Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011961.1 Corchorus olitorius cultivar O-4 contig11994, 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: 41330
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3022 original size:422 final size:421
Alignment explanation
Indices: 2167--3160 Score: 1189
Period size: 422 Copynumber: 2.3 Consensus size: 421
2157 AGTTGTGTGA
* ** * * * * *
2167 AATCGGACATCTGGATCAAAAATTATATAATATTAAATAGACCATCAATTGAAACCATAAAATTT
1 AATCGGACATGTAAATCGAAAATTATATGATATTAAATAGACCAGCAATCGAAACCA-CAAATTT
* * * * *
2232 CGGAAGCATTTTTTAAAATTGAAACATAAAAGTTAGCTTTTGAGTCCCTAATGAAAGTTGTAGAT
65 CGGAAGCATTTTTTTAAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGAT
* * * * * * *
2297 CATGAATTTACCTTTTAATAGACACCTGAATTCCCATGATTTAACAAATAGAATAAAGAAAAAAA
130 CATGAAATTACCTTTTAATAGACACCTGAAATCACATGAATCAACAAATAGAAAAAAAAAAAAAA
* * *
2362 AATCGAAGCGTTAAATCGAGTAAATAAGAATTTGTAAAGGACTAAATAGTATAAAGTAGAAAACT
195 AAGCGAAGCGTTAAATCGAGTAAATAAGAATTAGTAAAGGACTAAATAGTATAAAGTAGAAAAAT
* *
2427 ATGAGAGTTATTTGATAAATAATCCGAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAA
260 ATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATC-----AC----
* *
2492 AAATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAGCTTTCAGGTCCTTCTTGAAA
316 --A-T--CTTTTGAACCCTTAACGAAACTCGTAGATCAAATTTAGCTTTCAGGTCCTTCATGAAA
* *
2557 GTCGTAGATCATACAATAACTTTTTAACCGACACTTGAATAACTTT
376 GTCGTAGATCATACAATAACCTTTTAACCGACACTTAAATAACTTT
*
2603 AATCGGATATGTAAATCGAAAATTATATGATATTAAATAGACCAGCAATCGAAACCACCAAATTT
1 AATCGGACATGTAAATCGAAAATTATATGATATTAAATAGACCAGCAATCGAAACCA-CAAATTT
* * *
2668 CGGAAGCTTTTTTTTTAAATTGAAACATAAAAATTGGCTTTTGAGTCATTCATGAAAGTTGTAGG
65 CGGAAGC-ATTTTTTTAAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGA
* *
2733 TCATGAAATTACCTTTTAATAGACACCT-AAATCA-ACTTAATCAGACAAATATAACAAAAAATA
129 TCATGAAATTACCTTTTAATAGACACCTGAAATCACA-TGAATCA-ACAAATAGAA-AAAAAA-A
* * * * *
2796 AAAATAAAGCTTAAGTGTTAAATCGATTAAGAT-AGAATTAGTAAATGACTAAATGGTATAAAGT
190 AAAA-AAAGC-GAAGCGTTAAATCGAGTAA-ATAAGAATTAGTAAAGGACTAAATAGTATAAAGT
2860 AGAAAAATATGAG-GATCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGA-C-C
252 AGAAAAATATGAGAG-TCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCAC
*
2922 -T-TTTT-AACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTC-GAGTCCTTCATGAAAGTCG
316 ATCTTTTGAACCCTTAACGAAACTCGTAGATCAAATTTAGCTTTCAG-GTCCTTCATGAAAGTCG
*
2983 TAGATCATGCAATAACCTTTTAACCGACACTTAAATAACTTT
380 TAGATCATACAATAACCTTTTAACCGACACTTAAATAACTTT
* ** *
3025 AATTGGACATGTGGATCGAAAATTATATGATATATAAGATAGACCAGCAATCGAAAACCACAGAT
1 AATCGGACATGTAAATCGAAAATTATATGATAT-TAA-ATAGACCAGCAATCG-AAACCACAAAT
* * * * * *
3090 TTCAGAAGCATTTTTTTGAATCGAAACATAAAAATTGACTTTTGAATCCTTCATGAAAGTAGTAG
63 TTCGGAAGCATTTTTTTAAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAG
3155 ATCATG
128 ATCATG
3161 GAACAATCTT
Statistics
Matches: 488, Mismatches: 57, Indels: 39
0.84 0.10 0.07
Matches are distributed among these distances:
421 1 0.00
422 119 0.24
423 61 0.12
424 27 0.06
425 6 0.01
426 1 0.00
434 1 0.00
435 1 0.00
436 70 0.14
437 85 0.17
438 4 0.01
439 5 0.01
440 6 0.01
441 99 0.20
442 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (421 bp):
