Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015477.1 Corchorus olitorius cultivar O-4 contig15510, 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: 17288
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 11--45 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 GTGGGTGGCT
11 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:718 original size:21 final size:21
Alignment explanation
Indices: 692--731 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
682 ATTGGATATA
692 TGAAACCCCAAGGTTTCAATT
1 TGAAACCCCAAGGTTTCAATT
713 TGAAACCCCAAGGTTTCAA
1 TGAAACCCCAAGGTTTCAA
732 GCTTTTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
TGAAACCCCAAGGTTTCAATT
Found at i:1074 original size:20 final size:21
Alignment explanation
Indices: 1035--1076 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1025 CCTCTCATGG
**
1035 AGCTTGGAATTTTCTTCATCA
1 AGCTTGGAATTTTCACCATCA
1056 AGCTTGG-ATTTTCACCATCA
1 AGCTTGGAATTTTCACCATCA
1076 A
1 A
1077 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (21 bp):
AGCTTGGAATTTTCACCATCA
Found at i:8524 original size:12 final size:12
Alignment explanation
Indices: 8507--8531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8497 ATATTGATGC
8507 TATTGTTGGGAA
1 TATTGTTGGGAA
8519 TATTGTTGGGAA
1 TATTGTTGGGAA
8531 T
1 T
8532 CAATGGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (12 bp):
TATTGTTGGGAA
Found at i:15376 original size:331 final size:338
Alignment explanation
Indices: 14737--15414 Score: 1073
Period size: 331 Copynumber: 2.0 Consensus size: 338
14727 TCCACCCAAG
*
14737 ATACTATGTAGTCAATTTAGAAAAAAAAAAAAAAAAACACAATATGAGTGAAATATTCATAATAA
1 ATACTATGTAGTCAATTTAG---AAAAAAAAAAAAAACACAATATGAGTGAAATATGCATAATAA
14802 GTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGCGCTTACTTCCCTAAGTGA
63 GTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGCG-----TTCCCT-A-TGA
* *
14867 AGGTCCTCTCGTAGTAAAAGAGGGCTCAGAATTGCTGTAAAGTTGAGGGAAAATGGCGAAAAGGA
121 AGGTACTCTCGTAGTAAAAGAGGGCTCAGAATTGCTGTAAAGTTGAGGGAAAATGACGAAAAGGA
14932 GGAGACGAAAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTGACATCCCGGAT
186 GGAGACGAAAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTGACATCCCGGAT
* * *
14997 ACCAAGATGCCCTATTCAATTTTTATTGAAACATTATTAAGAAAATCAATAATAATAACTAAATA
251 ACCAAGATGCCCTATTCAACTTTTATTGAAACATCATCAAGAAAATCAATAATAATAACTAAATA
15062 AATTCAACATATTTTCAAAGTAC
316 AATTCAACATATTTTCAAAGTAC
* * *
15085 ATACTGTGTAGTCAATTTAG-AAAAAAAAACAAACACAATATGAGTGAAATATGCATGATAAGTA
1 ATACTATGTAGTCAATTTAGAAAAAAAAAAAAAACACAATATGAGTGAAATATGCATAATAAGTA
* *
15149 TTATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTT-G-G-T-GCT-T-AAGGTACTCTC
66 TAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGCGTTCCCTATGAAGGTACTCTC
*
15208 GTAGTAAAAGAGGGCTCAGAATTGCTGTAAAGTTGAGGGAGAATGACGAAAAGGAGGAGACGAAA
131 GTAGTAAAAGAGGGCTCAGAATTGCTGTAAAGTTGAGGGAAAATGACGAAAAGGAGGAGACGAAA
*
15273 ACTGGACCCCTGTTGCTGTGTACATAATGTCACCAGTGTTGTTGACATCCCGGATACCAAGATGC
196 ACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTGACATCCCGGATACCAAGATGC
* * *
15338 CTTATTCAACTTTTCTTGAAACATCATCAAGAAAATCAATAATAATAAGTAAATAAATTCAACAT
261 CCTATTCAACTTTTATTGAAACATCATCAAGAAAATCAATAATAATAACTAAATAAATTCAACAT
