Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009153.1 Corchorus capsularis cultivar CVL-1 contig09174, 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: 39056
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:15752 original size:13 final size:13
Alignment explanation
Indices: 15734--15762 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15724 TAGTCCTCTG
15734 ATACCAAGGGATA
1 ATACCAAGGGATA
15747 ATACCAAGGGATA
1 ATACCAAGGGATA
15760 ATA
1 ATA
15763 GGATCGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (13 bp):
ATACCAAGGGATA
Found at i:16398 original size:13 final size:13
Alignment explanation
Indices: 16379--16410 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16369 TAGCCTTGGT
16379 CATTATTACACAC
1 CATTATTACACAC
*
16392 TATTATTACACAC
1 CATTATTACACAC
16405 CATTAT
1 CATTAT
16411 CATGACACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (13 bp):
CATTATTACACAC
Found at i:16495 original size:10 final size:11
Alignment explanation
Indices: 16455--16498 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
16445 AAGTCTACAT
*
16455 CACACTTAAAA
1 CACACTTAATA
*
16466 CACTCTTAA-A
1 CACACTTAATA
16476 CACACTTAATA
1 CACACTTAATA
16487 CACAC-TAATA
1 CACACTTAATA
16497 CA
1 CA
16499 TATATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (11 bp):
CACACTTAATA
Found at i:26112 original size:21 final size:21
Alignment explanation
Indices: 26088--26161 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
26078 CTTGATGCAA
*
26088 CCACTCCTCCAATTGATTCTT
1 CCACTGCTCCAATTGATTCTT
* *
26109 CCACGGCTCCAATTGAATCTT
1 CCACTGCTCCAATTGATTCTT
* * * *
26130 CAATTGCTCGAATTGATCCTT
1 CCACTGCTCCAATTGATTCTT
*
26151 CCACTGTTCCA
1 CCACTGCTCCA
26162 TCACTTCCAT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.22, C:0.34, G:0.11, T:0.34
Consensus pattern (21 bp):
CCACTGCTCCAATTGATTCTT
Found at i:27080 original size:1 final size:1
Alignment explanation
Indices: 27074--27098 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
27064 TCTGGTTGCC
27074 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
27099 GAAATGGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34809 original size:30 final size:28
Alignment explanation
Indices: 34773--34869 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 28
34763 CGGGCATCTG
*
34773 ACGTGGCATACCACGTGTGCCAAAAATGCC
1 ACGTGGCATGCCACGTGT--CAAAAATGCC
* * *
34803 ACGTGGCATGCCACATGTACAAAAAGGAC
1 ACGTGGCATGCCACGTGT-CAAAAATGCC
* *
34832 ACATGGCACGCCACGTGTCAAAAATGCC
1 ACGTGGCATGCCACGTGTCAAAAATGCC
*
34860 ACGTGCCATG
1 ACGTGGCATG
34870 TGTCATTTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 15 0.28
29 23 0.43
30 16 0.30
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (28 bp):
ACGTGGCATGCCACGTGTCAAAAATGCC
Found at i:35278 original size:19 final size:18
Alignment explanation
Indices: 35256--35292 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
35246 AAAAAATCTT
35256 TTAAAAAATTTAAAAAAAA
1 TTAAAAAA-TTAAAAAAAA
35275 TTAAAAAATTAAAAAAAA
1 TTAAAAAATTAAAAAAAA
35293 AAGAAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TTAAAAAATTAAAAAAAA
Found at i:35293 original size:19 final size:19
Alignment explanation
Indices: 35256--35293 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35246 AAAAAATCTT
*
35256 TTAAAAAATTTAAAAAAAA
1 TTAAAAAATTAAAAAAAAA
35275 TTAAAAAATTAAAAAAAAA
1 TTAAAAAATTAAAAAAAAA
35294 AGAAAATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
TTAAAAAATTAAAAAAAAA
Found at i:35299 original size:19 final size:19
Alignment explanation
Indices: 35258--35299 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35248 AAAATCTTTT
* **
35258 AAAAAATTTAAAAAAAATT
1 AAAAAATTAAAAAAAAAAG
35277 AAAAAATTAAAAAAAAAAG
1 AAAAAATTAAAAAAAAAAG
35296 AAAA
1 AAAA
35300 TGGCCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAAATTAAAAAAAAAAG
Found at i:35408 original size:15 final size:14
Alignment explanation
Indices: 35357--35449 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
35347 TTATGATTAG
*
35357 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
35371 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
35384 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
35397 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
35410 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
35423 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
35436 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
35449 T
1 T
35450 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:35417 original size:26 final size:26
Alignment explanation
Indices: 35388--35455 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
35378 TACTTAGTTT
35388 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
35414 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
35440 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
35456 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:38006 original size:19 final size:18
Alignment explanation
Indices: 37982--38017 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37972 TGAAGATTTC
37982 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
38001 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
38018 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.