Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018034.1 Corchorus olitorius cultivar O-4 contig18067, 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: 54162
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:238 original size:31 final size:31
Alignment explanation
Indices: 151--219 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
141 TTATTAGTGA
* *
151 GGTCAATACTATAAAACTTTCATTTTAATGG
1 GGTCAATACAATAAATCTTTCATTTTAATGG
*
182 GGTCAATACAATAAATCTTTCATTTTAGTGG
1 GGTCAATACAATAAATCTTTCATTTTAATGG
213 GGTCAAT
1 GGTCAAT
220 TAGTAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (31 bp):
GGTCAATACAATAAATCTTTCATTTTAATGG
Found at i:2915 original size:16 final size:15
Alignment explanation
Indices: 2894--2923 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2884 TTCTCATCCC
2894 TATATATATGTATGTG
1 TATATATATG-ATGTG
2910 TATATATATGATGT
1 TATATATATGATGT
2924 TAGAATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATATATATGATGTG
Found at i:8764 original size:10 final size:9
Alignment explanation
Indices: 8748--8773 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
8738 TTTTTGAACC
8748 CAAAAAAAA
1 CAAAAAAAA
8757 CAAAAAAAA
1 CAAAAAAAA
8766 CAAAAAAA
1 CAAAAAAA
8774 GGATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:18554 original size:67 final size:66
Alignment explanation
Indices: 18437--19149 Score: 755
Period size: 67 Copynumber: 10.7 Consensus size: 66
18427 AGTAAAGTTT
* * *
18437 TATTTTCTCTTTCCAGAAGTACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTT
1 TATTTTC-ATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTTT-GTCTTTTTGCATTTAAGTT
18502 TAG
64 TAG
* *
18505 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTATCTTTTTGCATTCAAGTTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGT-TTGTCTTTTTGCATTTAAGTTT
*
18570 TG
65 AG
* * *
18572 TATTTTGATTTACC-GAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTG-TTTTCAAGT
1 TATTTTCATTT-CCAGAAATACCCTTTCGGTCAAAGGGTCAG-TTTGTCTTTTTGCATTT-AAGT
18635 TTAG
63 TTAG
* * * * *
18639 TATTTTCGTTTCCATAAATAACCTTTCGATCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGT-TTGTCTTTTTGCATTTAAGTTT
*
18704 TG
65 AG
* * *
18706 TATTTTGATTTCCAGAAATACCATTTCGGTCAAA-GGTCGGTTTTGTCTTTTTGC-TTTCAAGTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAG-TTTGTCTTTTTGCATTT-AAGTT
18769 TAG
64 TAG
* * *
18772 TATTTTCGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTACATTCAAGTTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGT-TTGTCTTTTTGCATTTAAGTTT
*
18837 TG
65 AG
* * *
18839 TATTTTGATTTCCAGAAATACCCTTTCGGTCAAATGGTCGGTTTTGTCTTTTTGC-TTTCAAGTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAG-TTTGTCTTTTTGCATTT-AAGTT
18903 TAG
64 TAG
* * * *
18906 TATTTTCGTTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAGGTTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTTT-GTCTTTTTGCATTTAAGTTT
18971 AG
65 AG
* * * * * *
18973 T-TTTAC-TTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAG
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTTT-GTC---TTTTTGCATTTAAG
*
19036 TCTAG
62 TTTAG
* * * * *
19041 T-CTTTC-TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTGAGT
1 TATTTTCATTTCCAGA-AATACCCTTTCGGTCAAAGGGTCAGTT-TGTC-TTTTTGCATTTAAGT
19104 TTA-
63 TTAG
* * * * *
19107 -CTTTTGATTTCCAAAAATACCCTTTCGGTGAAAGGGTAAGTTT
1 TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTTT
19150 CATCATTTCC
Statistics
Matches: 550, Mismatches: 72, Indels: 49
0.82 0.11 0.07
Matches are distributed among these distances:
65 40 0.07
66 97 0.18
67 340 0.62
68 46 0.08
69 26 0.05
70 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (66 bp):
TATTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTTTGTCTTTTTGCATTTAAGTTTA
G
Found at i:18696 original size:134 final size:134
Alignment explanation
Indices: 18446--19143 Score: 902
Period size: 134 Copynumber: 5.2 Consensus size: 134
18436 TTATTTTCTC
* * **
18446 TTTCCAGAAGTACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTT-AAGTTTAGTATTT
1 TTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGC-TTTCAAGTTTAGTATTT
* *
18510 TCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTATCTTTTTGCATTCAAGTTTTGTAT
65 TCGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTAT
18575 TTTGA
