Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016464.1 Corchorus capsularis cultivar CVL-1 contig16485, 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: 41503
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:669 original size:33 final size:33
Alignment explanation
Indices: 630--696 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
620 AAAGTATGAT
*
630 TATAGAAAAGGTATAATACTATCAACTAATTTA
1 TATAGAAAAGATATAATACTATCAACTAATTTA
663 TATAGAAAAGATATAATACTATCAACTAATTTA
1 TATAGAAAAGATATAATACTATCAACTAATTTA
696 T
1 T
697 TAATTTTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.34
Consensus pattern (33 bp):
TATAGAAAAGATATAATACTATCAACTAATTTA
Found at i:4586 original size:18 final size:18
Alignment explanation
Indices: 4563--4637 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
4553 AACGTTCTTT
4563 TTTTTGTAAAAAGATTGA
1 TTTTTGTAAAAAGATTGA
*
4581 TTTTTGTAAAAGGATTAGGAAA
1 TTTTTGTAAAAAGATT--G--A
* *
4603 TTTTTTGTGAAAAGATTTA
1 -TTTTTGTAAAAAGATTGA
*
4622 TTTTTGTAAAAGGATT
1 TTTTTGTAAAAAGATT
4638 AGGATATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
18 29 0.63
19 1 0.02
20 1 0.02
22 1 0.02
23 14 0.30
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (18 bp):
TTTTTGTAAAAAGATTGA
Found at i:4607 original size:41 final size:41
Alignment explanation
Indices: 4562--4641 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
4552 TAACGTTCTT
4562 TTTTTTGTAAAAAGATTGATTTTTGTAAAAGGATTAGGAAA
1 TTTTTTGTAAAAAGATTGATTTTTGTAAAAGGATTAGGAAA
* *
4603 TTTTTTGTGAAAAGATTTATTTTTGTAAAAGGATTAGGA
1 TTTTTTGTAAAAAGATTGATTTTTGTAAAAGGATTAGGA
4642 TATATTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (41 bp):
TTTTTTGTAAAAAGATTGATTTTTGTAAAAGGATTAGGAAA
Found at i:4799 original size:6 final size:6
Alignment explanation
Indices: 4781--4822 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
4771 GTTTAGACTT
4781 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
4823 TATTATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:7630 original size:28 final size:25
Alignment explanation
Indices: 7578--7629 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
7568 TATTACACTC
7578 TAGAAGAAGAGAAAGGGTGTTATAA
1 TAGAAGAAGAGAAAGGGTGTTATAA
* *
7603 TAGAAGAAGAGAAGGGGTGTTGTAA
1 TAGAAGAAGAGAAAGGGTGTTATAA
7628 TA
1 TA
7630 AAGCAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (25 bp):
TAGAAGAAGAGAAAGGGTGTTATAA
Found at i:9928 original size:16 final size:16
Alignment explanation
Indices: 9907--9937 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9897 ACATTACTTA
*
9907 CTTCTTTCTTCTTCTT
1 CTTCTTCCTTCTTCTT
9923 CTTCTTCCTTCTTCT
1 CTTCTTCCTTCTTCT
9938 CTCTATAGTC
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTCTTCCTTCTTCTT
Found at i:11166 original size:10 final size:10
Alignment explanation
Indices: 11148--11201 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
11138 AGGTGGGGGC
*
11148 TTTCCTTCTT
1 TTTCTTTCTT
11158 TTTCTTTCTT
1 TTTCTTTCTT
11168 TCTT-TTT-TT
1 T-TTCTTTCTT
*
11177 TTTTTTTC-T
1 TTTCTTTCTT
*
11186 TTTCTTTATT
1 TTTCTTTCTT
11196 TTTCTT
1 TTTCTT
11202 AAATGTGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 2 0.05
9 13 0.35
10 20 0.54
11 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:11170 original size:14 final size:14
Alignment explanation
Indices: 11147--11201 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
11137 GAGGTGGGGG
*
11147 CTTTCCTTCTTTTT
1 CTTTCTTTCTTTTT
11161 CTTTCTTTCTTTTT
1 CTTTCTTTCTTTTT
*
11175 -TTT-TTT-TTTCT
1 CTTTCTTTCTTTTT
*
11186 -TTTCTTTATTTTT
1 CTTTCTTTCTTTTT
11199 CTT
1 CTT
11202 AAATGTGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 7 0.20
12 6 0.17
13 7 0.20
14 15 0.43
