment explanation
Indices: 6615--6839 Score: 194
Period size: 41 Copynumber: 5.3 Consensus size: 43
6605 AGTCACCAAG
* * ** * * *
6615 CACATTTATAACATAGGGACAATTCTCTTTCTAAAGTCCTCAAG
1 CACATTTATAACACAGGGGCACCTCTATATC-AAAGTCCTCAAA
*
6659 CACATTTATAACACAGAGGCACC-C-ATATCAAAGTCC-CAAA
1 CACATTTATAACACAGGGGCACCTCTATATCAAAGTCCTCAAA
* *
6699 GCACAATTATAACACAGGGGCACCTCTATTTCAAAGTCCTCAAA
1 -CACATTTATAACACAGGGGCACCTCTATATCAAAGTCCTCAAA
* * ** *
6743 CACATTTATAACA-AAGAG-AAATCTATATCAAAGTCCCCAAA
1 CACATTTATAACACAGGGGCACCTCTATATCAAAGTCCTCAAA
* * * *
6784 CACAATTATAACACAGGGGCAATCCTCTCTA--GAAGTCATCAAA
1 CACATTTATAACACAGGGGC-A-CCTCTATATCAAAGTCCTCAAA
6827 CACATTTATAACA
1 CACATTTATAACA
6840 AAGAGACATC
Statistics
Matches: 145, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
40 3 0.02
41 59 0.41
42 10 0.07
43 45 0.31
44 23 0.16
45 5 0.03
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (43 bp):
CACATTTATAACACAGGGGCACCTCTATATCAAAGTCCTCAAA
Found at i:6752 original size:84 final size:82
Alignment explanation
Indices: 6603--6880 Score: 310
Period size: 84 Copynumber: 3.3 Consensus size: 82
6593 TTCTTTCCCT
* * * * ** *
6603 AAAGTCACCAAGCACATTTATAACATAGGGACAATTCTCTTTCTAAAGTCCTCAAGCACATTTAT
1 AAAGTC-CCAAACACAATTATAACACAGGGGCACCTCT-TTTC-AAAGTCCTCAAACACATTTAT
* * *
6668 AACACAGAGGCACCCATATC
63 AACAAAGAGACATCCATATC
6688 AAAGTCCCAAAGCACAATTATAACACAGGGGCACCTCTATTTCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCAAA-CACAATTATAACACAGGGGCACCTCT-TTTCAAAGTCCTCAAACACATTTATA
* *
6753 ACAAAGAGAAATCTATATC
64 ACAAAGAGACATCCATATC
* *
6772 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTC-TCT-AGAAGTCATCAAACACATTTA
1 AAAGT-CCCAAACACAATTATAACACAGGGGC-A-CCTCTTTTCA-AAGTCCTCAAACACATTTA
6835 TAACAAAGAGACATCCATA-C
62 TAACAAAGAGACATCCATATC
6855 TAAAGTCCCTAAACACAATTATAACA
1 -AAAGTCCC-AAACACAATTATAACA
6881 GAAGGGCAAT
Statistics
Matches: 169, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
83 5 0.03
84 122 0.72
85 38 0.22
86 4 0.02
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.22
Consensus pattern (82 bp):
AAAGTCCCAAACACAATTATAACACAGGGGCACCTCTTTTCAAAGTCCTCAAACACATTTATAAC
AAAGAGACATCCATATC
Found at i:9476 original size:578 final size:578
Alignment explanation
Indices: 8381--9539 Score: 2075
Period size: 578 Copynumber: 2.0 Consensus size: 578
8371 GAAGGGCTAG
*
