Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004984.1 Corchorus capsularis cultivar CVL-1 contig05002, 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: 6378
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:164 original size:28 final size:26
Alignment explanation
Indices: 93--149 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
83 TGGATTTCTC
*
93 TCAACAAAATTTCAAGTTATGGCGAAT
1 TCAAAAAAATTTCAAGTTATGGC-AAT
120 TCAAAAAAATTTTCAAGTTATGGC-AT
1 TCAAAAAAA-TTTCAAGTTATGGCAAT
146 TCAA
1 TCAA
150 GAAGGAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 14 0.50
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (26 bp):
TCAAAAAAATTTCAAGTTATGGCAAT
Found at i:2741 original size:166 final size:165
Alignment explanation
Indices: 2261--2741 Score: 587
Period size: 162 Copynumber: 2.9 Consensus size: 165
2251 TGAGTCATTT
2261 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCC-CAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAA-TTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * *
2325 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTATAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTTG
* * *
2390 ATGGGGATCTTTTA-TTAATTCTACTACTCTATTAAA
130 GTGGGGATCTTTTAGTT-ATTCCACTACCCTATTAAA
* * * * * * *
2426 GTCCATTGAGAAATGACCAAAAA--GA-TTATTCAATCCCTTAAAGAATCAAAAGCTAAGACATT
1 GTCAATTGAGAAATGACCAAAAATTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* * * * ** * *
2488 TAAGTAATCTACCAAGTAGGAAAAGATGAAAAAAA-AAGTTCTCTAACTCCAAAAGCAAGCCTTG
66 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCC-TCATCAATCCTTG
* * *
2552 GTAGGGATTTTTTAGTAATTCCACTACCCTATTAAA
130 GTGGGGATCTTTTAGTTATTCCACTACCCTATTAAA
*
2588 GTCAATTGAGAAATGACCAAAAATTCTAGTTATTTAATCCCCTCAAGAATTAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAATT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * **
2653 TTAATTAATCTGCCAAGTGGGAAAAAACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGGG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTTG
2718 GTGGGGATCTTTTAGTTATTCCAC
130 GTGGGGATCTTTTAGTTATTCCAC
2742 ATGTTTATTC
Statistics
Matches: 257, Mismatches: 51, Indels: 15
0.80 0.16 0.05
Matches are distributed among these distances:
161 22 0.09
162 111 0.43
163 1 0.00
165 23 0.09
166 88 0.34
167 12 0.05
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAATTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTTGG
TGGGGATCTTTTAGTTATTCCACTACCCTATTAAA
Found at i:6100 original size:104 final size:106
Alignment explanation
Indices: 5960--6223 Score: 399
Period size: 107 Copynumber: 2.5 Consensus size: 106
5950 AATTTTTCTA
**
5960 ACCTTTAAAATAAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTT
1 ACCTTTAAAATAAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTT
*
6023 ATTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
65 ATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* * *
6064 ACCTTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCTTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
6129 TTTCTAAAATCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* *
6171 ACCCTTAAAATAAAAATAAAATTTGAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCTTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
6224 GGCTAAACTT
Statistics
Matches: 145, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 12 0.08
104 31 0.21
105 35 0.24
107 67 0.46
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (106 bp):
ACCTTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Done.