Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012334.1 Corchorus olitorius cultivar O-4 contig12367, 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: 41467
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:5722 original size:18 final size:18
Alignment explanation
Indices: 5699--5733 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5689 GCATACATTG
5699 ATTTAATCAGAGTACTTA
1 ATTTAATCAGAGTACTTA
*
5717 ATTTAATTAGAGTACTT
1 ATTTAATCAGAGTACTT
5734 TCATAGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTTAATCAGAGTACTTA
Found at i:9977 original size:51 final size:51
Alignment explanation
Indices: 9893--10138 Score: 334
Period size: 51 Copynumber: 4.8 Consensus size: 51
9883 AGTTCCCATT
* *
9893 AAAGTATTCAATTTAAG-T-TTTTCAAATTGGGAAAGTTCCCATCAATTTTC
1 AAAGTATTCAATTT-AGCTCTTTTCAAATTGGGAAAGTTCCCACCAATCTTC
* *
9943 AAAGTATTCAATTTAGCTCTTTTCAAATTAGGAAAGTTCCAACCAATCTTC
1 AAAGTATTCAATTTAGCTCTTTTCAAATTGGGAAAGTTCCCACCAATCTTC
* *
9994 AAAGTATTCAATTTAGCTCTTTTCAAATTGGGAAAGTTCCCACCAGTTTTC
1 AAAGTATTCAATTTAGCTCTTTTCAAATTGGGAAAGTTCCCACCAATCTTC
* *
10045 AAAGTATTCAATCTAGCTCTTTTTCAAATTGGGAAAGTTCCCACCAGTCTTC
1 AAAGTATTCAATTTAGCTC-TTTTCAAATTGGGAAAGTTCCCACCAATCTTC
* * * *
10097 GAAGTATTCAATTTAGGTTTTTTTTTAAATTGGGAAAGTTCC
1 AAAGTATTCAATTTA-G-CTCTTTTCAAATTGGGAAAGTTCC
10139 AATCAGGTTT
Statistics
Matches: 176, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
49 2 0.01
50 15 0.09
51 93 0.53
52 44 0.25
53 21 0.12
54 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (51 bp):
AAAGTATTCAATTTAGCTCTTTTCAAATTGGGAAAGTTCCCACCAATCTTC
Found at i:10158 original size:103 final size:99
Alignment explanation
Indices: 9893--10159 Score: 322
Period size: 103 Copynumber: 2.6 Consensus size: 99
9883 AGTTCCCATT
* *
9893 AAAGTATTCAATTTAAG-TTTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTT
1 AAAGTATTCAATTT-AGTTTTTTCAAATTGGGAAAGTTCCCATCAGTTTT--AAGTATTCAATCT
9957 AGCTCTTTTCAAATTAGGAAAGTTCCAACCAATCTTC
63 AGCTCTTTTCAAATTAGGAAAGTTCCAACCAATCTTC
* *
9994 AAAGTATTCAATTTAGCTCTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCT
1 AAAGTATTCAATTTAG-TTTTTTCAAATTGGGAAAGTTCCCATCAGTTTT--AAGTATTCAATCT
* * *
10059 AGCTCTTTTTCAAATTGGGAAAGTTCCCACCAGTCTTC
63 AGCTC-TTTTCAAATTAGGAAAGTTCCAACCAATCTTC
* * * *
10097 GAAGTATTCAATTTAGGTTTTTTTTTAAATTGGGAAAGTTCCAATCAGGTTTT-AGTTTTCAAT
1 AAAGTATTCAATTTA-G--TTTTTTCAAATTGGGAAAGTTCCCATCA-GTTTTAAGTATTCAAT
10160 TCAGGGAAAG
Statistics
Matches: 146, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
100 2 0.01
101 14 0.10
102 48 0.33
103 52 0.36
104 1 0.01
105 24 0.16
106 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (99 bp):
AAAGTATTCAATTTAGTTTTTTCAAATTGGGAAAGTTCCCATCAGTTTTAAGTATTCAATCTAGC
TCTTTTCAAATTAGGAAAGTTCCAACCAATCTTC
Found at i:29885 original size:11 final size:11
Alignment explanation
Indices: 29869--29894 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29859 GTTTTAGATC
29869 TTTTCTTCTAG
1 TTTTCTTCTAG
29880 TTTTCTTCTAG
1 TTTTCTTCTAG
29891 TTTT
1 TTTT
29895 TAGGCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:30684 original size:15 final size:16
Alignment explanation
Indices: 30658--30693 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
30648 CTTTGTTTTG
30658 TTTCTAGTTTAATTGC
1 TTTCTAGTTTAATTGC
30674 TTTCT-GTTTAATTGC
1 TTTCTAGTTTAATTGC
30689 TTTCT
1 TTTCT
30694 TTCAACCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (16 bp):
TTTCTAGTTTAATTGC
Found at i:32275 original size:26 final size:26
Alignment explanation
Indices: 32233--32285 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
32223 GATTGTACTT
* *
32233 ACCAGAAAACGGTCCATTTCTGAGAA
1 ACCAGAAAACGGGCCATTCCTGAGAA
* *
32259 ACCAGAAAATGGGCCATTCCTTAGAA
1 ACCAGAAAACGGGCCATTCCTGAGAA
32285 A
1 A
32286 GTTAGAGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (26 bp):
ACCAGAAAACGGGCCATTCCTGAGAA
Done.