Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010113.1 Corchorus olitorius cultivar O-4 contig10145, 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: 2278
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Found at i:367 original size:98 final size:97
Alignment explanation
Indices: 195--380 Score: 259
Period size: 98 Copynumber: 1.9 Consensus size: 97
185 TGACCTGGAA
*
195 TATTTTTCCTCAATTTTTTGACCAAAATACTAATAAAAATATATAATTCAACACCAAAAATATTG
1 TATTTTTCCTCAATTTTTTGACCAAAATACTAAAAAAAATATATAATTCAACACCAAAAATATTG
*
260 AAGATCTTTTAACGCTTCTAATAGACCCGAAT
66 AAGAGCTTTTAACGCTTCTAATAGACCCGAAT
* ** *
292 TATTTTTCCTCAA-TTTTTGGCCACGATACTCATAAAAAAATATATAATTCAACGCCAAAAAGT-
1 TATTTTTCCTCAATTTTTTGACCAAAATACT-A-AAAAAAATATATAATTCAACACCAAAAA-TA
* *
355 TTGAAGGGCTTTTAACGTTTCTAATA
63 TTGAAGAGCTTTTAACGCTTCTAATA
381 TCGTTTTTCC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
96 14 0.18
97 14 0.18
98 49 0.63
99 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (97 bp):
TATTTTTCCTCAATTTTTTGACCAAAATACTAAAAAAAATATATAATTCAACACCAAAAATATTG
AAGAGCTTTTAACGCTTCTAATAGACCCGAAT
Found at i:1890 original size:334 final size:333
Alignment explanation
Indices: 283--2241 Score: 2187
Period size: 336 Copynumber: 5.9 Consensus size: 333
273 GCTTCTAATA
* * *
283 GACCCGAATTATTTTTCCTCAATTTTTGGCCACGATACTCATAAAAAAATATATAATTCAACGCC
1 GACCCGAAATATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAAATATATAATTCAACGCC
*
348 AAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTTTCCTAAATTAAAA
66 AAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAA--TTTTTTCCTAAATTAAAT
*
413 TCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGA
129 TCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGA
* ** * *
478 GATTTGGTTAGATGAATATAGTTATTTTAACGACTCTCGGCGCCGAAAATCATGCAAAACAGGGC
194 GATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCAAAAAATCATGCAAAACTGAGC
* * *
543 CGGTGTCCCGGAACGCGATTTTTGCTAAAAACC---AT-G--ACGTACACGATTTCGGCTATAGT
259 CGGTGCCCCGGAACGCG-TTTTTGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTATAAT
602 TTTGCAAAAATT
322 TTTGCAAAAATT
* * * * * * * * *
614 GACCAGGAATATATTTCCACAATTTTTGAGCAAAATACT-A-ATAAAAATATATAATTAAACACC
1 GACCCGAAATATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAAATATATAATTCAACGCC
* * * * * * * ** *
677 GAAAA-TATTGAAGGGTTTTTCAA-GCTCCTAATATCGTGTTCCCTATTTTTTATTAAATTAATT
66 AAAAAGT-TTGAAGGGCTTTT-AACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAATTAAAT
*** *
740 TAAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAAT-CATATGTGGCTG
129 TCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCA-ATATGGCTG
* * * ***
804 AGAATTGGGTAGATGTATATAGATATTTTAACGAC-CGTCGGCATTAAAAATCATGCAAAACTGA
193 AGATTTGGTTAGATGAATATAGATATTTTAACGACTC-TCGGCGCAAAAAATCATGCAAAACTGA
* ** * * * *
868 GTCTATGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAA
257 GCCGGTGCCCCGGAACGCGTTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTATAA
933 TTTTGCAAAAATT
321 TTTTGCAAAAATT
* * * *
946 GACCTGAATTATTTTTCCTCAATTTTTGGCCACGATACTCATAAAAAAAAATATATAATTCAACG
1 GACCCGAAATATTTTTCCTCAATTTTTGACCACAATACTCAT--AAAAAAATATATAATTCAACG
* * * *
1011 CCAAAAATTTTGAAGGGCTTTTAACGTTTCCAATATCGATTTTCCAATTTTTTCCTAAATGAAAA
64 CCAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAAT-TAAA
* * * *
1076 TT-TGATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAAAATCTTCAAATCCAATATGGCTA
128 TTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTG
* * * *
1140 AGATTTGGTTAGATGAATATAGATATTATAACGACTCTTGGCTCCAAAAATCATGCAAAACTGAG
