Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015545.1 Corchorus olitorius cultivar O-4 contig15578, 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: 12985
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1623 original size:451 final size:455
Alignment explanation
Indices: 777--1687 Score: 1685
Period size: 451 Copynumber: 2.0 Consensus size: 455
767 ATTATTATAA
777 ATAAAGGTGAAATTAATACCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTA
1 ATAAAGGTGAAATTAATACCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTA
842 GAAAAGTTAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATACTCCAATTAACCTG
66 GAAAAGTTAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATACTCCAATTAACCTG
*
907 TTCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTGAAGAA
131 TTCCATCTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTGAAGAA
972 TTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATG
196 TTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATG
1037 TTTCTGTTTTTTGTTGGAATAATAAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
261 TTTCTGTTTTTTGTTGGAATAATAAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
1102 ACTTCTTAGCTTCTGCGTTTTGATAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAAGGCGA
326 ACTTCTTAGCTTCTGCGTTTTGATAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAAGGCGA
* *
1167 AAAGTTTAAAAACTGACTCTTGAGAGGTA-TCTT-AGTTAAAAAGCTGTCATCTGATATCTTTAC
391 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTAATATCTTTAC
**
1230 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCT-
1 ATAAAGGTGAAATTAATACCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTA
1294 G-AAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAAT-CTCCAATTAACCT
66 GAAAAGTT-AAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATACTCCAATTAACCT
1357 GTTCCATCTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGG-TAATTTTTTTTTTGAAGA
130 GTTCCATCTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTGAAGA
1421 A-TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
195 ATTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
1485 GTTTCTGTTTTTTGTTGGAATAATAAATTTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGA
260 GTTTCTGTTTTTTGTTGGAATAATAAA-TTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGA
1550 CAACTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATG-AGG
324 CAACTTCTTAGCTTCTGCGTTTTGAT-AATATATTTAAAGGAGTTTAAAGTTAGAATCATGAAGG
1614 CGAAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTAATATCT
388 CG-AAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTAATATCT
1679 TTAC
452 TTAC
1683 ATAAA
1 ATAAA
1688 TCGTACTTAA
Statistics
Matches: 447, Mismatches: 5, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
449 90 0.20
450 87 0.19
451 128 0.29
452 47 0.11
453 95 0.21
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (455 bp):
ATAAAGGTGAAATTAATACCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTA
GAAAAGTTAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATACTCCAATTAACCTG
TTCCATCTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTGAAGAA
TTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATG
TTTCTGTTTTTTGTTGGAATAATAAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACA
ACTTCTTAGCTTCTGCGTTTTGATAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAAGGCGA
AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTAATATCTTTAC
Found at i:4156 original size:29 final size:29
Alignment explanation
Indices: 4120--4178 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4110 CCTCTGGAAA
4120 TGCAACTTGAATTTTCTTTGATTAAATGT
1 TGCAACTTGAATTTTCTTTGATTAAATGT
4149 TGCAACTTGAATTTTCTTTGATTAAATGT
1 TGCAACTTGAATTTTCTTTGATTAAATGT
4178 T
1 T
4179 CAGATAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (29 bp):
TGCAACTTGAATTTTCTTTGATTAAATGT
Found at i:5187 original size:21 final size:21
Alignment explanation
Indices: 5163--5210 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
5153 CTCCTCCCAT
5163 AAGAGACACTCCGGCTCCAGC
1 AAGAGACACTCCGGCTCCAGC
* *
5184 AAGAGTCGCTCCGGCTCCAGC
1 AAGAGACACTCCGGCTCCAGC
*
5205 TAGAGA
1 AAGAGA
5211 AGCATACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.12
Consensus pattern (21 bp):
AAGAGACACTCCGGCTCCAGC
Found at i:5553 original size:2 final size:2
Alignment explanation
Indices: 5546--5581 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5536 TCTTATACAT
5546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5582 GTCATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.