Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012797.1 Corchorus capsularis cultivar CVL-1 contig12818, 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: 44541
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:421 original size:29 final size:29
Alignment explanation
Indices: 352--427 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 29
342 GGTCCGATTG
* * *
352 TTTAATTAAAAATAATTTAGAAATTATTAT
1 TTTAATT-AAAATATTTTAAAAAATATTAT
382 TTTAAATTTAAAATATTTTAAAAAATATT-T
1 TTT-AA-TTAAAATATTTTAAAAAATATTAT
412 TTTATATTAAAATATT
1 TTTA-ATTAAAATATT
428 GCAAAATCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 11 0.28
30 8 0.20
31 19 0.47
32 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TTTAATTAAAATATTTTAAAAAATATTAT
Found at i:6066 original size:17 final size:17
Alignment explanation
Indices: 6032--6072 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6022 TACTTTTATT
6032 TATAGTATAGATAGATAA
1 TATA-TATAGATAGATAA
* *
6050 TATATATATATATATAA
1 TATATATAGATAGATAA
6067 TATATA
1 TATATA
6073 CGAACTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
TATATATAGATAGATAA
Found at i:6141 original size:13 final size:13
Alignment explanation
Indices: 6106--6142 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6096 AAATTTCCAA
*
6106 AATAAGTATATTT
1 AATAAGTATTTTT
6119 AATAA-T-TTTTT
1 AATAAGTATTTTT
6130 AATAAGTATTTTT
1 AATAAGTATTTTT
6143 TTAGTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (13 bp):
AATAAGTATTTTT
Found at i:7793 original size:16 final size:16
Alignment explanation
Indices: 7772--7804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7762 GTTGGTATAC
7772 ACACACACACAAACAT
1 ACACACACACAAACAT
*
7788 ACACACACACAGACAT
1 ACACACACACAAACAT
7804 A
1 A
7805 ACTTGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.36, G:0.03, T:0.06
Consensus pattern (16 bp):
ACACACACACAAACAT
Found at i:9548 original size:11 final size:11
Alignment explanation
Indices: 9521--9559 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9511 TTAATCGATT
9521 AATTTTTTATA
1 AATTTTTTATA
*
9532 ATATTTTTTATT
1 A-ATTTTTTATA
*
9544 AATTTTATATA
1 AATTTTTTATA
9555 AATTT
1 AATTT
9560 CAGTGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
AATTTTTTATA
Found at i:9769 original size:32 final size:32
Alignment explanation
Indices: 9733--9804 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
9723 CAAATTGATA
* * *
9733 GACAAAATAGCCCTCGAATTTTGACATAGA-AT
1 GACAAAATAACCCTCAAATTTTGACA-AAATAT
9765 GACAAAATAACCCTCAAATTTTGACAAAATAT
1 GACAAAATAACCCTCAAATTTTGACAAAATAT
9797 GACAAAAT
1 GACAAAAT
9805 GTTCTTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (32 bp):
GACAAAATAACCCTCAAATTTTGACAAAATAT
Found at i:13343 original size:105 final size:105
Alignment explanation
Indices: 13154--13344 Score: 258
Period size: 105 Copynumber: 1.8 Consensus size: 105
13144 AAACTTGAAA
* * * * ** *
13154 CTCCTCCAAAGAATTAGCTACGACATCCTCTTTATCACCTTCATAAATAATGAGATCTCCACTAG
1 CTCCTCCAAAGAATCAGCCACGACATCCTCTTTATCACCTTAAAAAATAACAAGATCTCCACCAG
* *
13219 CATGATTTCTTTCAATCGAATGAAAACTATCACCCACAAT
66 CAAGATTTCTTCCAATCGAATGAAAACTATCACCCACAAT
* *
13259 CTCCTCCAAAGAATCAGCCACGACATTCTCTTTA-CTGCCTTAAAAAATAACAAGATCTCCACCA
1 CTCCTCCAAAGAATCAGCCACGACATCCTCTTTATC-ACCTTAAAAAATAACAAGATCTCCACCA
*
13323 GCAAGATTTCTTCCATTCGAAT
65 GCAAGATTTCTTCCAATCGAAT
13345 TATAACTGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 1 0.01
105 72 0.99
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (105 bp):
CTCCTCCAAAGAATCAGCCACGACATCCTCTTTATCACCTTAAAAAATAACAAGATCTCCACCAG
CAAGATTTCTTCCAATCGAATGAAAACTATCACCCACAAT
Found at i:18263 original size:6 final size:6
Alignment explanation
Indices: 18254--18283 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18244 CAACAACAAC
18254 AACCCA AACCCA AACCCA AACCCA AACCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA
18284 TCAGCATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:24257 original size:23 final size:22
Alignment explanation
Indices: 24215--24274 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
24205 CCGGGTGGGA
24215 AAAAATA-TTTAATTGT-TTTTT
