Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005018.1 Corchorus capsularis cultivar CVL-1 contig05036, 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: 2174
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:661 original size:308 final size:309
Alignment explanation
Indices: 71--1158 Score: 1072
Period size: 308 Copynumber: 3.4 Consensus size: 309
61 GGAAAAAAAT
71 GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT
1 GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT
136 CTGAGTATTGTGGCAAAGAATCAAGGAAAAATTTTTCGGGTCAGTTTTTTTAACCGAAATCGTAT
66 CTGAGTATTGTGGCAAAGAATCAAGGAAAAA-TTTTCGGGTCAG--TTTTTAACCGAAATCGTAT
* * * *
201 ACGTCACGGGTTTTGGCTAAAAACGCAATTTGGGTCCCGACTCAATTTTGCATGATTTTTGGCGT
128 ACGTCACGAGTTTTGACTAAAAACACAATTGGGGTCCCGACTCAATTTTGCATGATTTTTGGCGT
* *
266 AAAGACTCCTTGAAATATCTATATTCACCTAACCAAATCTCAGTCACATTGGATTTAATGATTTG
193 AAAGACTCCTTGAAATATCTATATTCACCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
* *
331 ATTTTATGAGCATTTGAATCTTGTTTCGATTTAATTAAGATAA-TT-AATT-C-
258 ATTTTATGAGCATCTAAATCTTGTTTCGATTTAATT-AGA-AATTTAAATTCCA
*
381 GGAAAAACGGTATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT
1 GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT
* *
446 CTGAGTATTGTGGCAAAGAATCAAGGAAGAAATTTTCGGGTCAG-TTTTAGCCGAAATCGTGTAC
66 CTGAGTATTGTGGCAAAGAATCAAGGAA-AAATTTTCGGGTCAGTTTTTAACCGAAATCGTATAC
510 GTCACGAGTTTTGACTAAAAACACAATCTGGGGTCCCGACTCAATTTTGCATGATTTTTGGCGTA
130 GTCACGAGTTTTGACTAAAAACACAAT-TGGGGTCCCGACTCAATTTTGCATGATTTTTGGCGTA
* * *
575 TAGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGA
194 AAGACTCCTTGAAATATCTATATTCACCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGA
640 TTTTATGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTAAATTCCGAAAAAA
259 TTTTATGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTAAATTCC------A
* * ** * *
697 TGGAAAAACGATATTTGAAGCGTCAAAAGCCCTTCAATCATTTTTTGCGTTGAATTATATA-TTT
1 -GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATC-TTTTTGGCATTGAATTATATACTTT
** * *
761 TTCCTGAGTATTGTGGTCAAA-AATTGAGGAAAAATTTTTTGGATCAGTTTTTGCAAAATTTTAG
64 TT-CTGAGTATTGTGG-CAAAGAATCAAGGAAAAA-TTTTCGGGTCAGTTTTT-----A----A-
* * * * * * * * *
825 TCGTAATCGTGTACTAACTATCACG-GTTTTTGGCTAAAAACAC-GTTCCTGGGCCCCGGCTTAA
116 CCGAAATC--GTA-T-AC-GTCACGAG-TTTTGACTAAAAACACAATT--GGGGTCCCGACTCAA
* * * * * * * *
888 TTTTGCTTTGATTTTTGATGCCTAGAG-C-CCTTGAAATTTCAATATTCATCTAACCAAATTTAA
173 TTTTGC-ATGATTTTTG--GCGTAAAGACTCCTTGAAATATCTATATTCACCTAACCAAATCTCA
* * * * * * *
951 GCCACGTTGGATTTAGGGATAT-ATTTTTTCGAGCATAC-GAATCTTGTTTTGATTTGATTAGAA
235 GCCACATTGGATTTAAGGATTTGATTTTAT-GAGCAT-CTAAATCTTGTTTCGATTTAATTAGAA
*
1014 A-TT-AATTCGGAAAAAAA
298 ATTTAAATTC-------CA
* * * * *
1031 TGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGTATTAAATTATATATATTT
1 -GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATA-CTTT
* * * ** *
1096 TTTTGAGAATTTTGGCAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTTTTAACCGAAATCGT
64 TTCTGAGTATTGTGGCAAAGAATCAAGG-AAAAATTTTCGGGTCAGTTTTTAACCGAAATCGT
1159 GTACTAACCA
Statistics
Matches: 658, Mismatches: 68, Indels: 92
0.80 0.08 0.11
Matches are distributed among these distances:
306 2 0.00
307 47 0.07
308 133 0.20
309 1 0.00
310 104 0.16
311 3 0.00
317 41 0.06
318 50 0.08
319 8 0.01
322 2 0.00
324 7 0.01
325 1 0.00
329 7 0.01
331 2 0.00
332 2 0.00
333 30 0.05
334 113 0.17
335 97 0.15
336 2 0.00
337 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (309 bp):
GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT
CTGAGTATTGTGGCAAAGAATCAAGGAAAAATTTTCGGGTCAGTTTTTAACCGAAATCGTATACG
TCACGAGTTTTGACTAAAAACACAATTGGGGTCCCGACTCAATTTTGCATGATTTTTGGCGTAAA
GACTCCTTGAAATATCTATATTCACCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGATT
TTATGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTAAATTCCA
Found at i:1991 original size:21 final size:21
Alignment explanation
Indices: 1965--2005 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1955 TAAAATGGGG
**
1965 TTTGCTATTTACCGCCCCCCT
1 TTTGCTAAATACCGCCCCCCT
1986 TTTGCTAAATACCGCCCCCC
1 TTTGCTAAATACCGCCCCCC
2006 CCCCCCCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.44, G:0.10, T:0.32
Consensus pattern (21 bp):
TTTGCTAAATACCGCCCCCCT
Done.