Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006972.1 Corchorus capsularis cultivar CVL-1 contig06993, 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: 62093
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:17223 original size:29 final size:31
Alignment explanation
Indices: 17159--17235 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
17149 TGTTCTAATT
* **
17159 CTAATTCAAAATTCTTCTTACTGCCAAAAATT
1 CTAATTCAAAATTC-TCTTACTGCAAAAAACC
*
17191 CTAATTCAAAA-TC-CTTCCTGCAAAAAACC
1 CTAATTCAAAATTCTCTTACTGCAAAAAACC
*
17220 CTAATTCAAGATTCTC
1 CTAATTCAAAATTCTC
17236 CACTCTTCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 22 0.58
30 2 0.05
31 3 0.08
32 11 0.29
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (31 bp):
CTAATTCAAAATTCTCTTACTGCAAAAAACC
Found at i:17662 original size:18 final size:18
Alignment explanation
Indices: 17641--17677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17631 GATAATTCTA
17641 CTCCCAATAATAAGGTTT
1 CTCCCAATAATAAGGTTT
* *
17659 CTCCCAATATTAGGGTTT
1 CTCCCAATAATAAGGTTT
17677 C
1 C
17678 CAAAATGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (18 bp):
CTCCCAATAATAAGGTTT
Found at i:25665 original size:18 final size:17
Alignment explanation
Indices: 25638--25671 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25628 AAAATACAAG
*
25638 AAAGAAAAACTTCCATC
1 AAAGAAAAACATCCATC
25655 AAAGCAAAAACATCCAT
1 AAAG-AAAAACATCCAT
25672 AACAAAGAAT
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:0.56, C:0.24, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAGAAAAACATCCATC
Found at i:27967 original size:30 final size:29
Alignment explanation
Indices: 27933--28007 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 29
27923 CAAATTGGGG
*
27933 CTAAATCTTTTAAACTTACTTAATTTGAGT
1 CTAAA-CTTTTAAACTTACTTAATTTAAGT
*
27963 CTAAACCTTTCCAAACTTACTTAATTTAAGT
1 CTAAA-CTTT-TAAACTTACTTAATTTAAGT
*
27994 CTAAACCTTTAAAC
1 CTAAACTTTTAAAC
28008 ATGACAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.10
30 12 0.31
31 23 0.59
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (29 bp):
CTAAACTTTTAAACTTACTTAATTTAAGT
Found at i:27979 original size:31 final size:31
Alignment explanation
Indices: 27944--28003 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
27934 TAAATCTTTT
*
27944 AAACTTACTTAATTTGAGTCTAAACCTTTCC
1 AAACTTACTTAATTTAAGTCTAAACCTTTCC
27975 AAACTTACTTAATTTAAGTCTAAACCTTT
1 AAACTTACTTAATTTAAGTCTAAACCTTT
28004 AAACATGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (31 bp):
AAACTTACTTAATTTAAGTCTAAACCTTTCC
Found at i:30300 original size:27 final size:28
Alignment explanation
Indices: 30240--30310 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
30230 CCTACGTGGC
**
30240 TTTTTTAATATTTTTTTTTATTTTTCAAA
1 TTTTTTAATA-TTTTTTTTAAATTTCAAA
* *
30269 ATTTTAAATATTTTTTTTAAATTT-AAA
1 TTTTTTAATATTTTTTTTAAATTTCAAA
30296 TTTTTTAATATTTTT
1 TTTTTTAATATTTTT
30311 AAACCGGGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 16 0.44
28 12 0.33
29 8 0.22
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTTTAATATTTTTTTTAAATTTCAAA
Found at i:31723 original size:11 final size:11
Alignment explanation
Indices: 31707--31783 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 11
31697 GAGGTAGAGA
31707 AAAAGAAGAAG
1 AAAAGAAGAAG
31718 AAAAGAAGAAG
1 AAAAGAAGAAG
*
31729 AAAGAGAAAAGACG
1 AAA-AG--AAGAAG
*
31743 AAAGGGAGAAAAAG
1 AAA---AGAAGAAG
*
31757 AAAAGAA-AAT
