Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002631.1 Corchorus olitorius cultivar O-4 contig02633, 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, 790
Length: 1318
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Found at i:477 original size:155 final size:152
Alignment explanation
Indices: 1--1318 Score: 1917
Period size: 155 Copynumber: 8.5 Consensus size: 152
1 TTTGCCAAATCGAAGTCAATTCAAAACGGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGT
1 TTTGCCAAATCGAAGTCAATTCAAAAC-GGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGT
* * *
66 GTTCCAAATGAGCTAAAATTTCACAGTGGACAT-GTCTCAAAAAAAGTGATTATAGTTAGGCCAT
65 GTTCCAAATGAGCTAAAACTCCACAGTGGA-ATAATCTC-AAAAAA-TGATTATAGTTAGGCCAT
130 AAACAATGGAAAGAAAAGCTTTGAGG
127 AAACAATGGAAAGAAAAGCTTTGAGG
* * * *
156 TTTGCCAAATCGATGTCGATTACAAAACGGTTCTAATGGGGCCCCTAGAAAGGCCCAAAATAACA
1 TTTGCCAAATCGAAGTCAATT-CAAAACGGATCTAAT-GGGCCCC--GAAAGGCCCAAAATTACA
* * * *
221 AGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACCGAAAATGATTATAGTTTTGT
62 AGTGTTCCAAATGAGCT-AAAACTCCACAGTGGAATAATCTCA--AAAAATGATTATAG-TTAGG
286 CCATAAACAATGGAAAGAAAAGCTTTGAGG
123 CCATAAACAATGGAAAGAAAAGCTTTGAGG
316 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
* * *
381 TTCCAAATGAGCTAAAATTTCACAGTGGACAT-GTCTACAAAAAAGTGAGTTATAGTTAGGCCAT
66 TTCCAAATGAGCTAAAACTCCACAGTGGA-ATAATCT-CAAAAAA-TGA-TTATAGTTAGGCCAT
445 AAACAATGGAAAGAAAAGCTTTGAGG
127 AAACAATGGAAAGAAAAGCTTTGAGG
* * * * *
471 TTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGGCCCTGAAAGGCCCAAAATAACAAGT
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAAT-GGGCCCCGAAAGGCCCAAAATTACAAGT
* * *
536 GTTCCAAATGAGCTAAAACTCCACAGTGGAGTAATCTCACCAAAATGATTATAGTT-TGCCATAA
65 GTTCCAAATGAGCTAAAACTCCACAGTGGAATAATCTCA-AAAAATGATTATAGTTAGGCCATAA
600 ACAATGGAAAGAAAAGCTTTGAGG
129 ACAATGGAAAGAAAAGCTTTGAGG
624 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
* * *
689 TTCCAAATGAGCTAAAATTTCACAGTGGACAT-GTCTCAAAAAAGTGATTATAGTTAGGCCATAA
66 TTCCAAATGAGCTAAAACTCCACAGTGGA-ATAATCTCAAAAAA-TGATTATAGTTAGGCCATAA
753 ACAATGGAAAGAAAAGCTTTGAGG
129 ACAATGGAAAGAAAAGCTTTGAGG
* * * * *
777 TTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGCCCTGAAAGGCCCAAAATAACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
* * * *
842 TTACCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACCAAAATGATTATAGTTTGTCCATA
66 TT-CCAAATGAGCT-AAAACTCCACAGTGGAATAATCTCA-AAAAATGATTATAGTTAGGCCATA
907 AACAATGGAAAGAAAAGCTTTGAGG
128 AACAATGGAAAGAAAAGCTTTGAGG
932 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
* * *
997 TTCCAAATGAGCTAAAATTTCACAGTGGACA-ATGTCTCAAAAAAGTGAGTTATAGTTAGGCCAT
66 TTCCAAATGAGCTAAAACTCCACAGTGGA-ATA-ATCTCAAAAAA-TGA-TTATAGTTAGGCCAT
1061 AAACAATGGAAAGAAAAGCTTTGAGG
127 AAACAATGGAAAGAAAAGCTTTGAGG
* * * * *
1087 TTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGCCCTGAAAGGCCCAAAATAACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
* * * *
1152 TTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACCAAAATGATTATAGTTTGTCCATAA
66 TTCCAAATGAGCT-AAAACTCCACAGTGGAATAATCTCA-AAAAATGATTATAGTTAGGCCATAA
*
1217 ACAATGGGAAGAAAAGCTTTGAGG
129 ACAATGGAAAGAAAAGCTTTGAGG
1241 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1306 TTCCAAATGAGCT
66 TTCCAAATGAGCT
Statistics
Matches: 1047, Mismatches: 86, Indels: 61
0.88 0.07 0.05
Matches are distributed among these distances:
151 4 0.00
152 70 0.07
153 177 0.17
154 154 0.15
155 362 0.35
156 140 0.13
158 43 0.04
159 41 0.04
160 56 0.05
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (152 bp):
TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
TTCCAAATGAGCTAAAACTCCACAGTGGAATAATCTCAAAAAATGATTATAGTTAGGCCATAAAC
AATGGAAAGAAAAGCTTTGAGG
