Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013758.1 Corchorus capsularis cultivar CVL-1 contig13779, 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: 11914
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:362 original size:190 final size:188
Alignment explanation
Indices: 6--370 Score: 436
Period size: 190 Copynumber: 1.9 Consensus size: 188
1 GTTGA
* *
6 CATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTGATTATGAAATGGGGTATGTGTCA
1 CATGTGTACCCTTAGGGAATATGTATTAATATTAAATAATTAATTATGAAATGGGGTATGTGT--
* * * * *
71 ACTTTTAACCCGCTTATGGAATCCAAAATTTATACTGACAGTGTATTGTATAATAATCCTATAAG
64 AC---T-ACCCGCTCATGAAATCCAAAATTTATACAGACAATGTATTGTATAATAATCCTATAAA
* **
136 AAAATTTATGCAATACACTGTCACTGTAGTTTAGCAGACTGCACGCACGGGGTTTAAGGGTTAT
125 AAAAATTATAAAATACACTGTCACTGTAGTTTAGCAGACTGCACGCACGGGGTTTAAGGGTTAT
*
200 CATGTGT-CCTCTTAGGGAATATGTATTAATATTTTATATTAATTAATTATGAAATGGGGTATGT
1 CATGTGTACC-CTTAGGGAATATGTATTAATA--TTA-AATAATTAATTATGAAATGGGGTATGT
*
264 GT-C-ACCCGCTCATGAAATTCAAAA-TT-TACAGACAATGTATTGTATAATAACAATCCTATAA
62 GTACTACCCGCTCATGAAATCCAAAATTTATACAGACAATGTATTGTATAAT---AATCCTATAA
* *
325 AAAAAATTATAAAATACACTGTTAGTAG-AGTTTAGCAGACTGCACG
124 AAAAAATTATAAAATACACTGTCACT-GTAGTTTAGCAGACTGCACG
371 TGCATGACTT
Statistics
Matches: 149, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
187 20 0.13
188 2 0.01
189 18 0.12
190 48 0.32
191 1 0.01
193 2 0.01
194 29 0.19
196 3 0.02
197 26 0.17
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (188 bp):
CATGTGTACCCTTAGGGAATATGTATTAATATTAAATAATTAATTATGAAATGGGGTATGTGTAC
TACCCGCTCATGAAATCCAAAATTTATACAGACAATGTATTGTATAATAATCCTATAAAAAAAAT
TATAAAATACACTGTCACTGTAGTTTAGCAGACTGCACGCACGGGGTTTAAGGGTTAT
Found at i:808 original size:16 final size:16
Alignment explanation
Indices: 783--813 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
773 TCTACAAATT
783 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
799 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
814 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:3945 original size:86 final size:86
Alignment explanation
Indices: 3839--3999 Score: 288
Period size: 86 Copynumber: 1.9 Consensus size: 86
3829 GGATTAACAA
*
3839 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
3904 AA-ACAAATAAATTAAAAATAG
66 AATA-AAATAAATTAAAAATAG
*
3925 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
3990 AATAAAATAA
66 AATAAAATAA
4000 TAATAAAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 71 0.99
87 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.34
Consensus pattern (86 bp):
AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
AATAAAATAAATTAAAAATAG
Found at i:4014 original size:75 final size:75
Alignment explanation
Indices: 3934--4203 Score: 443
Period size: 75 Copynumber: 3.6 Consensus size: 75
3924 GAATTAATAA
3934 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
3999 ATAATAAAGT
66 ATAATAAAGT
* *
4009 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAGGAAATAAACTA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
4074 ATAATAAAGT
66 ATAATAAAGT
* *
4084 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTATGAGATATTTTAAGAAAT-AAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAT-
*
4148 AATAATAAAGAA
65 AATAATAAAG-T
*
4160 TGAGAATATTTCCCTAAATCTTGCCAGAATTGTGGGAGATTTAG
1 TGAGAATATTT-TCTAAATCTTGCCA-AATTGTGGGAGATTTAG
4204 AAAATATTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
74 3 0.02
75 139 0.77
76 11 0.06
77 13 0.07
78 15 0.08
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (75 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
ATAATAAAGT
Found at i:4112 original size:150 final size:156
Alignment explanation
Indices: 3846--4203 Score: 496
Period size: 150 Copynumber: 2.3 Consensus size: 156
3836 CAAAATTAAT
* *
3846 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAACAAA
1 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG---ACAAA
* *
3911 TAAATTAAAAATAGAATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAG
63 TAAACTAAAAATA-AA-TAAT-ATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAG
3976 GAGATATTTTAAGAAATAAA-ATAATAATAAAG
125 GAGATATTTTAAGAAATAAATA-AATAATAAAG
* *
4008 -TTGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTT-AG-GAAATAA
1 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGACAAATAA
* * *
4070 ACTAATAAT-AA-AGT-TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTATGAGATA
66 ACTAAAAATAAATAATATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATA
4132 TTTTAAGAAATAAATAAATAATAAAG
131 TTTTAAGAAATAAATAAATAATAAAG
*
4158 AATGAGAATATTTCCCTAAATCTTGCCAGAATTGTGGGAGATTTAG