130 TTTGA
*
18580 TTTACC-GAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGTTTTCAAGTTTAGTATTT
1 TTT-CCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTT
* * *
18644 TCGTTTCCATAAATAACCTTTCGATCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTAT
65 TCGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTAT
18709 TTTGA
130 TTTGA
*
18714 TTTCCAGAAATACCATTTCGGTCAAA-GGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTTT
1 TTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTTT
*
18778 CGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTACATTCAAGTTTTGTATT
66 CGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTATT
18843 TTGA
131 TTGA
*
18847 TTTCCAGAAATACCCTTTCGGTCAAATGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTTT
1 TTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTTT
* * *
18912 CGTTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGT-TTCGTCTTTTTGCATTCAGGTTTAG--T
66 CGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTGCATTCAAGTTTTGTAT
18974 TTT-A
130 TTTGA
* * * * ** * *
18978 CTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTT-AAGTCTAGT
1 -TTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTC---TTTTTGC-TTTCAAGTTTAGT
* * * * **
19042 -CTTTC-TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAAT-TCTGTCATTCTTGCATTTGAG-
61 ATTTTCGTTTCCAGA-AATACCCTTTCGGTCAAAGGGTCAGTCT-TGTC-TTTTTGCATTCAAGT
19103 -TT-TACTTTTGA
123 TTTGTA-TTTTGA
* *
19114 TTTCCAAAAATACCCTTTCGGTGAAAGGGT
1 TTTCCAGAAATACCCTTTCGGTCAAAGGGT
19144 AAGTTTCATC
Statistics
Matches: 505, Mismatches: 42, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
131 1 0.00
132 37 0.07
133 142 0.28
134 263 0.52
135 58 0.11
136 4 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (134 bp):
TTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTATTTT
CGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTATT
TTGA
Found at i:18906 original size:267 final size:264
Alignment explanation
Indices: 18445--19143 Score: 930
Period size: 267 Copynumber: 2.6 Consensus size: 264
18435 TTTATTTTCT
*
18445 CTTTCCAGAAGTACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTTTAGTATTT
1 CTTTCCAGAAATACCCTTTCGGTCAAA-GGTCAGTTTCATCTTTTTGCATTTAAGTTTAGTATTT
*
18510 TCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTATCTTTTTGCATTCAAGTTTTGTAT
65 TC-TTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTAT
*
18575 TTTGATTTACC-GAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGTTTTCAAGTTTAG
129 TTTGATTT-CCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAG
*
18639 TATTTTCGTTTCCATAAATAACCTTTCGATCAAAGGGTCAGTCTT-GTCTTTTTGCATTCAAGTT
193 TATTTTCGTTTCCAGAAATAACCTTTCGATCAAAGGGTCAGT-TTCGTCTTTTTGCATTCAAGTT
*
18703 TTGTATTTTGA
257 TAG--TTTT-A
* * **
18714 -TTTCCAGAAATACCATTTCGGTCAAAGGTCGGTTTTGTCTTTTTGC-TTTCAAGTTTAGTATTT
1 CTTTCCAGAAATACCCTTTCGGTCAAAGGTCAGTTTCATCTTTTTGCATTT-AAGTTTAGTATTT
*
18777 TCGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTACATTCAAGTTTTGTAT
65 TC-TTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTAT
*
18842 TTTGATTTCCAGAAATACCCTTTCGGTCAAATGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGT
129 TTTGATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGT
* * * *
18907 ATTTTCGTTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTCAGGTTTA
194 ATTTTCGTTTCCAGAAATAACCTTTCGATCAAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTA
18972 GTTTTA
259 GTTTTA
* * * * *
18978 CTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT-
1 CTTTCCAGAAATACCCTTTCGGTC-AAAGGTCAGTTTCATC---TTTTTGCATTTAAGTTTAGTA
* * * * **
19042 CTTTCTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAAT-TCTGTCATTCTTGCATTTGAG--T
62 TTTTCTTTCCAGA-AATACCCTTTCGGTCAAAGGGTCAGTCT-TGTC-TTTTTGCATTCAAGTTT
* *
19104 T-TACTTTTGATTTCCAAAAATACCCTTTCGGTGAAAGGGT
124 TGTA-TTTTGATTTCCAGAAATACCCTTTCGGTCAAAGGGT
19144 AAGTTTCATC
Statistics
Matches: 382, Mismatches: 35, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
264 1 0.00
265 24 0.06
266 21 0.05
267 252 0.66
268 57 0.15
269 24 0.06
270 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (264 bp):
CTTTCCAGAAATACCCTTTCGGTCAAAGGTCAGTTTCATCTTTTTGCATTTAAGTTTAGTATTTT
CTTTCCAGAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTTGTATTT
TGATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCTTTCAAGTTTAGTAT
TTTCGTTTCCAGAAATAACCTTTCGATCAAAGGGTCAGTTTCGTCTTTTTGCATTCAAGTTTAGT
TTTA
Found at i:29453 original size:17 final size:17
Alignment explanation
Indices: 29431--29466 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29421 TGTTCAATTA
29431 AACTTTTAAATAGGACC
1 AACTTTTAAATAGGACC
29448 AACTTTTAAATAGGACC
1 AACTTTTAAATAGGACC
29465 AA
1 AA
29467 ATTGGGCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
AACTTTTAAATAGGACC
Found at i:29689 original size:132 final size:132
Alignment explanation
Indices: 29465--29727 Score: 517
Period size: 132 Copynumber: 2.0 Consensus size: 132
29455 AAATAGGACC
29465 AAATTGGGCCTGAACGTTAGCAAATGGCACCAAATTAGGTTGCTAACGTTTAAAAAGATTTAGAT
1 AAATTGGGCCTGAACGTTAGCAAATGGCACCAAATTAGGTTGCTAACGTTTAAAAAGATTTAGAT
*
29530 CCAATTTGGGTATTAGTCCTACTATTCAAGCAACGATCAATTTAGGCTTAATCCTTTAAATTAAA
66 CCAATTTGGGTATTACTCCTACTATTCAAGCAACGATCAATTTAGGCTTAATCCTTTAAATTAAA
29595 AT
131 AT
29597 AAATTGGGCCTGAACGTTAGCAAATGGCACCAAATTAGGTTGCTAACGTTTAAAAAGATTTAGAT
1 AAATTGGGCCTGAACGTTAGCAAATGGCACCAAATTAGGTTGCTAACGTTTAAAAAGATTTAGAT
29662 CCAATTTGGGTATTACTCCTACTATTCAAGCAACGATCAATTTAGGCTTAATCCTTTAAATTAAA
66 CCAATTTGGGTATTACTCCTACTATTCAAGCAACGATCAATTTAGGCTTAATCCTTTAAATTAAA
29727 A
131 A
29728 CTAGGCTTAA
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 130 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (132 bp):
AAATTGGGCCTGAACGTTAGCAAATGGCACCAAATTAGGTTGCTAACGTTTAAAAAGATTTAGAT
CCAATTTGGGTATTACTCCTACTATTCAAGCAACGATCAATTTAGGCTTAATCCTTTAAATTAAA
AT
Found at i:29744 original size:25 final size:25
Alignment explanation
Indices: 29704--29755 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29694 ACGATCAATT
*
29704 TAGGCTTAATCCTTTAAATTAAAAC
1 TAGGCTTAATCCTTTAAATCAAAAC
** *
29729 TAGGCTTAATTTTTTAGATCAAAAC
1 TAGGCTTAATCCTTTAAATCAAAAC
29754 TA
1 TA
29756 ATTTTTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (25 bp):
TAGGCTTAATCCTTTAAATCAAAAC
Found at i:32704 original size:7 final size:7
Alignment explanation
Indices: 32692--32716 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32682 AATAATATAT
32692 ATTATTG
1 ATTATTG
32699 ATTATTG
1 ATTATTG
32706 ATTATTG
1 ATTATTG
32713 ATTA
1 ATTA
32717 ATCTCGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
ATTATTG
Found at i:36074 original size:31 final size:30
Alignment explanation
Indices: 35977--36074 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
35967 GGCTAAATAT
*
35977 CCAAATTGAGTCTAAACCTTTTGCAAGTTGC-
1 CCAAATTGAGTCTAAA-CTTTT-CAAGATGCA
* * * * * *
36008 TCAATTTGAGCCTAAACCTTT-AAGGTGAA
1 CCAAATTGAGTCTAAACTTTTCAAGATGCA
36037 CCAAATTGAGTCTAAACATTTTCAAGATGCA
1 CCAAATTGAGTCTAAAC-TTTTCAAGATGCA
36068 CCAAATT
1 CCAAATT
36075 AGGCCTAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 5 0.10
29 14 0.27
30 7 0.13
31 26 0.50
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (30 bp):
CCAAATTGAGTCTAAACTTTTCAAGATGCA
Found at i:42448 original size:21 final size:21
Alignment explanation
Indices: 42419--42460 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42409 TCGCTCGGTC
*
42419 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
42439 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
42461 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:43857 original size:33 final size:30
Alignment explanation
Indices: 43795--43879 Score: 86
Period size: 33 Copynumber: 2.8 Consensus size: 30
43785 AATAATTTTC
*
43795 ATTATCATATATTTA-TT-TTTTTAGATAA
1 ATTATCATATATTTATTTATTTTTAAATAA
43823 ATTATCATATATTTATTTAACTTTTGTAAATAA
1 ATTATCATATATTTATTT-A-TTTT-TAAATAA
*
43856 ATATAT-TTATATTTCATTTATTTT
1 AT-TATCATATATTT-ATTTATTTT
43880 GAATTTATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 15 0.31
29 2 0.04
32 8 0.17
33 16 0.33
34 7 0.15
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (30 bp):
ATTATCATATATTTATTTATTTTTAAATAA
Found at i:48054 original size:19 final size:19
Alignment explanation
Indices: 48030--48069 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
48020 TTGTAATACC
*
48030 TTTCTATTAGTTCTTAAAT
1 TTTCTATTAGTCCTTAAAT
48049 TTTCTATTAGTCCTTAAAT
1 TTTCTATTAGTCCTTAAAT
48068 TT
1 TT
48070 GTGTGAGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTATTAGTCCTTAAAT
Done.