Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019258.1 Corchorus olitorius cultivar O-4 contig19291, 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: 36932
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1888 original size:15 final size:16
Alignment explanation
Indices: 1865--1907 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1855 TTCAAAATTA
*
1865 TTTTAAAAAATTATT-
1 TTTTAAAAAAATATTC
*
1880 TTTTGAAAAAATATTC
1 TTTTAAAAAAATATTC
1896 TTTTAATAAAAA
1 TTTTAA-AAAAA
1908 ATGTGATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTTAAAAAAATATTC
Found at i:1899 original size:16 final size:15
Alignment explanation
Indices: 1865--1906 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1855 TTCAAAATTA
1865 TTTTAAAAAATTATT
1 TTTTAAAAAATTATT
1880 TTTTGAAAAAA-TATT
1 TTTT-AAAAAATTATT
1895 CTTTTAATAAAA
1 -TTTTAA-AAAA
1907 AATGTGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATTATT
Found at i:11335 original size:151 final size:151
Alignment explanation
Indices: 10898--11377 Score: 701
Period size: 151 Copynumber: 3.2 Consensus size: 151
10888 TTGTTGGAAA
* * * * *
10898 TATTGGAATTTCTACTCTGAATAAGTTACATTTGTTAGTTTGAAAGATCGTAGGGTAGCCTATTA
1 TATTGGAATTTCTACTCTGGATAATTTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTA
* * * ** *
10963 TTTGCTTGCTCAATAACTCGTTCCAACATATAAAAGTTCGTTAATTCATGCTTAGTCTTAGTTTG
66 TATGCTTGCTCAACAGCTCGTTCCAATGTATAAAAGTTCGTTAATTCATGCTTAGTTTTAGTTTG
** *
11028 AAAGATTATAAACCAATCTGT
131 AAAGATTATAGGCTAATCTGT
* *
11049 TATTGGAATGTCTACTCTGGATAATTTACATTTTTGTTAGTTTGGAAGATCATAGGCTAACCTAT
1 TATTGGAATTTCTACTCTGGATAATTTACA--TTTGTTAGTTTGAAAGATCATAGGCTAACCTAT
* * * *
11114 T-TATGCTTGCCCAACAGCTTGTTCCAATGTATAAAAGTTTGTGAATTCATGCTTAGTTTTAGTT
64 TATATGCTTGCTCAACAGCTCGTTCCAATGTATAAAAGTTCGTTAATTCATGCTTAGTTTTAGTT
**
11178 CCAAAGATTATAGGCTAATCTGT
129 TGAAAGATTATAGGCTAATCTGT
11201 TATTGGAATTTCTACTCTGGATAATTTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTA
1 TATTGGAATTTCTACTCTGGATAATTTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTA
* *
11266 TATGCTTGCTCAACAGCTCGTTCCAATGTTTGAAAGTTCGTTAATTCATGCTTAGTTTTAGTTTG
66 TATGCTTGCTCAACAGCTCGTTCCAATGTATAAAAGTTCGTTAATTCATGCTTAGTTTTAGTTTG
*
11331 AAAGATTATAGGCTAATCTAT
131 AAAGATTATAGGCTAATCTGT
*
11352 AATTGGAATTTCTACTCTGGATAATT
1 TATTGGAATTTCTACTCTGGATAATT
11378 ATATTCCTTA
Statistics
Matches: 292, Mismatches: 34, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
150 33 0.11
151 129 0.44
152 100 0.34
153 30 0.10
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (151 bp):
TATTGGAATTTCTACTCTGGATAATTTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTA
TATGCTTGCTCAACAGCTCGTTCCAATGTATAAAAGTTCGTTAATTCATGCTTAGTTTTAGTTTG
AAAGATTATAGGCTAATCTGT
Found at i:11368 original size:303 final size:307
Alignment explanation
Indices: 10801--11377 Score: 804
Period size: 303 Copynumber: 1.9 Consensus size: 307
10791 ATAGAGAACA
* * *
10801 ATTTTGCTTGCTCAACAGCTAGTTCCAATATATAAAAGTTCATCACTTCATGTTTAGTTTTAGCT
1 ATTTTGCTTGCCCAACAGCTAGTTCCAATATATAAAAGTTCATCAATTCATGCTTAGTTTTAGCT
*
10866 CCAAAGATCATAGGCTAATATGTTGTTGGAAATATTGGAATTTCTACTCTGAATAAGTTACATTT
66 CCAAAGATCATAGGCTAATATGCTGTT----ATATTGGAATTTCTACTCTGAATAAGTTACATTT
* * * * *
10931 GTTAGTTTGAAAGATCGTAGGGTAGCCTATTATTTGCTTGCTCAATAACTCGTTCCAACATATAA
127 GTTAGTTTGAAAGATCATAGGCTAACCTATTATATGCTTGCTCAACAACTCGTTCCAACATATAA
* *
10996 AAGTTCGTTAATTCATGCTTAGTCTTAGTTTGAAAGATTATAAACCAATCTGTTATTGGAATGTC
192 AAGTTCGTTAATTCATGCTTAGTCTTAGTTTGAAAGATTATAAACCAATCTATAATTGGAATGTC
11061 TACTCTGGATAATTTACATTTTTGTTAGTTTGGAAGATCATAGGCTAACCT
257 TACTCTGGATAATTTACATTTTTGTTAGTTTGGAAGATCATAGGCTAACCT
* * ** * *
11112 ATTTATGCTTGCCCAACAGCTTGTTCCAATGTATAAAAGTTTGTGAATTCATGCTTAGTTTTAGT
