Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011200.1 Corchorus capsularis cultivar CVL-1 contig11221, 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: 18339
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:3274 original size:41 final size:42
Alignment explanation
Indices: 3196--3275 Score: 128
Period size: 41 Copynumber: 1.9 Consensus size: 42
3186 TATATATTTA
3196 AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
1 AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
*
3238 AGAGATAATTAT-G-GATTATATTTATTAACCATATTATC
1 AGAGATAATTATGGTGATTATA-TAATTAACCATATTATC
3276 TACATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 7 0.19
41 17 0.47
42 12 0.33
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (42 bp):
AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
Found at i:3348 original size:92 final size:92
Alignment explanation
Indices: 3170--3341 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 92
3160 CAATTAACTC
*
3170 TTAACCATATTATCCATATATATTTAAGAGATAATTATGGTGATTATATAATTAACCATATTATC
1 TTAACCATATTATCCATAAATATTTAAGAGATAATTATGGTGATTATATAATTAACCATATTATC
* *
3235 CATAGAGATAATTATGGATTATATTTA
66 CATAAAGATAATTATGAATTATATTTA
* **
3262 TTAACCATATTATCTACATAAATA-TT-AGAGATAA-TAT-G-GATTATATTTATTAGTCATATT
1 TTAACCATATTATC--CATAAATATTTAAGAGATAATTATGGTGATTATA-TAATTAACCATATT
**
3322 ATCTTTAAAGATAATTATGA
63 ATCCATAAAGATAATTATGA
3342 CAATTATCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
89 7 0.10
90 28 0.41
91 3 0.04
92 22 0.32
93 2 0.03
94 7 0.10
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (92 bp):
TTAACCATATTATCCATAAATATTTAAGAGATAATTATGGTGATTATATAATTAACCATATTATC
CATAAAGATAATTATGAATTATATTTA
Found at i:3683 original size:28 final size:28
Alignment explanation
Indices: 3651--3706 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3641 ACCAAATGTC
3651 AAGTGGCACTCAATAAGGATCTTGTACA
1 AAGTGGCACTCAATAAGGATCTTGTACA
*
3679 AAGTGGCACTCAATAAGGATCTTTTACA
1 AAGTGGCACTCAATAAGGATCTTGTACA
3707 TAAAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (28 bp):
AAGTGGCACTCAATAAGGATCTTGTACA
Found at i:7749 original size:25 final size:25
Alignment explanation
Indices: 7715--7764 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
7705 TTTGATTTAA
*
7715 TATTATTATTATATATA-TAAATTAT
1 TATTAGTATTATATATACT-AATTAT
*
7740 TATTAGTATTATCTATACTAATTAT
1 TATTAGTATTATATATACTAATTAT
7765 AATGTGAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTAGTATTATATATACTAATTAT
Found at i:7910 original size:36 final size:34
Alignment explanation
Indices: 7858--7930 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 34
7848 ATTTAAATAA
7858 AAAAAAAAACTCCCTATTAAATTAGTTACCCATT
1 AAAAAAAAACTCCCTATTAAATTAGTTACCCATT
* * *
7892 AAAAAACAACTACTCCTATTAAGTTAGTTATCCATT
1 AAAAAAAAACT-C-CCTATTAAATTAGTTACCCATT
7928 AAA
1 AAA
7931 CTTCTTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 10 0.29
35 1 0.03
36 23 0.68
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (34 bp):
AAAAAAAAACTCCCTATTAAATTAGTTACCCATT
Found at i:12910 original size:28 final size:28
Alignment explanation
Indices: 12879--12945 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
12869 ACAATTGTAA
12879 TTATTATTTTACTTCTCATAATTA-TT-TT
1 TTATTATTTTACTT-T-ATAATTATTTATT
*
12907 TTATT-TTTTA-TTTATATTTATTTATT
1 TTATTATTTTACTTTATAATTATTTATT
12933 TTATTTATTTTAC
1 TTA-TTATTTTAC
12946 ATAAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 6 0.18
25 3 0.09
26 7 0.21
27 7 0.21
28 10 0.30
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (28 bp):
TTATTATTTTACTTTATAATTATTTATT
Found at i:12919 original size:14 final size:15
Alignment explanation
Indices: 12900--12936 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
12890 CTTCTCATAA
*
12900 TTATTTTTTATTT-T
1 TTATTTTATATTTAT
12914 TTA-TTTATATTTAT
1 TTATTTTATATTTAT
12928 TTATTTTAT
1 TTATTTTAT
12937 TTATTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 8 0.40
14 7 0.35
15 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTTATATTTAT
Found at i:12937 original size:9 final size:9
