Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013293.1 Corchorus olitorius cultivar O-4 contig13326, 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: 35447
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:487 original size:25 final size:25
Alignment explanation
Indices: 454--502 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
444 TCTGCAGAAC
*
454 ACATGAAAAGGTGTATTTTTATGAA
1 ACATGAAAAGGTGTATTTCTATGAA
* *
479 ACATGAAAATGTGTCTTTCTATGA
1 ACATGAAAAGGTGTATTTCTATGA
503 GGGATTGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (25 bp):
ACATGAAAAGGTGTATTTCTATGAA
Found at i:2635 original size:5 final size:5
Alignment explanation
Indices: 2625--2652 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2615 TTTGACCCAT
2625 TGGGG TGGGG TGGGG TGGGG TGGGG TGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG TGG
2653 ACCCAATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (5 bp):
TGGGG
Found at i:25248 original size:5 final size:5
Alignment explanation
Indices: 25238--25262 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25228 TGCAGCACAC
25238 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
25263 GTAATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:31720 original size:33 final size:33
Alignment explanation
Indices: 31678--31748 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
31668 CGTTGAAAAA
31678 TATTACTAAATCTTTATAATTTGTAGAAAACAT
1 TATTACTAAATCTTTATAATTTGTAGAAAACAT
31711 TATTACTAAATCTTTATAATTTGTAGAAAACAT
1 TATTACTAAATCTTTATAATTTGTAGAAAACAT
31744 TATTA
1 TATTA
31749 TATCTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (33 bp):
TATTACTAAATCTTTATAATTTGTAGAAAACAT
Found at i:32125 original size:16 final size:16
Alignment explanation
Indices: 32104--32149 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
32094 CAAGTTGTAA
32104 AGTAATCTTATTAATT
1 AGTAATCTTATTAATT
32120 AGTAATCTTATTAATT
1 AGTAATCTTATTAATT
*
32136 AGTAACCTTATTAA
1 AGTAATCTTATTAA
32150 CTGAGCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (16 bp):
AGTAATCTTATTAATT
Found at i:32876 original size:202 final size:200
Alignment explanation
Indices: 32158--33421 Score: 1610
Period size: 202 Copynumber: 6.4 Consensus size: 200
32148 AACTGAGCTT
* * *
32158 TTTCATAATTAATTAA-ATATTAAATATTAACACATATTCCCTAAGGCGACACATGTCAACCCTT
1 TTTCATAATTAATTAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
* ** * * * * *
32222 ACACATCGCCCGTGCAGTCTGCTAAACTCTACTGTCGGTGTATTCTATAATTTTTCTTATATGAT
66 AAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGAT
* * *
32287 TATTATACAATACATTGTAAGTGTAAATTTTGGACTCCATAAACGGGTTAA-AAGGTTGACACAT
131 TATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAA-GTTGACACAT
*
32351 A-CTCA
195 ACCCCA
* * *
32356 TTTCATAATTAATTAA-ATGTTTAATATTAATACATATTCCCTAAGGAGACACATGCCAACCCTT
1 TTTCATAATTAATTAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
* * * * *
32420 AAACCCCACACGTGCAGTCTGCTAAGCTCCACTGACGGTGTATTATACAAATTTTCTTATAGGGA
66 AAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATA-GGA
* * *
32485 TTATTATGCAATACACTGTCAGTGTAAATTTTGGACTCCATAAGTGGGTTAAGAGGTTGACACAT
130 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
32550 A-CCCA
195 ACCCCA
32555 TTTCATAATTAATTAA-ATATTTAATATTAATTAAGACATATTCCCTAAGGGGACACATGTCAAC
1 TTTCATAATTAATTAATATATTTAATATTAA-T---ACATATTCCCTAAGGGGACACATGTCAAC
* * *
32619 CCTTAAACCCCACACGTGCAGTCTGCTAAGA-TCCACTAACAGTGTATTGTATAATTTTTCTTAT
62 CCTTAAACCCCGCACGTGCAGTCTGCTAA-ACTCCACTGACGGTGTATTGTATAATTTTTCTTAT
* * * * *
32683 AGGGATTACTATACAATACACTGTCGGTGTAAATTTTGGACTCTATAAGTGGGTT-AGAAAGTCG
126 A-GGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAG-AAGTTG
*
32747 CCACATACCCCA
189 ACACATACCCCA
* *
32759 TTTCATAATTAATTAAATATATTTAATATCAATACATATTCCCTAAGGGGACACATGTTAACCCT
1 TTTCATAATTAATT-AATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* * *
32824 TAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGTA
65 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGA
*
32889 ATATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
130 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
*
32954 ATCCCA
195 ACCCCA
* * *
32960 TTTC-----------ATA-A-TT-A-ATT--CACATATTCCCTAATGGGACACATATCAACCCTT
1 TTTCATAATTAATTAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
* * * *
