Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014228.1 Corchorus capsularis cultivar CVL-1 contig14249, 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: 35636
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1206 original size:52 final size:51
Alignment explanation
Indices: 1058--1207 Score: 156
Period size: 51 Copynumber: 2.8 Consensus size: 51
1048 CCTCTGGTAT
* * * *
1058 AGAAATCTCCTTCCATCAGTAAAGCAAAAACCCAAAAAAAAAAAAAAGAGGAAAGA
1 AGAAATCTCCTTCGATGAGTAAAGC-AAAA-CC---AGAAAAAAAAAGAAGAAAGA
*** *
1114 AGAAATCTCCTTCGATGAGTAAAGCAAAACCAGGGGAAAAAAGAAGAAATA
1 AGAAATCTCCTTCGATGAGTAAAGCAAAACCAGAAAAAAAAAGAAGAAAGA
* *
1165 AGAAATCTCCTTCGATTGAGTGAAGCAAAACTAGAAAAAAAAA
1 AGAAATCTCCTTCGA-TGAGTAAAGCAAAACCAGAAAAAAAAA
1208 AATGAAGAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 29 0.36
52 22 0.28
54 2 0.03
55 4 0.05
56 23 0.29
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.14
Consensus pattern (51 bp):
AGAAATCTCCTTCGATGAGTAAAGCAAAACCAGAAAAAAAAAGAAGAAAGA
Found at i:8787 original size:112 final size:114
Alignment explanation
Indices: 8567--8794 Score: 388
Period size: 115 Copynumber: 2.0 Consensus size: 114
8557 TAATAGTTTA
* *
8567 CATTTAGGAATTTTGGGTTTATTATTGGTGATTGAACAAAAAGGATTTCTGTGGAATGTTTTTTT
1 CATTTAGGAATTTTGGCTTTATTATTGGTGATTGAACAAAAAGGATTTCTGTGGAATGTGTTTTT
*
8632 GTTTTTTTGTGGTTCTATGCTTAGAACTGTTTTTCTGATTTATATTAATT
66 G-TTTTTTGTGGTTCTATGCCTAGAACTGTTTTTCTGATTTATATTAATT
**
8682 CATTTAGGAATTTTGGCTTTATTATTGGTGATTGAACGGAAAGGATTTCTGTGGAATG-GTTTTT
1 CATTTAGGAATTTTGGCTTTATTATTGGTGATTGAACAAAAAGGATTTCTGTGGAATGTGTTTTT
8746 G-TTTTTGTGGTTCTATGCCTAGAACTGTTTTTCTGATTTATATTAATT
66 GTTTTTTGTGGTTCTATGCCTAGAACTGTTTTTCTGATTTATATTAATT
8794 C
1 C
8795 GTGTTAATAT
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
112 47 0.44
114 6 0.06
115 55 0.51
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.50
Consensus pattern (114 bp):
CATTTAGGAATTTTGGCTTTATTATTGGTGATTGAACAAAAAGGATTTCTGTGGAATGTGTTTTT
GTTTTTTGTGGTTCTATGCCTAGAACTGTTTTTCTGATTTATATTAATT
Found at i:9253 original size:28 final size:28
Alignment explanation
Indices: 9213--9268 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
9203 AAGTTAATTC
*
9213 ATTTATTTTGATGACTGAATTTCTGTTT
1 ATTTATTGTGATGACTGAATTTCTGTTT
*
9241 ATTTATTGTGATGACTGAATTTTTGTTT
1 ATTTATTGTGATGACTGAATTTCTGTTT
9269 TTAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.57
Consensus pattern (28 bp):
ATTTATTGTGATGACTGAATTTCTGTTT
Found at i:9579 original size:21 final size:21
Alignment explanation
Indices: 9553--9603 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
9543 GGATGAAGAC
9553 TCTGATGAGGATGAGAGCGAT
1 TCTGATGAGGATGAGAGCGAT
*
9574 TCTGATGAGGATGAGAGTGAT
1 TCTGATGAGGATGAGAGCGAT
9595 TCTGATGAG
1 TCTGATGAG
9604 AGCGATTCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.27
Consensus pattern (21 bp):
TCTGATGAGGATGAGAGCGAT
Found at i:9582 original size:15 final size:15
Alignment explanation
Indices: 9583--9614 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9573 TTCTGATGAG
*
9583 GATGAGAGTGATTCT
1 GATGAGAGCGATTCT
9598 GATGAGAGCGATTCT
1 GATGAGAGCGATTCT
9613 GA
1 GA
9615 GAGTGGAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.28
Consensus pattern (15 bp):
GATGAGAGCGATTCT
Found at i:9669 original size:2 final size:2
Alignment explanation
Indices: 9662--9686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9652 ATTTTTAATT
9662 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9687 TCTTATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11501 original size:58 final size:58
Alignment explanation
Indices: 11411--11527 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
11401 ATTTCAACTA
11411 AATTTCTACTACCACTAACAAGGGTAATTTAGATAACTTAGGAAAAAGTTGCATTGGG
1 AATTTCTACTACCACTAACAAGGGTAATTTAGATAACTTAGGAAAAAGTTGCATTGGG
*
11469 AATTTCTACTACCACTAACAAGGGTAATTTAGATAACTTAGGTAAAAGTTGCATTGGG
1 AATTTCTACTACCACTAACAAGGGTAATTTAGATAACTTAGGAAAAAGTTGCATTGGG
11527 A
1 A
11528 TTTAAAAAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (58 bp):
AATTTCTACTACCACTAACAAGGGTAATTTAGATAACTTAGGAAAAAGTTGCATTGGG
Found at i:11744 original size:1 final size:1
Alignment explanation
Indices: 11738--11773 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
11728 TTTATGTATC
