Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010058.1 Corchorus capsularis cultivar CVL-1 contig10079, 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: 4764
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Found at i:79 original size:18 final size:17
Alignment explanation
Indices: 52--85 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42 ATGCGTGGTG
*
52 AAAAAAGAAAAGAGAAA
1 AAAAAAGAAAAAAGAAA
69 AAAAGAAGAAAAAAGAA
1 AAAA-AAGAAAAAAGAA
86 GGAAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:904 original size:35 final size:35
Alignment explanation
Indices: 857--1295 Score: 783
Period size: 35 Copynumber: 12.6 Consensus size: 35
847 TGTAGTCATC
*
857 AGGTCAGTGTTGATCTCATTCCAAGAAG-TTTCTAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTC-AG
892 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
927 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTGCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
962 AGGTCAGAGTTGATCTCATTTCAAGAAGTTTCCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
997 A-GTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1031 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1066 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
1101 AGATCAGAGTTGATCTCATTCCAGGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
1136 AGGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1171 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1206 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1241 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
1276 AGGTCAGAGTTGATCGCATT
1 AGGTCAGAGTTGATCTCATT
1296 TTCAGTATTT
Statistics
Matches: 389, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
34 32 0.08
35 353 0.91
36 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (35 bp):
AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
Found at i:1318 original size:35 final size:35
Alignment explanation
Indices: 1279--1535 Score: 390
Period size: 35 Copynumber: 7.3 Consensus size: 35
1269 TTTTCAGAGG
*
1279 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1314 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
1349 TCAGAGTTGATCGCATTTTTAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1384 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
1419 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
1454 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * * *
1489 TCAGAGGTGATCTCA-TTTCAAGAAATTTCCGATGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
1524 TCAGAGTTGATC
1 TCAGAGTTGATC
1536 CAGAGTAGTT
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
34 4 0.02
35 200 0.98
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:1318 original size:105 final size:104
Alignment explanation
Indices: 857--1535 Score: 734
Period size: 105 Copynumber: 6.5 Consensus size: 104
847 TGTAGTCATC
* * * * *
857 AGGTCAGTGTTGATCTCATTCCAAGAAGTTTCTAGAGGTCAGAGTTGATCTCATTCCAAGAAGTT
1 AGGTCAGAGTTGATCTCATTTCAAGAATTTTCCA-AGATCAGAGTTGATCTCATTCCAAGAAGTT
*
922 TTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTGCAG
65 TTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
962 AGGTCAGAGTTGATCTCATTTCAAGAAGTTTCC-AGAGTCAGAGTTGATCTCATTCCAAGAAGTT
1 AGGTCAGAGTTGATCTCATTTCAAGAATTTTCCAAGA-TCAGAGTTGATCTCATTCCAAGAAGTT
1026 TTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
65 TTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
1066 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTT-CAGAGATCAGAGTTGATCTCATTCCAGGAAGT
1 AGGTCAGAGTTGATCTCATTTCAAGAA-TTTTCCA-AGATCAGAGTTGATCTCATTCCAAGAAGT
*
1130 TTTCAGAGGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAG
64 TTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
1171 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTT-CAGAGGTCAGAGTTGATCTCATTCCAAGAAGT
1 AGGTCAGAGTTGATCTCATTTCAAGAA-TTTTCCA-AGATCAGAGTTGATCTCATTCCAAGAAGT
1235 TTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
64 TTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* * * * *
1276 AGGTCAGAGTTGATCGCATTTTC-AGTATTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTAG
1 AGGTCAGAGTTGATCTCA-TTTCAAGAATTTTCCAA-GATCAGAGTTGATCTCA-TTCCAAGAAG
* * * *** *
1339 TTTCCA-ACGATCAGAGTTGATCGCATTTTTAGAAGTTTCCA-
63 TTTTCAGA-GGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* * * * * * *
1380 ACGATCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTA
1 A-GGTCAGAGTTGATCTCA-TTTCAAGAATTTTCCAA-GATCAGAGTTGATCTCA-TTCCAAGAA
* * * * * *
1443 GTTTCCA-ATGATCAGAGTTGATCACATTTTC-AGTAGTTTCCA-
62 GTTTTCAGA-GGTCAGAGTTGATCTCA-TTCCAAGAAGTTTTCAG
** * * *
1485 ACAATCAGAGGTGATCTCATTTCAAGAAATTTCCGATGATCAGAGTTGATC
1 A-GGTCAGAGTTGATCTCATTTCAAGAATTTTCC-AAGATCAGAGTTGATC
1536 CAGAGTAGTT
Statistics
Matches: 523, Mismatches: 38, Indels: 26
0.89 0.06 0.04
Matches are distributed among these distances:
103 2 0.00
104 104 0.20
105 404 0.77
106 13 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (104 bp):
AGGTCAGAGTTGATCTCATTTCAAGAATTTTCCAAGATCAGAGTTGATCTCATTCCAAGAAGTTT
TCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
Found at i:2811 original size:75 final size:75
Alignment explanation
Indices: 2730--2997 Score: 450
Period size: 75 Copynumber: 3.6 Consensus size: 75
2720 AAAATAATAA
*
2730 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGAAATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
2795 ATAATAAAGT
66 ATAATAAAGT
2805 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
2870 ATAATAAAGT
66 ATAATAAAGT
* *
2880 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATCTTTTAAGAAAT-AAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAT-
*
2944 AATAATAAAGAA
65 AATAATAAAG-T
*
2956 TGAGAATATTTCTCTAAATCTTGCCAGATTGTGGG-GATTTAG
1 TGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAG
2998 AAAATATTAA
Statistics
Matches: 184, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
74 4 0.02
75 141 0.77
76 18 0.10
77 21 0.11
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (75 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
ATAATAAAGT
Done.