Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024474.1 Corchorus olitorius cultivar O-4 contig24507, 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: 7290
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Found at i:687 original size:21 final size:22
Alignment explanation
Indices: 659--745 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
649 AAGCTTACCG
659 ATCTCATAGTGAGGTTATCAAA
1 ATCTCATAGTGAGGTTATCAAA
*
681 A-CTCATAGAGAGGTTA-CAAA
1 ATCTCATAGTGAGGTTATCAAA
* *
701 ATTTCATAG-GAAGGTTTATTAAA
1 ATCTCATAGTG-AGG-TTATCAAA
* * *
724 ATTTAATAGTTAGGTTATCAAA
1 ATCTCATAGTGAGGTTATCAAA
746 GTTTAATATG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.11
21 23 0.43
22 11 0.20
23 14 0.26
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (22 bp):
ATCTCATAGTGAGGTTATCAAA
Found at i:738 original size:23 final size:22
Alignment explanation
Indices: 670--836 Score: 107
Period size: 22 Copynumber: 7.7 Consensus size: 22
660 TCTCATAGTG
* *
670 AGGTTATCAAAA-CTCATA-GA
1 AGGTTATCAAAATTTAATAGGA
*
690 GAGGTTA-CAAAATTTCATAGGA
1 -AGGTTATCAAAATTTAATAGGA
* **
712 AGGTTTATTAAAATTTAATAGTT
1 AGG-TTATCAAAATTTAATAGGA
*
735 AGGTTATCAAAGTTTAATATGG-
1 AGGTTATCAAAATTTAATA-GGA
* * * *
757 AGTTTATCACAATTTCATAGGTT
1 AGGTTATCAAAATTTAATAGG-A
*
780 A--TTATCAAAATTTAATAACG-
1 AGGTTATCAAAATTTAAT-AGGA
*
800 TGGTTATCAAAATTTAATAGGA
1 AGGTTATCAAAATTTAATAGGA
822 TA-GTTATCAAAATTT
1 -AGGTTATCAAAATTT
837 CATAAAAATA
Statistics
Matches: 116, Mismatches: 18, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.04
21 31 0.27
22 64 0.55
23 16 0.14
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTAATAGGA
Found at i:750 original size:22 final size:23
Alignment explanation
Indices: 691--836 Score: 114
Period size: 22 Copynumber: 6.7 Consensus size: 23
681 ACTCATAGAG
* *
691 AGGTTA-CAAAATTTCATAGG-A
1 AGGTTATCAAAATTTAATAGGTT
*
712 AGGTTTATTAAAATTTAATA-GTT
1 AGG-TTATCAAAATTTAATAGGTT
*
735 AGGTTATCAAAGTTTAATATGG--
1 AGGTTATCAAAATTTAATA-GGTT
* * *
757 AGTTTATCACAATTTCATAGGTT
1 AGGTTATCAAAATTTAATAGGTT
*
780 A--TTATCAAAATTTAATAACG-T
1 AGGTTATCAAAATTTAAT-AGGTT
*
801 -GGTTATCAAAATTTAATAGGAT
1 AGGTTATCAAAATTTAATAGGTT
823 A-GTTATCAAAATTT
1 AGGTTATCAAAATTT
837 CATAAAAATA
Statistics
Matches: 100, Mismatches: 13, Indels: 23
0.74 0.10 0.17
Matches are distributed among these distances:
21 21 0.21
22 64 0.64
23 14 0.14
24 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (23 bp):
AGGTTATCAAAATTTAATAGGTT
Found at i:794 original size:43 final size:44
Alignment explanation
Indices: 716--841 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 44
706 ATAGGAAGGT
* * * ** *
716 TTATTAAAATTTAATA-GTTAGGTTATCAAAGTTTAATATGGAGT
1 TTATCAAAATTTAATAGGATA-GTTATCAAAATTTAATAACGAGG
* * * *
760 TTATCACAATTTCATAGGTTA-TTATCAAAATTTAATAACGTGG
1 TTATCAAAATTTAATAGGATAGTTATCAAAATTTAATAACGAGG
*
803 TTATCAAAATTTAATAGGATAGTTATCAAAATTTCATAA
1 TTATCAAAATTTAATAGGATAGTTATCAAAATTTAATAA
842 AAATATTCAA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 35 0.51
44 29 0.43
45 4 0.06
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTAATAGGATAGTTATCAAAATTTAATAACGAGG
Found at i:5029 original size:20 final size:20
Alignment explanation
Indices: 4992--5030 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4982 TACTATTATT
4992 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
