Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006466.1 Corchorus olitorius cultivar O-4 contig06491, 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: 10034
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Found at i:3109 original size:16 final size:16
Alignment explanation
Indices: 3091--3129 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3081 CAAGAGATGT
3091 TTTTC-AAGAAAATTG
1 TTTTCAAAGAAAATTG
**
3106 TTTTCAAAGAAAAAGG
1 TTTTCAAAGAAAATTG
3122 TTTTCAAA
1 TTTTCAAA
3130 AATGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (16 bp):
TTTTCAAAGAAAATTG
Found at i:5409 original size:64 final size:64
Alignment explanation
Indices: 5320--6015 Score: 907
Period size: 64 Copynumber: 10.9 Consensus size: 64
5310 TGTTAGAAAG
* * *
5320 AATTTTCAGACGTTGATTGGAAGACGATCTTGTCTAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
5384 AATTTTCAAAAGTTGATCGGGAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
5447 AAGTTTTAAGGAGTTGATCTGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTCTCTCAAC
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
5511 AATTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * ** *
5575 AGTTTTAAGGAGTTGATCCAAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * * *
5639 AGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTGAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * *
5703 AAATTTCAGAAGTTGATCAGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
5766 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * * *
5830 AGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAATACGCCAGAAGATGGTTTTTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * * *
5894 AATTTTCAGAAGTTGATCGGAACACGATCTTGTTAAAAATTACACTAGAAGATAGTTTCTCGAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAC
* * * * *
5958 AACGTTTCAGAAGTTGATCGGAAGATGATCTTGTTAAG-AGATGCACCAGAAGACGGTT
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAG-TACACCAGAAGATGGTT
6016 ATTTAGAAAT
Statistics
Matches: 553, Mismatches: 72, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
63 112 0.20
64 395 0.71
65 46 0.08
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:5557 original size:191 final size:192
Alignment explanation
Indices: 5320--6015 Score: 988
Period size: 191 Copynumber: 3.6 Consensus size: 192
5310 TGTTAGAAAG
* * *
5320 AATTTTCAGACGTTGATTGGAAGACGATCTTGTCTAGAAGTACACCAGAAGATGGTTTCTCAACA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
* *
5385 ATTTTCAAAAGTTGATCGGGAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAG
66 ATTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
* * * * * * *
5450 TTTTAAGGAGTTGATCTGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTCTCTCAAC
131 TTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
* *
5511 AATTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
* * **
5576 GTTTT-AAGGAGTTGATCCAAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
66 ATTTTCAA-AAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
*
5640 GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTGAAA
130 GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
* * *
5703 AAATTTCAGAAGTTGATCAGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTTTCTCAACA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
* *
5767 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAGAG
66 ATTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
*
5832 TTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAATACGCCAGAAGATGGTTTTTCAAA
131 TTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
* * * * * *
5894 AATTTTCAGAAGTTGATCGGAACACGATCTTGTTAAAAATTACACTAGAAGATAGTTTCTCGAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAC
* * * * * *
5958 AACGTTTCAGAAGTTGATCGGAAGATGATCTTGTTAAG-AGATGCACCAGAAGACGGTT
65 AA-TTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAG-TACACCAGAAGATGGTT
6016 ATTTAGAAAT
Statistics
Matches: 454, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
190 2 0.00
191 324 0.71
192 80 0.18
193 48 0.11
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (192 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
ATTTTCAAAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
TTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
Found at i:5791 original size:255 final size:255
Alignment explanation
Indices: 5340--6015 Score: 992
Period size: 255 Copynumber: 2.6 Consensus size: 255
5330 CGTTGATTGG
* * * *
5340 AAGACGATCTTGTCTAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAAAAGTTGATCGGG
1 AAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGA
* * ** * * *
5405 AGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAGTTTTAAGGAGTTGATCTGAA
66 AGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTGAAAAAATTTCAGAAGTTGATCAGAA
*
5470 GACGATCTTGTTAAAAGTACACCAGAAGATGGTCTCTCAACAATTTTCAAAAGTTGATCGGAAGA
131 GACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAAAAGTTGATCGGAAGA
*
5535 CGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTAAGGAGTTGATCCA
196 CGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAGAGTTTTAAGGAGTTGATCCA
* * *
5595 AAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGGAGTTGATCGGA
1 AAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGA
*
5660 AGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTGAAAAAATTTCAGAAGTTGATCAGAA
66 AGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTGAAAAAATTTCAGAAGTTGATCAGAA
*
5725 GACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGATCGGAAGA
131 GACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAAAAGTTGATCGGAAGA
* **
5790 CGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAGAGTTTTCAGGAGTTGATCGG
196 CGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAGAGTTTTAAGGAGTTGATCCA
* * *
5850 AAGACGATCTTGTCAAGAAATACGCCAGAAGATGGTTTTTCAAAAATTTTCAGAAGTTGATCGGA
1 AAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGA
* * * * * * * ** *
5915 ACACGATCTTGTTAAAAATTACACTAGAAGATAGTTTCTCGAAAACGTTTCAGAAGTTGATCGGA
66 AGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTT-TTGAAAAAATTTCAGAAGTTGATCAGA
* * * *
5980 AGATGATCTTGTTAAGAGATGCACCAGAAGACGGTT
130 AGACGATCTTGTTAAAAG-TACACCAGAAGATGGTT
6016 ATTTAGAAAT
Statistics
Matches: 378, Mismatches: 41, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
255 324 0.86
256 39 0.10
257 15 0.04
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (255 bp):
AAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGA
AGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTGAAAAAATTTCAGAAGTTGATCAGAA
GACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAAAAGTTGATCGGAAGA
CGATCTTGTCAAGAAGTACACCAGAAAATGGTTTCTCAAGAGTTTTAAGGAGTTGATCCA
Done.