8381 TTCTAAGCTTGATCTAACTATAGATCCATCCAATTATATCCTCATAGGCCTCATAATTCAATAAT
1 TTCTAAGCTTGATCTAACTATAGATCCATCCAATTATATCCTCACAGGCCTCATAATTCAATAAT
8446 CATCAAGATCATAAGATTAAAACAGGGATTTGCAATCTATCTACCAGGAACAAACATCAAATAAT
66 CATCAAGATCATAAGATTAAAACAGGGATTTGCAATCTATCTACCAGGAACAAACATCAAATAAT
* * **
8511 AAGCACAGAAATCTCACCATAATCAATTGATTTGATTCACCAATGGATAAGAAGTATTAAGAATT
131 AAGCACAGAAATCTCACCATAATCAATTGATTAGATTCACCAAAGGATAAGAAACATTAAGAATT
* * *
8576 TAGCTACTCATGGATTTAGGAAAATCCATGAGAGGCATAAGAAAACTTACAAGAGTAGAAGGCGA
196 TAGCTACTCATGGATTTAGGAAAATCCATGAAAGACATAAGAAAACTTACAAGACTAGAAGGCGA
* * * * *
8641 AATCCTCCTCCTTGAAACCCTATGTTTGTCGCACCTCTCTATGCAAAGAGAGGGTGTCGATACAC
261 AATCATCCTCCTTGAAACCCTAGGTTTGCCGCACCTCTCTATGCAAAGAGAGGATGTCGACACAC
*
8706 CTAGCCTAAAACTAGAGAAAAACTAAATTATTTTCTAAGAAAAAGATGATAGAGAATTGTTTGGG
326 CTAGCCTAAAACTAGAGAAAAACTAAATTATTTTCTAAGAAAAAGATGATAGAGAATTGTGTGGG
*
8771 ATTGGGTTAGATAAGGTGGCTATTTATAGTGGACAAATTAGACTCCTTATAGACTTAAGAAAGGG
391 ATTGGGTTAGAAAAGGTGGCTATTTATAGTGGACAAATTAGACTCCTTATAGACTTAAGAAAGGG
*
8836 TCTAGGACGGTTTTAAGGCTGACTTGGTCTCCAAGTTGGCTTAAAAGTCTTCCTGGAGTCAAAAT
456 TCTAGGACGGTTTTAAGGCTGACTTGGTCTCCAAGTTGGCTTAAAAGTCTTCCTAGAGTCAAAAT
* *
8901 CCTTGTGAAAATAGGACTCTAGAAACTTCTTGATTTGTGCAGGAACTTCGACGTCAAA
521 CCTTGTGAAAATAGGACTCTAGAAAATTCTTGATTTGTGCAGGAACTTCGACATCAAA
8959 TTCTAAGCTTGATCTAACTATAGATCCATCCAATTATATCCTCACAGGCCTCATAATTCAATAAT
1 TTCTAAGCTTGATCTAACTATAGATCCATCCAATTATATCCTCACAGGCCTCATAATTCAATAAT
*
9024 CATCAAGATCATAAGATTAAAACAGGGATTTGCAATTTATCTACCAGGAACAAACATCAAATAAT
66 CATCAAGATCATAAGATTAAAACAGGGATTTGCAATCTATCTACCAGGAACAAACATCAAATAAT
9089 AAGCACAGAAATCTCACCATAATCAATTGATTAGATTCACCAAAGGATAAGAAACATTAAGAATT
131 AAGCACAGAAATCTCACCATAATCAATTGATTAGATTCACCAAAGGATAAGAAACATTAAGAATT
*
9154 TAGTTACTCATGGATTTAGGAAAATCCATGAAAGACATAAGAAAACTTACAAGACTAGAAGGCGA
196 TAGCTACTCATGGATTTAGGAAAATCCATGAAAGACATAAGAAAACTTACAAGACTAGAAGGCGA
* *
9219 AATCATCCTTCTTGAAACCCTAGGTTTGCCGCACCTCTCTATGCAAAGAGAGGATGTTGACACAC
261 AATCATCCTCCTTGAAACCCTAGGTTTGCCGCACCTCTCTATGCAAAGAGAGGATGTCGACACAC
*
9284 CTAGCCTAAAACTAGAGAAAAACTAAATTATTTTCTAAGAAAACGATGATAGAGAATTGTGTGGG
326 CTAGCCTAAAACTAGAGAAAAACTAAATTATTTTCTAAGAAAAAGATGATAGAGAATTGTGTGGG
*
9349 ATTGGGTTAGAAAAGGTGGCTATTTATAGTGGACAAATTAGACTCCTTATAGACTTAGGAAAGGG
391 ATTGGGTTAGAAAAGGTGGCTATTTATAGTGGACAAATTAGACTCCTTATAGACTTAAGAAAGGG
*