11738 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11774 ACATTAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15460 original size:50 final size:50
Alignment explanation
Indices: 15339--15531 Score: 370
Period size: 50 Copynumber: 3.9 Consensus size: 50
15329 ATAAGTTTAG
*
15339 TTTTATCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAA-TTT
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
15388 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
15438 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
15488 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAA
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAA
15532 TTTCCTTTTT
Statistics
Matches: 142, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
49 45 0.32
50 97 0.68
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.61
Consensus pattern (50 bp):
TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
Found at i:15541 original size:99 final size:98
Alignment explanation
Indices: 15339--15541 Score: 354
Period size: 99 Copynumber: 2.1 Consensus size: 98
15329 ATAAGTTTAG
*
15339 TTTTATCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTTTTTTTCCTTTTTAAA
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTTTTTTTCCTTTTTAAA
*
15404 GTTTGTCATTTCTCTATTTTGTAATTAAAATTTT
66 GTTTGTCATTTCTCTATTTTGTAATT-AAATTTC
15438 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTTTTTTTTCCTTTTTAA
1 TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAA-TTTTTTTTTCCTTTTTAA
15503 AGTTTGTCATTTCTCTATTTTGTAATT-AATTTC
65 AGTTTGTCATTTCTCTATTTTGTAATTAAATTTC
*
15536 CTTTTT
1 TTTTTT
15542 GGTTGTTAAC
Statistics
Matches: 100, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 10 0.10
99 45 0.45
100 45 0.45
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (98 bp):
TTTTTTCCTTTTTAAAGTTTGTCATTTCTCTATTTTGTAATTAAAATTTTTTTTTCCTTTTTAAA
GTTTGTCATTTCTCTATTTTGTAATTAAATTTC
Found at i:19365 original size:7 final size:7
Alignment explanation
Indices: 19353--19389 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
19343 GGGTTTTGTC
19353 GGGCGGT
1 GGGCGGT
19360 GGGCGGT
1 GGGCGGT
19367 GGGCGGT
1 GGGCGGT
19374 GGGCGGT
1 GGGCGGT
*
19381 GGGGGGT
1 GGGCGGT
19388 GG
1 GG
19390 TGAGAGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.11, G:0.76, T:0.14
Consensus pattern (7 bp):
GGGCGGT
Found at i:29487 original size:10 final size:10
Alignment explanation
Indices: 29468--29500 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
29458 CTCAGCAGAG
29468 CAGAGGAAAA
1 CAGAGGAAAA
*
29478 CAGAGAAAAA
1 CAGAGGAAAA
29488 CAGAGGAAAA
1 CAGAGGAAAA
29498 CAG
1 CAG
29501 GGGATTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.12, G:0.27, T:0.00
Consensus pattern (10 bp):
CAGAGGAAAA
Found at i:33647 original size:6 final size:6
Alignment explanation
Indices: 33636--33662 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
33626 ATGTGCCAAA
33636 CTTCGT CTTCGT CTTCGT CTTCGT CTT
1 CTTCGT CTTCGT CTTCGT CTTCGT CTT
33663 AATTACCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
CTTCGT
Found at i:33924 original size:2 final size:2
Alignment explanation
Indices: 33917--33949 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33907 AATTAACGGA
33917 AT 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 AT A
33950 GATCAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35364 original size:31 final size:32
Alignment explanation
Indices: 35326--35396 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
35316 TTGGGTACCT
* *
35326 GAACCCGAAATGACCCGAATCC-AAACGACCC
1 GAACCCGAAATGACCCAAACCCAAAACGACCC
*
35357 GAACCCGAAATGACCCAAACCCAAAATGACCC
1 GAACCCGAAATGACCCAAACCCAAAACGACCC
35389 GAACCCGA
1 GAACCCGA
35397 TCAACCCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.06
Consensus pattern (32 bp):
GAACCCGAAATGACCCAAACCCAAAACGACCC
Found at i:35377 original size:16 final size:16
Alignment explanation
Indices: 35326--35396 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
35316 TTGGGTACCT
35326 GAACCCGAAATGACCC
1 GAACCCGAAATGACCC
* *
35342 GAATCC-AAACGACCC
1 GAACCCGAAATGACCC
35357 GAACCCGAAATGACCC
1 GAACCCGAAATGACCC
* *
35373 AAACCCAAAATGACCC
1 GAACCCGAAATGACCC
35389 GAACCCGA
1 GAACCCGA
35397 TCAACCCGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.28
16 33 0.72
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.06
Consensus pattern (16 bp):
GAACCCGAAATGACCC
Done.