Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014285.1 Corchorus capsularis cultivar CVL-1 contig14306, 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: 21273
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1983 original size:28 final size:28
Alignment explanation
Indices: 1941--2015 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
1931 AACGCATGCT
*
1941 GTCTGATATACCAGAGGGAAGATTTTCC
1 GTCTGATATATCAGAGGGAAGATTTTCC
1969 GTCTGATATATCAGAGGGAAGATTTTCC
1 GTCTGATATATCAGAGGGAAGATTTTCC
* ***
1997 ATCTCCCATATCAGAGGGA
1 GTCTGATATATCAGAGGGA
2016 GACACCCTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (28 bp):
GTCTGATATATCAGAGGGAAGATTTTCC
Found at i:6097 original size:21 final size:21
Alignment explanation
Indices: 6062--6114 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
6052 ACAGCAGCTG
* *
6062 ATGGAGTCGACTGCTCGAA-TA
1 ATGGAGTCAAATGCTC-AACTA
6083 ATGGAGTCAAATGCTCAACTTA
1 ATGGAGTCAAATGCTCAAC-TA
6105 A-GGAGTCAAA
1 ATGGAGTCAAA
6115 CAACTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.82
22 3 0.11
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
ATGGAGTCAAATGCTCAACTA
Found at i:7352 original size:137 final size:137
Alignment explanation
Indices: 7190--7458 Score: 538
Period size: 137 Copynumber: 2.0 Consensus size: 137
7180 GGGGGGGCCA
7190 TTTTTTATACCTCAATTTACAATTGAGGATAAATTGATCTTTGCATAAAATATATTGAGATGTGT
1 TTTTTTATACCTCAATTTACAATTGAGGATAAATTGATCTTTGCATAAAATATATTGAGATGTGT
7255 GGTCAAGATTTAATCAAAAATCCTGAAGAAACTTAGTTTCTGCACCACCCTAGTTCTGATAAAAT
66 GGTCAAGATTTAATCAAAAATCCTGAAGAAACTTAGTTTCTGCACCACCCTAGTTCTGATAAAAT
7320 CAAGATT
131 CAAGATT
7327 TTTTTTATACCTCAATTTACAATTGAGGATAAATTGATCTTTGCATAAAATATATTGAGATGTGT
1 TTTTTTATACCTCAATTTACAATTGAGGATAAATTGATCTTTGCATAAAATATATTGAGATGTGT
7392 GGTCAAGATTTAATCAAAAATCCTGAAGAAACTTAGTTTCTGCACCACCCTAGTTCTGATAAAAT
66 GGTCAAGATTTAATCAAAAATCCTGAAGAAACTTAGTTTCTGCACCACCCTAGTTCTGATAAAAT
7457 CA
131 CA
7459 GGAAAATCTT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (137 bp):
TTTTTTATACCTCAATTTACAATTGAGGATAAATTGATCTTTGCATAAAATATATTGAGATGTGT
GGTCAAGATTTAATCAAAAATCCTGAAGAAACTTAGTTTCTGCACCACCCTAGTTCTGATAAAAT
CAAGATT
Found at i:8438 original size:156 final size:155
Alignment explanation
Indices: 8019--8430 Score: 485
Period size: 156 Copynumber: 2.6 Consensus size: 155
8009 TATAGATCAT
* * *
8019 CTTGGCTAAGTTTCATCTCAAACGGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGGA
1 CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGGA
* * * * * *
8084 CAGTTTGGGGTGTGAAACCAACTTCACTATGAAAGGGAGTTCGTTTTTACTTAGAAATTTTCCAT
66 CAGTTTGGGGAGAGAAACCAAGTTCACCATG-AAGGGAGCTCGGTTTTACTTAGAAATTTTCCAT
* * *
8149 AGTTTTTTTGGAGATAATCTAAGCCTA
130 AGTTCTTGTGGAAATAATCTAAGCC-A
* * * ** * *
8176 CTGGTGTAAA--TTCAGCTTTAT-TGTACTTAAGATGAAAAACTTATACATGTTTTTCATTTAAG
1 CTTG-GCAAAGTTTCATCTCAATCAG-ACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAG
* * * * *
8238 GACAGTTTGGGAAGAAAAACCAAGTTCACCATCAAAGGGAGCTCGGTTTTACTTATAATTTTTTC
64 GACAGTTTGGGGAGAGAAACCAAGTTCACCAT-GAAGGGAGCTCGGTTTTACTTAGAA-ATTTTC
8303 CATAG-TCTTGTGGAAATAATCTAAGTCC-
127 CATAGTTCTTGTGGAAATAATCTAAG-CCA
*
8331 CTTGGCAAAGTTTCATCTCAATCAGACTT-AGAAGGAAAAACTTATGCATGTTTTTCATTTAAGG
1 CTTGGCAAAGTTTCATCTCAATCAGACTTAAG-ATGAAAAACTTATGCATGTTTTTCATTTAAGG
8395 ACAGTTTGGGGAGAGAAACCAAGTTCACCATGAAGG
65 ACAGTTTGGGGAGAGAAACCAAGTTCACCATGAAGG
8431 AGGGCTCGAA
Statistics
Matches: 212, Mismatches: 34, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
154 4 0.02
155 10 0.05
156 179 0.84
157 16 0.08
158 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (155 bp):
CTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGGA
CAGTTTGGGGAGAGAAACCAAGTTCACCATGAAGGGAGCTCGGTTTTACTTAGAAATTTTCCATA
GTTCTTGTGGAAATAATCTAAGCCA
Found at i:19979 original size:34 final size:34
Alignment explanation
Indices: 19936--20004 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
19926 TGTTCTCTTT
19936 GGTTACAGGGAAACTGAGGGTAGTTTCGACTCTA
1 GGTTACAGGGAAACTGAGGGTAGTTTCGACTCTA
19970 GGTTACAGGGAAACTGAGGGTAGTTTCGACTCTA
1 GGTTACAGGGAAACTGAGGGTAGTTTCGACTCTA
20004 G
1 G
20005 ACGGAAGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.26
Consensus pattern (34 bp):
GGTTACAGGGAAACTGAGGGTAGTTTCGACTCTA
Found at i:20926 original size:11 final size:11
Alignment explanation
Indices: 20910--20934 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20900 TCAAGCATCC
20910 ACAACCTCAAT
1 ACAACCTCAAT
20921 ACAACCTCAAT
1 ACAACCTCAAT
20932 ACA
1 ACA
20935 TTCAAGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (11 bp):
ACAACCTCAAT
Done.