Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011944.1 Corchorus capsularis cultivar CVL-1 contig11965, 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: 20629
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:390 original size:20 final size:21
Alignment explanation
Indices: 365--406 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
355 TCTTGGGTTC
365 TACTCTCAC-GAAATGTGAGT
1 TACTCTCACGGAAATGTGAGT
*
385 TACTCTCACGGAATTGTGAGT
1 TACTCTCACGGAAATGTGAGT
406 T
1 T
407 TTCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TACTCTCACGGAAATGTGAGT
Found at i:6380 original size:27 final size:24
Alignment explanation
Indices: 6325--6383 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
6315 TTAATTAAAT
*
6325 GTGTTTATTTTTTGACCAAAAATA
1 GTGTTTATTTTTTGACCAAAAAAA
* *
6349 TTGTTTATTTATTCTGGCCAAAAAAA
1 GTGTTTATTT-TT-TGACCAAAAAAA
6375 GGTGTTTAT
1 -GTGTTTAT
6384 AGTTACTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 9 0.32
25 2 0.07
26 10 0.36
27 7 0.25
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (24 bp):
GTGTTTATTTTTTGACCAAAAAAA
Found at i:6655 original size:2 final size:2
Alignment explanation
Indices: 6648--6681 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6638 TTAGAAAAAC
6648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6682 ACAAACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7136 original size:28 final size:28
Alignment explanation
Indices: 7104--7159 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
7094 AACAAGCTGA
7104 AAATCGCTTTAAGCTTTCAATTTTCTCT
1 AAATCGCTTTAAGCTTTCAATTTTCTCT
7132 AAATCGCTTTAAGCTTTCAATTTTCTCT
1 AAATCGCTTTAAGCTTTCAATTTTCTCT
7160 TTTTCAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (28 bp):
AAATCGCTTTAAGCTTTCAATTTTCTCT
Found at i:11988 original size:21 final size:22
Alignment explanation
Indices: 11943--12046 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 22
11933 TTTACTGAAT
* *
11943 TACTGATTACCATCATTA-TTT-
1 TACTGATTA-CTTCTTTACTTTG
11964 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTTCTTTACTTTG
11985 TACTGATTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
12008 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
12028 TACTGATTACTAT-TTTACT
1 TACTGATTACT-TCTTTACT
12047 CTTACTAATT
Statistics
Matches: 69, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
19 5 0.07
20 6 0.09
21 32 0.46
22 21 0.30
23 5 0.07
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (22 bp):
TACTGATTACTTCTTTACTTTG
Found at i:12034 original size:64 final size:63
Alignment explanation
Indices: 11961--12098 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 63
11951 ACCATCATTA
* * * *
11961 TTTTACTGATTA-T-TCTTTACTTTGTACTGATTACTATTTTACTCTTGT-TGATTACCTTCTTA
1 TTTTACTGATTACTAT-TTTACTCT-TACTAATTACCATTTTACTCTT-TCAGA-TACCTTCTTA
12023 CT
62 CT
*
12025 TTTTACTGATTACTATTTTACTCTTACTAATTACCATTTTACTCTTTCAGATACCTTTTTACT
1 TTTTACTGATTACTATTTTACTCTTACTAATTACCATTTTACTCTTTCAGATACCTTCTTACT
12088 TTTTACTGATT
1 TTTTACTGATT
12099 GCATGCTATT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 23 0.35
64 34 0.52
65 8 0.12
66 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (63 bp):
TTTTACTGATTACTATTTTACTCTTACTAATTACCATTTTACTCTTTCAGATACCTTCTTACT
Found at i:12057 original size:21 final size:21
Alignment explanation
Indices: 11963--12070 Score: 96
Period size: 21 Copynumber: 5.1 Consensus size: 21
11953 CATCATTATT
*
11963 TTACTGATTA-T-TCTTTACTT
1 TTACTGATTACTAT-TTTACTC
11983 TGTACTGATTACTATTTTACTC
1 T-TACTGATTACTATTTTACTC
** * *
12005 TTGTTGATTACCT-TCTTACTTT
1 TTACTGATTA-CTATTTTAC-TC
12027 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
* *
12048 TTACTAATTACCATTTTACTC
1 TTACTGATTACTATTTTACTC
12069 TT
1 TT
12071 TCAGATACCT
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.01
21 45 0.63
22 24 0.34
23 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.55
