Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021062.1 Corchorus olitorius cultivar O-4 contig21095, 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, 783
Length: 1306
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:282 original size:154 final size:154
Alignment explanation
Indices: 1--1306 Score: 1936
Period size: 154 Copynumber: 8.4 Consensus size: 154
*
1 TTATAGTTAGGCCATAAACAATGGAAAG-AAAGACATTTGAGGTTTGCCAAATGGAAGACAATTC
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CA-TTGAGGTTTGCCAAATCGAAGACAATTC
65 AAAACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
64 AAAACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
130 ACAGTGTACTAACCTCACCAAAATGA
129 ACAGTGGACTAACCTCACCAAAATGA
* * *
156 TTATAGTTAGGCCGTACACGATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
*
221 AACGGAACGAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
66 AACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
286 AGTGGACTAATCTCACCAAAATGA
131 AGTGGACTAACCTCACCAAAATGA
* * * *
310 TTATAGTTAGACCATAAACAATTGAAATAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
** * * *
375 AACGTCACTAATGGTCCCCGATAGGCC-TAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
66 AACGGAACTAATGGGCCTCGATA-GCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
439 CAGTGGACTAATCTCACCAAAATGA
130 CAGTGGACTAACCTCACCAAAATGA
* *
464 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGATAATTCAA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
* * *
529 AACGGAACTAATGGGCCTCGATAGGCACAAAATAACAATTGTTCCAAATAAGCTAAAAACTTCAC
66 AACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
594 AGTGGACTAACATCACCAAAATGA
131 AGTGGACTAACCTCACCAAAATGA
* * * *
618 TAATAGTTAGGCCATGAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAA-GCATTGAGGTTTGCCAAATCGAAGACAATTCA
*** * * *
683 AAACATCACTGATGGGCCCCGATAGGCC-TAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAACGGAACTAATGGGCCTCGATA-GCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
747 ACAGTGGACTAATCTCACCAAAATGA
129 ACAGTGGACTAACCTCACCAAAATGA
* * *
773 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGATAATTTAA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
* *
838 AACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCAC
66 AACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
903 AGTGGACTAACATCACCAAAATGA
131 AGTGGACTAACCTCACCAAAATGA
* * * * *
927 TAATAGTTAGGCCATGAACAATGGAAAGAAAAGGAATTGAGGCTTGCCAAATCGAAGACGATTCA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAA-GCATTGAGGTTTGCCAAATCGAAGACAATTCA
*** * *
992 AAACATCACTGATGGGCCCCGATAGGCC-CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAACGGAACTAATGGGCCTCGATA-GCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
1056 ACAGTGGACTAATCTCACCAAAATGA
129 ACAGTGGACTAACCTCACCAAAATGA
* * *
1082 TTATAGTTAGGACATAAACAATGGAAAAAGAAAGCATTGAGGTTTGCCAAATCGAAGATAATTCA
1 TTATAGTTAGGCCATAAACAATGGAAAGA-AAAGCATTGAGGTTTGCCAAATCGAAGACAATTCA
** * *
1147 AAACAAAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCA
65 AAACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
1212 CAGTGGACTAACATCACCCAAAATGA
130 CAGTGGACTAACCTCA-CCAAAATGA
* * *
1238 TAATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCA
1 TTATAGTTAGGCCATAAACAATGGAAAGAAAA-GCATTGAGGTTTGCCAAATCGAAGACAATTCA
1303 AAAC
65 AAAC
Statistics
Matches: 1030, Mismatches: 109, Indels: 23
0.89 0.09 0.02
Matches are distributed among these distances:
153 4 0.00
154 553 0.54
155 394 0.38
156 79 0.08
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAA
AACGGAACTAATGGGCCTCGATAGCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTAACCTCACCAAAATGA
Found at i:799 original size:309 final size:309
Alignment explanation
Indices: 3--1306 Score: 2186
Period size: 309 Copynumber: 4.2 Consensus size: 309
1 TT
* *
3 ATAGTTAGGCCATAAACAATGGAAAG-AAA-GACATTTGAGGTTTGCCAAATGGAAGACAATTCA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGA-A-TTGAGGTTTGCCAAATCGAAGACGATTCA
*** *
66 AAACGGAACTAATGGGCCTCGATA-GCCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
64 AAACATCACTAATGGGCCCCGATAGGCC-CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* * * * * *
130 ACAGTGTACTAACCTCACCAAAATGATTATAGTTAGGCCGTACACGATGGAAAGAAAAGCATTGA
128 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGA
* * *
195 GGTTTGCCAAATCGAAGACAATTCAAAACGGAACGAATGGGCCTCGATAGCCACAAAATAACAAG
193 GGTTTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAG
* *
260 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC-TCACCAAAATGATT
258 TGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAA-CATCACCAAAATGATA
* * * *
312 ATAGTTAGACCATAAACAATTGAAATAAAA-GCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* * *
376 ACGTCACTAATGGTCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 ACATCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
441 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGT
131 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGT
*
506 TTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAATTGT
196 TTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGT
571 TCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATGATA
261 TCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATGATA
*
620 ATAGTTAGGCCATGAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* *
685 ACATCACTGATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 ACATCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
750 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGT
131 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGT
*
815 TTGCCAAATCGAAGATAATTTAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGT
196 TTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGT
880 TCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATGATA
261 TCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATGATA
* *
929 ATAGTTAGGCCATGAACAATGGAAAGAAAAGGAATTGAGGCTTGCCAAATCGAAGACGATTCAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
*
994 ACATCACTGATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 ACATCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* * *
1059 GTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAAAGAAAGCATTGAGG
131 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA-AAAGCAATGAGG
**
1124 TTTGCCAAATCGAAGATAATTCAAAACAAAACTAATGGGCCTCGATAGGCACAAAATAACAAGTG
195 TTTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTG
1189 TTCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCCAAAATGATA
260 TTCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCA-CCAAAATGATA
1240 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
1305 AC
66 AC
Statistics
Matches: 946, Mismatches: 43, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
307 1 0.00
308 276 0.29
309 477 0.50
310 116 0.12
311 76 0.08
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (309 bp):
ATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAA
ACATCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGT
TTGCCAAATCGAAGATAATTCAAAACGGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGT
TCCAAATAAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATGATA
Done.