Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023514.1 Corchorus olitorius cultivar O-4 contig23547, 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: 14821
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:39 original size:22 final size:22
Alignment explanation
Indices: 14--60 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4 CATAGCGAGG
* *
14 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
36 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
58 TTA
1 TTA
61 CTAATAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:195 original size:22 final size:22
Alignment explanation
Indices: 144--223 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
134 CTCAGTGTTG
*
144 GTTATCAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATAGGGAA
* *
166 GTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGGGAA
* * *
188 GTCT-TCAAAATTTCTTACGGAG
1 GT-TATCAAAATTTCATAGGGAA
*
210 GTTAACAAAATTTC
1 GTTATCAAAATTTC
224 TTACGGAGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.96
23 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAA
Found at i:242 original size:21 final size:22
Alignment explanation
Indices: 193--243 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
183 GTGAGGTCTT
193 CAAAATTTCTTACGGAGGTTAA
1 CAAAATTTCTTACGGAGGTTAA
215 CAAAATTTCTTACGGAGGTTAA
1 CAAAATTTCTTACGGAGGTTAA
237 -AAAATTT
1 CAAAATTT
244 TATAAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
CAAAATTTCTTACGGAGGTTAA
Found at i:301 original size:22 final size:22
Alignment explanation
Indices: 276--328 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
266 TATAGTATCG
*
276 TTATTAAAATTTCATAAGAAGA
1 TTATCAAAATTTCATAAGAAGA
*
298 TTATCAAAATTTCATAAGGAGA
1 TTATCAAAATTTCATAAGAAGA
*
320 TCATCAAAA
1 TTATCAAAA
329 ATAGTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGAAGA
Found at i:363 original size:22 final size:22
Alignment explanation
Indices: 338--380 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
328 AATAGTGTAA
338 TTATCATAATTTAATAAGAATG
1 TTATCATAATTTAATAAGAATG
* *
360 TTATCATAATTTCATATGAAT
1 TTATCATAATTTAATAAGAAT
381 ATTTCATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (22 bp):
TTATCATAATTTAATAAGAATG
Found at i:6175 original size:105 final size:106
Alignment explanation
Indices: 5995--6256 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 106
5985 AATGTTTCTA
* * **
5995 ACCCTTAAGATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTGTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTGTATATTTTA
*
6058 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
6098 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTGTATATTTTA
*
6163 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* *
6205 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGTTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
6257 AGGCTAAACT
Statistics
Matches: 145, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 26 0.18
104 15 0.10
105 37 0.26
107 67 0.46
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTGTATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:14570 original size:29 final size:28
Alignment explanation
Indices: 14526--14581 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
14516 TTCTTCAAAC
*
14526 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
14554 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
14582 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.