1 AATGAGAATATTT-TCTAAATCTTGCCA-AATTGTGGGAGATTTAG
4204 AAAATATTAA
Statistics
Matches: 181, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
150 70 0.39
151 12 0.07
152 15 0.08
153 17 0.09
154 2 0.01
156 13 0.07
160 2 0.01
161 50 0.28
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (156 bp):
AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGACAAATAA
ACTAAAAATAAATAATATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATA
TTTTAAGAAATAAATAAATAATAAAG
Found at i:7793 original size:15 final size:14
Alignment explanation
Indices: 7746--7784 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
7736 TTAAAAATGC
* *
7746 TTTTCAAGAAAGTG
1 TTTTCAAAAAAGGG
7760 TTTTCAAAAAAGGG
1 TTTTCAAAAAAGGG
7774 TTTTCTAAAAA
1 TTTTC-AAAAA
7785 TTGGTTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (14 bp):
TTTTCAAAAAAGGG
Found at i:8141 original size:26 final size:26
Alignment explanation
Indices: 8119--8169 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
8109 GAAAAAAATG
8119 AAGAAAAGAA-TTGAAAAAGAAAAGAA
1 AAGAAAAGAAGTTGAAAAAGAAAA-AA
*
8145 AAGAAAAGAAGTTGAAAAAGCAAAA
1 AAGAAAAGAAGTTGAAAAAGAAAAA
8170 GATGGAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.08
Consensus pattern (26 bp):
AAGAAAAGAAGTTGAAAAAGAAAAAA
Found at i:8428 original size:37 final size:37
Alignment explanation
Indices: 8350--8426 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
8340 ATGAAGAAGA
* * *
8350 TTTTCTTCAAAGTGTGAACTTTTCACAAGAAAAAATG
1 TTTTCCTCAAAGTGTCAACTTTTCAAAAGAAAAAATG
8387 TTTTCCTCAAAGTG-CAATCTTTTCAAAAG-AAAAATG
1 TTTTCCTCAAAGTGTCAA-CTTTTCAAAAGAAAAAATG
8423 TTTT
1 TTTT
8427 TCAAAAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTTCCTCAAAGTGTCAACTTTTCAAAAGAAAAAATG
Found at i:9643 original size:35 final size:35
Alignment explanation
Indices: 9597--10221 Score: 570
Period size: 35 Copynumber: 17.9 Consensus size: 35
9587 CTGTGCGGTC
*
9597 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATATCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
*
9632 TTTCAAGAAGTTTT-AGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* *
9666 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
*
9701 TATCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* *
9736 TTTCAAGAAGTTTTCAGAGGTCATAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* *
9771 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
*
9806 TATCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
*
9841 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* * *
9876 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* *
9911 TTTTC-A-TAGTTTTCAGAGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
* *
9945 TTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCGCA
1 -TTTCAAGAAGTTTT-CAGA-GATCAGAGTTGATCTCA
* * * *
9980 TTTTC-AGTAGTTTCCA-ACGATCAAAGTTGATATCA
1 -TTTCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA
* *
10015 TTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCGCA
1 -TTTCAAGAAGTTTT-CAGA-GATCAGAGTTGATCTCA
* * *
10050 TTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCGCA
1 -TTTCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA
** * * *
10085 TTTTTAGTA-TTTTCCA-ACGATCAAAGTTGATCGCA
1 TTTCAAGAAGTTTT-CAGA-GATCAGAGTTGATCTCA
* * *
10120 TTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCACA
1 -TTTCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA
* * * *
10155 TTTTC-AGTAGTTTCCA-ACAATCAGAGGTGATCTCA
1 -TTTCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA
* * *
10190 TTTCAAGAAATTCTC-GTTGATCAGAGTTGATC
1 TTTCAAGAAGTTTTCAG-AGATCAGAGTTGATC
10222 CAGAGGAGTT
Statistics
Matches: 526, Mismatches: 49, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
34 81 0.15
35 430 0.82
36 15 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
Found at i:11519 original size:85 final size:85
Alignment explanation
Indices: 11419--11649 Score: 417
Period size: 85 Copynumber: 2.7 Consensus size: 85
11409 AAAATAATAA
* *
11419 AATTTGTAAAAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATGTTTTAAGA
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
*
11484 AATAAAAATTATAAAGATTT
66 AATAAAAATGATAAAGATTT
*
11504 AATTTGTAAATAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
11569 AATAAAAATGATAAAGATTT
66 AATAAAAATGATAAAGATTT
*
11589 AATTTGTAAAGAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTT
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTT
11650 TAGATTTAAT
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 141 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (85 bp):
AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
AATAAAAATGATAAAGATTT
Done.