Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017038.1 Corchorus olitorius cultivar O-4 contig17071, 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: 46390
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9208 original size:12 final size:12
Alignment explanation
Indices: 9191--9220 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
9181 ATCCAGGCTT
9191 AGTTAGAAATCC
1 AGTTAGAAATCC
9203 AGTTAGAAATCC
1 AGTTAGAAATCC
9215 AGTTAG
1 AGTTAG
9221 GCTTAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (12 bp):
AGTTAGAAATCC
Found at i:17344 original size:29 final size:27
Alignment explanation
Indices: 17312--17366 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
17302 TATATTTTTT
17312 TTAAAAAAATCTGATTTTAAAATTTTTAG
1 TTAAAAAAATC--ATTTTAAAATTTTTAG
* *
17341 TTAATAAAATCCTTTTAAAATTTTTA
1 TTAAAAAAATCATTTTAAAATTTTTA
17367 TTGTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (27 bp):
TTAAAAAAATCATTTTAAAATTTTTAG
Found at i:21520 original size:28 final size:28
Alignment explanation
Indices: 21480--21535 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
21470 TCAATTTTGT
21480 TTCCTCATCTAAAGTGTGTAGCACTTAA
1 TTCCTCATCTAAAGTGTGTAGCACTTAA
*
21508 TTCCTCCTCTAAAGTGTGTAGCACTTAA
1 TTCCTCATCTAAAGTGTGTAGCACTTAA
21536 ACAAAAACTA
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:0.23, G:0.14, T:0.36
Consensus pattern (28 bp):
TTCCTCATCTAAAGTGTGTAGCACTTAA
Found at i:22176 original size:22 final size:22
Alignment explanation
Indices: 22148--22299 Score: 142
Period size: 22 Copynumber: 6.5 Consensus size: 22
22138 TGGAAATATT
*
22148 TTTGCAGAGCATTATTTACCAC
1 TTTGCAGAGCATTATTTTCCAC
*
22170 TTTGCAGAGCATTATTTTCTAC
1 TTTGCAGAGCATTATTTTCCAC
22192 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
22214 TTTGCAGAGTGCATTATTTTCTTCAAC
1 TTTGCAGA--GCATTATTTTC--C-AC
* *** ***
22241 TTCAGCTTTGCATTATTGGAAACATC
1 TT-TGCAGAGCATTATT--TTCCA-C
22267 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
22289 TTTGCAGAGCA
1 TTTGCAGAGCA
22300 CTTCTTGTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
22 61 0.59
23 2 0.02
24 11 0.11
25 11 0.11
26 13 0.12
27 4 0.04
28 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (22 bp):
TTTGCAGAGCATTATTTTCCAC
Found at i:29870 original size:29 final size:29
Alignment explanation
Indices: 29827--29892 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 29
29817 CCATCCTCTT
29827 CTGATTATGGGAGAGGAGTGGAGAGGTCCA
1 CTGATT-TGGGAGAGGAGTGGAGAGGTCCA
29857 CTGATTTGGGAGAGGAGTGGAGAGGTCCA
1 CTGATTTGGGAGAGGAGTGGAGAGGTCCA
29886 CTGATTT
1 CTGATTT
29893 TTCCAAGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.24, C:0.11, G:0.41, T:0.24
Consensus pattern (29 bp):
CTGATTTGGGAGAGGAGTGGAGAGGTCCA
Found at i:30073 original size:17 final size:17
Alignment explanation
Indices: 30047--30080 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30037 AATCGATACG
30047 TATTTGTATAAAGTATC
1 TATTTGTATAAAGTATC
* *
30064 TATTTTTATAATGTATC
1 TATTTGTATAAAGTATC
30081 AGTAGCGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTTGTATAAAGTATC
Found at i:30243 original size:56 final size:56
Alignment explanation
Indices: 30151--30379 Score: 277
Period size: 56 Copynumber: 4.1 Consensus size: 56
30141 TTTGACTAGG
* * *
30151 GGAACGGATGATTGAGCGAGACTTTCTGCGGGGAGGAATTCTCAATGTCGACGAGA
1 GGAACTGATGATTGAGCAAGACTTCCTGCGGGGAGGAATTCTCAATGTCGACGAGA
* *
30207 GGAAGTGATGATTGAGCGAGACTTCCTGCGGGGAGGAATT-T-AATGTCGACGAGA
1 GGAACTGATGATTGAGCAAGACTTCCTGCGGGGAGGAATTCTCAATGTCGACGAGA
* * * ** * *
30261 GGAACTGGTGATTGAACAAGACTTCATGTAGGGAGG-ATTCTCAAGGTCGACGACA
1 GGAACTGATGATTGAGCAAGACTTCCTGCGGGGAGGAATTCTCAATGTCGACGAGA
** * *
30316 GGAACTGATGATTGAGCAAGACTTCCTAAGGTGAGGAATTCTCAA-GCTGGACGAGA
1 GGAACTGATGATTGAGCAAGACTTCCTGCGGGGAGGAATTCTCAATG-TCGACGAGA
30372 GGAACTGA
1 GGAACTGA
30380 GGGAGATAAA
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
53 3 0.02
54 43 0.29
55 42 0.28
56 60 0.41