5012 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
5031 TATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:5427 original size:44 final size:44
Alignment explanation
Indices: 5358--5480 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
5348 ATCTCTGTGT
* ** * *
5358 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCA-TGAGGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTCCATTG-GGA
*
5402 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTCCATTGGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATTGGGA
* *
5446 GGTTATCAAAATTTCTTAGTGTGGTTACCAGAATT
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATT
5481 TCATAGGATC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 64 0.94
45 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATTGGGA
Found at i:5471 original size:22 final size:21
Alignment explanation
Indices: 5356--5548 Score: 91
Period size: 22 Copynumber: 8.8 Consensus size: 21
5346 TTATCTCTGT
*
5356 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTC-TTAG
* * * *
5378 ATGGTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTC-TTAG
* * *
5400 GAGGTTATCAAAATTCCATAG
1 GTGGTTATCAAAATTTCTTAG
* * *
5421 TGTGGTTACCAAAATTCCATTGG
1 -GTGGTTATCAAAATTTC-TTAG
*
5444 GAGGTTATCAAAATTTCTTAG
1 GTGGTTATCAAAATTTCTTAG
* * *
5465 TGTGGTTACCAGAATTTCATAG
1 -GTGGTTATCAAAATTTCTTAG
* *
5487 GATCAAGTTATTAAAATTTCTTAG
1 G-T--GGTTATCAAAATTTCTTAG
* ** *
5511 GAAGGTTATTGAAA-TTCATAG
1 G-TGGTTATCAAAATTTCTTAG
*
5532 TGTGGTTATCACAATTT
1 -GTGGTTATCAAAATTT
5549 TATAGAAAGG
Statistics
Matches: 127, Mismatches: 36, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
21 20 0.16
22 89 0.70
23 2 0.02
24 16 0.13
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
GTGGTTATCAAAATTTCTTAG
Found at i:5507 original size:46 final size:44
Alignment explanation
Indices: 5403--5510 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
5393 TCATGAGGAG
* * * * *
5403 GTTATCAAAATTCCATAGTGTGGTTACCAAAATTCCATTGGGAG
1 GTTATCAAAATTTCTTAGTGTGGTTACCAAAATTCCATAGGCAA
* *
5447 GTTATCAAAATTTCTTAGTGTGGTTACCAGAATTTCATAGGATCAA
1 GTTATCAAAATTTCTTAGTGTGGTTACCAAAATTCCATAGG--CAA
*
5493 GTTATTAAAATTTCTTAG
1 GTTATCAAAATTTCTTAG
5511 GAAGGTTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 36 0.67
46 18 0.33
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (44 bp):
GTTATCAAAATTTCTTAGTGTGGTTACCAAAATTCCATAGGCAA
Found at i:5683 original size:22 final size:22
Alignment explanation
Indices: 5572--6457 Score: 285
Period size: 22 Copynumber: 40.7 Consensus size: 22
5562 CCCAAAGAGA
* **
5572 TTATCAAAATGTCATAACGAGG
1 TTATCAAAATTTCATAGTGAGG
5594 TTAT-AAGAATTTCATAGT-ATGG
1 TTATCAA-AATTTCATAGTGA-GG
* * * *
5616 TTAACAAAATTTTATAAG-AAGA
1 TTATCAAAATTTCAT-AGTGAGG
* ** *
5638 TTA-CTAATATTTCACGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
5660 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* ** * *
5682 TTATCAAATTTTTTTAATGTGG
1 TTATCAAAATTTCATAGTGAGG
*
5704 TTATCAAAATTTCATA-TGAAGT
1 TTATCAAAATTTCATAGTG-AGG
* *
5726 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
5751 AATACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
5773 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
** *
5794 TTATGGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
**
5818 ATTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTGAGG
* *