AATCGGACATGTAAATCGAAAATTATATGATATTAAATAGACCAGCAATCGAAACCACAAATTTC
GGAAGCATTTTTTTAAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGATC
ATGAAATTACCTTTTAATAGACACCTGAAATCACATGAATCAACAAATAGAAAAAAAAAAAAAAA
AGCGAAGCGTTAAATCGAGTAAATAAGAATTAGTAAAGGACTAAATAGTATAAAGTAGAAAAATA
TGAGAGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCACATCTTTTGAA
CCCTTAACGAAACTCGTAGATCAAATTTAGCTTTCAGGTCCTTCATGAAAGTCGTAGATCATACA
ATAACCTTTTAACCGACACTTAAATAACTTT
Found at i:3353 original size:168 final size:168
Alignment explanation
Indices: 2955--3370 Score: 427
Period size: 168 Copynumber: 2.5 Consensus size: 168
2945 TAGATCAAAT
* * * *
2955 TTAGCTTTCGAGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTAAATA
1 TTAGCTTTTGAGTCCTTCATGAAAGTAGTAGATCATG-AATAACCTTTTAACGGACACTTGAATA
* * * *
3020 ACTTTAATTGGACATGTGGATCGAAAATTATATGATATATAAGATAGACCAGCAATCGAAAACCA
65 ATTTTAATCGGACATCTAGATCGAAAATTATATGATATATAAGATAGACCAGCAATCGAAAACCA
* * *
3085 CAGATTTCAGAAGCATTTTTTTGAATCGAAACATAAAAA
130 CAAATTTCAGAAGCATGTTTTAGAATCGAAACATAAAAA
* * *
3124 TT-GACTTTTGAATCCTTCATGAAAGTAGTAGATCATGGAACAATC-TTTAGATCGG-CACTTGA
1 TTAG-CTTTTGAGTCCTTCATGAAAGTAGTAGATCAT-GAATAACCTTTTA-A-CGGACACTTGA
* * * *
3186 ATAATTTTAACCGGACATCTAGATC-AAAATTATAT-ATCACTTTAA-ATAGACC-GTTAATTG-
62 ATAATTTTAATCGGACATCTAGATCGAAAATTATATGAT-A-TATAAGATAGACCAG-CAATCGA
* * *
3246 AAACCGCCAAATTTC-GAAAGCATGTTTTAGACTCGAAATATAAAAA
124 AAACC-ACAAATTTCAG-AAGCATGTTTTAGAATCGAAACATAAAAA
* * * * *
3292 TTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCATAGAATTACCTTTTAAGGGACACTTGAATC
1 TTAGCTTTTGAGTCCTTCATGAAAGTAGTAGATCAT-GAATAACCTTTTAACGGACACTTGAATA
*
3357 ATCTTAATCGGACA
65 ATTTTAATCGGACA
3371 AATAAAACTA
Statistics
Matches: 203, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
167 11 0.05
168 117 0.58
169 72 0.35
170 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (168 bp):
TTAGCTTTTGAGTCCTTCATGAAAGTAGTAGATCATGAATAACCTTTTAACGGACACTTGAATAA
TTTTAATCGGACATCTAGATCGAAAATTATATGATATATAAGATAGACCAGCAATCGAAAACCAC
AAATTTCAGAAGCATGTTTTAGAATCGAAACATAAAAA
Found at i:3701 original size:2 final size:2
Alignment explanation
Indices: 3696--3788 Score: 114
Period size: 2 Copynumber: 44.5 Consensus size: 2
3686 TGTTTTTTAT
* *
3696 TA TA TA TA TA AA TA TA TA TGA TA TA TA TC TA TA TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA
* *
3740 TA TA TA TA TA TGA TA TA TA TC TA TA TA TGA TA TA GA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
3784 TA TA T
1 TA TA T
3789 TTAACTTTAC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
2 71 0.90
3 8 0.10
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3721 original size:17 final size:17
Alignment explanation
Indices: 3699--3788 Score: 119
Period size: 17 Copynumber: 5.2 Consensus size: 17
3689 TTTTTATTAT
*
3699 ATATATAAATATATATG
1 ATATATATATATATATG
*
3716 ATATATATCTATATATG
1 ATATATATATATATATG
3733 ATATATATATATATATATG
1 --ATATATATATATATATG
*
3752 ATATATATCTATATATG
1 ATATATATATATATATG
*
3769 ATATAGATATATATAT-
1 ATATATATATATATATG
3785 ATAT
1 ATAT
3789 TTAACTTTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
16 4 0.06
17 45 0.69
19 16 0.25
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATATATATATATATG
Found at i:3747 original size:36 final size:36
