Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023256.1 Corchorus olitorius cultivar O-4 contig23289, 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: 21295
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4713 original size:28 final size:28
Alignment explanation
Indices: 4642--4713 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
4632 AAGTTCTAAT
* *
4642 TTATATATACTTATAAATTATTCAATTTTA
1 TTATAT-TATTTAT-AATTATTCAATTATA
* * *
4672 TTAT-GTATAATATAATTATTTAATTATA
1 TTATATTAT-TTATAATTATTCAATTATA
4700 TTATATTATTTATA
1 TTATATTATTTATA
4714 TATAATACGG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
28 23 0.70
29 6 0.18
30 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (28 bp):
TTATATTATTTATAATTATTCAATTATA
Found at i:5840 original size:81 final size:81
Alignment explanation
Indices: 5705--5868 Score: 265
Period size: 81 Copynumber: 2.0 Consensus size: 81
5695 CGGCATTGAT
*
5705 CCGGTTGAACCGGTCGGTTTACCGACTTTTTTCATTTTGAAAAATTAAAAAAAAAACAATTGCAA
1 CCGGTTGAACCGGCCGGTTTACCGACTTTTTTCATTTTGAAAAATTAAAAAAAAAACAATTGCAA
5770 ATGGTAAGAATCGAAC
66 ATGGTAAGAATCGAAC
* **** *
5786 CCGGTTGAACCGGCCGGTTTACCGACTTTTTTCATTTTGAAAATTTTTTTAAAAAACAATTGTAA
1 CCGGTTGAACCGGCCGGTTTACCGACTTTTTTCATTTTGAAAAATTAAAAAAAAAACAATTGCAA
5851 ATGGTAAGAATCGAAC
66 ATGGTAAGAATCGAAC
5867 CC
1 CC
5869 AACATGCTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (81 bp):
CCGGTTGAACCGGCCGGTTTACCGACTTTTTTCATTTTGAAAAATTAAAAAAAAAACAATTGCAA
ATGGTAAGAATCGAAC
Found at i:11604 original size:28 final size:28
Alignment explanation
Indices: 11572--11628 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
11562 ATGTTATCTT
11572 ACCCTAGATTTTCTTACTATAGAATGCC
1 ACCCTAGATTTTCTTACTATAGAATGCC
11600 ACCCTAGATTTTCTTACTATAGAATGCC
1 ACCCTAGATTTTCTTACTATAGAATGCC
11628 A
1 A
11629 TATAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (28 bp):
ACCCTAGATTTTCTTACTATAGAATGCC
Found at i:19664 original size:200 final size:194
Alignment explanation
Indices: 19309--19824 Score: 637
Period size: 189 Copynumber: 2.7 Consensus size: 194
19299 TACCTAGCAG
* * * *
19309 AAAAAAAGGCATTGTATTATGTATTTGATTTATTAAC-GA---ATTCATT--CATTGCCATGTAT
1 AAAAAAAAGCATTGTACTATGGATTTGATTTATTAACAAATTCATTCATTGCCATTGCCATGTAT
19368 TTGTCTCCTCAATAAGGAGTAC-AAAATTTTATAAAAAGTAAAAAATTGCACATTAAAATTAAAT
66 TTGTCTCCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCAC------ATTAAAT
* * *
19432 TAAATTTGGTAGCTTGGATACAATTTTATCT-AAGGTTCGGTCTGGACTTGAAATCATTAATTTG
125 TAAATTTGGTAGCTTGGATACAATTTTATCTAAAAGTTCGGTCTGGACTTAAAAGCATTAATTTG
19496 TTAAAA
190 TT-AAA
19502 AAAAAAAAGCATTGTACTATGGATTTGATTTATTCAACAAATTCATTCATTGCCAATTTGCCATG
1 AAAAAAAAGCATTGTACTATGGATTTGATTTATT-AACAAATTCATTCATTGCC-A-TTGCCATG
* *
19567 TATTTGTCACCTCCTCGATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACACTAAAT
63 TATTTGT---CTCCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAAT
* * *
19632 TCAATTTGGTAGCTTGGATATAATTTTATCTAAAAAGTTTGGTCTGGACTTAAAAGCATTAATTT
125 TAAATTTGGTAGCTTGGATACAATTTTATCT-AAAAGTTCGGTCTGGACTTAAAAGCATTAATTT
**
19697 GTTTTA
189 GTTAAA
* * * *
19703 CAAAAAAGGCATTGTACTATGTATTTGATTTATTAACGAATTCATTCATTGCCA-TG--A---AT
1 AAAAAAAAGCATTGTACTATGGATTTGATTTATTAACAAATTCATTCATTGCCATTGCCATGTAT
*
19762 TTGTCTCCTCCATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATTAAA
66 TTGTCTCCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATTAAA
19825 ATTCAATTCA
Statistics
Matches: 287, Mismatches: 21, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
189 56 0.20
192 6 0.02
193 31 0.11
194 3 0.01
195 2 0.01
197 2 0.01
198 7 0.02
199 1 0.00
200 54 0.19
201 33 0.11
202 46 0.16
205 17 0.06
206 29 0.10
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (194 bp):
AAAAAAAAGCATTGTACTATGGATTTGATTTATTAACAAATTCATTCATTGCCATTGCCATGTAT
TTGTCTCCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATTAAATT
TGGTAGCTTGGATACAATTTTATCTAAAAGTTCGGTCTGGACTTAAAAGCATTAATTTGTTAAA
Found at i:19835 original size:200 final size:197
Alignment explanation
Indices: 19309--19851 Score: 668
Period size: 200 Copynumber: 2.8 Consensus size: 197
19299 TACCTAGCAG
* *
19309 AAAAAAAGGCATTGTATTATGTATTTGATTTATTAACGAATTCATTCATTGCCATGTATTTGTCT
1 AAAAAAAGGCATTGTACTATGTATTTGATTTATTAACGAATTCATTCATTGCCATGAATTTGTCT
19374 CCTCAATAAGGAGTAC-AAAATTTTATAAAAAGTAAAAAATTGCACATTAAAATTAAATT-A---
66 CCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATT-AAATTAAATTAATTC
* * * *
19434 AATTTGGTAGCTTGGATACAATTTTATCTAAGGTTCGGTCTGGACTTGAAATCATTAATTTGTTA
130 AATTTGGTAGCTTGGATATAATTTTATCTAAAGTTCGGTCTGGACTTAAAAGCATTAATTTGTTA
19499 AAA
195 AAA
* * *
19502 AAAAAAAAGCATTGTACTATGGATTTGATTTATTCAACAAATTCATTCATTGCCAATTTGCCATG
1 AAAAAAAGGCATTGTACTATGTATTTGATTTATT-AACGAATTCATTCATTGCC-A--TG--A--
* *
19567 TATTTGTCACCTCCTCGATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCAC-----AC
58 -ATTTGT---CTCCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAAT
*
19627 T--A--AATTCAATTTGGTAGCTTGGATATAATTTTATCTAAAAAGTTTGGTCTGGACTTAAAAG
119 TAAATTAATTCAATTTGGTAGCTTGGATATAATTTTATCT--AAAGTTCGGTCTGGACTTAAAAG
**
19688 CATTAATTTGTT-TTA
182 CATTAATTTGTTAAAA
*
19703 CAAAAAAGGCATTGTACTATGTATTTGATTTATTAACGAATTCATTCATTGCCATGAATTTGTCT
1 AAAAAAAGGCATTGTACTATGTATTTGATTTATTAACGAATTCATTCATTGCCATGAATTTGTCT
*
19768 CCTCCATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATTAAAATTCAATT
66 CCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATT-AAATT-AATT
*
19833 CAA-TTGGTTGCTTGGATAT
129 CAATTTGGTAGCTTGGATAT
19852 CTTTTTGAGA
Statistics
Matches: 299, Mismatches: 21, Indels: 54
0.80 0.06 0.14
Matches are distributed among these distances:
189 47 0.16
192 6 0.02
193 31 0.10
194 20 0.07
195 2 0.01
197 6 0.02
198 1 0.00
199 16 0.05
200 55 0.18
201 32 0.11
202 37 0.12
205 17 0.06
206 29 0.10
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (197 bp):
AAAAAAAGGCATTGTACTATGTATTTGATTTATTAACGAATTCATTCATTGCCATGAATTTGTCT
CCTCAATAAGGAGTACAAAAATTTTATAAAAAGTAAAAAATTGCACATTAAATTAAATTAATTCA
ATTTGGTAGCTTGGATATAATTTTATCTAAAGTTCGGTCTGGACTTAAAAGCATTAATTTGTTAA
AA
Found at i:20319 original size:49 final size:49
Alignment explanation
Indices: 20251--20349 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
20241 GACTCCTCAT
20251 TCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTATTTGAAA
1 TCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTATTTGAAA
20300 TCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTATTTGAAA
1 TCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTATTTGAAA
20349 T
1 T
20350 GTATGTTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (49 bp):
TCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTATTTGAAA
Done.