Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013811.1 Corchorus capsularis cultivar CVL-1 contig13832, 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: 36828
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1289 original size:3 final size:3
Alignment explanation
Indices: 1281--1318 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1271 TAATTTAAAT
1281 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1319 ATAAACACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1305 original size:17 final size:17
Alignment explanation
Indices: 1283--1322 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1273 ATTTAAATTA
1283 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1300 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1317 A-AATAA
1 ATAATAA
1323 ACACATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:1306 original size:20 final size:19
Alignment explanation
Indices: 1276--1322 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1266 TTTCATAATT
1276 TAAATTAATAATAATAATAA
1 TAAA-TAATAATAATAATAA
1296 TAATATAATAATAATAATAA
1 TAA-ATAATAATAATAATAA
1316 TAAATAA
1 TAAATAA
1323 ACACATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.15
20 21 0.81
21 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAATAATAATAATAA
Found at i:3740 original size:6 final size:6
Alignment explanation
Indices: 3715--3769 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
3705 GCGCTCCTAG
* * * *
3715 TTAATT TTAAATA TTCATT TAAATT TAAATT TTAATT TTAATT TTAATT
1 TTAATT TT-AATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
3764 TTAATT
1 TTAATT
3770 ATGAACTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (6 bp):
TTAATT
Found at i:4200 original size:22 final size:22
Alignment explanation
Indices: 4175--4219 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4165 AAATAGGTTT
*
4175 AGAATCCTTACAAGACTAAGAA
1 AGAATCCTAACAAGACTAAGAA
4197 AGAATCCTAACAAGACTAAGAA
1 AGAATCCTAACAAGACTAAGAA
4219 A
1 A
4220 AGGGTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (22 bp):
AGAATCCTAACAAGACTAAGAA
Found at i:5985 original size:22 final size:22
Alignment explanation
Indices: 5950--5994 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5940 AAATAGGTTT
*
5950 AGAATCTTAACAAGACTAAGAA
1 AGAATCCTAACAAGACTAAGAA
*
5972 AGAATCCTAGCAAGACTAAGAA
1 AGAATCCTAACAAGACTAAGAA
5994 A
1 A
5995 AGGATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (22 bp):
AGAATCCTAACAAGACTAAGAA
Found at i:9389 original size:20 final size:19
Alignment explanation
Indices: 9357--9394 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
9347 ACATTGACAT
9357 ATACATAATTATGTACACAC
1 ATACATAATTATGT-CACAC
9377 ATACATACA-TATGTCACA
1 ATACATA-ATTATGTCACA
9395 ACATTTTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 12 0.71
21 1 0.06
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (19 bp):
ATACATAATTATGTCACAC
Found at i:14932 original size:7 final size:7
Alignment explanation
Indices: 14920--14953 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
14910 ACCTGTATGA
14920 ATCATCC
1 ATCATCC
14927 ATCATCC
1 ATCATCC
14934 ATCATCC
1 ATCATCC
14941 ATCATCC
1 ATCATCC
14948 ATCATC
1 ATCATC
14954 ATGCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCATCC
Found at i:24708 original size:16 final size:16
Alignment explanation
Indices: 24650--24708 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
24640 AATCGGTTTT
* *
24650 GAAGAAAGAAGAACGAA
1 GAAGAAAAAAGAA-AAA
* *
24667 GAAGGAAAAGGAAAAA
1 GAAGAAAAAAGAAAAA
24683 GAA-AATAAAAGAAAAA
1 GAAGAA-AAAAGAAAAA
24699 GAAGAAAAAA
1 GAAGAAAAAA
24709 AAATTAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 1 0.03
16 21 0.62
17 12 0.35
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (16 bp):
GAAGAAAAAAGAAAAA
Found at i:26877 original size:2 final size:2
Alignment explanation
Indices: 26870--26931 Score: 88
Period size: 2 Copynumber: 29.5 Consensus size: 2
26860 TAATATGTAG
*
26870 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
26913 TA TA GTA TA TA TA GTA TA T
1 TA TA -TA TA TA TA -TA TA T
26932 GCATGGAATG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 49 0.89
3 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26886 original size:21 final size:18
Alignment explanation
Indices: 26870--26931 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 18
26860 TAATATGTAG
26870 TATATATATATATATATA
1 TATATATATATATATATA
*
26888 TATATATAGTATATATGTA
1 TATATATA-TATATATATA
26907 TATATATATAGTATATATA
1 TATATATATA-TATATATA
26926 GTATAT
1 -TATAT
26932 GCATGGAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.26
19 24 0.62
20 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (18 bp):
TATATATATATATATATA
Found at i:33365 original size:14 final size:14
Alignment explanation
Indices: 33343--33379 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
33333 TGTGTATACT
*
33343 AAAACTAAAACTAC
1 AAAATTAAAACTAC
*
33357 AAAATTAAAATTAC
1 AAAATTAAAACTAC
33371 AAAATTAAA
1 AAAATTAAA
33380 CATTTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAACTAC
Found at i:33428 original size:66 final size:66
Alignment explanation
Indices: 33358--33486 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
33348 TAAAACTACA
*
33358 AAATTAAAATTACAAAATTAAACATTTTCAAATCCAGATTAAACATTCATATGATTTTTTTAAAT
1 AAATTAAAATTACAAAATTAAACATTTCCAAATCCAGATTAAACATTCATATGATTTTTTTAAAT
33423 T
66 T
* *
33424 AAATTAAAATTACAAAATTCACCATTTCCAAATCCAGATTAAACATTCATATGATTTTTTTAA
1 AAATTAAAATTACAAAATTAAACATTTCCAAATCCAGATTAAACATTCATATGATTTTTTTAA
33487 TAAATTGAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (66 bp):
AAATTAAAATTACAAAATTAAACATTTCCAAATCCAGATTAAACATTCATATGATTTTTTTAAAT
T
Found at i:33548 original size:15 final size:15
Alignment explanation
Indices: 33523--33559 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
33513 TTTATAAAAC
33523 TAAAGAATTAAAGAAA
1 TAAA-AATTAAAGAAA
33539 TAAAAATTAAAGAAA
1 TAAAAATTAAAGAAA
*
33554 CAAAAA
1 TAAAAA
33560 CTACTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (15 bp):
TAAAAATTAAAGAAA
Done.