Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011124.1 Corchorus olitorius cultivar O-4 contig11157, 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: 2991
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Found at i:650 original size:331 final size:332
Alignment explanation
Indices: 40--791 Score: 1206
Period size: 331 Copynumber: 2.3 Consensus size: 332
30 AACTGTGATG
* ** * * * *
40 GTACACGATTTCGGCAAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCGTCAATTTTTAACCG
1 GTACACAATTTCGGCAAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAA-TTTTAACC-
* * * * * * *
105 C--AATACACGTAAAAATATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCATGCTTCTAAT
64 CAAAATACTCATAAAAATATATAATTCAACACCAAAAAGATTGATAGGATTTTCAAGCATCTAAT
*
168 ATCATTTTTCCTATTTTTTTCTGAATTAATTTCTAATTCAGGTGAAATTGGTTTCTAATGCTCGT
129 ATCATATTTCCTATTTTTTTCTGAATTAATTTCTAATTCAGGTGAAATTGGTTTCTAATGCTCGT
233 AAAAACAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTTGCTGAATAGAGATATTTCAATGAG
194 AAAAACAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTTGCTGAATAGAGATATTTCAATGAG
*
298 TCCTGACGCCAAAAATAATCCAAAACTCAGTCGGAGCCCCAGAACGCGTTTTTAGCTAAATATCG
259 TCCTGACGCCAAAAATAATCCAAAACTCAGTCGGAGCCCCAGAACGCGTTTTTAGCTAAATACCG
363 TGATGGTTA
324 TGATGGTTA
*
372 GTACACAATTTCGGCAAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAAGTTTAACCCA
1 GTACACAATTTCGGCAAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTAACCCA
*
437 AAATACTCATAAAAATATATAATTCAACACCAAAAATATTGGA-AGGATTTT-AAGCATCTAATA
66 AAATACTCATAAAAATATATAATTCAACACCAAAAAGATT-GATAGGATTTTCAAGCATCTAATA
*
500 TCATATTTCCTATTTTTTTCTGAATTAATTTCTTATTCAGGTGAAATTGGTTTCTAATGCTCGTA
130 TCATATTTCCTATTTTTTTCTGAATTAATTTCTAATTCAGGTGAAATTGGTTTCTAATGCTCGTA
565 AAAACAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTTGCTGAATAGAGATATTTCAATGAGT
195 AAAACAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTTGCTGAATAGAGATATTTCAATGAGT
**
630 CCTGACGCCAAAAATAATCCAAAACTCAGTCGGAGCCCTGGAACGCGTTTTTAGCTAAATACCGT
260 CCTGACGCCAAAAATAATCCAAAACTCAGTCGGAGCCCCAGAACGCGTTTTTAGCTAAATACCGT
695 GATGGTTA
325 GATGGTTA
* *** *
703 GTACACAATTTCGGCTAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTTGGCTA
1 GTACACAATTTCGGCAAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTAACCCA
*
768 AAATACTCATAAAATTATATAATT
66 AAATACTCATAAAAATATATAATT
792 TGGTATCTTA
Statistics
Matches: 389, Mismatches: 28, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
330 1 0.00
331 297 0.76
332 89 0.23
333 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (332 bp):
GTACACAATTTCGGCAAAATTTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTAACCCA
AAATACTCATAAAAATATATAATTCAACACCAAAAAGATTGATAGGATTTTCAAGCATCTAATAT
CATATTTCCTATTTTTTTCTGAATTAATTTCTAATTCAGGTGAAATTGGTTTCTAATGCTCGTAA
AAACAAATCCTTCAATCCATTGTGGCTGAGATTTTCTTTGCTGAATAGAGATATTTCAATGAGTC
CTGACGCCAAAAATAATCCAAAACTCAGTCGGAGCCCCAGAACGCGTTTTTAGCTAAATACCGTG
ATGGTTA
Found at i:1818 original size:11 final size:11
Alignment explanation
Indices: 1802--1837 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1792 TTAGCTAAAT
1802 ATTTTTCCTTA
1 ATTTTTCCTTA
1813 ATTTTTCCTTA
1 ATTTTTCCTTA
1824 A-TTTTCCTTA
1 ATTTTTCCTTA
1834 ATTT
1 ATTT
1838 CTAGTACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTTCCTTA
Found at i:1828 original size:10 final size:10
