Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021130.1 Corchorus olitorius cultivar O-4 contig21163, 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: 38565
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5832 original size:30 final size:30
Alignment explanation
Indices: 5796--5857 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
5786 GTTAATAAGC
5796 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
*
5826 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
5856 CA
1 CA
5858 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGAAAAGT
Found at i:7498 original size:13 final size:13
Alignment explanation
Indices: 7480--7504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7470 TACTATATAG
7480 ATAAATATTGTGA
1 ATAAATATTGTGA
7493 ATAAATATTGTG
1 ATAAATATTGTG
7505 GACTAAGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
ATAAATATTGTGA
Found at i:7926 original size:31 final size:31
Alignment explanation
Indices: 7901--8001 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
7891 ACACATTACA
*
7901 TGCCATGTGTCACTTTTTGGTACACATGGCG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
** * *
7932 TGATACATGTCACTTTTTGGTACACGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
* *
7963 TGCCACGTGTCGCTTTTTGGTACACGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
7994 TGCCACGT
1 TGCCACGT
8002 CAGATACCGT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.34
Consensus pattern (31 bp):
TGCCACGTGTCACTTTTTGGTACACATGGCG
Found at i:15431 original size:18 final size:19
Alignment explanation
Indices: 15400--15439 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
15390 TTCTCTCTTG
* *
15400 TTTTTCTTTCTTTGGTTAT
1 TTTTTCTCTCTTTGGTGAT
15419 TTTTTCTCT-TTTGGTGAT
1 TTTTTCTCTCTTTGGTGAT
15437 TTT
1 TTT
15440 CTTTTCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.72
Consensus pattern (19 bp):
TTTTTCTCTCTTTGGTGAT
Found at i:17165 original size:21 final size:19
Alignment explanation
Indices: 17139--17197 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
17129 CGCTGCTCTA
*
17139 ATAATCTCATCTGTATAGT
1 ATAATCTCATCTGTACAGT
* *
17158 ACATAATCTAATATGTACAGT
1 --ATAATCTCATCTGTACAGT
*
17179 GTAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
17198 TGCCAAACAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:28328 original size:30 final size:30
Alignment explanation
Indices: 28292--28438 Score: 107
Period size: 31 Copynumber: 4.8 Consensus size: 30
28282 GGCCCGTATC
* *
28292 CTTTTTGTGCACGA-GGCATGTCATGTGTCA
1 CTTTTTGTACAC-ATGGCATGCCATGTGTCA
*
28322 CTTTTTGGTACACATGGCGTGCCATGTGTCA
1 CTTTTT-GTACACATGGCATGCCATGTGTCA
* * ** * * *
28353 CTTTTTGGTATATATGGTGTGTCACGTGTCG
1 CTTTTT-GTACACATGGCATGCCATGTGTCA
* * ** *
28384 CTTTTTTGTACACGTGGCGTGCCACATGTCG
1 C-TTTTTGTACACATGGCATGCCATGTGTCA
28415 CTTTTTGGTACACATGGCATGCCA
1 CTTTTT-GTACACATGGCATGCCA
28439 CGTTGGACAC
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
30 12 0.12
31 79 0.82
32 5 0.05
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (30 bp):
CTTTTTGTACACATGGCATGCCATGTGTCA
Found at i:28350 original size:31 final size:31
Alignment explanation
Indices: 28316--28441 Score: 153
Period size: 31 Copynumber: 4.1 Consensus size: 31
28306 GGCATGTCAT
*
28316 GTGTCACTTTTTGGTACACATGGCGTGCCAT
1 GTGTCACTTTTTGGTACACATGGCGTGCCAC
* * * *
28347 GTGTCACTTTTTGGTATATATGGTGTGTCAC
1 GTGTCACTTTTTGGTACACATGGCGTGCCAC
* * *
28378 GTGTCGCTTTTTTGTACACGTGGCGTGCCAC
1 GTGTCACTTTTTGGTACACATGGCGTGCCAC
* * *
28409 ATGTCGCTTTTTGGTACACATGGCATGCCAC
1 GTGTCACTTTTTGGTACACATGGCGTGCCAC
28440 GT
1 GT
28442 TGGACACCAA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.37
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACATGGCGTGCCAC
Found at i:32373 original size:18 final size:18
Alignment explanation
Indices: 32352--32395 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
32342 ACCCGCTTCT
32352 ACTCCTCCACCAACCGCC
1 ACTCCTCCACCAACCGCC
* * **
32370 ACTCCACCACCGACTTCC
1 ACTCCTCCACCAACCGCC
32388 ACTCCTCC
1 ACTCCTCC
32396 TCCCACTTCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.59, G:0.05, T:0.16
Consensus pattern (18 bp):
ACTCCTCCACCAACCGCC
Found at i:32548 original size:63 final size:65