1 AAAAATATTTTAATT-TCTTTTT
24236 AAGAAATATTTTAATTTCTTTTT
1 AA-AAATATTTTAATTTCTTTTT
* *
24259 CAATATATTTT-ATTTC
1 AAAAATATTTTAATTTC
24275 ATGGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 7 0.21
22 14 0.41
23 13 0.38
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (22 bp):
AAAAATATTTTAATTTCTTTTT
Found at i:25220 original size:7 final size:7
Alignment explanation
Indices: 25188--25230 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
25178 ATTTAAATTA
25188 TATATAT
1 TATATAT
*
25195 CATATAT
1 TATATAT
* *
25202 TAAATAAA
1 TATAT-AT
25210 TATATAT
1 TATATAT
25217 TATATAT
1 TATATAT
25224 TATATAT
1 TATATAT
25231 AAAAATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (7 bp):
TATATAT
Found at i:29992 original size:21 final size:22
Alignment explanation
Indices: 29968--30013 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29958 TTTTCTATTT
*
29968 TTTTTACCAT-TTTTATATGTA
1 TTTTTACCATATTTTATAAGTA
*
29989 TTTTTACCCTATTTTATAAGTA
1 TTTTTACCATATTTTATAAGTA
30011 TTT
1 TTT
30014 GTGTTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTTACCATATTTTATAAGTA
Found at i:30173 original size:19 final size:18
Alignment explanation
Indices: 30149--30185 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
30139 GAAGTTCGTG
30149 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
30168 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
30186 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:31747 original size:21 final size:21
Alignment explanation
Indices: 31723--31762 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31713 ACTGGCGGGC
31723 TTTACTTGCTGAGGAAGGCAT
1 TTTACTTGCTGAGGAAGGCAT
31744 TTTACTTGCTGAGGAAGGC
1 TTTACTTGCTGAGGAAGGC
31763 GAACTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCAT
Found at i:31949 original size:17 final size:17
Alignment explanation
Indices: 31911--31943 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31901 CTCATGATAC
31911 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
31928 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
31944 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:37756 original size:13 final size:13
Alignment explanation
Indices: 37738--37772 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
37728 ATAATTATTG
37738 TTTGCTTTATTAA
1 TTTGCTTTATTAA
37751 TTTGCTTTATTAA
1 TTTGCTTTATTAA
37764 TTTGCTTTA
1 TTTGCTTTA
37773 GATTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:37780 original size:6 final size:6
Alignment explanation
Indices: 37769--37800 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
37759 ATTAATTTGC
37769 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
37801 GTTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:40990 original size:32 final size:32
Alignment explanation
Indices: 40951--41021 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
40941 CCATGCCCGG
40951 CCATGCCCGACCCTTGCCAAGCCATCCACGCA
1 CCATGCCCGACCCTTGCCAAGCCATCCACGCA
* *
40983 CCATGCCCGGCCCTTGCCAAGCCATCCGCGCA
1 CCATGCCCGACCCTTGCCAAGCCATCCACGCA
41015 CCATGCC
1 CCATGCC
41022 GCGCCACCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13
Consensus pattern (32 bp):
CCATGCCCGACCCTTGCCAAGCCATCCACGCA
Found at i:43233 original size:10 final size:10
Alignment explanation
Indices: 43218--43242 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43208 GTCCCTGCTC
43218 AATTCCAGAA
1 AATTCCAGAA
43228 AATTCCAGAA
1 AATTCCAGAA
43238 AATTC
1 AATTC
43243 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:44180 original size:13 final size:13
Alignment explanation
Indices: 44162--44196 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
44152 ATAATTATTG
44162 TTTGCTTTATTAA
1 TTTGCTTTATTAA
44175 TTTGCTTTATTAA
1 TTTGCTTTATTAA
44188 TTTGCTTTA
1 TTTGCTTTA
44197 GATTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:44204 original size:6 final size:6
Alignment explanation
Indices: 44193--44224 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44183 ATTAATTTGC
44193 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
44225 GTTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.