Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010947.1 Corchorus olitorius cultivar O-4 contig10979, 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: 15869
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:1941 original size:35 final size:35
Alignment explanation
Indices: 1895--2578 Score: 653
Period size: 35 Copynumber: 19.6 Consensus size: 35
1885 TTCTCGATTG
* *
1895 GACTCGGTGTAGCATCTCCAAAGTTGAA-TCCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACT-CAGAT
1930 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* * *
1965 GACTCGGTGTGGCATTTTCAAAGTTGAA-TCCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACT-CAGAT
*
2000 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
*
2035 GACTCGGTGTAGCATCTTCAAAGATGAACTCATAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
*
2070 GACTCGGTGTAGCATCTTCAAAGTTGAA-TCCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACT-CAGAT
*
2105 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
2140 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
*
2175 GACTCGGTGTAGCATCTTCAAAGTTGAA-TCCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACT-CAGAT
* *
2210 GACTCGGTGTAGCATCATCAAAGATGAACTCGGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
*
2245 GACTCGGTGTAGCATCTTCAAAGATGAATTCAGAT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* *
2280 GACTCGGTGTAGCATCTTC-AATATGGACTCAG-T
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* * *
2313 GGGCTCGGTGCAGCAAATCTTCAAATAGATCAGAA---AAAT
1 -GACTCGGTGTAGC--ATCTTC-AA-AGAT--GAACTCAGAT
* *
2352 -ACTCGGTGTAGCATCTTC-AATATGGACTCAG-T
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* * * *
2384 GGGCTCGGTGCAGCAAATCATCAAATA-G-A-TCAGGAT
1 -GACTCGGTGTAGC--ATCTTCAAAGATGAACTCA-GAT
* * *
2420 GACTCGGTGTAGCATCTTC-AATATGGACTTAG-T
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* * * *
2453 GGGCTCGGTGCAACAAATCTTCAAATA-G-A-TCAGGAT
1 -GACTCGGTGTAGC--ATCTTCAAAGATGAACTCA-GAT
* *
2489 GACTCGGTGTAGCATCTTC-AATATGGACTCAG-T
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
* * *
2522 GGGCTCGGTGCAGCAAATCTTCAAATA-G-A-TCAGGAT
1 -GACTCGGTGTAGC--ATCTTCAAAGATGAACTCA-GAT
*
2558 GACTCGGTTTAGCATCTTCAA
1 GACTCGGTGTAGCATCTTCAA
2579 TATGGACCTA
Statistics
Matches: 550, Mismatches: 55, Indels: 90
0.79 0.08 0.13
Matches are distributed among these distances:
30 2 0.00
32 12 0.02
33 26 0.05
34 67 0.12
35 380 0.69
36 33 0.06
37 22 0.04
38 2 0.00
39 4 0.01
41 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (35 bp):
GACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT
Found at i:2077 original size:105 final size:105
Alignment explanation
Indices: 1895--2300 Score: 724
Period size: 105 Copynumber: 3.9 Consensus size: 105
1885 TTCTCGATTG
* * *
1895 GACTCGGTGTAGCATCTCCAAAGTTGAA-TCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
1 GACTCGGTGTAGCATCTTCAAAGATGAACT-CGGATGACTCGGTGTAGCATCTTCAAAGATGAAC
* *
1959 TCAGATGACTCGGTGTGGCATTTTCAAAGTTGAATCCAGAT
65 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
2000 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
*
2065 CATATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
66 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
2105 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
2170 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
66 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
* *
2210 GACTCGGTGTAGCATCATCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAATT
1 GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
2275 CAGATGACTCGGTGTAGCATCTTCAA
66 CAGATGACTCGGTGTAGCATCTTCAA
2301 TATGGACTCA
Statistics
Matches: 291, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
