Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005029.1 Corchorus capsularis cultivar CVL-1 contig05047, 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: 2378
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Found at i:616 original size:88 final size:87
Alignment explanation
Indices: 334--649 Score: 426
Period size: 88 Copynumber: 3.7 Consensus size: 87
324 ATTATCATTA
* * * * * *
334 TTAAATATATATCCTAAATCTCCCACAATCTGACAAGATTTAAAGAAATATTCTCATTACTATTC
1 TTAAA-ATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCATTATTATTC
* * * *
399 AATCTTTATTATTTATTTA-TTTC
64 TATTTTTATAATTTGTTTATTTTC
* *
422 TTAAAATATCTCCTAAATCTCCCACAGTTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
487 TTTTTATAATTTG----TTTTC
66 TTTTTATAATTTGTTTATTTTC
* * *
505 TTAAAATATCTCCTAAACCTTCCACAATTTCGCAAGATTTAGAAAATATTCTCATTATTAAATCT
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATT-ATTCT
570 ATTTTTATAATTTGTTTATTTTC
65 ATTTTTATAATTTGTTTATTTTC
*
593 TTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTA
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTA
650 ATTGTTTTGT
Statistics
Matches: 206, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
83 59 0.29
84 18 0.09
86 30 0.15
87 33 0.16
88 66 0.32
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (87 bp):
TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
TTTTTATAATTTGTTTATTTTC
Found at i:629 original size:171 final size:171
Alignment explanation
Indices: 334--649 Score: 458
Period size: 171 Copynumber: 1.8 Consensus size: 171
324 ATTATCATTA
* *
334 TTAAATATATATCCTAAATCTCCCACAATCTGACAAGATTTAAAGAAATATTCTCATTACTATTC
1 TTAAATATATATCCTAAACCTCCCACAATCTGACAAGATTTAAAGAAATATTCTCATTACTAATC
* * *
399 AATCTTTATTATTTATTTATTTCTTAAAATATCTCCTAAATCTCCCACAGTTTGGCAAGATTTAG
66 AATCTTTATAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAG
464 AAAATATTCTCATTATTATTCTATTTTTATAATTTGTTTTC
131 AAAATATTCTCATTATTATTCTATTTTTATAATTTGTTTTC
* * * * *
505 TTAAA-ATATCTCCTAAACCTTCCACAATTTCG-CAAGATTTAGA-AAATATTCTCATTATTAAA
1 TTAAATATATATCCTAAACCTCCCACAATCT-GACAAGATTTAAAGAAATATTCTCATTACT-AA
* * * *
567 TCTATTTTTATAATTTGTTTATTTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATT
64 TCAATCTTTATAATTTATTTA-TTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATT
632 TAGAAAATATTCTCATTA
128 TAGAAAATATTCTCATTA
650 ATTGTTTTGT
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
169 15 0.12
170 49 0.38
171 64 0.50
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (171 bp):
TTAAATATATATCCTAAACCTCCCACAATCTGACAAGATTTAAAGAAATATTCTCATTACTAATC
AATCTTTATAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAG
AAAATATTCTCATTATTATTCTATTTTTATAATTTGTTTTC
Found at i:1389 original size:20 final size:20
Alignment explanation
Indices: 1350--1386 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
1340 AATTGGTTGA
1350 ATACAAAACTCTCTCAAATT
1 ATACAAAACTCTCTCAAATT
1370 ATAC-AAACTCTCTCAAA
1 ATACAAAACTCTCTCAAA
1387 ATTTAGTGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
ATACAAAACTCTCTCAAATT
Found at i:1961 original size:35 final size:35
Alignment explanation
Indices: 1916--2378 Score: 654
Period size: 35 Copynumber: 13.3 Consensus size: 35
1906 AACTCCTCTG
* *
1916 GATCAACTCTGATC-TTCGGAAACTTCTTG-AAATGA
1 GATCAACTCTGATCGTT-GGAAACTAC-TGAAAATGC
* * * *
1951 GATCACCTCTGATTGTTGGAAACTACTAAAAATGT
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
1986 GATCAACTCTGACCGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
2021 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
2056 GATCAACTCTGATCATTGGAAACTACTGAAAAT--
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
2089 G--CAACTCTGATCGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
2122 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
2157 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
* * *
2192 GATCAACTCTGATCTTTGGAAACTTCTGAAAATGT
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
2227 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
2262 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
* *
2297 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
* * * *
2332 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AAATGA
1 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGC
2367 GATCAACTCTGA
1 GATCAACTCTGA
Statistics
Matches: 389, Mismatches: 31, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
31 29 0.07
33 2 0.01
34 3 0.01
35 351 0.90
36 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
Done.