Alignment explanation
Indices: 12912--12944 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
12902 ATTTTTTATT
12912 TTTTATTTA
1 TTTTATTTA
12921 TATTTATTTA
1 T-TTTATTTA
12931 TTTTATTTA
1 TTTTATTTA
12940 TTTTA
1 TTTTA
12945 CATAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:12937 original size:13 final size:13
Alignment explanation
Indices: 12905--12942 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
12895 CATAATTATT
12905 TTTTATTT-TTTA
1 TTTTATTTATTTA
12917 TTTATATTTATTTA
1 TTT-TATTTATTTA
12931 TTTTATTTATTT
1 TTTTATTTATTT
12943 TACATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 14 0.58
14 7 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:15717 original size:330 final size:332
Alignment explanation
Indices: 15113--15752 Score: 1068
Period size: 331 Copynumber: 1.9 Consensus size: 332
15103 ATTAAATTGA
* *
15113 TAAGAATGTAAGATTATTAAATTTATTGATAGCATAACAATTGTTTTAATAACTTCTATATCTAT
1 TAAGAATGTAAGATTATTAAATTTATTGATAGCATAACAATTCTTTTAATAACCTCTATATCTAT
* * *
15178 TTTAGTAATCTTAATTTGATAATGGAGAAATTATTAGATGGATCAGCTCTACCAAGTCATTCATG
66 TTTAGTAATCTTAATTTGATAATGGAGAAATTATTAGATAGACCAGCTCCACCAAGTCATTCATG
*
15243 GTCTCGATCAATAAGATCGTTACACGTCAGATTTTTTCCTAAAATTCAGGAACAAATTAAGCACC
131 GTCCCGATCAATAAGATCGTTACACGTCAGATTTTTTCCTAAAATTCAGGAACAAATTAAGCACC
* * ** *
15308 AGCTTTAGTTCCAACTTTAACCAGGTGAGATTTATAAGTTAATCCTCTAAATTTAGTATATTAAT
196 AGCTTTAGTCCCAACTTTAACCAGGTGAGATTTACAAGGCAAGCCTCTAAATTTAGTATATTAAT
* *
15373 TTGGTAGGGTTTTAGAAATTGTA-GAAAAAAATCTGGCGTGTCATGATCTGGTGAAAGTTTATTA
261 TTGGTAGGGTTTTAGAAATTGTAGGAAAAAAATCTGACGTGTCACGATCTGGTGAAAGTTTATTA
15437 AAGTTTT
326 AAGTTTT
* *
15444 TAAGAATGTAAGATTATTAAATTTATTGATAGCATCATAATTCTTTTAATAACCTCTATATCTAT
1 TAAGAATGTAAGATTATTAAATTTATTGATAGCATAACAATTCTTTTAATAACCTCTATATCTAT
*
15509 TTTAGTAATCTTAATTTGATAATGGAGAAATTATTAGATAGACCAGGTCCACCAAGTCATTCATG
66 TTTAGTAATCTTAATTTGATAATGGAGAAATTATTAGATAGACCAGCTCCACCAAGTCATTCATG
* * * *
15574 GTCCCGATCATTAAGTTCG-TACGCGTTAGATTTTTTCCTAAAATTCAGGAACAAATTAAGCACC
131 GTCCCGATCAATAAGATCGTTACACGTCAGATTTTTTCCTAAAATTCAGGAACAAATTAAGCACC
* *
15638 AGCTTTAGTCCCAACTTTAACCAGGTGTGATTTACAGGGCAAGCCTCTAAATTTAGTATATTAAT
196 AGCTTTAGTCCCAACTTTAACCAGGTGAGATTTACAAGGCAAGCCTCTAAATTTAGTATATTAAT
15703 TTGGTAGGGTTTTAGAAATTGTAGGAAAAAAATCTGACGTGTCACGATCT
261 TTGGTAGGGTTTTAGAAATTGTAGGAAAAAAATCTGACGTGTCACGATCT
15753 TATTGATCGG
Statistics
Matches: 286, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
330 124 0.43
331 162 0.57
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (332 bp):
TAAGAATGTAAGATTATTAAATTTATTGATAGCATAACAATTCTTTTAATAACCTCTATATCTAT
TTTAGTAATCTTAATTTGATAATGGAGAAATTATTAGATAGACCAGCTCCACCAAGTCATTCATG
GTCCCGATCAATAAGATCGTTACACGTCAGATTTTTTCCTAAAATTCAGGAACAAATTAAGCACC
AGCTTTAGTCCCAACTTTAACCAGGTGAGATTTACAAGGCAAGCCTCTAAATTTAGTATATTAAT
TTGGTAGGGTTTTAGAAATTGTAGGAAAAAAATCTGACGTGTCACGATCTGGTGAAAGTTTATTA
AAGTTTT
Found at i:16798 original size:160 final size:160
Alignment explanation
Indices: 16534--16856 Score: 646
Period size: 160 Copynumber: 2.0 Consensus size: 160
16524 TTTTGATAGC
16534 ATCATGTAACTAACCTTTGAAACTTTTTTTATTAACCTTTGTTAACTTTAAGGTTTAACATATAA
1 ATCATGTAACTAACCTTTGAAACTTTTTTTATTAACCTTTGTTAACTTTAAGGTTTAACATATAA
16599 TTTAATATATCAATCTATATTTTCAATTTTAAACCTTGATTTCTTTTTTGTCTTCTCATTTTTTT
66 TTTAATATATCAATCTATATTTTCAATTTTAAACCTTGATTTCTTTTTTGTCTTCTCATTTTTTT
16664 AAGGTGAGGCGATATTATATTTAATTATTT
131 AAGGTGAGGCGATATTATATTTAATTATTT
16694 ATCATGTAACTAACCTTTGAAACTTTTTTTATTAACCTTTGTTAACTTTAAGGTTTAACATATAA
1 ATCATGTAACTAACCTTTGAAACTTTTTTTATTAACCTTTGTTAACTTTAAGGTTTAACATATAA
16759 TTTAATATATCAATCTATATTTTCAATTTTAAACCTTGATTTCTTTTTTGTCTTCTCATTTTTTT
66 TTTAATATATCAATCTATATTTTCAATTTTAAACCTTGATTTCTTTTTTGTCTTCTCATTTTTTT
16824 AAGGTGAGGCGATATTATATTTAATTATTT
131 AAGGTGAGGCGATATTATATTTAATTATTT
16854 ATC
1 ATC
16857 TTTGAACACC
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (160 bp):
ATCATGTAACTAACCTTTGAAACTTTTTTTATTAACCTTTGTTAACTTTAAGGTTTAACATATAA
TTTAATATATCAATCTATATTTTCAATTTTAAACCTTGATTTCTTTTTTGTCTTCTCATTTTTTT
AAGGTGAGGCGATATTATATTTAATTATTT
Done.