5841 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
5863 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
5885 TTATCAAAATTTCATAGATG-GG
1 TTATCAAAATTTCATAG-TGAGG
* ** *
5907 TCAAAAAAATTTTATA--GAGG
1 TTATCAAAATTTCATAGTGAGG
** *
5927 TTATCAAAATTTCATAAAGAGA
1 TTATCAAAATTTCATAGTGAGG
5949 TTATCAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
**
5971 TTA-CCGAA--T--TAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
5988 TTAT-AAAACTTTTATTA-TG-GAG
1 TTATCAAAA-TTTCA-TAGTGAG-G
* *
6010 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
6030 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
6052 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * * *
6073 TAGATCAAAATTCCTTAGT-ATG
1 T-TATCAAAATTTCATAGTGAGG
* * *
6095 TAGATCAAAATTTCAT-GGGAGA
1 T-TATCAAAATTTCATAGTGAGG
*
6117 TTGA-CAAAATTTCATAATGAGG
1 TT-ATCAAAATTTCATAGTGAGG
* ** *
6139 TTATAAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
6161 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
* * *
6177 TTACCAAGATTTCAAAAG-GAGG
1 TTATCAAAATTTC-ATAGTGAGG
* *
6199 TTATTAAAATTTTATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* **
6221 TTTATCAAAGTTTCATAGCAAGG
1 -TTATCAAAATTTCATAGTGAGG
* * *
6244 TTATCACAATTTGATAGT-ATGA
1 TTATCAAAATTTCATAGTGA-GG
* * *
6266 TTATCAAAATTTCAAAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
6288 TTA-CTAACAATTT-ATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
** ** *
6310 TT-TTTAAATTTCATAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
6331 TTATCAATATATGATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
6353 TTATCAACATCTCATAGTGGTGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
6376 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAGTGAGG
6398 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
6420 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
*
6442 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
6458 AGAATATTTC
Statistics
Matches: 629, Mismatches: 161, Indels: 148
0.67 0.17 0.16
Matches are distributed among these distances:
16 8 0.01
17 13 0.02
18 2 0.00
19 4 0.01
20 42 0.07
21 60 0.10
22 409 0.65
23 60 0.10
24 1 0.00
25 20 0.03
26 6 0.01
27 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:6167 original size:87 final size:86
Alignment explanation
Indices: 6012--6171 Score: 193
Period size: 87 Copynumber: 1.8 Consensus size: 86
6002 TTATGGAGTA
* ** * *
6012 ATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTATGTAGA
1 ATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATAAAAAAATCATAGGAGGTAGA
6077 TCAAAATTCCTTAGTATGTAG
66 TCAAAATTCCTTAGTATGTAG
6098 ATCAAAATTTCATGGGA-GAT-TGACAAAATTTCATAATG-AGGTTATAAAAAAATCATAGGGAG
1 ATCAAAATTTCA-GGGAGGATAT--CAAAATTTCAT-ATGAAGGTTATAAAAAAATCATA-GGAG
*
6160 GT-TATCAAAATT
61 GTAGATCAAAATT
6172 TGTAGTTACC
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
85 1 0.02
86 15 0.24
87 40 0.63
88 7 0.11
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (86 bp):
ATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATAAAAAAATCATAGGAGGTAGA
TCAAAATTCCTTAGTATGTAG
Found at i:6523 original size:2 final size:2
Alignment explanation
Indices: 6516--6542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6506 CTAAAACTAG
6516 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6543 TACTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.