193 AGATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCAAAAAATCATGCAAAACTGAG
* * * * * *
1205 ACGGTGACCTGAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAA
258 CCGGTGCCCCG-GA-ACGCGTTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTATA
*
1270 ATTTTGCAAAAATA
320 ATTTTGCAAAAATT
* * * ** * *
1284 GACCCGAATTATTTTTCC-AAAGTTTTTGGCCACGGTGCTCATAAAAAAGTATATAATTCAACGC
1 GACCCGAAATATTTTTCCTCAA-TTTTTGACCACAATACTCATAAAAAAATATATAATTCAACGC
*
1348 CAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAATTAAAAT
65 CAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAATTAAATT
* * *
1413 CTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGAG
130 CTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGAG
* * * *
1478 ATTTGGTTAAATGAATATAGTTATTTTAACGACTCTCGGCGTC-GAAAATCATGCAAAACTGAGT
195 ATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCG-CAAAAAATCATGCAAAACTGAGC
* *
1542 CGGTGCCTCGGAACGCGTTTCTTTCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTATAATT
259 CGGTGCCCCGGAACGCGTTT-TTGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTATAATT
1607 TTGCAAAAATT
323 TTGCAAAAATT
* * * * *
1618 GACCCGAAATATTTTTCCAT-AATTTTTAACCGA-AATACTCTTAAGAAAACATATAATTCAATG
1 GACCCGAAATATTTTTCC-TCAATTTTTGACC-ACAATACTCATAAAAAAATATATAATTCAACG
*
1681 ACAAAAAGTTTGAAGGG-TTTTAACGTTTCTAATATCGTTTTTCCAATGCTTTTTACCT-AATTA
64 CCAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAAT--TTTTT-CCTAAATTA
* * * * ** * * * *
1744 ATTTCTGATTAAATCGAAACAAGAATCAGAAGCTCGTAAAAAGATCTTCTTAAATCCATTGTGGC
126 AATTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGC
* * * * * * * ** * * *
1809 TGAGATTTGATTTGAT-AATATTGATATTTCAAGGAGTCTCAGCGCAAAAAAAGAAGAAAAACTA
191 TGAGATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCAAAAAATCATGCAAAACTG
* * **
1873 AGCC-ATGGCCCCGGAACGCGTTTCTAGCCAAAAACTATGATGGTTAGTACACGATTTCGGCTAT
256 AGCCGGT-GCCCCGGAACGCGTTT-TTGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAT
*
1937 AATTTAGCAAAAATT
319 AATTTTGCAAAAATT
* * * *
1952 GACCAGGAATATTTTTCCTCAAATTTTTGACCAAAATACTCCTAAAAAAATATATAATTCAACGC
1 GACCCGAAATATTTTTCCTC-AATTTTTGACCACAATACTCATAAAAAAATATATAATTCAACGC
* * * * * * * *
2017 CAAAAAGTTTGAAGGGATTTTAAAGCTACTAATATCGTGTTCCCTATTTTTTCCTAAATTAATTT
65 CAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAATTAAATT
* ** *
2082 CTGATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCTTATGTGGCTGAG
130 CTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGAG
* * * * * * * *
2147 AATTGGGTAGGTGAATATAGATAATTTAACGACTCTCGGCACCAAAAATCAGGCAAAACAGAGCC
195 ATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCAAAAAATCATGCAAAACTGAGCC
** *
2212 TATGCCCCGAAACGCGTTTTTAGCCAAAAA
260 GGTGCCCCGGAACGCGTTTTT-GCCAAAAA
2242 AAATCGTGAT
Statistics
Matches: 1365, Mismatches: 221, Indels: 80
0.82 0.13 0.05
Matches are distributed among these distances:
326 8 0.01
327 144 0.11
328 1 0.00
329 53 0.04
330 5 0.00
331 31 0.02
332 61 0.04
333 38 0.03
334 315 0.23
335 199 0.15
336 402 0.29
337 13 0.01
338 95 0.07
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (333 bp):
GACCCGAAATATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAAATATATAATTCAACGCC
AAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTTTTTCCAATTTTTTCCTAAATTAAATTC
TGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAATATGGCTGAGA
TTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCAAAAAATCATGCAAAACTGAGCCG
GTGCCCCGGAACGCGTTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTATAATTTTG
CAAAAATT
Done.