Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008432.1 Corchorus capsularis cultivar CVL-1 contig08453, 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: 17833
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:232 original size:59 final size:59
Alignment explanation
Indices: 140--255 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 59
130 CCAACTCCTA
* **
140 TCTTTTTGGAACATTGTTTCTAATACAAGTTAGACCATGATCGAAATCAATTGTCACTG
1 TCTTTTTGGAACATTGTTTCTAATACAAGTTAGACCATAAAAGAAATCAATTGTCACTG
* * *
199 TCTTTTTGGAACTTTGTTTCTAATATATGTTAGACCATAAAAGAAATCAATTGTCAC
1 TCTTTTTGGAACATTGTTTCTAATACAAGTTAGACCATAAAAGAAATCAATTGTCAC
256 GACTTTTCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (59 bp):
TCTTTTTGGAACATTGTTTCTAATACAAGTTAGACCATAAAAGAAATCAATTGTCACTG
Found at i:1513 original size:11 final size:11
Alignment explanation
Indices: 1475--1507 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1465 TATATAGATA
1475 AATTATCAAA-T
1 AATTAT-AAATT
1486 AATTATAAATT
1 AATTATAAATT
1497 AATTATAAATT
1 AATTATAAATT
1508 TGTTATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATAAATT
Found at i:3832 original size:2 final size:2
Alignment explanation
Indices: 3827--3864 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3817 ATTAAGAGAG
3827 TA TA 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 TA TA
3865 AGCTAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4384 original size:2 final size:2
Alignment explanation
Indices: 4377--4407 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4367 TTTAAATTAT
4377 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 T
4408 TCTTATTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6685 original size:17 final size:17
Alignment explanation
Indices: 6663--6697 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6653 ATTTGTCTTT
6663 TGTATGTGCTATATATA
1 TGTATGTGCTATATATA
*
6680 TGTATGTGCTATTTATA
1 TGTATGTGCTATATATA
6697 T
1 T
6698 ATATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (17 bp):
TGTATGTGCTATATATA
Found at i:6753 original size:27 final size:27
Alignment explanation
Indices: 6715--6767 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6705 ATATAAATCC
6715 TATCATCTGATCAACGGGATTGTCTGG
1 TATCATCTGATCAACGGGATTGTCTGG
* *
6742 TATCCTCTGATCCACGGGATTGTCTG
1 TATCATCTGATCAACGGGATTGTCTG
6768 ATACCAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (27 bp):
TATCATCTGATCAACGGGATTGTCTGG
Found at i:7074 original size:37 final size:37
Alignment explanation
Indices: 7024--7094 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
7014 CAATACAATT
*
7024 AATAATTCTACTTTGTAGAATTGACATAATTGGAATC
1 AATAATTCTACTTTGTACAATTGACATAATTGGAATC
* *
7061 AATAATTGTACTTTGTACTATTGACATAATTGGA
1 AATAATTCTACTTTGTACAATTGACATAATTGGA
7095 GACAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (37 bp):
AATAATTCTACTTTGTACAATTGACATAATTGGAATC
Found at i:7346 original size:5 final size:5
Alignment explanation
Indices: 7336--7382 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
7326 TATATATATA
* *
7336 TATCT TATCT TATCT TATCT TATCT TA-C- TATCT TATTT TCTCT TATC
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATC
7383 ACTACTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 32 0.89
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (5 bp):
TATCT
Found at i:7486 original size:13 final size:13
Alignment explanation
Indices: 7468--7493 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7458 TTTAAATAAG
7468 TATTCTTTTTAGT
1 TATTCTTTTTAGT
7481 TATTCTTTTTAGT
1 TATTCTTTTTAGT
7494 AAAACGGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TATTCTTTTTAGT
Found at i:7845 original size:2 final size:2
Alignment explanation
Indices: 7838--7865 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7828 TCAAAACCAA
7838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7866 GTAATTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12416 original size:12 final size:12
Alignment explanation
Indices: 12399--12500 Score: 129
Period size: 12 Copynumber: 8.6 Consensus size: 12
12389 GGAGAAACCT
12399 AAGTTCTTCATC
1 AAGTTCTTCATC
12411 AAGTTCTTCA-C
1 AAGTTCTTCATC
*
12422 TAAGTT-TTCACC
1 -AAGTTCTTCATC
*
12434 AAGTTCTTCACC
1 AAGTTCTTCATC
*
12446 AAGTTTTTC-TAC
1 AAGTTCTTCAT-C
12458 AAGTTCTTCATC
1 AAGTTCTTCATC
*
12470 AAGTTCTTCAAC
1 AAGTTCTTCATC
12482 AAGTTCTTCATC
1 AAGTTCTTCATC
12494 AAGTTCT
1 AAGTTCT
12501 CCACCGATCA
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.12
12 69 0.86
13 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (12 bp):
AAGTTCTTCATC
Found at i:13973 original size:15 final size:16
Alignment explanation
Indices: 13953--13985 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13943 TTGATAGGTT
13953 TAATTAAAG-GAAATC
1 TAATTAAAGAGAAATC
*
13968 TAATTAGAGAGAAATC
1 TAATTAAAGAGAAATC
13984 TA
1 TA
13986 TCAAGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (16 bp):
TAATTAAAGAGAAATC
Found at i:16085 original size:6 final size:6
Alignment explanation
Indices: 16074--16100 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16064 AAAGCAAAGC
16074 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
16101 ACAGATTATA
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:16112 original size:12 final size:13
Alignment explanation
Indices: 16097--16141 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
16087 AATCTAAATC
*
16097 TAAAACAGATT-A
1 TAAAGCAGATTAA
*
16109 TAAAGCAAATTAA
1 TAAAGCAGATTAA
16122 TAAAGCAGATTAA
1 TAAAGCAGATTAA
16135 TAAAGCA
1 TAAAGCA
16142 AACAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:16148 original size:25 final size:25
Alignment explanation
Indices: 16097--16149 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
16087 AATCTAAATC
*
16097 TAAAACAGATTATAAAGCAAATTAA
1 TAAAACAGATTATAAAGCAAATCAA
*
16122 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAACAGATT-ATAAAGCAAATCAA
16147 TAA
1 TAA
16150 TTAAAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (25 bp):
TAAAACAGATTATAAAGCAAATCAA
Done.