1 ATTT-TGCTTGCCCAACAGCTAGTTCCAATATATAAAAGTTCATCAATTCATGCTTAGTTTTAGC
* * *
11177 TCCAAAGATTATAGGCT-A-AT-CTG-T-TATTGGAATTTCTACTCTGGATAATTTACATTTGTT
65 TCCAAAGATCATAGGCTAATATGCTGTTATATTGGAATTTCTACTCTGAATAAGTTACATTTGTT
* ** * *
11237 AGTTTGAAAGATCATAGGCTAACCTATTATATGCTTGCTCAACAGCTCGTTCCAATGTTTGAAAG
130 AGTTTGAAAGATCATAGGCTAACCTATTATATGCTTGCTCAACAACTCGTTCCAACATATAAAAG
* ** * *
11302 TTCGTTAATTCATGCTTAGTTTTAGTTTGAAAGATTATAGGCTAATCTATAATTGGAATTTCTAC
195 TTCGTTAATTCATGCTTAGTCTTAGTTTGAAAGATTATAAACCAATCTATAATTGGAATGTCTAC
11367 TCTGGATAATT
260 TCTGGATAATT
11378 ATATTCCTTA
Statistics
Matches: 235, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
303 158 0.67
308 1 0.00
309 2 0.01
310 2 0.01
311 5 0.02
312 67 0.29
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (307 bp):
ATTTTGCTTGCCCAACAGCTAGTTCCAATATATAAAAGTTCATCAATTCATGCTTAGTTTTAGCT
CCAAAGATCATAGGCTAATATGCTGTTATATTGGAATTTCTACTCTGAATAAGTTACATTTGTTA
GTTTGAAAGATCATAGGCTAACCTATTATATGCTTGCTCAACAACTCGTTCCAACATATAAAAGT
TCGTTAATTCATGCTTAGTCTTAGTTTGAAAGATTATAAACCAATCTATAATTGGAATGTCTACT
CTGGATAATTTACATTTTTGTTAGTTTGGAAGATCATAGGCTAACCT
Found at i:19712 original size:18 final size:18
Alignment explanation
Indices: 19682--19720 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19672 ATCATATATC
19682 ATATAGTAGTATACTAGT
1 ATATAGTAGTATACTAGT
*
19700 ATATCAGTA-TATAGTAGT
1 ATAT-AGTAGTATACTAGT
19718 ATA
1 ATA
19721 CTGGTAGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (18 bp):
ATATAGTAGTATACTAGT
Found at i:35191 original size:23 final size:23
Alignment explanation
Indices: 35161--35225 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
35151 CACAATTGCT
35161 TGGCGCCCGATCACTTCCAAACC
1 TGGCGCCCGATCACTTCCAAACC
35184 TGGCGCCCGATCACTTCCAAACC
1 TGGCGCCCGATCACTTCCAAACC
*
35207 TGGCGACCGA-CTACTTCCA
1 TGGCGCCCGATC-ACTTCCA
35226 TAACGCGGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.18
Consensus pattern (23 bp):
TGGCGCCCGATCACTTCCAAACC
Found at i:35389 original size:26 final size:27
Alignment explanation
Indices: 35328--35395 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
35318 AACCAGCTGG
*
35328 CACC-CCACACGTGACCTCCAAACGTA
1 CACCTCCACACGTGACCTCCAAACGGA
*
35354 CGACCT-CACACGTGATCTCC-AACGGA
1 C-ACCTCCACACGTGACCTCCAAACGGA
*
35380 CACCTCCACATGTGAC
1 CACCTCCACACGTGAC
35396 ATCGCGCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.11
26 15 0.43
27 16 0.46
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.15
Consensus pattern (27 bp):
CACCTCCACACGTGACCTCCAAACGGA
Found at i:36106 original size:23 final size:23
Alignment explanation
Indices: 36069--36154 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
36059 CACAATTGTT
*
36069 TGGCGCCCGACCACTTCCAAACC
1 TGGCGCTCGACCACTTCCAAACC
*
36092 TGGCGCTCGATCACTTCCAAACC
1 TGGCGCTCGACCACTTCCAAACC
*
36115 TGGCGAC-CGACTACTTCCATAACGC
1 TGGCG-CTCGACCACTTCCA-AAC-C
36140 -GGCGCTCGACCACTT
1 TGGCGCTCGACCACTT
36155 GTGACCACAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 37 0.69
24 16 0.30
25 1 0.02
ACGTcount: A:0.21, C:0.41, G:0.20, T:0.19
Consensus pattern (23 bp):
TGGCGCTCGACCACTTCCAAACC
Found at i:36297 original size:26 final size:28
Alignment explanation
Indices: 36240--36303 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
36230 AGCTGGCATC
* *
36240 CCACACGTGACCTCCAAACGTACGACCT
1 CCACATGTGACCTCCAAACGGACGACCT
*
36268 -CACATGTGATCTCC-AACGGAC-ACCT
1 CCACATGTGACCTCCAAACGGACGACCT
36293 CCACATGTGAC
1 CCACATGTGAC
36304 ATCGCGCGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 4 0.13
26 15 0.48
27 12 0.39
ACGTcount: A:0.28, C:0.39, G:0.16, T:0.17
Consensus pattern (28 bp):
CCACATGTGACCTCCAAACGGACGACCT
Done.