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTCTTTCTTTTT
Found at i:11184 original size:15 final size:15
Alignment explanation
Indices: 11156--11201 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
11146 GCTTTCCTTC
* *
11156 TTTTTCTTTCTTTCT
1 TTTTTTTTTTTTTCT
11171 TTTTTTTTTTTTTCT
1 TTTTTTTTTTTTTCT
* *
11186 TTTCTTTATTTTTCT
1 TTTTTTTTTTTTTCT
11201 T
1 T
11202 AAATGTGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTTCT
Found at i:11184 original size:19 final size:21
Alignment explanation
Indices: 11156--11198 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
11146 GCTTTCCTTC
11156 TTTTTCTTTC-TTTCTTT-TT
1 TTTTTCTTTCTTTTCTTTATT
*
11175 TTTTTTTTTCTTTTCTTTATT
1 TTTTTCTTTCTTTTCTTTATT
11196 TTT
1 TTT
11199 CTTAAATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTCTTTCTTTTCTTTATT
Found at i:29852 original size:30 final size:30
Alignment explanation
Indices: 29818--29879 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
29808 CCTATACCAA
* *
29818 CCATTGAGAGTGTAACAAATAGGAGCAACT
1 CCATTGAAAATGTAACAAATAGGAGCAACT
*
29848 CCATTGAAAATGTAACAAATAGGAGGAACT
1 CCATTGAAAATGTAACAAATAGGAGCAACT
29878 CC
1 CC
29880 GTGATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (30 bp):
CCATTGAAAATGTAACAAATAGGAGCAACT
Found at i:30134 original size:8 final size:8
Alignment explanation
Indices: 30121--30155 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
30111 TTGTGCCTAA
30121 ATATTATT
1 ATATTATT
30129 ATATTATT
1 ATATTATT
30137 ATATTATT
1 ATATTATT
30145 ATTATT-TT
1 A-TATTATT
30153 ATA
1 ATA
30156 AGATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 2 0.08
8 20 0.77
9 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATATTATT
Found at i:35278 original size:1 final size:1
Alignment explanation
Indices: 35272--35318 Score: 94
Period size: 1 Copynumber: 47.0 Consensus size: 1
35262 TGTCACAAGG
35272 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35319 GCATACATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38916 original size:35 final size:35
Alignment explanation
Indices: 38855--38949 Score: 160
Period size: 35 Copynumber: 2.8 Consensus size: 35
38845 TAATTTGACA
38855 GGACTCC-TTGTGAGAG--TTTGTATTGGTTTTTG
1 GGACTCCTTTGTGAGAGCTTTTGTATTGGTTTTTG
*
38887 GGACTCCTTTGTGAGAGCTTTTGTTTTGGTTTTTG
1 GGACTCCTTTGTGAGAGCTTTTGTATTGGTTTTTG
38922 GGACTCCTTTGTGAGAGCTTTTGTATTG
1 GGACTCCTTTGTGAGAGCTTTTGTATTG
38950 TCTTTGTACA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 7 0.12
33 9 0.16
35 42 0.72
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (35 bp):
GGACTCCTTTGTGAGAGCTTTTGTATTGGTTTTTG
Found at i:39563 original size:30 final size:30
Alignment explanation
Indices: 39529--39601 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
39519 GTAGTTTACA
** *
39529 GTAGTTTTCTTTTTTGGTACTTTTAAATTG
1 GTAGTTTTCTTTTTTGACACATTTAAATTG
39559 GTAGTTTTCTTTTTTGACACATTTAAATTG
1 GTAGTTTTCTTTTTTGACACATTTAAATTG
*
39589 GTAATTTTCTTTT
1 GTAGTTTTCTTTT
39602 AAGTGATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.59
Consensus pattern (30 bp):
GTAGTTTTCTTTTTTGACACATTTAAATTG
Found at i:40237 original size:1 final size:1
Alignment explanation
Indices: 40231--40264 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
40221 AGATTTCCGA
40231 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40265 CCAATTTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41469 original size:2 final size:2
Alignment explanation
Indices: 41462--41498 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41452 GCTTTCCATG
41462 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
41499 CTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.