Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012684.1 Corchorus olitorius cultivar O-4 contig12717, 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: 25808
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:10024 original size:31 final size:31
Alignment explanation
Indices: 9983--10061 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 31
9973 CGTTTCTGTT
* *
9983 TTTAGGCTCAAATTGGTCAATTTTTGAAAGG
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGG
10014 TTTAGACTCAAATTGAG-CAACTTTTGAAAGG
1 TTTAGACTCAAATTG-GTCAACTTTTGAAAGG
10045 TTTAGACTCAAATTGGT
1 TTTAGACTCAAATTGGT
10062 GGCTAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 42 0.95
32 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGG
Found at i:10976 original size:42 final size:43
Alignment explanation
Indices: 10926--11019 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
10916 AATGCATTAC
* *
10926 CTAA-ATTCTACT-TCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
10967 CTAATATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG
11012 CTAATATT
1 CTAATATT
11020 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
45 35 0.74
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:15130 original size:35 final size:35
Alignment explanation
Indices: 15065--15131 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
15055 GATCCTCTTT
* *
15065 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
* * *
15100 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT
15132 AAAGAGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
Found at i:19727 original size:22 final size:22
Alignment explanation
Indices: 19701--19750 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
19691 ACTATAATAT
* *
19701 CAAAAAATTACAGGGAGATTAA
1 CAAAAAATGACAGAGAGATTAA
** *
19723 CAAAATCTGACAGAGAGATTAT
1 CAAAAAATGACAGAGAGATTAA
19745 CAAAAA
1 CAAAAA
19751 TCATAGGAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.18
Consensus pattern (22 bp):
CAAAAAATGACAGAGAGATTAA
Found at i:19764 original size:21 final size:21
Alignment explanation
Indices: 19738--19780 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19728 TCTGACAGAG
19738 AGATTATCAAAA-ATCATAGGA
1 AGATTA-CAAAATATCATAGGA
*
19759 AGATTACAAAATTTCATAGGA
1 AGATTACAAAATATCATAGGA
19780 A
1 A
19781 AGTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (21 bp):
AGATTACAAAATATCATAGGA
Found at i:19818 original size:22 final size:23
Alignment explanation
Indices: 19741--19845 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 23
19731 GACAGAGAGA
* *
19741 TTATCAAAA-ATCATAGG-AAGA
1 TTATCAAAATTTCATAGGAAAGT
19762 TTA-CAAAATTTCATAGGAAAGT
1 TTATCAAAATTTCATAGGAAAGT
* * *
19784 TTATTAAAATTTCATAGTAATG-
1 TTATCAAAATTTCATAGGAAAGT
* *
19806 TTATCAAAGTTTCTTATGG--AGT
1 TTATCAAAATTTCATA-GGAAAGT
* *
19828 TTATCACAATTTTATAGG
1 TTATCAAAATTTCATAGG
19846 TAATTGGTGG
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.08
21 13 0.20
22 31 0.48
23 16 0.25
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAAAGT
Found at i:24277 original size:22 final size:22
Alignment explanation
Indices: 24249--24348 Score: 66
Period size: 22 Copynumber: 4.6 Consensus size: 22
24239 CAGATGATCG
24249 AAATTTCATAGTGTAACTATCA
1 AAATTTCATAGTGTAACTATCA
* ***
24271 AAATTTCATAATGTGGTTA-CA
1 AAATTTCATAGTGTAACTATCA
*
24292 AAAGTTTCATA---TAAGGTAATCA
1 AAA-TTTCATAGTGTAA-CT-ATCA
* *
24314 AAATTTCATATTGT-GCTTATCA
1 AAATTTCATAGTGTAAC-TATCA
24336 AAATTTCATAGTG
1 AAATTTCATAGTG
24349 AGATTAATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 13 0.22
22 43 0.72
23 1 0.02
24 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTCATAGTGTAACTATCA
Found at i:24322 original size:21 final size:21
Alignment explanation
Indices: 24267--24324 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
24257 TAGTGTAACT
** *
24267 ATCAAAATTTCATAATGTGGTT
1 ATCAAAATTTCAT-ATAAGGTA
24289 A-CAAAAGTTTCATATAAGGTA
1 ATCAAAA-TTTCATATAAGGTA
24310 ATCAAAATTTCATAT
1 ATCAAAATTTCATAT
24325 TGTGCTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATATAAGGTA
Found at i:24419 original size:22 final size:21
Alignment explanation
Indices: 24266--24433 Score: 96
Period size: 22 Copynumber: 7.7 Consensus size: 21
24256 ATAGTGTAAC
24266 TATCAAAATTTCATAATGT-GGT
1 TATCAAAATTTCAT-A-GTAGGT
24288 TA-CAAAAGTTTCATA-TAAGGT
1 TATCAAAA-TTTCATAGT-AGGT
* *
24309 AATCAAAATTTCATATTGT-GCT
1 TATCAAAATTTCATA--GTAGGT
*
24331 TATCAAAATTTCATAGTGAGAT
1 TATCAAAATTTCATAGT-AGGT
* * *
24353 TAAT-GAAA-TTCTATAAGGAAGT
1 T-ATCAAAATTTC-AT-AGTAGGT
* * *
24375 TATCAACATTCCATAGGGAGGT
1 TATCAAAATTTCATA-GTAGGT
24397 TATCAAAATTTCATAGTATGGT
1 TATCAAAATTTCATAGTA-GGT
*
24419 TATCCAAATTTCATA
1 TATCAAAATTTCATA
24434 ATGTACCAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 25 0.22
22 79 0.69
23 6 0.05
24 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATAGTAGGT
Found at i:24593 original size:22 final size:22
Alignment explanation
Indices: 24515--24657 Score: 97
Period size: 22 Copynumber: 6.5 Consensus size: 22
24505 CATATAGAGA
* * *
24515 TTATCACAATTTTATAGTGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
24537 TTATCAAAATTTTATAGTTTGG
1 TTATCAAAATTTCATAGTGTGG
* *
24559 TGACCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
24581 TTATCAAAGTTTCACAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
24603 TTTTCACAATTTCTTAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
** * * *
24625 TTATCAAAATAACATAGCGAGA
1 TTATCAAAATTTCATAGTGTGG
24647 TTATCAAAATT
1 TTATCAAAATT
24658 CTATAATAAG
Statistics
Matches: 95, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Done.