Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024584.1 Corchorus olitorius cultivar O-4 contig24617, 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: 23238
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Found at i:6788 original size:10 final size:11
Alignment explanation
Indices: 6764--6792 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
6754 AATTCTCTCC
6764 TTTGTGTGTTT
1 TTTGTGTGTTT
6775 TTTGTGTG-TT
1 TTTGTGTGTTT
6785 TTTGTGTG
1 TTTGTGTG
6793 GAAGCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (11 bp):
TTTGTGTGTTT
Found at i:14386 original size:13 final size:14
Alignment explanation
Indices: 14359--14389 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
14349 AATTCTTCCC
14359 ATCAATAAGAATAA
1 ATCAATAAGAATAA
14373 ATCAATAA-AATAA
1 ATCAATAAGAATAA
14386 ATCA
1 ATCA
14390 CCAAATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAATAAGAATAA
Found at i:14712 original size:13 final size:14
Alignment explanation
Indices: 14685--14715 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
14675 AATTCTTCCC
14685 ATCAATAAGAATAA
1 ATCAATAAGAATAA
14699 ATCAATAA-AATAA
1 ATCAATAAGAATAA
14712 ATCA
1 ATCA
14716 CCAAATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAATAAGAATAA
Found at i:15019 original size:13 final size:14
Alignment explanation
Indices: 14992--15022 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
14982 AATTCTTCCC
14992 ATCAATAAGAATAA
1 ATCAATAAGAATAA
15006 ATCAATAA-AATAA
1 ATCAATAAGAATAA
15019 ATCA
1 ATCA
15023 CCAAATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAATAAGAATAA
Found at i:15092 original size:307 final size:308
Alignment explanation
Indices: 14235--15147 Score: 1605
Period size: 307 Copynumber: 2.9 Consensus size: 308
14225 GCAGTTTTTC
*
14235 AAATTCTTTTTCCATTTTTTGTCCATATTTCAAACAATCCCTCCGTACACGCCAGGAAAACCTCA
1 AAATTCTTTTTCCATTTTTTGTCCATATTCCAAACAATCCCTCCGTACACGCCAGGAAAACCTCA
14300 TATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAAT
66 TATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAAT
*
14365 AAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAAAATTTCATA
131 AAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCATA
14430 TATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGATAGAAAAAAAAATACAA
196 TATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGAT-GAAAAAAAAATACAA
14495 GAATAGGAAATCAATAGTAGTAGTAGTAGTAGTAAGTATTTTACAAAACCCAAACTAGAAATTCG
260 GAATAGGAAATC------------A--A-TAGT-AGTATTTTACAAAACCCAAACTAGAAATTCG
*
14560 AAATTTTTTTTCCATTTTTTTGTCCATATTCCAAACAATCCCTCCGTACACGCCAGGAAAACCTC
1 AAATTCTTTTTCCA-TTTTTTGTCCATATTCCAAACAATCCCTCCGTACACGCCAGGAAAACCTC
14625 ATATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAA
65 ATATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAA
14690 TAAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCAT
130 TAAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCAT
14755 ATATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGATGAAAAAAAAATACAA
195 ATATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGATGAAAAAAAAATACAA
14820 GAATAGGAAATCAATAGTA-TATTTTACAAAACCCAAACTAGAAATTCG
260 GAATAGGAAATCAATAGTAGTATTTTACAAAACCCAAACTAGAAATTCG
*
14868 AAATTCTTTTTCCATTTTTTGTCCATATTCCAAACAATCCCTCCATACACGCCAGGAAAACCTCA
1 AAATTCTTTTTCCATTTTTTGTCCATATTCCAAACAATCCCTCCGTACACGCCAGGAAAACCTCA
14933 TATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAAT
66 TATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAAT
14998 AAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCATA
131 AAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCATA
*
15063 TATTGAACTTCATATAGAAAAGAAATAACCAATCTGATGACAAACTGAT-AAAAAAAAATACAAG
196 TATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGATGAAAAAAAAATACAAG
15127 AATAGGAAATCAATAGTAGTA
261 AATAGGAAATCAATAGTAGTA
15148 GTAGTAGTAA
Statistics
Matches: 580, Mismatches: 6, Indels: 22
0.95 0.01 0.04
Matches are distributed among these distances:
306 33 0.06
307 230 0.40
308 42 0.07
309 1 0.00
310 4 0.01
311 1 0.00
313 1 0.00
325 40 0.07
326 228 0.39
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (308 bp):
AAATTCTTTTTCCATTTTTTGTCCATATTCCAAACAATCCCTCCGTACACGCCAGGAAAACCTCA
TATATTAAATTAAAATTTCTTAAAATAGGTGTTGGGGGAGTCATTATGAAATTCTTCCCATCAAT
AAGAATAAATCAATAAAATAAATCACCAAATCAATAAAAATGAATTAACGCCAAAGAATTTCATA
TATTGAACTTCATATAGAAAAGGAATAACCAATCTGATGACAAACTGATGAAAAAAAAATACAAG
AATAGGAAATCAATAGTAGTATTTTACAAAACCCAAACTAGAAATTCG
Found at i:16158 original size:2 final size:2
Alignment explanation
Indices: 16151--16182 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16141 ATTTATTATC
16151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16183 TGTAAAACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19453 original size:3 final size:3
Alignment explanation
Indices: 19445--19511 Score: 55
Period size: 3 Copynumber: 22.7 Consensus size: 3
19435 AATATACAAG
* * * * *
19445 ATA ATA ATA ATA ATA AAA ATA AGA CTA AT- GTC ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
19492 ATA ATG ATG ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
19512 TTATTAGGAG
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Done.