Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023469.1 Corchorus olitorius cultivar O-4 contig23502, 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, 960
Length: 1601
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Found at i:31 original size:21 final size:21
Alignment explanation
Indices: 1--114 Score: 160
Period size: 21 Copynumber: 5.4 Consensus size: 21
*
1 AATGATCTTGGAACCTTCTCC
1 AATGAACTTGGAACCTTCTCC
*
22 AATGAACTTGGAACCTTTTCC
1 AATGAACTTGGAACCTTCTCC
43 AATGAACTTGGAACCTTCTCC
1 AATGAACTTGGAACCTTCTCC
*
64 AATGAGCTTGGAA-CTTGCTCC
1 AATGAACTTGGAACCTT-CTCC
*
85 AATGAGCTTGGAA-CTTGCTCC
1 AATGAACTTGGAACCTT-CTCC
106 AATGAACTT
1 AATGAACTT
115 CTAGCATCTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 84 0.97
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (21 bp):
AATGAACTTGGAACCTTCTCC
Found at i:500 original size:154 final size:154
Alignment explanation
Indices: 217--1601 Score: 2128
Period size: 154 Copynumber: 9.0 Consensus size: 154
207 TGGCACATCA
* * * *
217 CATAAACAATGGAAAGAAAAGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAACAGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
282 GGGACCCGATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTTAAAACTTCACAGTGGACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
347 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* * * * **
371 CAAAAACAATGGAAAGAAAGGCATCGAAGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
436 GGTCCCCGATAGTCCCAAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
501 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
525 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
590 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
655 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
679 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
*
744 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
809 TCACCAAAATGATAATAATTAGGC
131 TCACCAAAATGATTATAGTTAGGC
833 CATAAACAATGGAAAGAAAAGCATTTAGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
1 CATAAACAATGGAAAGAAAAGCA-TT-GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * * *
898 ATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAA
64 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
963 TCTTACCAAAATGATTATAGTTAGGC
129 TCTCACCAAAATGATTATAGTTAGGC
*
989 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
1054 GGGCCTCGATAGGACCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTACATAGTGTACTAAT
66 GGGCCCCGATAGG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
**
1118 CTCAAAAAAATGATTATAGTTAGGC
130 CTCACCAAAATGATTATAGTTAGGC
*
1143 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
1208 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCTCACAGTGGACAAATA
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
1273 TCACCAAAATGATAATAATTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* * * *
1297 CATAAACAATGGAAAGAAAAG-AATGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
1361 GGGCCCCGAAAGGCCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATAT
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-AT
*
1425 CTTACCAAAATGATTATAGTTAGGC
130 CTCACCAAAATGATTATAGTTAGGC
* * * * *
1450 CATAAACAATGGATAGAAAAGACTTTGAGGTTTTGCCAAATCGAAGTCGATTCAAAACGGTACTA
1 CATAAACAATGGAAAGAAAAG-CATTGAGG-GTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * * * *
1515 ATGAGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATCAGCTAAAAAATTTCACAGTGGACTA
64 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTA
*
1580 ATCTCAACAAAAATGATTATAG
128 ATCTC-ACCAAAATGATTATAG
Statistics
Matches: 1141, Mismatches: 79, Indels: 18
0.92 0.06 0.01
Matches are distributed among these distances:
152 1 0.00
153 167 0.15
154 681 0.60
155 38 0.03
156 217 0.19
157 21 0.02
158 16 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGC
Found at i:1103 original size:464 final size:460
Alignment explanation
Indices: 217--1601 Score: 2189
Period size: 464 Copynumber: 3.0 Consensus size: 460
207 TGGCACATCA
* * * *
217 CATAAACAATGGAAAGAAAAGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAACAGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* *
282 GGGACCCGATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTTAAAACTTCACAGTGGACTAATC
66 GGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * * *
347 TCACCAAAATGATTATAGTTAGGCCAAAAACAATGGAAAGAAAGGCATCGAAGGTTGCCAAATCG
130 TCACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGCAT-GAGGGTTGCCAAATCG
** * * *
412 AAGACGATTCAAAACGTCACTAATGGTCCCCGATAGTCCCAAAATAACAAGTGTTACAAATGAGC
194 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
*
477 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
259 TAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
542 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCA
324 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCA
*
607 AAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACCAAAATGATTATA
389 AAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACAAAAATGATTATA
672 GTTAGGC
454 GTTAGGC
679 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
744 GGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGGCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
809 TCACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGCATTTAGAGGGTTGCCAAAT
130 TCACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGCA--T-GAGGGTTGCCAAAT
*
874 CGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
192 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * *
939 GCTAAAAACTACATAGTGTACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
257 GCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1004 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGCACTAATGGGCCTCGATAGGAC
322 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGG-C
*
1069 CCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTACATAGTGTACTAATCTCAAAAAAATGATT
386 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACAAAAATGATT
1133 ATAGTTAGGC
451 ATAGTTAGGC
*
1143 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACGGAACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
1208 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCTCACAGTGGACAAATA
66 GGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
1273 TCACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGAATGAGGTTTGCCAAATCGA
130 TCACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGCATGAGGGTTGCCAAATCGA
* * * * *
1338 AGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAATTGTTCCAAATGAGCT
195 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
1403 AAAAACTTCACAGTGGAC-ATATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGA
260 AAAAACTTCACAGTGGACTA-ATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* * * * * * *
1467 AAAGACTTTGAGGTTTTGCCAAATCGAAGTCGATTCAAAACGGTACTAATGAGCCCCGAAAGGCC
324 AAAG-CATTGAGG-GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCC
* * * * * *
1532 TAAAATAACAAGTGTTCCAAATCAGCTAAAAAATTTCACAGTGGACTAATCTCAACAAAAATGAT
387 CAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTACATAGTGTACTAATCTC-ACAAAAATGAT
1597 TATAG
450 TATAG
Statistics
Matches: 856, Mismatches: 56, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
460 1 0.00
461 139 0.16
462 199 0.23
463 43 0.05
464 428 0.50
465 46 0.05
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (460 bp):
CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
CACCAAAATGATAATAATTAGGCCATAAACAATGGAAAGAAAAGCATGAGGGTTGCCAAATCGAA
GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
AAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAA
ATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACAAAAATGATTATAGT
TAGGC
Done.