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (56 bp):
GGAACTGATGATTGAGCAAGACTTCCTGCGGGGAGGAATTCTCAATGTCGACGAGA
Found at i:30643 original size:21 final size:22
Alignment explanation
Indices: 30613--30659 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
30603 TCTATGAAAT
*
30613 TGTGTTTGAACTTGTT-TTAAG
1 TGTGTCTGAACTTGTTCTTAAG
*
30634 TGTGTCTGAACTTGTTCTTGAG
1 TGTGTCTGAACTTGTTCTTAAG
30656 TGTG
1 TGTG
30660 ATCAAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.49
Consensus pattern (22 bp):
TGTGTCTGAACTTGTTCTTAAG
Found at i:34679 original size:13 final size:13
Alignment explanation
Indices: 34661--34686 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34651 GCACTGAACT
34661 ACAAATTTTTTCC
1 ACAAATTTTTTCC
34674 ACAAATTTTTTCC
1 ACAAATTTTTTCC
34687 TTCACAATAC
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ACAAATTTTTTCC
Found at i:37982 original size:107 final size:107
Alignment explanation
Indices: 37801--38081 Score: 431
Period size: 107 Copynumber: 2.6 Consensus size: 107
37791 TTTTCTAATG
* ** *
37801 CTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTT
* *
37864 CTAAAACCCTATAACAATAAATTATTAATCATGTAATTTACC
66 CTAAAACCCTATAACAATAAATTAATAATCATGAAATTTACC
* *
37906 CTTAAAATAAAAATAAAATTTTAATTTGGGTCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTT
* **
37971 CTAAAATCCTATAACAATAAATTAATAATTTTGAAATTTACC
66 CTAAAACCCTATAACAATAAATTAATAATCATGAAATTTACC
* *
38013 CTTGAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTT
38078 CTAA
66 CTAA
38082 GAGTCTATAA
Statistics
Matches: 160, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
105 24 0.15
106 14 0.09
107 122 0.76
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (107 bp):
CTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTT
CTAAAACCCTATAACAATAAATTAATAATCATGAAATTTACC
Found at i:39806 original size:12 final size:12
Alignment explanation
Indices: 39785--39814 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39775 GCAAGAAATG
39785 CATCAACATCAC
1 CATCAACATCAC
*
39797 CATCACCATCAC
1 CATCAACATCAC
39809 CATCAA
1 CATCAA
39815 TGGTAAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (12 bp):
CATCAACATCAC
Found at i:40406 original size:28 final size:27
Alignment explanation
Indices: 40373--40429 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
40363 AGTCTCACAC
40373 AACCTGGAGCTTCTTTTGAGCCTCACCT
1 AACCTGGAGCTTC-TTTGAGCCTCACCT
*
40401 AACCTGGAGCTTCTTTGAGTCTCACCT
1 AACCTGGAGCTTCTTTGAGCCTCACCT
40428 AA
1 AA
40430 AACCCTAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.32
Consensus pattern (27 bp):
AACCTGGAGCTTCTTTGAGCCTCACCT
Found at i:40425 original size:27 final size:28
Alignment explanation
Indices: 40363--40429 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
40353 CAAATTCCCA
40363 AGTCTCACAC-AACCTGGAGCTTCTTTTG
1 AGTCTCAC-CTAACCTGGAGCTTCTTTTG
*
40391 AGCCTCACCTAACCTGGAGCTTC-TTTG
1 AGTCTCACCTAACCTGGAGCTTCTTTTG
40418 AGTCTCACCTAA
1 AGTCTCACCTAA
40430 AACCCTAGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.30
Consensus pattern (28 bp):
AGTCTCACCTAACCTGGAGCTTCTTTTG
Found at i:46083 original size:78 final size:77
Alignment explanation
Indices: 45954--46121 Score: 257
Period size: 78 Copynumber: 2.2 Consensus size: 77
45944 TTGTTTAAAC
*
45954 TTTTATAGTTTTACTCAACCAAAAACTCTATATTTATTTAATTAAATCTAATATCTTTATAACTA
1 TTTTATA-TTTTACTCAACCAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTA
*
46019 TTTTATTTTACCA
65 TTTTAGTTTACCA
* * *
46032 TTTTACTATTTTACTCAACTAAATACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACCAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTA
46097 TTTTAGTTTACCA
65 TTTTAGTTTACCA
46110 -TTTATTATTTTA
1 TTTTA-TATTTTA
46122 ATTAAAAAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
77 11 0.13
78 70 0.84
79 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (77 bp):
TTTTATATTTTACTCAACCAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTAT
TTTAGTTTACCA
Done.