Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013705.1 Corchorus capsularis cultivar CVL-1 contig13726, 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: 12541
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:1545 original size:321 final size:316
Alignment explanation
Indices: 1019--1922 Score: 1072
Period size: 318 Copynumber: 2.8 Consensus size: 316
1009 GTGTTCTAGC
* * * *
1019 CCCGTCTCAATTTTGCATGATTTTTGGCGCAGTGAGTCCTTGAAATATCTATTTTCATCGAACCA
1 CCCGACTCAATTTTGCATGATTTTTGGCGCAAT-ACTCCTTGAAATATCTATATTCATCGAACCA
* * * *
1084 AATCTCAGCCATATTGGATATAAGGATTT-TTTTTCCGAGCATCTCAATCTTATTTCGATTTAAT
65 AATCTCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * *
1148 TAGAAATTAATTCGAAAAAAATG-GAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTT
129 TAGAAATTAATTCGAAAAAAATGAGAAAATGATATTAGAAGCGTGAAAAACTCGTCAATCTTTTT
* *
1212 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGATAAAACTTTTCAGGTTA
194 GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAG--AAAAC-TTTCAGGTCA
* * *
1277 GTTTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTTGCCTAAAAACGCGTT-TGGAGT
256 GTTTTTAGCCAAAATCGTGTACTAACCATCACGG-ATTTTGACTAAAAACGCCTTCTGGAGT
***
1338 CCCGACTCAATTTTGCATGATTTTTGGCGCAAATACTCCTTGCTTTATCTATATTCATCGAACCA
1 CCCGACTCAATTTTGCATGATTTTTGGCGC-AATACTCCTTGAAATATCTATATTCATCGAACCA
* * * *
1403 AATGTCAGCCACATTAGATATATGGATTTGTTATTACGAGCATCTGAATCTTGTTTAGATTTAAT
65 AATCTCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * *
1468 TAGAAATTAATTCGGAAAAAATGAAAAAATGATATTAGAAGCGTGAAAAACTCGTTAATCTTTTT
129 TAGAAATTAATTCGAAAAAAATGAGAAAATGATATTAGAAGCGTGAAAAACTCGTCAATCTTTTT
* *
1533 GGCGTTGAATTATATGTTTTTTATGAGTATTGTGGAAAAAAATTGAGAAAACTTTCAGGTCAGTT
194 GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAACTTTCAGGTCAGTT
* * * *
1598 TTTAGCCGAAATCGTGTACTAACTATCACTGATTTTGACTAAAAACGCCTTCTGGGGT
259 TTTAGCCAAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCCTTCTGGAGT
* ** * * * * * ** *
1656 CACGACTCTGTTTTACATGGTTTTTGGCACTGAGACTCCTTGAAATATCT-TCATT-AGTTTAAT
1 CCCGACTCAATTTTGCATGATTTTTGGCGC-AATACTCCTTGAAATATCTAT-ATTCA-TCGAAC
* * **
1719 CAAATCT-AGGCCACATTGAATTTAAGGATTTGTTTTTACGTGCATAAGAATCTTGTTTCGATTT
63 CAAATCTCA-GCCACATTG-ATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * *
1783 AATTAGAAATTAATTCAGAAAAAAAT-ATGAAAATGATATTAAAAGCGTG-AAAAGTCCTCCAAT
126 AATTAGAAATTAATTC-GAAAAAAATGA-GAAAATGATATTAGAAGCGTGAAAAACTCGT-CAAT
* * *
1846 CTTTTTGGCGTTGAATTATATATATTTTTATGAGTGTT-TTGCCAAAAATTGAGGAAAAATCTTT
188 CTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTGTGGCAAAAAATTGA-G-AAAA-CTTT
*
1910 CGGGTCA-TTTTTA
249 CAGGTCAGTTTTTA
1923 CCATCATGGT
Statistics
Matches: 502, Mismatches: 68, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
317 21 0.04
318 165 0.33
319 148 0.29
320 68 0.14
321 90 0.18
322 10 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (316 bp):
CCCGACTCAATTTTGCATGATTTTTGGCGCAATACTCCTTGAAATATCTATATTCATCGAACCAA
ATCTCAGCCACATTGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
GAAATTAATTCGAAAAAAATGAGAAAATGATATTAGAAGCGTGAAAAACTCGTCAATCTTTTTGG
CGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAACTTTCAGGTCAGTTTT
TAGCCAAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCCTTCTGGAGT
Found at i:5971 original size:15 final size:15
Alignment explanation
Indices: 5951--5980 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5941 ATCAGGCTGC
*
5951 CACGATACACGATAT
1 CACGATACACAATAT
5966 CACGATACACAATAT
1 CACGATACACAATAT
5981 TTCAACCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Done.