1 AAAAGAAGAAG
31767 AAAAGAAGAAG
1 AAAAGAAGAAG
31778 ATAAAG
1 A-AAAG
31784 TAATAACTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
10 9 0.17
11 21 0.39
12 6 0.11
14 15 0.28
16 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:31729 original size:17 final size:16
Alignment explanation
Indices: 31704--31783 Score: 56
Period size: 17 Copynumber: 4.8 Consensus size: 16
31694 GTCGAGGTAG
*
31704 AGAAAAAGAAGAAGAAA
1 AGAAGAAGAA-AAGAAA
31721 AGAAGAAGAAAGAGAAA
1 AGAAGAAGAAA-AGAAA
* **
31738 AGACGAA-AGGGAGAAAA
1 AGAAGAAGA-AAAG-AAA
*
31755 AGAA-AAGAAAATAAA
1 AGAAGAAGAAAAGAAA
31770 AGAAGAAGATAAAG
1 AGAAGAAGA-AAAG
31784 TAATAACTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
15 7 0.15
16 11 0.23
17 30 0.62
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (16 bp):
AGAAGAAGAAAAGAAA
Found at i:31740 original size:14 final size:14
Alignment explanation
Indices: 31702--31765 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
31692 GGGTCGAGGT
31702 AGAGAAAAAGAAG-A
1 AGAG-AAAAGAAGAA
*
31716 AGAAAAGAAGAAGAA
1 AGAGAA-AAGAAGAA
*
31731 AGAGAAAAGACGAA
1 AGAGAAAAGAAGAA
*
31745 AGGGAGAAA-AAGAA
1 AGAGA-AAAGAAGAA
31759 A-AGAAAA
1 AGAGAAAA
31766 TAAAAGAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 3 0.07
13 4 0.10
14 25 0.61
15 9 0.22
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (14 bp):
AGAGAAAAGAAGAA
Found at i:36263 original size:25 final size:25
Alignment explanation
Indices: 36227--36318 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
36217 CAAGATTTAA
36227 AATTTATT-TATTATTATTACACAT
1 AATTTATTGTATTATTATTACACAT
* ****
36251 AATTTATTGTATTATCATTAGGTGT
1 AATTTATTGTATTATTATTACACAT
*** * *
36276 AATTTA-CACAATA-AATTACACAT
1 AATTTATTGTATTATTATTACACAT
36299 AATTTATTGTATTATTATTA
1 AATTTATTGTATTATTATTA
36319 TAAAGTCTAA
Statistics
Matches: 46, Mismatches: 19, Indels: 5
0.66 0.27 0.07
Matches are distributed among these distances:
23 11 0.24
24 14 0.30
25 21 0.46
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (25 bp):
AATTTATTGTATTATTATTACACAT
Found at i:39157 original size:2 final size:2
Alignment explanation
Indices: 39150--39192 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39140 TAGTCCCATT
*
39150 TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39192 T
1 T
39193 TTTTGATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:57793 original size:17 final size:17
Alignment explanation
Indices: 57773--57805 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57763 ACTACAAAGT
57773 TTTTCACTTT-TTTTCTA
1 TTTT-ACTTTATTTTCTA
57790 TTTTACTTTATTTTCT
1 TTTTACTTTATTTTCT
57806 TCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTACTTTATTTTCTA
Found at i:58859 original size:438 final size:430
Alignment explanation
Indices: 58043--59065 Score: 1180
Period size: 438 Copynumber: 2.4 Consensus size: 430
58033 TAAAAAAATC
* * * *
58043 TTTTTTTTGCTGGATTATTTATCAAATGATCCCTATGCTTTTATGCTTTATGCTATTTAGTCCCT
1 TTTTTTTTGCT-GATTATTTATCAAATGATCCTTATACTTTTATGCTTTATGCTATTTAATCCTT
* * * * * * * * * * * * *
58108 CAGAAATTCTGGATTGAACGACTGAACGTTTCGGCTTTAATTCTTTAATTTTTTTTGTTTTACTT
65 TA-CAATTATGGGTTGAATGATTTAACGTTTCGGCTTTTATT-TTT-GTATTTTCTGTTCTATTT
* * * * * *
58173 GTTCGATCAAGGTGATTCAAGTGTATGTTAAAAGGTAATTTTATGATCTATAACTTTCATAAAGG
127 GTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTACAACTTTCATAAA-G
* * * *
58238 ATCTCAAAAACCAATTTTCATGTTTCGATTCTAAAAAATGCTTCTTAAATTTGTCGTCTCGATTG
