Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021766.1 Corchorus olitorius cultivar O-4 contig21799, 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: 5551
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:1785 original size:27 final size:27
Alignment explanation
Indices: 1729--1896 Score: 160
Period size: 27 Copynumber: 6.3 Consensus size: 27
1719 AGTGAACTTA
* * * **
1729 AAATGACCGAAATG-CCCTTAGTGTAA
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
1755 AAATGACCAAGATGCCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
1782 AAATGACCAAAATGCCCCTGGATATGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* * **
1809 AAATGACCAAAATG-CCCTTAGTGTAA
1 AAATGACCAAAATGCCCCTGAATGTGC
* * *
1835 AAATGACCAAGATGCCCTTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
1862 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
1889 AAATGACC
1 AAATGACC
1897 CCAAAACCCC
Statistics
Matches: 113, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
26 31 0.27
27 82 0.73
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTGC
Found at i:1795 original size:53 final size:53
Alignment explanation
Indices: 1728--1896 Score: 160
Period size: 53 Copynumber: 3.2 Consensus size: 53
1718 AAGTGAACTT
* * *
1728 AAAATGACCGAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCTTAGTGTGAAAATGACCAAAATGCCCCTGAATGTG
* * * * * * * *
1781 TAAATGACCAAAATGCCCCTGGATATGCAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCTTAG-TGTGAAAATGACCAAAATGCCCCTGAATGTG
* * * * *
1834 AAAATGACCAAGATGCCCTTGAATGTGTAAATGACCAAAATGCCCCTGGACGTG
1 AAAATGACCAAAATGCCCTT-AGTGTGAAAATGACCAAAATGCCCCTGAATGTG
*
1888 CAAATGACC
1 AAAATGACC
1897 CCAAAACCCC
Statistics
Matches: 89, Mismatches: 24, Indels: 5
0.75 0.20 0.04
Matches are distributed among these distances:
53 60 0.67
54 29 0.33
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (53 bp):
AAAATGACCAAAATGCCCTTAGTGTGAAAATGACCAAAATGCCCCTGAATGTG
Found at i:1826 original size:80 final size:80
Alignment explanation
Indices: 1729--1896 Score: 300
Period size: 80 Copynumber: 2.1 Consensus size: 80
1719 AGTGAACTTA
*
1729 AAATGACCGAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
1 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
*
1794 TGCCCCTGGATATGC
66 TGCCCCTGGACATGC
*
1809 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCTTGAATGTGTAAATGACCAAAA
1 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
*
1874 TGCCCCTGGACGTGC
66 TGCCCCTGGACATGC
1889 AAATGACC
1 AAATGACC
1897 CCAAAACCCC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (80 bp):
AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
TGCCCCTGGACATGC
Found at i:2214 original size:50 final size:50
Alignment explanation
Indices: 2173--2332 Score: 266
Period size: 50 Copynumber: 3.2 Consensus size: 50
2163 CTTCCAAACT
2173 AATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
1 AATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
* *
2223 AATATTAAAAGGAACATCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
1 AATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
* * *
2273 AATCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATCC
1 AATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
*
2323 AATCTTAAAA
1 AATATTAAAA
2333 AAAGGTAATG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.33
Consensus pattern (50 bp):
AATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTC
Found at i:2453 original size:50 final size:50
Alignment explanation
Indices: 2391--2676 Score: 484
Period size: 50 Copynumber: 5.7 Consensus size: 50
2381 GTTTGAAATA
* *
2391 ACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGGCC-ATGTTGATTATTG
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA-GCCTATGTTGATAATTG
*
2441 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAATTG
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTG
* *
2491 ACTCGTATCGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAATTG
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTG
*
2541 ACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAATTG
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTG
*
2591 ACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTTGATAATTG
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTG
*
2641 ACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
2677 AAAGCATTCG
Statistics
Matches: 224, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
49 3 0.01
50 221 0.99
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTG
Found at i:2925 original size:91 final size:91
Alignment explanation
Indices: 2756--2959 Score: 290
Period size: 91 Copynumber: 2.2 Consensus size: 91
2746 AAGAAAATAC
*
2756 CTTGGAAAATAACTCTGAA-TCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAAAGGA
1 CTTGAAAAATAACTCT-AAGTCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAAAGGA
**
2820 CCAATGTGTGGTCAACTTGAAAAACAA
65 AAAATGTGTGGTCAACTTGAAAAACAA
2847 CTTGAAAAATAACTCTAAGTCTGATGTTGTAATTGAAAACTTCTTGATTGATGAT-AAAAGAGGA
1 CTTGAAAAATAACTCTAAGTCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAA-AGG-
*
2911 AAAAAT-TGCT-GTCAACTTGACAAACAA
64 AAAAATGTG-TGGTCAACTTGAAAAACAA
* *
2938 ATTGAAAAATAACTCTGAGTCT
1 CTTGAAAAATAACTCTAAGTCT
2960 AACGTTATGA
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
90 6 0.06
91 92 0.89
92 5 0.05
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (91 bp):
CTTGAAAAATAACTCTAAGTCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAAAGGAA
AAATGTGTGGTCAACTTGAAAAACAA
Found at i:3406 original size:50 final size:50
Alignment explanation
Indices: 3326--3421 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
3316 CTTAAATGCC
* * * * *
3326 CTTTGAAAGGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
*
3376 CTTTGAAAAGCAAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAAT
3422 TTTATTGTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (50 bp):
CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Done.