Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011487.1 Corchorus olitorius cultivar O-4 contig11520, 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, 949
Length: 1582
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Found at i:935 original size:154 final size:154
Alignment explanation
Indices: 654--1575 Score: 1451
Period size: 154 Copynumber: 6.0 Consensus size: 154
644 TTGTTTTACA
* * *
654 AAATCGAAGACGATTCAAAATGTCACTAATGGTCCCCGATAGGCCCAAACTAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* *
719 ATGAGCTAAAAACTTCACAGTGGACTAA-CATCACCAAAATTG-TAATAGCTAGGCCATAAACAA
66 ATGAGCTAAAAACTTCACAGTGGACTAATC-TCACCAAAA-TGATTATAGTTAGGCCATAAACAA
**
782 TGGAAAGAAAAGGAATTGAGGTTTTTC
129 TGGAAAGAAAA-GAATTGAGGTTTGCC
*
809 AAATCGAAGACGATTCAAAACGTCACTGATGGGCCCCGATAGG-CCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
873 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
938 GAAAGAAAAGAATTGAGGTTTGCC
131 GAAAGAAAAGAATTGAGGTTTGCC
** ** * * *
962 AAATCGAAGATAATTCAAAACGAAACTAATGGGCCTCGATAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* *
1027 ATAAGCTAAAAACTTCACAGTGGACTAA-CATCACCAAAATGATAATAGTTAGGCCATAAACAAT
66 ATGAGCTAAAAACTTCACAGTGGACTAATC-TCACCAAAATGATTATAGTTAGGCCATAAACAAT
1091 GGAAAGAAAAGGAATTGAGGTTTGCC
130 GGAAAGAAAA-GAATTGAGGTTTGCC
*
1117 AAATCGAAGACGATTCAAAACGTCACTGATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1182 ATGAGCTAAAAACTTCACAGTGGA-TAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
66 ATGAGCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
1246 GGAAAGAAAAGCATTGAGGTTTGCC
130 GGAAAGAAAAGAATTGAGGTTTGCC
** ** * * *
1271 AAATCGAAGATAATTCAAAACGAAACTAATGGGCCTCGAAAGGCCCAAAATAACCAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
*
1336 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAATATAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
*
1401 GAAAGAAAAGCATTGAGGTTTGCC
131 GAAAGAAAAGAATTGAGGTTTGCC
* *
1425 AAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGCTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
*
1490 ATGAGCTAAAAACTTCACAGTGGA-TAAATCTCACCAAAATGATTATAGTTAGACCATAAACAAT
66 ATGAGCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
1554 GGAAAGAAAAGCATTGAGGTTT
130 GGAAAGAAAAGAATTGAGGTTT
1576 TTCCGAA
Statistics
Matches: 709, Mismatches: 49, Indels: 19
0.91 0.06 0.02
Matches are distributed among these distances:
153 53 0.07
154 473 0.67
155 182 0.26
156 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGAATTGAGGTTTGCC
Found at i:1526 original size:463 final size:462
Alignment explanation
Indices: 654--1575 Score: 1451
Period size: 463 Copynumber: 2.0 Consensus size: 462
644 TTGTTTTACA
* * *
654 AAATCGAAGACGATTCAAAATGTCACTAATGGTCCCCGATAGGCCCAAACTAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
719 ATGAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATTGTAATAGCTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATTGTAATAGCTAGGCCATAAACAATG
** * ** * *
784 GAAAGAAAAGGAATTGAGGTTTTTCAAATCGAAGACGATTCAAAACGTCACTGATGGGCCCCGAT
131 GAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGAAACTAATGGGCCCCGAA
849 AGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
196 AGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
* *
914 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGATAATTCA
261 AATATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCA
* *
979 AAACGAAACTAATGGGCCTCGATAGACACAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCA
326 AAACGAAACTAATGGGCCCCGATAGACACAAAATAACAAGTGCTCCAAATAAGCTAAAAACTTCA
*
1044 CAGTGGACTAACATCACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGGAATTGA
391 CAGTGGACTAACATCACCAAAATGATAATAGTTAGACCATAAACAATGGAAAGAAAA-GAATTGA
1109 GGTTTGCC
455 GGTTTGCC
*
1117 AAATCGAAGACGATTCAAAACGTCACTGATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* *
1182 ATGAGCTAAAAACTTCACAGTGGA-TAA-ATCTCACCAAAA-TGATTATAGTTAGGCCATAAACA
66 ATGAGCTAAAAACTTCACAGTGGACTAACA--TCACCAAAATTG-TAATAGCTAGGCCATAAACA
* * *
1244 ATGGAAAGAAAA-GCATTGAGGTTTGCCAAATCGAAGATAATTCAAAACGAAACTAATGGGCCTC
128 ATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGAAACTAATGGGCCCC
*
1308 GAAAGGCCCAAAATAACCAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
193 GAAAGG-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
1373 AATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
257 AATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACAA
** * * * *
1438 TTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGCTCCAAATGAGCTAAAAAC
322 TTCAAAACGAAACTAATGGGCCCCGATAGACACAAAATAACAAGTGCTCCAAATAAGCTAAAAAC
* *
1503 TTCACAGTGGA-TAA-ATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGC
387 TTCACAGTGGACTAACA--TCACCAAAATGATAATAGTTAGACCATAAACAATGGAAAGAAAAGA
1566 ATTGAGGTTT
450 ATTGAGGTTT
1576 TTCCGAA
Statistics
Matches: 421, Mismatches: 32, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
461 2 0.00
462 67 0.16
463 352 0.84
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (462 bp):
AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAACATCACCAAAATTGTAATAGCTAGGCCATAAACAATG
GAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGAAACTAATGGGCCCCGAA
AGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
AATATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCA
AAACGAAACTAATGGGCCCCGATAGACACAAAATAACAAGTGCTCCAAATAAGCTAAAAACTTCA
CAGTGGACTAACATCACCAAAATGATAATAGTTAGACCATAAACAATGGAAAGAAAAGAATTGAG
GTTTGCC
Done.