Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012460.1 Corchorus olitorius cultivar O-4 contig12493, 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: 64138
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1772 original size:2 final size:2
Alignment explanation
Indices: 1765--1792 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1755 GCAATTCCAA
1765 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1793 TAATCTTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:25703 original size:33 final size:33
Alignment explanation
Indices: 25661--25726 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
25651 AAGCTTGCTA
25661 TTTACATTGGCTTGCCACATGTGTCTACTATGT
1 TTTACATTGGCTTGCCACATGTGTCTACTATGT
25694 TTTACATTGGCTTGCCACATGTGTCTACTATGT
1 TTTACATTGGCTTGCCACATGTGTCTACTATGT
25727 GTGTCATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (33 bp):
TTTACATTGGCTTGCCACATGTGTCTACTATGT
Found at i:28707 original size:41 final size:41
Alignment explanation
Indices: 28661--28742 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
28651 TCTGGTACTG
28661 TGTCCATAAATCACTAAGACACTAACAGACCAACAGGCCTT
1 TGTCCATAAATCACTAAGACACTAACAGACCAACAGGCCTT
28702 TGTCCATAAATCACTAAGACACTAACAGACCAACAGGCCTT
1 TGTCCATAAATCACTAAGACACTAACAGACCAACAGGCCTT
28743 AGCCACATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (41 bp):
TGTCCATAAATCACTAAGACACTAACAGACCAACAGGCCTT
Found at i:29911 original size:28 final size:28
Alignment explanation
Indices: 29861--29941 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
29851 AAACTCCGAC
* *
29861 TTGGAATTCACCTAGAGAAGTCTTAAAG
1 TTGGAATTCACCTAAAGAAGTCTCAAAG
* *
29889 TTGGAATTCACAC-AAAGAGGTCTCAAAT
1 TTGGAATTCAC-CTAAAGAAGTCTCAAAG
29917 TTGTCGAATTCACCTAGAA-AAGTCT
1 TTG--GAATTCACCTA-AAGAAGTCT
29942 TGAGTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 25 0.58
29 2 0.05
30 14 0.33
31 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (28 bp):
TTGGAATTCACCTAAAGAAGTCTCAAAG
Found at i:34287 original size:18 final size:17
Alignment explanation
Indices: 34264--34297 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34254 TGGTTGTTTA
*
34264 TGATTTTGTCCTTCTGAC
1 TGATTTT-TCCATCTGAC
34282 TGATTTTTCCATCTGA
1 TGATTTTTCCATCTGA
34298 AAAAGGGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.50
Consensus pattern (17 bp):
TGATTTTTCCATCTGAC
Found at i:40817 original size:36 final size:36
Alignment explanation
Indices: 40799--40871 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
40789 TACTATAGTT
40799 TGTGTATTCCTAATTAGTAGAGACTAGACCAGCTGA
1 TGTGTATTCCTAATTAGTAGAGACTAGACCAGCTGA
* *
40835 TGTGTATTCCTAATTAATAGAGACTAGACCATCTGA
1 TGTGTATTCCTAATTAGTAGAGACTAGACCAGCTGA
40871 T
1 T
40872 TGCCAGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTGTATTCCTAATTAGTAGAGACTAGACCAGCTGA
Found at i:40953 original size:34 final size:34
Alignment explanation
Indices: 40884--40953 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
40874 CCAGTTTTGT
* *
40884 ATTTGGCTACATTACACTTTCATTTATCAGTGAA
1 ATTTGGCTACAATACACTTTCATTTATCAGCGAA
* * *
40918 ATTTGGTTACAATCCACTTTTATTTATC-GCCGAA
1 ATTTGGCTACAATACACTTTCATTTATCAG-CGAA
40952 AT
1 AT
40954 CATGCCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (34 bp):
ATTTGGCTACAATACACTTTCATTTATCAGCGAA
Found at i:41412 original size:15 final size:16
Alignment explanation
Indices: 41387--41419 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
41377 AAATTTCAAT
41387 CAAAGAATAATCTTTC
1 CAAAGAATAATCTTTC
41403 CAAA-AATAATCTTTC
1 CAAAGAATAATCTTTC
41418 CA
1 CA
41420 CGAGGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.30
Consensus pattern (16 bp):
CAAAGAATAATCTTTC
Found at i:42568 original size:20 final size:20
Alignment explanation
Indices: 42540--42578 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42530 CATAAATGAA