9414 TCTAGGACGGTTTTAAGGCTGGCTTGGTCTCCAAGTTGGCTTAAAAGTCTTCCTAGAGTCAAAAT
456 TCTAGGACGGTTTTAAGGCTGACTTGGTCTCCAAGTTGGCTTAAAAGTCTTCCTAGAGTCAAAAT
* *
9479 CCTTGTGAAATTAGGACTCTAGAAAATTCTTGATTTGTGCAGGAACTTTGACATCAAA
521 CCTTGTGAAAATAGGACTCTAGAAAATTCTTGATTTGTGCAGGAACTTCGACATCAAA
9537 TTC
1 TTC
9540 GGGGTTGAAG
Statistics
Matches: 554, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
578 554 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (578 bp):
TTCTAAGCTTGATCTAACTATAGATCCATCCAATTATATCCTCACAGGCCTCATAATTCAATAAT
CATCAAGATCATAAGATTAAAACAGGGATTTGCAATCTATCTACCAGGAACAAACATCAAATAAT
AAGCACAGAAATCTCACCATAATCAATTGATTAGATTCACCAAAGGATAAGAAACATTAAGAATT
TAGCTACTCATGGATTTAGGAAAATCCATGAAAGACATAAGAAAACTTACAAGACTAGAAGGCGA
AATCATCCTCCTTGAAACCCTAGGTTTGCCGCACCTCTCTATGCAAAGAGAGGATGTCGACACAC
CTAGCCTAAAACTAGAGAAAAACTAAATTATTTTCTAAGAAAAAGATGATAGAGAATTGTGTGGG
ATTGGGTTAGAAAAGGTGGCTATTTATAGTGGACAAATTAGACTCCTTATAGACTTAAGAAAGGG
TCTAGGACGGTTTTAAGGCTGACTTGGTCTCCAAGTTGGCTTAAAAGTCTTCCTAGAGTCAAAAT
CCTTGTGAAAATAGGACTCTAGAAAATTCTTGATTTGTGCAGGAACTTCGACATCAAA
Found at i:20752 original size:71 final size:71
Alignment explanation
Indices: 20591--20781 Score: 249
Period size: 71 Copynumber: 2.7 Consensus size: 71
20581 CAGCCCATCC
* * * *
20591 CATGGTCATCTTCTCCATTGCGATTGTAGCCTAGGCAGTTCCCACATTTTGTAGTCCTTCGCACA
1 CATGATCATCTTCT-CATTGCGATTGTAGCCGAGGCAGTTCCCACATTTAGCAGTCCTTCGCACA
20656 ATCCTCA
65 ATCCTCA
* * *
20663 GATTATCCTCTTCTTCATTGCGATTGTAGCCGAGGCAG-TCCCACATTTAGCAGTCCTTCGCACA
1 CATGATCATCTTC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTAGCAGTCCTTCGCACA
* *
20727 ATTCTTA
65 ATCCTCA
* *
20734 CATGATCATCTTTCTCATTGCGATTGTAGCCGAGGTAGTTTCCACATT
1 CATGATCATC-TTCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATT
20782 GGTCGTTCCC
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 59 0.58
72 42 0.41
73 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (71 bp):
CATGATCATCTTCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTAGCAGTCCTTCGCACAA
TCCTCA
Found at i:21777 original size:20 final size:20
Alignment explanation
Indices: 21748--21786 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21738 GTTGAAGTGT
21748 CATAGCTGCGACAGAGACAA
1 CATAGCTGCGACAGAGACAA
*
21768 CATAGTTGCGACAGAGACA
1 CATAGCTGCGACAGAGACA
21787 GAAGCATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (20 bp):
CATAGCTGCGACAGAGACAA
Done.