105 290 1.00
106 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (105 bp):
GACTCGGTGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGAACT
CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGAT
Found at i:2634 original size:138 final size:138
Alignment explanation
Indices: 2277--2635 Score: 587
Period size: 138 Copynumber: 2.6 Consensus size: 138
2267 GATGAATTCA
2277 GATGACTCGGTGTAGCATCTTCAATATGGA-CTCAGTGGGCTCGGTGCAGCAAATCTTCAAATAG
1 GATGACTCGGTGTAGCATCTTCAATATGGACCT-AGTGGGCTCGGTGCAGCAAATCTTCAAATAG
***
2341 ATCAGAAAAATACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAATCATC
65 ATCAGAGTGAT--TCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAATCATC
2406 AAATAGATCAG
128 AAATAGATCAG
* *
2417 GATGACTCGGTGTAGCATCTTCAATATGGACTTAGTGGGCTCGGTGCAACAAATCTTCAAATAGA
1 GATGACTCGGTGTAGCATCTTCAATATGGACCTAGTGGGCTCGGTGCAGCAAATCTTCAAATAGA
* *
2482 TCAG-GATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAATCTTCAA
66 TCAGAG-TGATTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAATCATCAA
2546 ATAGATCAG
130 ATAGATCAG
* *
2555 GATGACTCGGTTTAGCATCTTCAATATGGACCTAGTGGGCTTGGTGCAGCAAATCTTCAAATAGA
1 GATGACTCGGTGTAGCATCTTCAATATGGACCTAGTGGGCTCGGTGCAGCAAATCTTCAAATAGA
2620 TCAGAGTGATTCGGTG
66 TCAGAGTGATTCGGTG
2636 AATCAAGCTA
Statistics
Matches: 204, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
138 136 0.67
139 1 0.00
140 66 0.32
141 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (138 bp):
GATGACTCGGTGTAGCATCTTCAATATGGACCTAGTGGGCTCGGTGCAGCAAATCTTCAAATAGA
TCAGAGTGATTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAATCATCAAA
TAGATCAG
Found at i:2800 original size:89 final size:90
Alignment explanation
Indices: 2597--2800 Score: 229
Period size: 90 Copynumber: 2.3 Consensus size: 90
2587 TAGTGGGCTT
* * * *
2597 GGTGCAGCAAATCTTCAAATAGATCA-GAGTGATTCGGTGAATCAAGCTAATGCGGTGCTTTACT
1 GGTGCAGCAAATCTTCAAACAGATTAGGA-AGATTCGGTGAATCAAGCTAATGCGGTGCTATACT
* * *
2661 TCTTCAATGTTCGACTCGGTGAGCTG
65 TCTTCAAAGATCGACTCGGTGAGCTC
*
2687 GGTGCAGCAAATCTTCAAATAGATTAGGAAGATTCGGTGAATCAAG-TCAATGCGGTGC-AT-C-
1 GGTGCAGCAAATCTTCAAACAGATTAGGAAGATTCGGTGAATCAAGCT-AATGCGGTGCTATACT
*
2748 TCTTCAAAGATCGGAATTCGGTGAGCTC
65 TCTTCAAAGATC-G-ACTCGGTGAGCTC
** *
2776 GGTGCAGCACGTTTTCAAACAGATT
1 GGTGCAGCAAATCTTCAAACAGATT
2801 CAGTAAATTA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
87 10 0.10
88 2 0.02
89 34 0.34
90 51 0.52
91 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (90 bp):
GGTGCAGCAAATCTTCAAACAGATTAGGAAGATTCGGTGAATCAAGCTAATGCGGTGCTATACTT
CTTCAAAGATCGACTCGGTGAGCTC
Found at i:12160 original size:30 final size:30
Alignment explanation
Indices: 11922--12159 Score: 172
Period size: 30 Copynumber: 7.5 Consensus size: 30
11912 CAAATAAACT
* *
11922 TAAAGTAATGATCCTAAGCCAGGATTAAAA
1 TAAAGCAATGATCCTAAACCAGGATTAAAA
* * *
11952 TAAAGCAATGATGCTAAATCAGGAATAAAA
1 TAAAGCAATGATCCTAAACCAGGATTAAAA
* * * *
11982 TGAAA-CAATCATCCTCAACTAGGACTAAGATTAA
1 T-AAAGCAATGATCCTAAACCAGGA-TTA-A--AA
* **
12016 CTTATGAAGCAATGATCCTAAACCATGATCGAAA
1 --TA--AAGCAATGATCCTAAACCAGGATTAAAA
* *
12050 TGAAACCAAATAAAGGTCCTAAACCAGGATTAAAA
1 T-AAAGC-AAT---GATCCTAAACCAGGATTAAAA
* *
12085 TAAAGCGATGATCCTAAACCGGGATTAAAA
1 TAAAGCAATGATCCTAAACCAGGATTAAAA
* *
12115 TAAAGCAATGATCCTCAACCATGATTAAAA
1 TAAAGCAATGATCCTAAACCAGGATTAAAA
*
12145 TAAAGCAACGATCCT
1 TAAAGCAATGATCCT
12160 CTCTGGTATC
Statistics
Matches: 161, Mismatches: 32, Indels: 30
0.72 0.14 0.13
Matches are distributed among these distances:
30 99 0.61
31 7 0.04
32 5 0.03
33 3 0.02
34 8 0.05
35 19 0.12
36 2 0.01
37 3 0.02
38 15 0.09
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (30 bp):
TAAAGCAATGATCCTAAACCAGGATTAAAA
Done.