Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009626.1 Corchorus capsularis cultivar CVL-1 contig09647, 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: 34973
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:5297 original size:18 final size:18
Alignment explanation
Indices: 5247--5301 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
5237 GACTCTTCCC
**
5247 TCTCTTTCTCTTTAAGTT
1 TCTCTTTCTCTTTCTGTT
* * *
5265 TTTCTTTCTCCTTCTCTT
1 TCTCTTTCTCTTTCTGTT
*
5283 TCTCTTTCTGTTTCTGTT
1 TCTCTTTCTCTTTCTGTT
5301 T
1 T
5302 AGGCTCTTCA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.25, G:0.05, T:0.65
Consensus pattern (18 bp):
TCTCTTTCTCTTTCTGTT
Found at i:6639 original size:11 final size:11
Alignment explanation
Indices: 6623--6657 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
6613 AAATATACAT
6623 TATGATAATAA
1 TATGATAATAA
6634 TATGATAATAA
1 TATGATAATAA
*
6645 TATAATAATAA
1 TATGATAATAA
6656 TA
1 TA
6658 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (11 bp):
TATGATAATAA
Found at i:7566 original size:2 final size:2
Alignment explanation
Indices: 7555--7605 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
7545 AGCAATGAAG
* *
7555 TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TG 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 TA TA
7596 TA TA TA TA TA
1 TA TA TA TA TA
7606 CACCTTTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18602 original size:17 final size:17
Alignment explanation
Indices: 18580--18641 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
18570 GTGGCGTGTT
18580 ATGTGCCACTTTTTGAA
1 ATGTGCCACTTTTTGAA
18597 ATGTGCCAC--TTT---
1 ATGTGCCACTTTTTGAA
18609 -T-TGCCACTTTTTGAA
1 ATGTGCCACTTTTTGAA
18624 ATGTGCCACTTTTTGAA
1 ATGTGCCACTTTTTGAA
18641 A
1 A
18642 CATGTGGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
10 6 0.16
11 1 0.03
12 3 0.08
15 3 0.08
16 1 0.03
17 24 0.63
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (17 bp):
ATGTGCCACTTTTTGAA
Found at i:18614 original size:27 final size:27
Alignment explanation
Indices: 18583--18638 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
18573 GCGTGTTATG
18583 TGCCACTTTTTGAAATGTGCCACTTTT
1 TGCCACTTTTTGAAATGTGCCACTTTT
18610 TGCCACTTTTTGAAATGTGCCACTTTT
1 TGCCACTTTTTGAAATGTGCCACTTTT
18637 TG
1 TG
18639 AAACATGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (27 bp):
TGCCACTTTTTGAAATGTGCCACTTTT
Found at i:18707 original size:31 final size:31
Alignment explanation
Indices: 18669--18754 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
18659 GACGTGTCAC
*
18669 GTGTCACTTTTTGGTACACATGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* *
18700 GTGTCACTTTTTGGTACATGTGGCGTGTCAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* *
18731 ATATCACTTTTTGGTACACGTGGC
1 GTGTCACTTTTTGGTACACGTGGC
18755 ATGTCGCATC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACAT
Found at i:22318 original size:13 final size:13
Alignment explanation
Indices: 22300--22328 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22290 AATTGCTATT
22300 GGATTTATGCAGA
1 GGATTTATGCAGA
22313 GGATTTATGCAGA
1 GGATTTATGCAGA
22326 GGA
1 GGA
22329 ATGAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (13 bp):
GGATTTATGCAGA
Found at i:25536 original size:12 final size:12
Alignment explanation
Indices: 25519--25543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25509 AGTAGTGCCT
25519 ATTTCCAGAAAC
1 ATTTCCAGAAAC
25531 ATTTCCAGAAAC
1 ATTTCCAGAAAC
25543 A
1 A
25544 GAGCATGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
ATTTCCAGAAAC
Found at i:26063 original size:28 final size:28
Alignment explanation
Indices: 26023--26078 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
26013 TAACTCAGCT
*
26023 CTACGCCCATACCTTACAGATCTTGATG
1 CTACGCCCATACCTTAAAGATCTTGATG
26051 CTACGCCCATACCTTAAAGATCTTGATG
1 CTACGCCCATACCTTAAAGATCTTGATG
26079 AAGATTGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (28 bp):
CTACGCCCATACCTTAAAGATCTTGATG
Found at i:26206 original size:18 final size:18
Alignment explanation
Indices: 26172--26206 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26162 ATAATGAGAA
*
26172 GAGAAGAAGAACGACAAG
1 GAGAAGAAGAACAACAAG
*
26190 GAGAAGAAGAATAACAA
1 GAGAAGAAGAACAACAA
26207 AAAAAAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.29, T:0.03
Consensus pattern (18 bp):
GAGAAGAAGAACAACAAG
Found at i:26594 original size:18 final size:18
Alignment explanation
Indices: 26571--26609 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
26561 TTTTGGTGTA
26571 ATTACACTTCTTCTTCTT
1 ATTACACTTCTTCTTCTT
26589 ATTACACTTCTTCTTCTT
1 ATTACACTTCTTCTTCTT
26607 ATT
1 ATT
26610 GTTTAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTACACTTCTTCTTCTT
Done.