15403 ATTTTCAAAGTA
326 ATTTTCAAAGTA
15415 GAATCAATCT
Statistics
Matches: 314, Mismatches: 16, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
331 208 0.66
332 1 0.00
335 2 0.01
336 1 0.00
342 1 0.00
343 1 0.00
344 81 0.26
348 19 0.06
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (338 bp):
ATACTATGTAGTCAATTTAGAAAAAAAAAAAAAACACAATATGAGTGAAATATGCATAATAAGTA
TAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGCGTTCCCTATGAAGGTACTCTC
GTAGTAAAAGAGGGCTCAGAATTGCTGTAAAGTTGAGGGAAAATGACGAAAAGGAGGAGACGAAA
ACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTGACATCCCGGATACCAAGATGC
CCTATTCAACTTTTATTGAAACATCATCAAGAAAATCAATAATAATAACTAAATAAATTCAACAT
ATTTTCAAAGTAC
Found at i:17052 original size:343 final size:344
Alignment explanation
Indices: 16405--17094 Score: 1231
Period size: 343 Copynumber: 2.0 Consensus size: 344
16395 AGTCCACCCA
16405 AGATACTGTATAGTCAATTTAGAAAAAAAAAACAAACACAATATGAATGAAATATGCATGATAAG
1 AGATACTGTATAGTCAATTTAGAAAAAAAAAACAAACACAATATGAATGAAATATGCATGATAAG
16470 TATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTGCTTACTTCCCTAAGTGAA
66 TATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTGCTTACTTCCCTAAGTGAA
*
16535 GGTCCTATCGTTGTAAAAGGAGCTCAGAATTGCTGTAAAGATGAGGGAAAATGGCGAAAAGGAGG
131 GGTCCTATCGTAGTAAAAGGAGCTCAGAATTGCTGTAAAGATGAGGGAAAATGGCGAAAAGGAGG
* * * *
16600 AGACGAGAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTGACATCCTGGATAC
196 AGAAGAAAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTAACATCCCGGATAC
16665 CAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCAATAATAATAACTAAATAAA
261 CAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCAATAATAATAACTAAATAAA
16730 TTCAACATATTTTCAAAGT
326 TTCAACATATTTTCAAAGT
* * *
16749 AGATACTGTGTAGTCAATTT-G-AAAAAAATACAAACACAATATGAGTGAAATATGCATGATAAG
1 AGATACTGTATAGTCAATTTAGAAAAAAAAAACAAACACAATATGAATGAAATATGCATGATAAG
16812 TATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTGCTTACTTCCCTAAGTGAA
66 TATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTGCTTACTTCCCTAAGTGAA
* * * *
16877 GGTCCTCTCGTAGTAAAAGAGGGCTCAGAATTGTTGTAAAGTTGAGGGAAAATGGCGAAAAGGAG
131 GGTCCTATCGTAGTAAAAG-GAGCTCAGAATTGCTGTAAAGATGAGGGAAAATGGCGAAAAGGAG
*
16942 GAGAAGAAAACTGGACCCCTGTTGCTGTGTACATAATGTCACCAGTGTTGTTAACATCCCGGATA
195 GAGAAGAAAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTAACATCCCGGATA
17007 CCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCAATAATAATAACTAAATAA
260 CCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCAATAATAATAACTAAATAA
*
17072 ATTCAACATATTTTGAAAGT
325 ATTCAACATATTTTCAAAGT
17092 AGA
1 AGA
17095 ATCAATCTAA
Statistics
Matches: 331, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
342 122 0.37
343 190 0.57
344 19 0.06
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (344 bp):
AGATACTGTATAGTCAATTTAGAAAAAAAAAACAAACACAATATGAATGAAATATGCATGATAAG
TATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTGCTTACTTCCCTAAGTGAA
GGTCCTATCGTAGTAAAAGGAGCTCAGAATTGCTGTAAAGATGAGGGAAAATGGCGAAAAGGAGG
AGAAGAAAACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTGTTGTTAACATCCCGGATAC
CAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCAATAATAATAACTAAATAAA
TTCAACATATTTTCAAAGT
Done.