191 AACTCAAAAACCAATTTTAATGTTTCGATTCTAAAAAATGCTTCTTAAATTTGTAGTCTCAATTG
* * * * *
58303 TCGGTCTATCTAATATTGTATAATTTTCGATCCACTTGTCTGATTGAGGTTTTTCAAGTGTCGGT
256 CCGGTCTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAGTTGTTCAAGTGTCGGT
* ** * * * *
58368 TAAAAGGTTATTGTGTAATCTATGACTTTTGTCAAGGGCGTGAAAGCTGAATTTGATTAATGAGT
321 TAAAAGGTTATTGTGTAATCTACGACTTTCATCAAAGGCATGAAAGCTGAATTTGATTAACGAAT
* *
58433 TTCGTGGAGGGTTCGAGAGGGAACTTTTATGTTTGGCCTCCATAAAAAA
386 TTCGTGGAGGATTCAAGAGGGAACTTTTATGTTTGG--T-C-TAAAAAA
58482 TATATTTTTTGCTGCATTATTTATCAAATGATCCTTATACTTTTATGCTTTATGCTATTTAATCC
1 T-T-TTTTTTGCTG-ATTATTTATCAAATGATCCTTATACTTTTATGCTTTATGCTATTTAATCC
* * **
58547 TTTACAATTATGGGTTGCATGATTTAATGCGTCGGCTTTTATTTTTGTATTTTCTGTTCTATTTG
63 TTTACAATTATGGGTTGAATGATTTAACGTTTCGGCTTTTATTTTTGTATTTTCTGTTCTATTTG
58612 TCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTACAACTTTCATGAAA-A
128 TCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTACAACTTTCAT-AAAGA
** * * * *
58676 ACTCAAAAGGCAATTTTAATGTTTTGATTTTAAAAAATGTTTCTTAAATTTTGTAGTTTCAATTG
192 ACTCAAAAACCAATTTTAATGTTTCGATTCTAAAAAATGCTTCTTAAA-TTTGTAGTCTCAATTG
* *
58741 CCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGTTCAAGTGTCGGT
256 CCGGTCTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAGTTGTTCAAGTGTCGGT
* * *
58806 TAAAAGGTTATTGTGTGATCTACGACTTTCATTAAAGGCATGAAAGTTGAATTTGATTAACGAAT
321 TAAAAGGTTATTGTGTAATCTACGACTTTCATCAAAGGCATGAAAGCTGAATTTGATTAACGAAT
* *
58871 TTCGTGGAGGATTCAAGAGGGAATTTTTATGTTTTGTCT------
386 TTCGTGGAGGATTCAAGAGGGAACTTTTATGTTTGGTCTAAAAAA
* * * * * *
58910 TTTTCTTTTGCTAGATTACTTATCTAATGA-CTTTCATACTTTTATACTTCATGCTATTGAATCC
1 TTTT-TTTTGCT-GATTATTTATCAAATGATCCTT-ATACTTTTATGCTTTATGCTATTTAATCC
* * * * *
58974 TTTACAATTATAGGTTGAATGATTTAACGTTTTGACTTTTGTTTTTGTATTTTTGTGTTCTATTT
63 TTTACAATTATGGGTTGAATGATTTAACGTTTCGGCTTTTATTTTTGTA-TTTTCTGTTCTATTT
* * *
59039 GTCCCATTAAGGCGATTCAAGTGTCTA
127 GTCCGATCAAGGTGATTCAAGTGTCTA
59066 CACGAAAAAC
Statistics
Matches: 499, Mismatches: 76, Indels: 29
0.83 0.13 0.05
Matches are distributed among these distances:
426 5 0.01
427 89 0.18
428 40 0.08
434 1 0.00
435 1 0.00
436 1 0.00
437 42 0.08
438 225 0.45
439 7 0.01
440 30 0.06
441 58 0.12
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (430 bp):
TTTTTTTTGCTGATTATTTATCAAATGATCCTTATACTTTTATGCTTTATGCTATTTAATCCTTT
ACAATTATGGGTTGAATGATTTAACGTTTCGGCTTTTATTTTTGTATTTTCTGTTCTATTTGTCC
GATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTACAACTTTCATAAAGAACTC
AAAAACCAATTTTAATGTTTCGATTCTAAAAAATGCTTCTTAAATTTGTAGTCTCAATTGCCGGT
CTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAGTTGTTCAAGTGTCGGTTAAAA
GGTTATTGTGTAATCTACGACTTTCATCAAAGGCATGAAAGCTGAATTTGATTAACGAATTTCGT
GGAGGATTCAAGAGGGAACTTTTATGTTTGGTCTAAAAAA
Found at i:61326 original size:18 final size:18
Alignment explanation
Indices: 61303--61343 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
61293 TCATAACAAG
61303 TTTATAATTAATTT-ATAA
1 TTTATAATT-ATTTGATAA
61321 TTTATAATTATTTGATAA
1 TTTATAATTATTTGATAA
61339 TTTAT
1 TTTAT
61344 TTTATATAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTATAATTATTTGATAA
Found at i:61755 original size:2 final size:2
Alignment explanation
Indices: 61748--61778 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61738 AGTAGGTTTA
61748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61779 CACATATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.