Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011809.1 Corchorus olitorius cultivar O-4 contig11842, 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: 2856
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Found at i:326 original size:154 final size:154
Alignment explanation
Indices: 1--2853 Score: 4047
Period size: 154 Copynumber: 18.6 Consensus size: 154
*
1 TTAGGCCATAAACATTGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * *
65 ACTAATGGTCCTCGATATGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
129 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
153 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * *
218 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA-CAAAAAAACTTCAAAGTGG
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGTGG
*
282 ACTAATCTTACCAAAATGATTATAG
130 ACTAATCTCACCAAAATGATTATAG
*
307 TTAGGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
** * *
372 ACTAATGGTCCTTGATATGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
437 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * *
461 TTAGGCCATAAACAATGGAACGAAAAGCAATGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * * *
526 CCTAATGGGCCCCGATAGGCCCAAAATAACAAGGGTTCCAAATGAGCTAAAAACTTCAAAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
591 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
*
615 TTAGGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * * *
680 ACTAATGGGCCCCGA-AGGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCAAAGTGG
66 ACTAATGGTCCCCGATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
744 ACTAATCTTACCAAAATGATTATAG
130 ACTAATCTCACCAAAATGATTATAG
* * * *
769 TTAGGCCATAAACAACGGAACGAAAAGACATACGAGGGTTGCCAAATACGATGACGATTCAAAAC
1 TTAGGCCATAAACAATGGAAAGAAAAG-CAT-TGAGGGTTGCCAAAT-CGAAGACGATTCAAAAC
* * *
834 GAAACTAATGGGCCCCGGA-AGGCCTAAAAT-ACAAGTGTTCCAAATGAGGCTAAAAACTTCACA
63 GGAACTAATGGTCCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGA-GCTAAAAACTTCACA
897 GTGGACTAATCTCACCAAAATGATTATAG
126 GTGGACTAATCTCACCAAAATGATTATAG
* * *
926 TTAGCCCATAAACAATGGAAA-CAAAGCATCGA-GGTTAGCCAAATCGAAGACGATTCAAAACGG
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT-GCCAAATCGAAGACGATTCAAAACGG
* * *
989 AACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGGCTAAAAAACGTTCACAG
65 AACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA-GCT-AAAAAC-TTCACAG
1054 TGGACTAATCTCACCAAAATGATTATAG
127 TGGACTAATCTCACCAAAATGATTATAG
* * *
1082 TTAGCCCATAAACAAAGG-AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTCAAAAACG
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA-TTC-AAAACG
** *
1146 TCACTAAATGGTCCCCGATAGGCCCAAAAATCACAAGTGTTCCAAAATGAGCTAAAAAACTTCAC
64 GAACT-AATGGTCCCCGATAGGCCC-AAAATAACAAGTGTTCC-AAATGAGCT-AAAAACTTCAC
*
1211 AGTGGACAAATCTCACCAAAATGATTATAG
125 AGTGGACTAATCTCACCAAAATGATTATAG
* * * *
1241 TTAGGCCAT-AACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACAGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * * *
1305 ACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCGAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
1370 CTTATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * * **
1394 TTAGGCCATAAACAATTGAAAGAAAGGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
*
1459 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1524 CAAATCTCACCAAAACGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * *
1548 TTAAGG-CATAAACAATGGAAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAAACAATTCAAAAC
1 TT-AGGCCATAAACAATGG--AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
* * *
1612 GGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
63 GGAACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
1677 GGACAAATCTCACCAAAATGATTATAG
128 GGACTAATCTCACCAAAATGATTATAG
* * * * * **
1704 TTAGGCCATAAACACTGGAAAAAAAAGCATTGAGGTTTACCAAATCGAAGAC-AATCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
*
1768 ACTAATGGTACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
1833 CTTATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * **
1857 TTAGGCCACAAACAAT----TG---A--A---A--GTT-CCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
*
1907 ACTAAT-GTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1971 CTAATCTCACCAATATGATTATAC
131 CTAATCTCACCAAAATGATTATAG
* * **
1995 TTAGGCCATAAACAAAGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* *
2060 ACTAATGGTCCCCGATAGGCCCAAAATCACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
2125 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * * **
2149 TTAGCCCATAAACAATGGAAAGAAAGGCGTCGAAGGTTGCCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* * *
2214 ACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTGCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
2279 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * * **
2303 TTAGGCCATAAACAATTGAAAGAAAGGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
2368 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2433 CTAATCTCACCAAAATGATTATAT
131 CTAATCTCACCAAAATGATTATAG
* * * * *
2457 TTAGGCCATAAACAATTGAAAGAAAGGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAAC-GA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* *
2521 CACTAGTGGTCCCCGATAGGCCCAACATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
66 -ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
2586 ACTTATCTCACCAAAATGATTATAG
130 ACTAATCTCACCAAAATGATTATAG
* * * * * * ***
2611 TTAGGCCATAAACAATTGAAAGAAAGGAATCGAAGGTTTCCAAATCGAAGACGATTCAAAACTTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* *
2676 ACTAATGGTCCCCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGCGAAAAACTTCACAGTGGA
66 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2741 CTTATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * *
2765 TTAGGCCATAAACTAAT-GAAAGAAAGGCATCGAAGGTTTCCAAATCGAAGACGATTCAAAACGT
1 TTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
*
2829 CACTAATGGTCCCCGATAGGCCCAA
65 AACTAATGGTCCCCGATAGGCCCAA
2854 CAT
Statistics
Matches: 2476, Mismatches: 177, Indels: 94
0.90 0.06 0.03
Matches are distributed among these distances:
138 104 0.04
139 19 0.01
141 1 0.00
142 1 0.00
144 1 0.00
145 1 0.00
146 1 0.00
147 1 0.00
150 1 0.00
152 25 0.01
153 300 0.12
154 1458 0.59
155 40 0.02
156 264 0.11
157 114 0.05
158 22 0.01
159 91 0.04
160 26 0.01
161 6 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAG
Done.