33008 AAACCCCACACGTGCATTCTGCTAAACTCCACTAAAGGTGTATTGTATAATTTTTCTTATAGGGA
66 AAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATA-GGA
* ** *
33073 TTATTATACAATACACTGTCAGTGTAAAATTTGGACTCCATAAGTTGGTTAAGAAATTGACACAT
130 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
*
33138 ACCACA
195 ACCCCA
* * *
33144 TTTCATAATAAATTATATATATTTAATATTGATACATATTCCCTAATGGGACACATGTCAACCCT
1 TTTCATAATTAATTA-ATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* *
33209 TAAACCTCGCACGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTTCTTATAGGA
65 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGA
* * * * *
33274 CTATTATACAATACACTATCAGTGTAAATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACAT
130 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
*
33339 ACCTCA
195 ACCCCA
* * *
33345 TTTCATAACTAATTAA-ATATTTAATATTAATACATATTTCCT-AGGGGACATATGTCAACCCTT
1 TTTCATAATTAATTAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
*
33408 AAACCTCGCACGTG
66 AAACCCCGCACGTG
33422 AAGATGTATT
Statistics
Matches: 937, Mismatches: 97, Indels: 64
0.85 0.09 0.06
Matches are distributed among these distances:
183 85 0.09
184 70 0.07
185 2 0.00
186 1 0.00
187 2 0.00
188 1 0.00
189 3 0.00
196 3 0.00
197 1 0.00
198 144 0.15
199 117 0.12
200 6 0.01
201 145 0.15
202 178 0.19
203 145 0.15
204 18 0.02
205 3 0.00
206 13 0.01
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (200 bp):
TTTCATAATTAATTAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
AAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGAT
TATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATA
CCCCA
Found at i:33300 original size:385 final size:385
Alignment explanation
Indices: 32590--33358 Score: 1231
Period size: 385 Copynumber: 2.0 Consensus size: 385
32580 ATTAATTAAG
*
32590 ACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCACACGTGCAGTCTGCTAAGATCCAC
1 ACATATTCCCTAAGGGGACACATATCAACCCTTAAACCCCACACGTGCAGTCTGCTAAGATCCAC
* *
32655 TAACAGTGTATTGTATAATTTTTCTTATAGGGATTACTATACAATACACTGTCGGTGTAAATTTT
66 TAACAGTGTATTGTATAATTTTTCTTATAGGGATTACTATACAATACACTGTCAGTGTAAAATTT
* * * *
32720 GGACTCTATAAGTGGGTTAGAAAGTCGCCACATACCCCATTTCATAATTAATTAAATATATTTAA
131 GGACTCCATAAGTGGGTTAGAAAGTCGACACATACCACATTTCATAATAAATTAAATATATTTAA
*
32785 TATCAATACATATTCCCTAAGGGGACACATGTTAACCCTTAAACCCCGCACATGCAGTCTGCTAA
196 TATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGCTAA
* * *
32850 ACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGTAATATTATACAATACACTGTCAGTGTA
261 ACTCCACTGACAGTGTATTGTATAATTTTTCTTATAGGAATATTATACAATACACTATCAGTGTA
* * * *
32915 AATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCC-CATTTCATAATTAATTC
326 AATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACATA-CCTCATTTCATAACTAATTC
* *
32975 ACATATTCCCTAATGGGACACATATCAACCCTTAAACCCCACACGTGCATTCTGCTAA-ACTCCA
1 ACATATTCCCTAAGGGGACACATATCAACCCTTAAACCCCACACGTGCAGTCTGCTAAGA-TCCA
*
33039 CTAA-AGGTGTATTGTATAATTTTTCTTATAGGGATTATTATACAATACACTGTCAGTGTAAAAT
65 CTAACA-GTGTATTGTATAATTTTTCTTATAGGGATTACTATACAATACACTGTCAGTGTAAAAT
* * *
33103 TTGGACTCCATAAGTTGGTTAAGAAA-TTGACACATACCACATTTCATAATAAATTATATATATT
129 TTGGACTCCATAAGTGGGTT-AGAAAGTCGACACATACCACATTTCATAATAAATTAAATATATT
** * * *
33167 TAATATTGATACATATTCCCTAATGGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTGC
193 TAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGC
*
33232 TAAACTCCACTGACAGTGTATTGTATAATTTTTCTTATAGGACTATTATACAATACACTATCAGT
258 TAAACTCCACTGACAGTGTATTGTATAATTTTTCTTATAGGAATATTATACAATACACTATCAGT
33297 GTAAATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACATACCTCATTTCATAACTAATT
323 GTAAATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACATACCTCATTTCATAACTAATT
33359 AAATATTTAA
Statistics
Matches: 353, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
384 4 0.01
385 344 0.97
386 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (385 bp):
ACATATTCCCTAAGGGGACACATATCAACCCTTAAACCCCACACGTGCAGTCTGCTAAGATCCAC
TAACAGTGTATTGTATAATTTTTCTTATAGGGATTACTATACAATACACTGTCAGTGTAAAATTT
GGACTCCATAAGTGGGTTAGAAAGTCGACACATACCACATTTCATAATAAATTAAATATATTTAA
TATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGCTAA
ACTCCACTGACAGTGTATTGTATAATTTTTCTTATAGGAATATTATACAATACACTATCAGTGTA
AATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACATACCTCATTTCATAACTAATTC
Done.