Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011803.1 Corchorus olitorius cultivar O-4 contig11836, 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, 865
Length: 1442
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Found at i:880 original size:154 final size:154
Alignment explanation
Indices: 1--1442 Score: 1891
Period size: 154 Copynumber: 9.3 Consensus size: 154
**
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATAATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * ** *
66 GGAACTAATGGGCCTCGATAGGCAGAAAATAACAAATGTTCCAAATGAGACT-AAAACTTCACAG
66 GTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAG
*
130 TGGACTAATCTCAATC-AAATGATTA
130 TGGACTAATCTC-ACCAAAATGATTA
**
155 TAGTTAGGACCAATAAACAATAGGAAAGAAAAGCATTGAAGGTTTGCCAAATCGAAGATAATTCA
1 TAGTTAGG-CC-ATAAACAAT-GGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCA
* * * * *
220 AAACGAAACTAATGGGCCTCGATAGGACAACAAAATAACAAGTAGTTACAAATAAGACT-AAAAC
62 AAACGTAACTAATGGGCCCCGATAGG-C-CCAAAATAACAAGT-GTTCCAAATGAG-CTAAAAAC
* *
284 TTACACAGTGGACTAATAGTCACCAAAATCATTA
123 TT-CACAGTGGACTAAT-CTCACCAAAATGATTA
* *
318 TAGTTAGTCCAT-AACAATGG-AAG-AAAGCATTGAGCTTTGCCAAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * ** * *
380 GTCACTAATCGGACCTTAGATAGGCCCAAAATAACAAGTAGTAGCCAAATGAGCTAAAAACTTTA
66 GTAACTAAT-GGGCC-CCGATAGGCCCAAAATAACAAGT-GT-TCCAAATGAGCTAAAAACTTCA
*
445 CAGTGGACTAATCTTACCAAAATCGATTA
127 CAGTGGACTAATCTCACCAAAAT-GATTA
* *
474 TAGTTAGTCCCGTAAACAATGG-AAG-AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
1 TAGTTAG-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
* * * * *
537 CGTCACTAACGGGCACCGATAAGGACCAAAATAACAAGTGTTCCAAATAAGCT-AAAACTTCACA
65 CGTAACTAATGGGCCCCGAT-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* *
601 GTGGACTAATGTCACC-AAATCATTA
129 GTGGACTAATCTCACCAAAATGATTA
* *
626 TAGTTAGTCCAT-AACAATGG-AAG-AAAGCATTGAGCTTTGCCAAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * ** * *
688 GTCACTAATCGGACCTTGAATAGGCCCAAAATAACAAGTAGTGCCAAATGAGCTAAAAACTTTAC
66 GTAACTAAT-GGGCCCCG-ATAGGCCCAAAATAACAAGT-GTTCCAAATGAGCTAAAAACTTCAC
*
753 AGTGGACTAATCTTACCAAAATGATTA
128 AGTGGACTAATCTCACCAAAATGATTA
* *
780 TAGTTAGTCCCTAAACAATGG-AAG-AAAGCATTGAGGTTTGCCAAATCGTAAGACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG-AAGACGATTCAAAA
* * *
843 CGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAG
65 CGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
908 TGGACTAATCTCACC-AAATGATTA
130 TGGACTAATCTCACCAAAATGATTA
* * *
932 TAGTTAGGCCATAACACAATGG-AAG-AAAGCATTGAGGTTTGCTAAATCGAAGAAGATTCAATA
1 TAGTTAGGCCATAA-ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
* * * * * *
995 CGTTACTAATGGG-CCCGATAGGTCC-AAATAACAAGT-TTCCAAATAAGCTTAAAAGTTCACAA
65 CGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* *
1057 TGGACTAATCTGACCAAATTGATTA
130 TGGACTAATCTCACCAAAATGATTA
* *
1082 TGGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAT
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
*
1147 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 GTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
1212 GGACTAATCTCACTAAAATGATTA
131 GGACTAATCTCACCAAAATGATTA
*
1236 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCGAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* *
1301 GGAACTAATGGGCCCCGATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 GTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1366 GGACTAATCTCACCAAAATGATTA
131 GGACTAATCTCACCAAAATGATTA
* *
1390 TAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTTGCCAATTCGAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAA
Statistics
Matches: 1155, Mismatches: 100, Indels: 65
0.88 0.08 0.05
Matches are distributed among these distances:
149 43 0.04
150 92 0.08
151 80 0.07
152 80 0.07
153 110 0.10
154 301 0.26
155 72 0.06
156 114 0.10
157 67 0.06
158 118 0.10
159 3 0.00
160 18 0.02
161 22 0.02
162 18 0.02
163 17 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
GTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
GGACTAATCTCACCAAAATGATTA
Found at i:1333 original size:457 final size:456
Alignment explanation
Indices: 1--1442 Score: 1956
Period size: 457 Copynumber: 3.1 Consensus size: 456