*
42540 ATTTGCAAAAATTATTATTT
1 ATTTGCAAAAATTAATATTT
* *
42560 ATTTTCAAATATTAATATT
1 ATTTGCAAAAATTAATATT
42579 AAATTCGGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTGCAAAAATTAATATTT
Found at i:44018 original size:48 final size:44
Alignment explanation
Indices: 43933--44066 Score: 166
Period size: 48 Copynumber: 3.0 Consensus size: 44
43923 CAATCCGCTA
*
43933 CTGCCACGTCATCATTGTTGACTAAGTCAACCCGCCACGTCATC
1 CTGCCACGTCATCATTGTTGACTAAGTCAACCTGCCACGTCATC
* * *
43977 CTGCCACGTCATCATTGACAGTTGACTGAGTCAACCTGCCACATCATG
1 CTGCCACGTCATCATT----GTTGACTAAGTCAACCTGCCACGTCATC
*
44025 CTGCCACGTCATC--TGTTGAC-CAGTCAACCTGCCACGTCATC
1 CTGCCACGTCATCATTGTTGACTAAGTCAACCTGCCACGTCATC
44066 C
1 C
44067 GTTGACCGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
41 19 0.24
42 6 0.08
44 16 0.20
46 1 0.01
48 37 0.47
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (44 bp):
CTGCCACGTCATCATTGTTGACTAAGTCAACCTGCCACGTCATC
Found at i:44267 original size:18 final size:17
Alignment explanation
Indices: 44243--44383 Score: 141
Period size: 18 Copynumber: 8.2 Consensus size: 17
44233 TATTTTCTGT
44243 CTGTTTGACCTCTTGGTC
1 CTGTTTGACCT-TTGGTC
*
44261 ATGTTTGACCTTTTGGTC
1 CTGTTTGACC-TTTGGTC
44279 CTGTTTGACCATTTGGTC
1 CTGTTTGACC-TTTGGTC
*
44297 CTGTTT----TCT-G-C
1 CTGTTTGACCTTTGGTC
* *
44308 TTGTTCGACCTCTTGGTC
1 CTGTTTGACCT-TTGGTC
44326 CTGTTTGACCTTTCGGTC
1 CTGTTTGACCTTT-GGTC
44344 CTGTTTGACCTTTCGGTC
1 CTGTTTGACCTTT-GGTC
44362 CTGTTTGACCTTTCGGTC
1 CTGTTTGACCTTT-GGTC
44380 CTGT
1 CTGT
44384 ATTTTAGCCC
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
11 5 0.05
12 1 0.01
13 2 0.02
15 1 0.01
16 1 0.01
17 3 0.03
18 91 0.87
19 1 0.01
ACGTcount: A:0.06, C:0.26, G:0.22, T:0.46
Consensus pattern (17 bp):
CTGTTTGACCTTTGGTC
Found at i:44295 original size:36 final size:36
Alignment explanation
Indices: 44243--44383 Score: 156
Period size: 36 Copynumber: 4.1 Consensus size: 36
44233 TATTTTCTGT
* *
44243 CTGTTTGACCTCTTGGTCATGTTTGACCTTTTGGTC
1 CTGTTTGACCTCTTGGTCCTGTTTGACCTTTCGGTC
*
44279 CTGTTTGACCAT-TTGGTCCTG--T----TTTCTG-C
1 CTGTTTGACC-TCTTGGTCCTGTTTGACCTTTCGGTC
* *
44308 TTGTTCGACCTCTTGGTCCTGTTTGACCTTTCGGTC
1 CTGTTTGACCTCTTGGTCCTGTTTGACCTTTCGGTC
44344 CTGTTTGACCT-TTCGGTCCTGTTTGACCTTTCGGTC
1 CTGTTTGACCTCTT-GGTCCTGTTTGACCTTTCGGTC
44380 CTGT
1 CTGT
44384 ATTTTAGCCC
Statistics
Matches: 87, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
28 1 0.01
29 18 0.21
30 4 0.05
31 1 0.01
34 1 0.01
35 7 0.08
36 54 0.62
37 1 0.01
ACGTcount: A:0.06, C:0.26, G:0.22, T:0.46
Consensus pattern (36 bp):
CTGTTTGACCTCTTGGTCCTGTTTGACCTTTCGGTC
Found at i:44304 original size:65 final size:64
Alignment explanation
Indices: 44217--44367 Score: 223
Period size: 65 Copynumber: 2.3 Consensus size: 64
44207 AGCTTGCTCC
* * * *
44217 GTTTGACCTTTCGTCCTATTTTCTG-TCTGTTTGACCTCTTGGTCATGTTTGACCTTTTGGTCCT
1 GTTTGACCTTTGGTCCTGTTTTCTGCT-TGTTCGACCTCTTGGTCATGTTTGACCTTTCGGTCCT
*
44281 GTTTGACCATTTGGTCCTGTTTTCTGCTTGTTCGACCTCTTGGTCCTGTTTGACCTTTCGGTCCT
1 GTTTGACC-TTTGGTCCTGTTTTCTGCTTGTTCGACCTCTTGGTCATGTTTGACCTTTCGGTCCT
44346 GTTTGACCTTTCGGTCCTGTTT
1 GTTTGACCTTT-GGTCCTGTTT
44368 GACCTTTCGG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
64 11 0.14
65 67 0.85
66 1 0.01
ACGTcount: A:0.07, C:0.25, G:0.21, T:0.48
Consensus pattern (64 bp):
GTTTGACCTTTGGTCCTGTTTTCTGCTTGTTCGACCTCTTGGTCATGTTTGACCTTTCGGTCCT
Found at i:63916 original size:14 final size:13
Alignment explanation
Indices: 63880--63918 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
63870 TATATATTAG
63880 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
63893 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
63907 AATTTTTTAAAT
1 AATTTTTTAAAT
63919 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.