Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020932.1 Corchorus olitorius cultivar O-4 contig20965, 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: 29288
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:3406 original size:90 final size:89
Alignment explanation
Indices: 3299--3476 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 89
3289 ACACATGAAT
* **
3299 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATAGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
3364 AATATTTAAAAATTAAAAAGGACAC
66 AATATTT-AAAATTAAAAAGGACAC
* *
3389 ATGATATATAATTCTTAATTTAATAGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATAGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
3454 AATATTTAAAATTAAAAAGGACA
66 AATATTTAAAATTAAAAAGGACA
3477 TTTTAGATAT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 16 0.19
90 67 0.81
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (89 bp):
ATGATAAATAATCCTTAATTTAATAGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
AATATTTAAAATTAAAAAGGACAC
Found at i:5080 original size:33 final size:33
Alignment explanation
Indices: 5038--5136 Score: 189
Period size: 33 Copynumber: 3.0 Consensus size: 33
5028 TTTATCTTGA
5038 GACCACCATGACAAACCGGGTCATTTGCTTTGC
1 GACCACCATGACAAACCGGGTCATTTGCTTTGC
5071 GACCACCATGACAAACCGGGTCATTTGCTTTGC
1 GACCACCATGACAAACCGGGTCATTTGCTTTGC
*
5104 GACCACCATGACAAACCGGATCATTTGCTTTGC
1 GACCACCATGACAAACCGGGTCATTTGCTTTGC
5137 AAGAAGTTTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (33 bp):
GACCACCATGACAAACCGGGTCATTTGCTTTGC
Found at i:5501 original size:88 final size:88
Alignment explanation
Indices: 5352--5535 Score: 316
Period size: 88 Copynumber: 2.1 Consensus size: 88
5342 ATATGATCAT
*
5352 AATTACAATTTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAGATTAATTTAGA
1 AATTACAATTTAAATAATTAATTGAGAAGATGAAAAACATATTAAGTTACAAAGATTAATTTAGA
5417 ATGTAACGTACATGTAAACATCC
66 ATGTAACGTACATGTAAACATCC
5440 AATTACAATTTAAATAATTAATTGAGAAGATGAAAAACATATTAAGTTACAAA-ATTTAATTTAG
1 AATTACAATTTAAATAATTAATTGAGAAGATGAAAAACATATTAAGTTACAAAGA-TTAATTTAG
* *
5504 AATGTAATGTACATGTGAACATCC
65 AATGTAACGTACATGTAAACATCC
*
5528 AATGACAA
1 AATTACAA
5536 ATAATATAGA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
87 1 0.01
88 90 0.99
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (88 bp):
AATTACAATTTAAATAATTAATTGAGAAGATGAAAAACATATTAAGTTACAAAGATTAATTTAGA
ATGTAACGTACATGTAAACATCC
Found at i:5687 original size:4 final size:4
Alignment explanation
Indices: 5678--5736 Score: 109
Period size: 4 Copynumber: 14.8 Consensus size: 4
5668 GGAGCCAAGA
*
5678 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5726 ATAC ATAC ATA
1 ATAC ATAC ATA
5737 TATATATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:5739 original size:2 final size:2
Alignment explanation
Indices: 5722--5757 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5712 ACATACATAC
* *
5722 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5758 TCCTTTCTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6522 original size:42 final size:43
Alignment explanation
Indices: 6471--6564 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
6461 AGTGCATTAC
* *
6471 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
6512 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
6557 CTAATATT
1 CTAATATT
6565 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:7642 original size:171 final size:171
Alignment explanation
Indices: 7350--7697 Score: 633
Period size: 171 Copynumber: 2.0 Consensus size: 171
7340 CTTAATCATA
* * * *
7350 AATATAAAAATAGTAAATTACAAAAAGGGGCAGCATGAAAAGTAAGGGTGGAAATTCATTGAGGG
1 AATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGG
*
7415 CCTTTTTAGTCACCCGAAAAGTGTGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATC
66 CCTTTTTAGTCACCCGAAAAATGTGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATC
7480 CTCAATTTGGCCTTTAAGTAATTTCCATTGTCACTAAAAAT
131 CTCAATTTGGCCTTTAAGTAATTTCCATTGTCACTAAAAAT
*
7521 AATATAGAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGG
1 AATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGG
*
7586 CCTTTTTAGTCACCCGAAAAATGTGAAAAGACCAAAAAAAGGCAAAAGGAGGCACCACATTAATC
66 CCTTTTTAGTCACCCGAAAAATGTGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATC
7651 CTCAATTTGGCCTTTAAGTAATTTCCATTGTCACTAAAAAT
131 CTCAATTTGGCCTTTAAGTAATTTCCATTGTCACTAAAAAT
7692 AATATA
1 AATATA
7698 TAGTATATAT
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (171 bp):
AATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGG
CCTTTTTAGTCACCCGAAAAATGTGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATC
CTCAATTTGGCCTTTAAGTAATTTCCATTGTCACTAAAAAT
Found at i:24379 original size:19 final size:20
Alignment explanation
Indices: 24342--24381 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
24332 AATTGCAGCA
24342 AAAAAAGTCTTCCGTTTTTG
1 AAAAAAGTCTTCCGTTTTTG
24362 AAAAAAGTCTTCCGTTTTTG
1 AAAAAAGTCTTCCGTTTTTG
24382 TAGGTCACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
AAAAAAGTCTTCCGTTTTTG
Done.