Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005538.1 Corchorus capsularis cultivar CVL-1 contig05556, 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: 21459
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:12598 original size:1 final size:1
Alignment explanation
Indices: 12592--12616 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12582 AAGAATCTGC
12592 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12617 GCAAGAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16129 original size:25 final size:25
Alignment explanation
Indices: 16084--16132 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16074 TTTTGAACTC
*
16084 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
16109 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
16133 ATATCTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:16132 original size:21 final size:21
Alignment explanation
Indices: 16084--16134 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
16074 TTTTGAACTC
16084 ATTATT-TATTATTTAAAATAT
1 ATTATTAT-TTATTTAAAATAT
16105 ATTTATTATTTATTTAATAATAT
1 A-TTATTATTTATTTAA-AATAT
16128 A-TATTAT
1 ATTATTAT
16135 ATCTTTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 7 0.26
22 13 0.48
23 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTATTTATTTAAAATAT
Found at i:21032 original size:335 final size:333
Alignment explanation
Indices: 20024--21381 Score: 2180
Period size: 335 Copynumber: 4.1 Consensus size: 333
20014 CGTGCCGCCC
* * * * *
20024 CAAAATTTTACACGAAATCGTGTGCTAACCATCACAGTTTTTGATCAAAAATGCGTTCCGGAGCC
1 CAAAATTTTACTCGAAATCGTGTCCTAACCATCACAATTTTGGACCAAAAATGCGTTCCGGAGCC
*
20089 CCGGCTCTGTTTTGCATGA-TTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGACAAA
66 CCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
20153 ATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTT
131 ATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTT
*
20218 AGAAATTAATTCGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTTG
196 AGAAATTAATTTGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTTG
20283 GCGTTGACTTG--TATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATC
261 GCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATC
*
20346 AATTTTAG
326 AATTTTGG
* * * *
20354 CAAAATTTTA-TCCGAAATCGTGTGCTAACCATCACAGTTTTTGACCAAAAATGCGTTCCAGAGC
1 CAAAATTTTACT-CGAAATCGTGTCCTAACCATCACAATTTTGGACCAAAAATGCGTTCCGGAGC
* * *
20418 CCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATA-C--T-TCCATCAT-ATA
65 CCCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCAT-TTGACA
*
20478 AAATCTTATCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTAT
129 AAATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTAT
20543 TTAGAAATTAATTTGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTT
194 TTAGAAATTAATTTGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTT
*
20608 TGGCGTTGACTTGTATAT-TTTTTTATGAGTATTGTGGCAAAAAATTGAGGAGAAATGTTTCGGA
259 TGGCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGA
20672 TCAATTTTGG
324 TCAATTTTGG
* *
20682 CAAAATTTTACTCGAAATCATGTCCTAACCATCATAATTTTGGACCAAAAATGCGTTCCGGAGCC
1 CAAAATTTTACTCGAAATCGTGTCCTAACCATCACAATTTTGGACCAAAAATGCGTTCCGGAGCC
*
20747 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
66 CCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
*
20812 ATCTTATCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTTGATTTATT
131 ATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAG-TTTTGATTTATT
20877 TAGAAATTAATTTGGAAAAATATGAAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTT
195 TAGAAATTAATTTGGAAAAATATG-AAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTT
20942 TGGCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGA
259 TGGCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGA
21007 TCAATTTTGG
324 TCAATTTTGG
* *
21017 CAAAATTTTACTCGAAATCATGTCCTAACCATCATAATTTTGGACCAAAAATGCGTTCCGGAGCC
1 CAAAATTTTACTCGAAATCGTGTCCTAACCATCACAATTTTGGACCAAAAATGCGTTCCGGAGCC
*
21082 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
66 CCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
* * *
21147 ATCTTACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATT
131 ATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTT
* * * * * * * ** * *
21212 AAAAATTAATTCGGGAAAAA-AAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTT
196 AGAAATTAATT-TGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTT
* * * * *
21276 GGCGTTGAGTTATATATATTTTTTAGGATTATTGTGGCCAAAAATTGAGGAGAAATGTTTCAGAT
260 GGCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGAT
21341 CAATTTTGG
325 CAATTTTGG
* * *
21350 TAAAATTTTACCCGAAATCGTGTACTAACCAT
1 CAAAATTTTACTCGAAATCGTGTCCTAACCAT
21382 AGTTATTAAA
Statistics
Matches: 968, Mismatches: 45, Indels: 27
0.93 0.04 0.03
Matches are distributed among these distances:
327 148 0.15
328 157 0.16
329 5 0.01
330 81 0.08
331 27 0.03
332 61 0.06
333 166 0.17
334 81 0.08
335 242 0.25
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (333 bp):
CAAAATTTTACTCGAAATCGTGTCCTAACCATCACAATTTTGGACCAAAAATGCGTTCCGGAGCC
CCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATCCATTTGACAAA
ATCTTACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTT
AGAAATTAATTTGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTTG
GCGTTGACTTGTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATC
AATTTTGG
Done.