Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000882.1 Corchorus olitorius cultivar O-4 contig00882, 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: 10715
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 ACCCAATGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3963 original size:7 final size:6
Alignment explanation
Indices: 3946--4015 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
3936 TATAACGTGG
* * *
3946 CTTTTT CTTTTT CATTTT CCTTTT CTTTTT -TTTTC CTTTTT -TTCTCTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT-T-TT
*
3994 -TTCTT CTTTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTT
4016 CTCCTTCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 8 0.15
6 41 0.77
7 4 0.08
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:3994 original size:10 final size:10
Alignment explanation
Indices: 3966--4015 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3956 TTCATTTTCC
*
3966 TTTTCTTTTT
1 TTTTCTCTTT
3976 TTTTC-CTTT
1 TTTTCTCTTT
3985 TTTTCTCTTT
1 TTTTCTCTTT
*
3995 TCTTCT-TTT
1 TTTTCTCTTT
*
4004 TCTTTTTCTTT
1 T-TTTCTCTTT
4015 T
1 T
4016 CTCCTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 12 0.36
10 17 0.52
11 4 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:4023 original size:26 final size:26
Alignment explanation
Indices: 3946--4024 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
3936 TATAACGTGG
*
3946 CTTTTTCTTTTTCATTT-TCCTT-TT
1 CTTTTTCTTTTTCTTTTCTCCTTCTT
* * *
3970 CTTTTTTTTTCCTTTTTTTCTCTTTTCTT
1 CTTTTTCTTT--TTCTTTTCTC-CTTCTT
3999 CTTTTTCTTTTTCTTTTCTCCTTCTT
1 CTTTTTCTTTTTCTTTTCTCCTTCTT
4025 TGTCAACCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
24 9 0.21
26 10 0.23
27 11 0.26
28 2 0.05
29 11 0.26
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (26 bp):
CTTTTTCTTTTTCTTTTCTCCTTCTT
Found at i:5284 original size:20 final size:21
Alignment explanation
Indices: 5242--5281 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5232 CTATATCTCA
5242 GGTCTATGTGACTAAAAAAAT
1 GGTCTATGTGACTAAAAAAAT
5263 GGTCTATGT-AGCTAAAAAA
1 GGTCTATGTGA-CTAAAAAA
5282 TGGCTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
GGTCTATGTGACTAAAAAAAT
Found at i:5815 original size:19 final size:19
Alignment explanation
Indices: 5797--5833 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5787 AATTAATTAT
5797 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
5815 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
5834 CTTAAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:6971 original size:29 final size:30
Alignment explanation
Indices: 6915--6986 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
6905 CATCAGAAAA
****
6915 GGGCTTATTTGGCTTTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCTGCACTTAAGAGTTCAG
6945 GGGCTTATTTGGCTGCACTTAA-AGTTCAG
1 GGGCTTATTTGGCTGCACTTAAGAGTTCAG
*
6974 GAGCTTATTTGGC
1 GGGCTTATTTGGC
6987 CGTTTTGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCTGCACTTAAGAGTTCAG
Found at i:7321 original size:34 final size:35
Alignment explanation
Indices: 7259--7328 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
7249 CTTCTTCTGC
7259 AGAATTTTTCTATCCTTGCTCAAGTAATTGGAGGT
1 AGAATTTTTCTATCCTTGCTCAAGTAATTGGAGGT
* *
7294 AGAATTTTTCTATCCTT-TTCAAGTAATTTGAGGT
1 AGAATTTTTCTATCCTTGCTCAAGTAATTGGAGGT
7328 A
1 A
7329 AAGAAGAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 16 0.48
35 17 0.52
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (35 bp):
AGAATTTTTCTATCCTTGCTCAAGTAATTGGAGGT
Found at i:9242 original size:11 final size:11
Alignment explanation
Indices: 9226--9265 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
9216 GTTAACTGGT
9226 CCACGTAGGTG
1 CCACGTAGGTG
9237 CCACGTAGGTG
1 CCACGTAGGTG
*
9248 CCATGTAGGATG
1 CCACGTAGG-TG
9260 CCACGT
1 CCACGT
9266 GTATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.20, C:0.28, G:0.33, T:0.20
Consensus pattern (11 bp):
CCACGTAGGTG
Found at i:9319 original size:21 final size:21
Alignment explanation
Indices: 9293--9332 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9283 TGAATTTTTA
* *
9293 TTTTATTTTATTTTTTTATCT
1 TTTTATTTAACTTTTTTATCT
9314 TTTTATTTAACTTTTTTAT
1 TTTTATTTAACTTTTTTAT
9333 AACCTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTTAACTTTTTTATCT
Found at i:9368 original size:31 final size:30
Alignment explanation
Indices: 9333--9408 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
9323 ACTTTTTTAT
*
9333 AACCTTATATCCTGAATTG-CTTGTTCAGGTA
1 AACCTTATATCCTGAATTGACTT-TT-AGGCA
*
9364 AACCTCATATCCTGAATTGCACTTTTAGGCA
1 AACCTTATATCCTGAATTG-ACTTTTAGGCA
*
9395 AACCTTATACCCTG
1 AACCTTATATCCTG
9409 TATTATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 34 0.87
32 2 0.05
33 3 0.08
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (30 bp):
AACCTTATATCCTGAATTGACTTTTAGGCA
Found at i:10395 original size:66 final size:67
Alignment explanation
Indices: 10299--10427 Score: 217
Period size: 66 Copynumber: 1.9 Consensus size: 67
10289 TCAAAACATG
* *
10299 CAGAAAGGGAGATAAACCAGTCTTTAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATATGAA
1 CAGAAAGGGAGATAAACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATATGAA
10364 TA
66 TA
10366 CAGAAAGGGAGA-AAGA-AAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATATG
1 CAGAAAGGGAGATAA-ACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATATG
10428 GAAAAATGAC
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 46 0.78
67 13 0.22
ACGTcount: A:0.51, C:0.09, G:0.24, T:0.16
Consensus pattern (67 bp):
CAGAAAGGGAGATAAACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATATGAA
TA
Done.