Alignment explanation
Indices: 1804--1837 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
1794 AGCTAAATAT
1804 TTTTCCTTAA
1 TTTTCCTTAA
1814 TTTTTCCTTAA
1 -TTTTCCTTAA
1825 TTTTCCTTAA
1 TTTTCCTTAA
1835 TTT
1 TTT
1838 CTAGTACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTCCTTAA
Found at i:2458 original size:331 final size:332
Alignment explanation
Indices: 1843--2788 Score: 1589
Period size: 331 Copynumber: 2.9 Consensus size: 332
1833 AATTTCTAGT
*
1843 ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACAAAA
1 ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
* * *
1908 AATATTTAAAGACTTTTGACGCTTCTAATATCATTTTTCCTATTTTTTTCTGAATTAATTTCTAT
66 AATATTTAAAGGCTTTTGATGCTTCTAATATCATTTTTCCTA-TTTTTTCTGAATTAATTTCTAA
* * *
1973 TTCATGTGAAAGTCGGTTTTTGATGCTTGTAATAACAAATCCTTTCTAA---ATTGTTGCTTAGA
130 TTCATGTGAAAGTCGGTTTCTGATGCTCGTAATAACAAATCC-TTC-AATCCATTGTGGCTTAGA
* *
2035 TACTCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAATTCATGCAAAACTGAGTCG
193 TTCTCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCG
*
2100 GAGCCCCGGAAAGCGTTTTTAGCTAAATACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTT
258 GAGCCCCGGAAAGCGTTTTTAGCTAAATACCGTGATGGTTAGTACACGATTTCGGCCAAATTTTT
*
2165 GTAAAAATTG
323 GCAAAAATTG
2175 ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
1 ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
2240 AATATTTAAAGGCTTTTGATGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTAATTTCTAAT
66 AATATTTAAAGGCTTTTGATGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTAATTTCTAAT
* * * *
2305 TCAGGTGAAA-TTGGTTTCTAATGCTCGTAATAACAAATCCTTCAATCCATTGTGGCTGAGATTC
131 TCATGTGAAAGTCGGTTTCTGATGCTCGTAATAACAAATCCTTCAATCCATTGTGGCTTAGATTC
*
2369 TCTTAGCTCAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGAG
196 TCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGAG
2434 CCCCGGAAAGCGTTTTTAGCTAAATACCGTGATGGTTAGTACACGATTTCGGCCAAATTTTTGCA
261 CCCCGGAAAGCGTTTTTAGCTAAATACCGTGATGGTTAGTACACGATTTCGGCCAAATTTTTGCA
*
2499 AATATTG
326 AAAATTG
*
2506 ACCTGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
1 ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
* *
2571 AATATTTAAAAGCTTTTGATGCTTCTAATATCATTTTTCCT-TTTTTT-TGAATTAATTTGTAAT
66 AATATTTAAAGGCTTTTGATGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTAATTTCTAAT
* * *
2634 TCTTGTGAAAGTCGGTTTCTGATGCTCGTAATAAAAAATTCTTCAATCCATTGTGGCTTAGATTC
131 TCATGTGAAAGTCGGTTTCTGATGCTCGTAATAACAAATCCTTCAATCCATTGTGGCTTAGATTC
* *
2699 TCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATAATGCAAAAATGAGTCGGAG
196 TCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGAG
*
2764 CCCCGGAATGCGTTTTTAGCTAAAT
261 CCCCGGAAAGCGTTTTTAGCTAAAT
2789 TATTGCAAAA
Statistics
Matches: 579, Mismatches: 31, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
328 2 0.00
329 26 0.04
330 167 0.29
331 280 0.48
332 104 0.18
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (332 bp):
ACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAAAATATATAATTCAACACCAAA
AATATTTAAAGGCTTTTGATGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTAATTTCTAAT
TCATGTGAAAGTCGGTTTCTGATGCTCGTAATAACAAATCCTTCAATCCATTGTGGCTTAGATTC
TCTTAGCTGAATAGAGATATTTCAATGAGTCCTGACGCCAAAAATCATGCAAAACTGAGTCGGAG
CCCCGGAAAGCGTTTTTAGCTAAATACCGTGATGGTTAGTACACGATTTCGGCCAAATTTTTGCA
AAAATTG
Done.