Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011748.1 Corchorus olitorius cultivar O-4 contig11781, 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: 1753
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Found at i:804 original size:289 final size:289
Alignment explanation
Indices: 5--819 Score: 1472
Period size: 288 Copynumber: 2.8 Consensus size: 289
1 TTAC
*
5 GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTTTGGCGTGTATGATCATATGTCGGCAAC
1 GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAC
70 AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAAA-ACTGATGGGTGCGAT
66 AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGC-AAAGACTGATGGGTGCGAT
* * *
134 CATACCAGCACTAATGCACCAGATCCCATCAGAACTCCGCAGTTAAGTGTGCTTGGGCGAGTGTA
130 CATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTA
* * *
199 GTACTAGGATGGTTGACCTCCTGGGAAGTCCTCGTGTTGCTCCCCTTTTTTCATTTTTATTTTCT
195 GTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTAGTTTCT
264 TTTCTTCTTCTTTCGAAATTTCTTATGGTA
260 TTTCTTCTTCTTTCGAAATTTCTTATGGTA
*
294 GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGTCGTGTATGATCATATGTCGGCAAC
1 GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAC
*
359 AATGCA-CGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACTGATGGGTGCGATC
66 AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATC
*
423 ATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCTTGCTTGGGCGAGAGTAG
131 ATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
*
488 TACTAAGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTAGTTTCTT
196 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTAGTTTCTT
*
553 TTCTTCTTCTTTCGAAATTTGTTATGGTA
261 TTCTTCTTCTTTCGAAATTTCTTATGGTA
* *
582 GACAATCGTTTCAAGTAAGCATTAAGTCTACAAACGTATGGCGTGTATGATCATATATCGGCAAC
1 GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAC
647 AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATC
66 AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATC
712 ATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
131 ATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
*
777 TACTAGGATGGGTGACCTCCTGGGAAGTTCTCGTGTTGCACCC
196 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
820 GCGTGTATGA
Statistics
Matches: 505, Mismatches: 19, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
287 2 0.00
288 272 0.54
289 231 0.46
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (289 bp):
GACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAC
AATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATC
ATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTAGTTTCTT
TTCTTCTTCTTTCGAAATTTCTTATGGTA
Found at i:856 original size:20 final size:20
Alignment explanation
Indices: 831--871 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
821 CGTGTATGAT
831 CATATGTCGGCAACAATGCA
1 CATATGTCGGCAACAATGCA
851 CATATGTCGGCAACAATGCA
1 CATATGTCGGCAACAATGCA
871 C
1 C
872 CGGATCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
CATATGTCGGCAACAATGCA
Found at i:1017 original size:218 final size:218
Alignment explanation
Indices: 633--1037 Score: 738
Period size: 218 Copynumber: 1.9 Consensus size: 218
623 CGTGTATGAT
*
633 CATATATCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAAGAC
1 CATATATCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAACAC
*
698 TGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGC
66 TGATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGC
* *
763 TTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTTCTCGTGTTGCACCCGCGTGTAT
131 TTGGGCGAGAGTAGTACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCGCGTGTAT
828 GATCATATGTCGGCAACAATGCA
196 GATCATATGTCGGCAACAATGCA
* *
851 CATATGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAACAC
1 CATATATCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAACAC
* *
916 TGATGGGTGTGATCATACCAGCACAAATGCACCGGATCCTATCAGAACTCCGCAGTTAAGCGTGC
66 TGATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGC
981 TTGGGCGAGAGTAGTACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
131 TTGGGCGAGAGTAGTACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
1038 CTTTTTTCAT
Statistics
Matches: 179, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 179 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (218 bp):
CATATATCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAACAC
TGATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGC
TTGGGCGAGAGTAGTACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCGCGTGTAT
GATCATATGTCGGCAACAATGCA
Found at i:1319 original size:507 final size:506
Alignment explanation
Indices: 345--1326 Score: 1793
Period size: 507 Copynumber: 1.9 Consensus size: 506
335 CGTGTATGAT
*
345 CATATGTCGGCAACAATGCACGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACT
1 CATATGTCGGCAACAATGCACGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACT
* *
410 GATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCTTGCT
66 GATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCT
*
475 TGGGCGAGAGTAGTACTAAGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCA
131 TGGGCGAGAGTAGTACTAAGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCA
* *
540 TTTTTAGTTTCTTTTCTTCTTCTTTCGAAATTTGTTATGGTAGACAATCGTTTCAAGTAAGCATT
196 TTTTTAGTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCATT
605 AAGTCTACAAACGTATGGCGTGTATGATCATATATCGGCAACAATGCACCGGATCCAATGAGATG
261 AAGTCTACAAACGTATGGCGTGTATGATCATATATCGGCAACAATGCACCGGATCCAATGAGATG
*
670 TGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGAT
326 TGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCAGAT
735 CCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGG
391 CCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGG
*
800 GAAGTTCTCGTGTTGCACCCGCGTGTATGATCATATGTCGGCAACAATGCA
456 GAAGTCCTCGTGTTGCACCCGCGTGTATGATCATATGTCGGCAACAATGCA
851 CATATGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAACAC
1 CATATGTCGGCAACAATGCA-CGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAACAC
* *
916 TGATGGGTGTGATCATACCAGCACAAATGCACCGGATCCTATCAGAACTCCGCAGTTAAGCGTGC
65 TGATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGC
*
981 TTGGGCGAGAGTAGTACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTC
130 TTGGGCGAGAGTAGTACTAAGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTC
* *
1046 ATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTGGACAATCGTATCAAGTAAGCAT
195 ATTTTTAGTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCAT
* *
1111 TAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAACAATGCACCGGATCCAATGAGAT
260 TAAGTCTACAAACGTATGGCGTGTATGATCATATATCGGCAACAATGCACCGGATCCAATGAGAT
* *
1176 GTGCTTATATATATTTATTATGCAAAGACTGATTGGTGCGATCATACCAGCATTAATGCACCAGA
325 GTGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCAGA
*
1241 TCCCATCAGAACTCCGCATTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTG
390 TCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTG
1306 GGAAGTCCTCGTGTTGCACCC
455 GGAAGTCCTCGTGTTGCACCC
1327 CTTTATTCAT
Statistics
Matches: 457, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
506 20 0.04
507 437 0.96
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (506 bp):
CATATGTCGGCAACAATGCACGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACT
GATGGGTGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCT
TGGGCGAGAGTAGTACTAAGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCA
TTTTTAGTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCATT
AAGTCTACAAACGTATGGCGTGTATGATCATATATCGGCAACAATGCACCGGATCCAATGAGATG
TGCTTATATATATTTATTATGCAAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCAGAT
CCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGG
GAAGTCCTCGTGTTGCACCCGCGTGTATGATCATATGTCGGCAACAATGCA
Found at i:1408 original size:72 final size:72
Alignment explanation
Indices: 1284--1428 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
1274 GCGAGAGTAG
1284 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTTTATTTTCTT
1349 TTCTTCT
66 TTCTTCT
* * *
1356 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTTTATTTTCTT
1421 TTCTTCT
66 TTCTTCT
1428 T
1 T
1429 CTTTCGAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (72 bp):
TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTTTATTTTCTT
TTCTTCT
Found at i:1659 original size:361 final size:361
Alignment explanation
Indices: 995--1753 Score: 1365
Period size: 361 Copynumber: 2.1 Consensus size: 361
985 GCGAGAGTAG
* *
995 TACTAGGATCGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
*
1060 TTCTTCTTCTTTCGAAATTTCTTATGGTGGACAATCGTATCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCATTAAGTCTTCAAACG
* *
1125 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGGATCCAATAAGATGTGCTTATACATAT
* * *
1190 TTATTATGCAAAGACTGATTGGTGCGATCATACCAGCATTAATGCACCAGATCCCATCAGAACTC
196 TTATTATGCAAAGACTGATGGGTGCGATCATACCAACACTAATGCACCAGATCCCATCAGAACTC
*
1255 CGCATTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
*
1320 TGCACCCCTTTATTCATTTTTATTTTCTTTTCTTCT
326 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
*
1356 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
*
1421 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCATTAAGTCTTCAAACG
*
1486 TATGGCGTGTATGATCATATGTCTGCAACAATGCACCGGATCCAATAAGATGTGCTTATACATAT
131 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGGATCCAATAAGATGTGCTTATACATAT
* * * *
1551 TTATTATGCGAAGACTGATGGGTGCGATCATACCAACACTAATGCACCGGTTCCCATTAGAACTC
196 TTATTATGCAAAGACTGATGGGTGCGATCATACCAACACTAATGCACCAGATCCCATCAGAACTC
1616 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
1681 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
326 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
1717 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTT
Statistics
Matches: 381, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
361 381 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (361 bp):
TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTATCAAGTAAGCATTAAGTCTTCAAACG
TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGGATCCAATAAGATGTGCTTATACATAT
TTATTATGCAAAGACTGATGGGTGCGATCATACCAACACTAATGCACCAGATCCCATCAGAACTC
CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
Done.