Alignment explanation
Indices: 32424--32551 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 65
32414 TCCAGTGACA
* * ** *
32424 GCTTCTCCTCCACCGGCTTCCACTCCTCCTCCAGCAACTCCGCCACCCGTTAGCTCCCCACCACC
1 GCTTCTCCTCCACC-GCTGCCACTCCTCCTCCAGCAACTCCCCCACCCGCCAGCCCCCCACCACC
32489 T
65 T
* *
32490 GCTTCTCCTCC-CC-CTGCCACTCCTCCTCCAGCTACTCCCCCTCCCGCCA---CCCCACCACCT
1 GCTTCTCCTCCACCGCTGCCACTCCTCCTCCAGCAACTCCCCCACCCGCCAGCCCCCCACCACCT
32550 GC
1 GC
32552 CACCCCTCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
60 13 0.23
63 30 0.54
65 2 0.04
66 11 0.20
ACGTcount: A:0.12, C:0.59, G:0.09, T:0.20
Consensus pattern (65 bp):
GCTTCTCCTCCACCGCTGCCACTCCTCCTCCAGCAACTCCCCCACCCGCCAGCCCCCCACCACCT
Found at i:32552 original size:45 final size:45
Alignment explanation
Indices: 32502--32626 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
32492 TTCTCCTCCC
* * *
32502 CCTGCCACTCCTCCTCCAGCTACTCCC-CCTCCCGCCACCCCACCA
1 CCTGCCACTCCTCCTCCAGCCAC-CCCACCACCAGCCACCCCACCA
* * * *
32547 CCTGCCACCCCTCCTCCCGCCACCCCACCACCAGCCACTCCTCCA
1 CCTGCCACTCCTCCTCCAGCCACCCCACCACCAGCCACCCCACCA
* *
32592 CCTGCAACTCCTCCTCCAGCAACCCCACCACCAGC
1 CCTGCCACTCCTCCTCCAGCCACCCCACCACCAGC
32627 TCCATTGGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 3 0.04
45 65 0.96
ACGTcount: A:0.17, C:0.63, G:0.07, T:0.13
Consensus pattern (45 bp):
CCTGCCACTCCTCCTCCAGCCACCCCACCACCAGCCACCCCACCA
Found at i:32560 original size:60 final size:61
Alignment explanation
Indices: 32443--32593 Score: 144
Period size: 60 Copynumber: 2.5 Consensus size: 61
32433 CCACCGGCTT
* * * ** *
32443 CCACTCCTCCTCCAGCAACTCCGCCACCCGTTAGCTCCCCACCACCTGCTTCTCCTCC-CCCTG
1 CCACTCCTCCTCCAGCAACTCCCCCACCCG-T-CCACCCCACCACCTGCCACCCCTCCTCCC-G
* *
32506 CCACTCCTCCTCCAGCTACTCCCCCTCCCG-CCACCCCACCACCTGCCACCCCTCCTCCCG
1 CCACTCCTCCTCCAGCAACTCCCCCACCCGTCCACCCCACCACCTGCCACCCCTCCTCCCG
* * * * *
32566 CCACCCCACCACCAGCCACTCCTCCACC
1 CCACTCCTCCTCCAGCAACTCCCCCACC
32594 TGCAACTCCT
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
60 43 0.59
61 3 0.04
63 27 0.37
ACGTcount: A:0.14, C:0.63, G:0.07, T:0.16
Consensus pattern (61 bp):
CCACTCCTCCTCCAGCAACTCCCCCACCCGTCCACCCCACCACCTGCCACCCCTCCTCCCG
Found at i:32611 original size:30 final size:30
Alignment explanation
Indices: 32479--32590 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 30
32469 CCCGTTAGCT
* **
32479 CCCCACCACCTGCTTCTCCTCC-CCCTGCCA
1 CCCCACCACCAGCCACTCCTCCTCCC-GCCA
* * * * *
32509 CTCCTCCTCCAGCTACTCCCCCTCCCGCCA
1 CCCCACCACCAGCCACTCCTCCTCCCGCCA
* *
32539 CCCCACCACCTGCCACCCCTCCTCCCGCCA
1 CCCCACCACCAGCCACTCCTCCTCCCGCCA
32569 CCCCACCACCAGCCACTCCTCC
1 CCCCACCACCAGCCACTCCTCC
32591 ACCTGCAACT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
30 63 0.95
31 3 0.05
ACGTcount: A:0.12, C:0.66, G:0.06, T:0.15
Consensus pattern (30 bp):
CCCCACCACCAGCCACTCCTCCTCCCGCCA
Found at i:32614 original size:15 final size:15
Alignment explanation
Indices: 32494--32611 Score: 83
Period size: 15 Copynumber: 7.9 Consensus size: 15
32484 CCACCTGCTT
* *
32494 CTCCTCCCCCTGCCA
1 CTCCTCCTCCAGCCA
*
32509 CTCCTCCTCCAGCTA
1 CTCCTCCTCCAGCCA
* *
32524 CTCCCCCTCCCGCCA
1 CTCCTCCTCCAGCCA
* * * *
32539 CCCCACCACCTGCCA
1 CTCCTCCTCCAGCCA
* *
32554 CCCCTCCTCCCGCCA
1 CTCCTCCTCCAGCCA
* * *
32569 CCCCACCACCAGCCA
1 CTCCTCCTCCAGCCA
* * *
32584 CTCCTCCACCTGCAA
1 CTCCTCCTCCAGCCA
32599 CTCCTCCTCCAGC
1 CTCCTCCTCCAGC
32612 AACCCCACCA
Statistics
Matches: 81, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 81 1.00
ACGTcount: A:0.14, C:0.64, G:0.07, T:0.15
Consensus pattern (15 bp):
CTCCTCCTCCAGCCA
Found at i:32625 original size:15 final size:15
Alignment explanation
Indices: 32535--32626 Score: 76
Period size: 15 Copynumber: 6.1 Consensus size: 15
32525 TCCCCCTCCC
*
32535 GCCACCCCACCACCT
1 GCCACCCCACCACCA
* * *
32550 GCCACCCCTCCTCCC
1 GCCACCCCACCACCA
32565 GCCACCCCACCACCA
1 GCCACCCCACCACCA
* * *
32580 GCCACTCCTCCACCT
1 GCCACCCCACCACCA
* * * *
32595 GCAACTCCTCCTCCA
1 GCCACCCCACCACCA
*
32610 GCAACCCCACCACCA
1 GCCACCCCACCACCA
32625 GC
1 GC
32627 TCCATTGGCT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 62 1.00
ACGTcount: A:0.20, C:0.63, G:0.08, T:0.10
Consensus pattern (15 bp):
GCCACCCCACCACCA
Done.