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:12058 original size:43 final size:43
Alignment explanation
Indices: 11976--12067 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
11966 CTGATTATTC
** *
11976 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACC-T
1 TTTACTTTGTACTGATTACTATTTTACTCTTACTAATTACCAT
*
12018 TCTTACTTTTTACTGATTACTATTTTACTCTTACTAATTACCAT
1 T-TTACTTTGTACTGATTACTATTTTACTCTTACTAATTACCAT
12062 TTTACT
1 TTTACT
12068 CTTTCAGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 41 0.93
44 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTACTTTGTACTGATTACTATTTTACTCTTACTAATTACCAT
Found at i:12406 original size:29 final size:29
Alignment explanation
Indices: 12373--12462 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
12363 TCCCTGATTA
12373 CTGATTTACTGATTACTATTACCTTGACT
1 CTGATTTACTGATTACTATTACCTTGACT
* * * *
12402 CTGATTAATCT-CTT--T-TTA-CTTAATT
1 CTGATTTA-CTGATTACTATTACCTTGACT
12427 ACTGATTTACTGATTACTATTACCTTGACT
1 -CTGATTTACTGATTACTATTACCTTGACT
12457 CTGATT
1 CTGATT
12463 AGTCTCTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 7 0.15
26 12 0.26
27 1 0.02
28 1 0.02
29 18 0.39
30 7 0.15
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (29 bp):
CTGATTTACTGATTACTATTACCTTGACT
Found at i:12416 original size:55 final size:55
Alignment explanation
Indices: 12369--12571 Score: 352
Period size: 55 Copynumber: 3.7 Consensus size: 55
12359 TTTTTCCCTG
12369 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
*
12424 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAGTCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* * * *
12479 ATTACTGATTTACTGATCACTATTACTTTGACTCTAATTAATCTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
*
12534 ATTACTGATTTACTGATTACTATTACTTTGACTCTGAT
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGAT
12572 AGTCAAAAAA
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 140 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
Found at i:12598 original size:23 final size:24
Alignment explanation
Indices: 12568--12615 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
12558 ACTTTGACTC
*
12568 TGATAGTCAAAAAAGGTAAA-GAA
1 TGATAGTCAAAAAAGGAAAATGAA
*
12591 TGATAGTCAAACAAGGAAAATGAA
1 TGATAGTCAAAAAAGGAAAATGAA
12615 T
1 T
12616 AAAAGAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (24 bp):
TGATAGTCAAAAAAGGAAAATGAA
Found at i:13489 original size:50 final size:49
Alignment explanation
Indices: 13383--13489 Score: 110
Period size: 50 Copynumber: 2.1 Consensus size: 49
13373 AGGTTAATCC
* * * *
13383 TTTATCAAAAATAGAGTCTTTTAATCTAAAGGCTTAGCTTTTATTAACAG
1 TTTATC-AAAATAGAGTCTTTTAATCTAAAGGATTAGCCTTTATCAACAA
* *
13433 TCTATCAAAATGAGAGTCTTTTAGAT-TAAA-GATTAGTCCTTTATCACCAA
1 TTTATCAAAAT-AGAGTCTTTTA-ATCTAAAGGATTAG-CCTTTATCAACAA
13483 TTTATCA
1 TTTATCA
13490 GAATTAGAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
49 10 0.21
50 35 0.74
51 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (49 bp):
TTTATCAAAATAGAGTCTTTTAATCTAAAGGATTAGCCTTTATCAACAA
Found at i:16336 original size:16 final size:16
Alignment explanation
Indices: 16315--16345 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16305 CCTTTAATAT
16315 AACTAATATGATTAAC
1 AACTAATATGATTAAC
*
16331 AACTAATATGGTTAA
1 AACTAATATGATTAA
16346 TGGCTAGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (16 bp):
AACTAATATGATTAAC
Found at i:16660 original size:28 final size:27
Alignment explanation
Indices: 16593--16671 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
16583 AGGTGAACTT
*
16593 AAAAATGACTAAAATGCCCCTGAGTGC
1 AAAAATGACCAAAATGCCCCTGAGTGC
* *
16620 AAAAATGACCAAAATTCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGAGTGC
*
16647 AAAAACTGACCAAAATGCCCTTGAG
1 AAAAA-TGACCAAAATGCCCCTGAG
16672 CGACCCTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
27 29 0.64
28 16 0.36
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGAGTGC
Done.