Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020955.1 Corchorus olitorius cultivar O-4 contig20988, 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: 14203
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5514 original size:35 final size:35
Alignment explanation
Indices: 5471--5639 Score: 218
Period size: 35 Copynumber: 4.9 Consensus size: 35
5461 CATTCAAGTT
*
5471 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAAG
* *
5506 TTTTCAAATGGGGAAAGTTCCCATCAGGTTTT-AG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAAG
* * *
5540 TTTTCAAATTGGGAAAGTTCCAATCAG-GTTTCAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAAG
* *
5574 TTTCCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAAG
* *
5609 TCTTCAGATTGGGAAAGTTCCCA-CTAGTTTT
1 TTTTCAAATTGGGAAAGTTCCCATC-AGTTTT
5640 CAAAGTATTC
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
33 3 0.03
34 55 0.47
35 59 0.50
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAAG
Found at i:5551 original size:69 final size:69
Alignment explanation
Indices: 5471--5639 Score: 225
Period size: 69 Copynumber: 2.4 Consensus size: 69
5461 CATTCAAGTT
*
5471 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATGGGGAAAGTTCCCATCAGGTT
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTCCAAATGGGGAAAGTTCCCATCA-GTT
5536 TT-AG
65 TTAAG
* * * * *
5540 TTTTCAAATTGGGAAAGTTCCAATCAG-GTTTCAGTTTCCAAATTGGGAAAGTTCCCATCAGTTT
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTCCAAATGGGGAAAGTTCCCATCAGTTT
5604 TCAAG
66 T-AAG
* * *
5609 TCTTCAGATTGGGAAAGTTCCCACTAGTTTT
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTT
5640 CAAAGTATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
67 5 0.06
68 29 0.34
69 49 0.58
70 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (69 bp):
TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTCCAAATGGGGAAAGTTCCCATCAGTTT
TAAG
Found at i:5640 original size:35 final size:35
Alignment explanation
Indices: 5471--5651 Score: 226
Period size: 34 Copynumber: 5.2 Consensus size: 35
5461 CATTCAAGTT
* *
5471 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
*
5506 TTTTCAAATGGGGAAAGTTCCCATCAGGTTTT--AG
1 TTTTCAAATTGGGAAAGTTCCCATCA-GTTTTCAAG
* *
5540 TTTTCAAATTGGGAAAGTTCCAATCAGGTTTC-AG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
*
5574 TTTCCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
* *
5609 TCTTCAGATTGGGAAAGTTCCCA-CTAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATC-AGTTTTC-AAG
*
5645 TATTCAA
1 TTTTCAA
5652 TATAGCTCTT
Statistics
Matches: 128, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
33 4 0.03
34 58 0.45
35 53 0.41
36 13 0.10
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
Found at i:5681 original size:52 final size:52
Alignment explanation
Indices: 5611--5847 Score: 368
Period size: 52 Copynumber: 4.6 Consensus size: 52
5601 TTTTCAAGTC
* * *
5611 TTCAGATTGGGAAAGTTCCCACTAGTTTTCAAAGTATTCAATATAGCTCTTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
* * *
5663 TTCGAATAGGGAAAGTTCCTACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
* *
5715 TTCAAATTGGGAAAGTT-CCACCAGTTTTCAAAGTATTCAATCTTGTTCTTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
*
5766 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
*
5818 TTCGAATTGGGAAAGTTCCCACCAGATTTT
1 TTCAAATTGGGAAAGTTCCCACCAG-TTTT
5848 AGTTTTCAAT
Statistics
Matches: 168, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
51 48 0.29
52 116 0.69
53 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (52 bp):
TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
Found at i:5752 original size:103 final size:104
Alignment explanation
Indices: 5611--5847 Score: 368
Period size: 103 Copynumber: 2.3 Consensus size: 104
5601 TTTTCAAGTC
* * *
5611 TTCAGATTGGGAAAGTTCCCACTAGTTTTCAAAGTATTCAATATAGCTCTTTTTCGAATAGGGAA
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATATAGCTCTTTTTCAAATAGGGAA
*
5676 AGTTCCTACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
66 AGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
* * * *
5715 TTCAAATTGGGAAAGTT-CCACCAGTTTTCAAAGTATTCAATCTTGTTCTTTTTCAAATTGGGAA
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATATAGCTCTTTTTCAAATAGGGAA
*
5779 AGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTT
66 AGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
*
5818 TTCGAATTGGGAAAGTTCCCACCAGATTTT
1 TTCAAATTGGGAAAGTTCCCACCAG-TTTT
5848 AGTTTTCAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
103 94 0.78
104 23 0.19
105 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (104 bp):
TTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATATAGCTCTTTTTCAAATAGGGAA
AGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCTTT
Found at i:9244 original size:38 final size:38
Alignment explanation
Indices: 9167--9267 Score: 177
Period size: 38 Copynumber: 2.7 Consensus size: 38
9157 ATTTTATTAA
* *
9167 TTTCCAAAATCTTCTTTTGG-ATTTCTTAAACTTTTAT
1 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTAT
9204 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTAT
1 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTAT
9242 TTTCCAAAATCTTCTTTTGGAATTAC
1 TTTCCAAAATCTTCTTTTGGAATTAC
9268 TCAATTAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
37 20 0.33
38 41 0.67
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.50
Consensus pattern (38 bp):
TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTAT
Found at i:10002 original size:42 final size:41
Alignment explanation
Indices: 9939--10019 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
9929 ATCAGGAACT
*
9939 AAATTGCATCAAATAGTAAATAAAATCCTAAAGCAGGGACC
1 AAATTGCATCAAATAGAAAATAAAATCCTAAAGCAGGGACC
** * * *
9980 AAATTGCATTTAATCAGAAAATAGAATCCTAGATCAGGGA
1 AAATTGCATCAAAT-AGAAAATAAAATCCTAAAGCAGGGA
10020 TCAGATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 12 0.36
42 21 0.64
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (41 bp):
AAATTGCATCAAATAGAAAATAAAATCCTAAAGCAGGGACC
Done.