Alignment explanation
Indices: 3697--3786 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
3687 GTTTTTTATT
*
3697 ATATATATAAATATATATGATATATATCTATATATG
1 ATATATATATATATATATGATATATATCTATATATG
3733 ATATATATATATATATATGATATATATCTATATATG
1 ATATATATATATATATATGATATATATCTATATATG
*
3769 ATATAGATATATATATAT
1 ATATATATATATATATAT
3787 ATTTAACTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATATATATATATATGATATATATCTATATATG
Found at i:13739 original size:27 final size:27
Alignment explanation
Indices: 13709--13797 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
13699 TATTTCTTAA
*
13709 TTGG-CATTAGGATCACTCAGGGGCATT
1 TTGGTCATTAGCA-CACTCAGGGGCATT
***
13736 TTGGTCATTTTTACACT-AGGGGCATT
1 TTGGTCATTAGCACACTCAGGGGCATT
* *
13762 TTGGTCATTCGCACATTCAGGGGCATT
1 TTGGTCATTAGCACACTCAGGGGCATT
13789 TTGGTCATT
1 TTGGTCATT
13798 TTAAGTTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.42
27 26 0.49
28 5 0.09
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (27 bp):
TTGGTCATTAGCACACTCAGGGGCATT
Found at i:13760 original size:26 final size:27
Alignment explanation
Indices: 13722--13799 Score: 113
Period size: 26 Copynumber: 2.9 Consensus size: 27
13712 GCATTAGGAT
*
13722 CACTCAGGGGCATTTTGGTCATTTTTA
1 CACTCAGGGGCATTTTGGTCATTTTCA
**
13749 CACT-AGGGGCATTTTGGTCATTCGCA
1 CACTCAGGGGCATTTTGGTCATTTTCA
*
13775 CATTCAGGGGCATTTTGGTCATTTT
1 CACTCAGGGGCATTTTGGTCATTTT
13800 AAGTTAGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 22 0.50
27 22 0.50
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (27 bp):
CACTCAGGGGCATTTTGGTCATTTTCA
Found at i:24176 original size:11 final size:12
Alignment explanation
Indices: 24159--24191 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
24149 AATGGTCTTC
24159 AAATCTTCAAAT
1 AAATCTTCAAAT
24171 -AATCTTC-AAT
1 AAATCTTCAAAT
24181 AAATCTTCAAA
1 AAATCTTCAAA
24192 CACGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.16
11 14 0.74
12 2 0.11
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATCTTCAAAT
Found at i:25668 original size:21 final size:21
Alignment explanation
Indices: 25639--25683 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
25629 TTGGAGCTCA
25639 TTGAATTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
*
25660 TTGAGTTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
25681 TTG
1 TTG
25684 TTTGATTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGAATTCAAAATTAGGGTTC
Found at i:32401 original size:21 final size:22
Alignment explanation
Indices: 32377--32422 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
32367 GGCTTGGAAT
*
32377 GGTGATGGCACGG-GCATGGCC
1 GGTGATGGCACGGTGAATGGCC
*
32398 GGTGGTGGCACGGTGAATGGCC
1 GGTGATGGCACGGTGAATGGCC
32420 GGT
1 GGT
32423 TGCGGCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (22 bp):
GGTGATGGCACGGTGAATGGCC
Found at i:35474 original size:23 final size:24
Alignment explanation
Indices: 35434--35478 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
35424 GGAAAAATAT
35434 ATTTTTTTATATTAAAAACGCAGA
1 ATTTTTTTATATTAAAAACGCAGA
35458 ATTTTTTT-T-TTAGAAAACGCA
1 ATTTTTTTATATTA-AAAACGCA
35479 AAAACTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (24 bp):
ATTTTTTTATATTAAAAACGCAGA
Done.