Found at i:699 original size:308 final size:307
Alignment explanation
Indices: 1--1318 Score: 2487
Period size: 308 Copynumber: 4.3 Consensus size: 307
1 TTTGCCAAATCGAAGTCAATTCAAAACGGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGT
1 TTTGCCAAATCGAAGTCAATTCAAAAC-GGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGT
66 GTTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTCAAAAAAAGTGATTATAGTTAGGCCATA
65 GTTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTC-AAAAAAGTGATTATAGTTAGGCCATA
131 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTACAAAACGGTTCTAATGGG
129 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATT-CAAAACGGTTCTAAT-GG
196 GCCCCTAGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATC
192 G-CCCT-GAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATC
261 TCACCGAAAATGATTATAGTTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
255 TCACC-AAAATGATTATAG-TTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
316 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
381 TTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTACAAAAAAGTGAGTTATAGTTAGGCCATA
66 TTCCAAATGAGCTAAAATTTCACAGTGGACATGTCT-CAAAAAAGTGA-TTATAGTTAGGCCATA
446 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGG
129 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAAT-GGG
511 CCCTGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTCCACAGTGGAGTAATCTCA
193 CCCTGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCA
575 CCAAAATGATTATAGTTTG-CCATAAACAATGGAAAGAAAAGCTTTGAGG
258 CCAAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
624 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
689 TTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTCAAAAAAGTGATTATAGTTAGGCCATAAA
66 TTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTCAAAAAAGTGATTATAGTTAGGCCATAAA
754 CAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGCCC
131 CAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGCCC
819 TGAAAGGCCCAAAATAACAAGTGTTACCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACC
196 TGAAAGGCCCAAAATAACAAGTGTT-CCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACC
884 AAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
260 AAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
932 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
997 TTCCAAATGAGCTAAAATTTCACAGTGGACAATGTCTCAAAAAAGTGAGTTATAGTTAGGCCATA
66 TTCCAAATGAGCTAAAATTTCACAGTGGAC-ATGTCTCAAAAAAGTGA-TTATAGTTAGGCCATA
1062 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGC
129 AACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGC
1127 CCTGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCAC
194 CCTGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCAC
*
1192 CAAAATGATTATAGTTTGTCCATAAACAATGGGAAGAAAAGCTTTGAGG
259 CAAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
1241 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1 TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
1306 TTCCAAATGAGCT
66 TTCCAAATGAGCT
Statistics
Matches: 995, Mismatches: 1, Indels: 20
0.98 0.00 0.02
Matches are distributed among these distances:
305 31 0.03
306 88 0.09
307 55 0.06
308 256 0.26
309 185 0.19
310 121 0.12
311 27 0.03
312 35 0.04
313 4 0.00
314 103 0.10
315 90 0.09
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (307 bp):
TTTGCCAAATCGAAGTCAATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAGTG
TTCCAAATGAGCTAAAATTTCACAGTGGACATGTCTCAAAAAAGTGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGCCC
TGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAGTAATCTCACCA
AAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGAGG
Done.