Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004076.1 Corchorus capsularis cultivar CVL-1 contig04084, 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: 10948
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:291 original size:75 final size:76
Alignment explanation
Indices: 79--274 Score: 306
Period size: 75 Copynumber: 2.6 Consensus size: 76
69 TTAAAATAAT
* * * *
79 AATGTGAATATTTTCTAAATCTTGTCAAATTATGGGAGATTTAGGAGATATTTTAAGAAATAAA-
1 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAAT
143 ATAATAATAAAG
66 A-AATAATAAAG
*
155 -TTGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAAT
1 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAAT
219 AAATAATAAAG
66 AAATAATAAAG
*
230 AATGAGAATATTTCTCTAAATCTTGCCAGATTGTGGAAGATTTAG
1 AATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAG
275 AAAATATCAA
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 68 0.62
76 12 0.11
77 30 0.27
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (76 bp):
AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAAT
AAATAATAAAG
Found at i:304 original size:77 final size:74
Alignment explanation
Indices: 84--304 Score: 246
Period size: 75 Copynumber: 2.9 Consensus size: 74
74 ATAATAATGT
* * * * * **
84 GAATATTTTCTAAATCTTGTCAAATTATGGGAGATTTAGGAGATATTTTAAGAAATAAAATAATA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAATATAATAAGAAATAAAA-AATA
*
149 ATAAAGTTGA
65 ATAAAGATGA
* * **
159 GAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAATAAATA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAATATAATAAGAAATAAA-AAATA
224 ATAAAGAATGA
65 ATAAAG-ATGA
* *
235 GAATATTTCTCTAAATCTTGCCAGATTGTGGAAGATTTAGAAAATATCAAATAA-TAATAAAAAA
1 GAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAATAT--AATAAGAAATAAAAAA
*
299 AAATAA
63 TAATAA
305 TTGACAAGAA
Statistics
Matches: 130, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
75 66 0.51
76 12 0.09
77 43 0.33
78 6 0.05
79 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (74 bp):
GAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAATATAATAAGAAATAAAAAATAA
TAAAGATGA
Found at i:2207 original size:67 final size:67
Alignment explanation
Indices: 2098--2225 Score: 238
Period size: 67 Copynumber: 1.9 Consensus size: 67
2088 ATATCCAGAA
* *
2098 ACTCAATCAAGCCCATGATTTGAGTCTTCCATGAAAGCAAATTGGTTTGATTCAGTTTGAGCCTG
1 ACTCAATCAAGCCCATGATTTGAGTCTTCCATAAAAGAAAATTGGTTTGATTCAGTTTGAGCCTG
2163 AG
66 AG
2165 ACTCAATCAAGCCCATGATTTGAGTCTTCCATAAAAGAAAATTGGTTTGATTCAGTTTGAG
1 ACTCAATCAAGCCCATGATTTGAGTCTTCCATAAAAGAAAATTGGTTTGATTCAGTTTGAG
2226 GGAAACAAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (67 bp):
ACTCAATCAAGCCCATGATTTGAGTCTTCCATAAAAGAAAATTGGTTTGATTCAGTTTGAGCCTG
AG
Found at i:10789 original size:78 final size:78
Alignment explanation
Indices: 10638--10793 Score: 224
Period size: 78 Copynumber: 2.0 Consensus size: 78
10628 CAGGAGCCAA
* * *
10638 GTCGACAATAGAAAGCCAAGGGGGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAGGGGGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
*
10703 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * *
10716 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGGCCCTATTGAAAGACCTG-AACATG
1 GTCGACAATAGAAAGCCAAGGGGGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TG
*
10780 TTCGTAGAAATCCT
65 TTCGCAGAAATCCT
10794 ATCTATGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 2 0.03
78 67 0.97
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.22
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGGGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAGAAATCCT
Done.