Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011810.1 Corchorus olitorius cultivar O-4 contig11843, 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: 2499
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Found at i:719 original size:154 final size:154
Alignment explanation
Indices: 1--2499 Score: 3760
Period size: 154 Copynumber: 16.2 Consensus size: 154
* * * *
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAACGGTCCCC-GATAGGCCCAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCCTAAAATAA
* *
65 CAAGTGCTCCAAACTGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
65 CAAGTGTTCCAAA-TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
130 GCCATAAACAATCGAAAGAAAAGGCAT
129 GCCATAAACAATGGAAAGAAAA-GCAT
* *
157 CGAAGGTTGCCAAATCGAAGACGATTCAAAACG-ACACTAATGGGCCCC-GATAGGCCCAAAATA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTA-ACTAATGGGCCCCGGA-AGGCCTAAAATA
*
220 ACAAGTGTTCCAAATCGAGCCTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTT
64 ACAAGTGTTCCAAAT-GAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
285 AGGCCATAAACAATAGGAAAGAAAAGCAT
127 AGGCCATAAACAAT-GGAAAGAAAAGCAT
* * *
314 CGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCT-AAAATAA
* *
379 CAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATTATTATAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
444 CCATAAACAATGGAAAG-AAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* *
468 CGAGGGTTGCCAAATCGAAGACGAGTTCAAAACGGGAACTAATGGGCCCCGAAAGGCCTAAAATA
1 CGAGGGTTGCCAAATCGAAGACGA-TTCAAAAC-GTAACTAATGGGCCCCGGAAGGCCTAAAATA
533 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
64 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
598 GCCAT-AACAATCGAAAGAAAAGCAT
129 GCCATAAACAATGGAAAGAAAAGCAT
* * *
623 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCCGGAAGGCCTAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG-CCCCGGAAGGCCTAAAATAA
*
688 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGGCAAAATGATTATAGTTAG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CCAAAATGATTATAGTTAG
*
753 CCCATAAACAATGGAAAGAAAAGCAT
129 GCCATAAACAATGGAAAGAAAAGCAT
* *
779 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAAC
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
844 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
*
909 CATAAACAATGGAAACAAAAGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* ** * * * *
933 TGAGCTTTGCCAAATCGAACACGATTCAAACCGTCACTAATGGGCCCC-GATAGGCCCAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCCTAAAATAA
* *
997 CATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC-CCTATAATGATTATAGTTAG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATTATAGTTAG
* *
1061 GCCATAAACAATCGAAAAAAAAGCAT
129 GCCATAAACAATGGAAAGAAAAGCAT
* * * * *
1087 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCCGATAGGCCAAAAAATA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCC-TAAAATA
*
1152 ACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
64 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
1217 GCCATAAACAATGGAAACAAAAGCAT
129 GCCATAAACAATGGAAAGAAAAGCAT
* * * * * *
1243 CGAGGGTTGCGAAATCGATGACGATTCAAATCGAAACTAATGGCCCCCGGAACGCCTAAAATAAC
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
* *
1308 AAGTGTTCCAAATAAGCTAAAAGCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
1373 CATAAACAATCGAAAGAAAAACAT
131 CATAAACAATGGAAAGAAAAGCAT
* * * * *
1397 TGAGGTTTCCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGAAAGGCCTAAAATAAC
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
* *
1462 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGTCTAATCTCACCAAAATGATTATAATTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1527 CATAAACAATGGAAAGAAAAGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* * *
1551 CGAGGGTTGCCAAATCAAAGACGATTCAAAACGTCACTAATGGGCCCC-GATAGGCCCAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCCTAAAATAA
* * *
1615 CAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTAAAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1680 CCATAAACAATGGAAAGAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* * ** * * ** *
1705 CAAGGGTTCCCAAATCGATTACGATTCAAAACTTCACTAATGGG-CCTTGATAGGCCCAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCCTAAAATAA
*
1769 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CAAAATGATTATAGTTAGC
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1833 CCATAAACAATGGAAACAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* * *
1858 CGAGGGTTGCCCAAATCGATGACGATTCAAAACGAAACTAATGGCCCCCGGAAGGCCTAAAATAA
1 CGAGGGTTG-CCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAA
1923 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1988 CCATAAACAATCGAAAGAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* * * *
2013 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC-GATAGGCCCAAAATAA
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGA-AGGCCTAAAATAA
* * *
2077 CAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGC
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
2142 CCATAAACAATGGAAAGAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* *
2167 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAAC
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
2232 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
2297 CATAAACAATGGCAACAAAAGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* * * * * * * *
2321 CGAGGGTTGCGAAATCGATGACGATTGAAATCGAAACTAATGGCCCCCGGAAGGCTTAAATTAAC
1 CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
* *
2386 AAGTGTTCCAAATAAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
2451 CATAAACAATCGAAAGAAAAACAT
131 CATAAACAATGGAAAGAAAAGCAT
* * *
2475 TGAGGTTTCCCAAATCGAAGACGAT
1 CGAGGGTTGCCAAATCGAAGACGAT
Statistics
Matches: 2150, Mismatches: 168, Indels: 52
0.91 0.07 0.02
Matches are distributed among these distances:
153 66 0.03
154 1323 0.62
155 269 0.13
156 345 0.16
157 115 0.05
158 32 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (154 bp):
CGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGGAAGGCCTAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCAT
Done.