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATA-ATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA-AGATTCAAAA
* * * *
65 CGGAACTAATGGGCCTCGATAGGCAGAAAATAACAAATGTTCCAAATGAGACTAAAACTTCACAG
65 CGTAACTAATGGGCC-CGATAGGC--CAAATAACAAGTGTTCCAAATAAG-CTAAAACTTCACAG
*
130 TGGACTAATCTCAATCAAATGATTATAGTTAGGACCAATAAACAATAGGAAAGAAAAGCATTGAA
126 TGGACTAATCT-AACCAAATGATTATAGTTAGG-CC-ATAAACAAT-GGAAAGAAAAGCATTG-A
** *
195 GGTTTGCCAAATCGAAGATAATTCAAAACGAAACTAATGGGCCTCGATAGGACAACAAAATAACA
186 GGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCTCGATAGG-C-CCAAAATAACA
* * * *
260 AGTAGTTACAAATAAGACT-AAAACTTACACAGTGGACTAATAGTCACCAAAATCATTATAGTTA
249 AGTAGTTCCAAATGAG-CTAAAAACTT-CACAGTGGACTAAT-CTCACCAAAATGATTATAGTTA
*
324 GTCCAT-AACAATGGAAGAAAGCATTGAGCTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
311 GTCCATAAACAATGGAAGAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
** ** *
388 TCGGACCTTAGATAGGCCCAAAATAACAAGTAGTAGCCAAATGAGCTAAAAACTTTACAGTGGAC
376 T-GGACC-CCGATAGGCCCAAAATAACAAGT--TTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
453 TAATCTTACCAAAATCGATTA
437 TAATCTCACCAAAAT-GATTA
* * *
474 TAGTTAGTCCCGTAAACAATGG-AAG-AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
1 TAGTTAG-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAA
* *
537 CGTCACTAACGGGCACCGATAAGGACCAAAATAACAAGTGTTCCAAATAAGCTAAAACTTCACAG
65 CGTAACTAATGGGC-CCGAT-AGG-CC-AAATAACAAGTGTTCCAAATAAGCTAAAACTTCACAG
* * * * *
602 TGGACTAATGTCACCAAATCATTATAGTTAGTCCAT-AACAATGG-AAG-AAAGCATTGAGCTTT
126 TGGACTAATCTAACCAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
** * *
664 GCCAAATCGAAGACGATTCAAAACGTCACTAATCGGACCTTGAATAGGCCCAAAATAACAAGTAG
191 GCCAAATCGAAGACGATTCAAAACGAAACTAAT-GGGCCTCG-ATAGGCCCAAAATAACAAGTAG
* * * *
729 TGCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTTACCAAAATGATTATAGTTAGTCCCTAA
254 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
*
794 ACAATGGAAGAAAGCATTGAGGTTTGCCAAATCGTAAGACGATTCAAAACGTCACTAATGGTCCC
319 ACAATGGAAGAAAGCATTGAGGTTTGCCAAATCG-AAGACGATTCAAAACGTCACTAATGGACCC
859 CGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-
383 CGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
923 AAATGATTA
448 AAATGATTA
* *
932 TAGTTAGGCCATAACACAATGG-AAG-AAAGCATTGAGGTTTGCTAAATCGAAGAAGATTCAATA
1 TAGTTAGGCCATAA-ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAA
* * *
995 CGTTACTAATGGGCCCGATAGGTCCAAATAACAAGT-TTCCAAATAAGCTTAAAAGTTCACAATG
65 CGTAACTAATGGGCCCGATAGG-CCAAATAACAAGTGTTCCAAATAAGC-TAAAACTTCACAGTG
* *
1059 GACTAATCTGACCAAATTGATTATGGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
128 GACTAATCTAACCAAA-TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
* * *
1124 CCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT-GTTC
192 CCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTAGTTC
* *
1188 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACA
257 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACA
* ** *
1253 ATGGAAAGAAAAGCATTGAGGTTTGCCGAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
322 ATGG-AAG-AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGACCCCG
* *
1318 ATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
385 ATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1383 ATGATTA
450 ATGATTA
* *
1390 TAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTTGCCAATTCGAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAA
Statistics
Matches: 871, Mismatches: 75, Indels: 59
0.87 0.07 0.06
Matches are distributed among these distances:
454 12 0.01
455 38 0.04
456 87 0.10
457 137 0.16
458 126 0.14
459 59 0.07
460 50 0.06
462 45 0.05
463 53 0.06
464 88 0.10
465 16 0.02
466 8 0.01
467 2 0.00
468 6 0.01
469 2 0.00
470 2 0.00
471 17 0.02
472 75 0.09
473 35 0.04
474 13 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (456 bp):
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAAC
GTAACTAATGGGCCCGATAGGCCAAATAACAAGTGTTCCAAATAAGCTAAAACTTCACAGTGGAC
TAATCTAACCAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
ATCGAAGACGATTCAAAACGAAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTAGTTCCAAA
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGG
AAGAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGC
CCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
A
Done.