Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007587.1 Corchorus capsularis cultivar CVL-1 contig07608, 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: 24553
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:1334 original size:21 final size:21
Alignment explanation
Indices: 1309--1350 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1299 ATCCTTAAAT
1309 CCCCAACACCATAGTTTTGTC
1 CCCCAACACCATAGTTTTGTC
1330 CCCCAACACCATAGTTTTGTC
1 CCCCAACACCATAGTTTTGTC
1351 TTGTACAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.10, T:0.29
Consensus pattern (21 bp):
CCCCAACACCATAGTTTTGTC
Found at i:14366 original size:12 final size:12
Alignment explanation
Indices: 14349--14376 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14339 CAATGGAGGT
14349 CGCAACCGCATC
1 CGCAACCGCATC
14361 CGCAACCGCATC
1 CGCAACCGCATC
14373 CGCA
1 CGCA
14377 TCAAGGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.50, G:0.18, T:0.07
Consensus pattern (12 bp):
CGCAACCGCATC
Found at i:22731 original size:336 final size:329
Alignment explanation
Indices: 22013--23021 Score: 959
Period size: 336 Copynumber: 3.0 Consensus size: 329
22003 AAACTTTACA
** ** *
22013 TCATCTAACCAAATCTCAGTAACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAAACTTGT
1 TCATCTAATAAAATCTCAGCCACATT-GATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
22078 TTTAATTTAATTAGAAATAAATTTAGAAAAAATAAGAAATATGATATTAAAAGTGCGAAAAGCCC
65 TTTGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAA-ACGATATTAAAAGCGTGAAAAGCCC
** ** * *
22143 TCTGATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCTAAAAATTGAGAAGAAAT
129 TCAAATCTTTTT-GAATTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAAAT
* * *
22208 CTTTCGTGTCAATTTTTACAAAATTTTATCCGAAATCGTGTACTAACTAACCATCACGGTTTTTG
193 CTTTCGAGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACT-A--ATCACGGTTTTTG
* * * *
22273 ACTAAACATACGTTCAAGGGACCCAACTCAATTTTGCATGATTTTTGTCTCCGAGACCACTTGAA
255 ACTAAAAATACGTTCAAGGGACCCAACTCAATTTTGCATGATTTTTGGCGCCAAGACCACTTGAA
22338 ATATCTATAT
320 ATATCTATAT
* *
22348 TCATCTAATCAAATCTCAGCCACATTAGATTTAAAAATTTCTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATAAAATCTCAGCCACATT-GATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
22413 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAACCATAATAAAAGCGTGAAAAGTCCT
65 TTTGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAACGATATTAAAAGCGTGAAAAGCCCT
* * *
22478 CAAATCTTTTTGAAATTAAATTATATATATTTTATAAGTATTTTATCCAAAAATTGAGGAAAAAA
130 CAAATCTTTTTG-AATTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGA-G-AAAAA
** * *
22543 AGT-TTTCGAGTCTTTTTTTTTTTGC-AAATTTTAGCCAAAATCGTGTACTAACT-ATCGCGGTT
191 A-TCTTTCGAGTC----AATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACTAATCACGGTT
** * * *
22605 TTTGACTAAAAATGTGTTTC-A-GGACCCCATCTCAGTTTTGCATGATTTTTGGCGCCAAGAATC
251 TTTGACTAAAAATACG-TTCAAGGGA-CCCAACTCAATTTTGCATGATTTTTGGCGCCAAG-ACC
*
22668 -CTTGAAATATCTGTAT
313 ACTTGAAATATCTATAT
* **
22684 TCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAG-ATTCTGAATCTTG
1 TCATCTAATAAAATCTCAGCCACATTG-ATTTAAAAATTTGTTTTTACGAGCA-TCTGAATCTTG
* * * *
22748 TTTTGATATAAATAGAAATTAATTCAGAAAAAAATACGAAAAACGATATTAAAATCGTGAAAAGC
64 TTTTGATTTAATTAGAAATTAATTCAG-AAAAAATAAG-AAAACGATATTAAAAGCGTGAAAAGC
* * * * * * * *
22813 CCTTCAATTTTTTTTGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAGAAATTGAGGAAA
127 CC-TCAAATCTTTTTGAATTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
* ** ** * *
22878 TATCTTTC-AGGTCAATTTTTGTAAAA--TTAGCTGAAATCGTGTAATAA-TCATCACGGTTTTT
190 AATCTTTCGA-GTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACTAATCACGG-TTTT
** * *** * * * *
22939 TG-CTAAAAACGCGTTC-CGGTG-CCCGGTTCAGTTTTGCATGATTTTCGGTGCCGAGACTC-CT
253 TGACTAAAAATACGTTCAAGG-GACCCAACTCAATTTTGCATGATTTTTGGCGCCAAGAC-CACT
*
23000 TGAAATACCTATAT
316 TGAAATATCTATAT
23014 TCATCTAA
1 TCATCTAA
23022 CCAAATCCCA
Statistics
Matches: 561, Mismatches: 87, Indels: 57
0.80 0.12 0.08
Matches are distributed among these distances:
329 1 0.00
330 55 0.10
331 34 0.06
332 13 0.02
333 4 0.01
334 41 0.07
335 125 0.22
336 157 0.28
337 28 0.05
338 59 0.11
339 12 0.02
340 26 0.05
341 6 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (329 bp):
TCATCTAATAAAATCTCAGCCACATTGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTT
TTGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAACGATATTAAAAGCGTGAAAAGCCCTC
AAATCTTTTTGAATTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAAATCTT
TCGAGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACTAATCACGGTTTTTGACTAAA
AATACGTTCAAGGGACCCAACTCAATTTTGCATGATTTTTGGCGCCAAGACCACTTGAAATATCT
ATAT
Done.