Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011543.1 Corchorus olitorius cultivar O-4 contig11576, 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: 3461
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Found at i:371 original size:20 final size:20
Alignment explanation
Indices: 346--384 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
336 AGGAAGAAGT
346 TTCAAGCTCATCAGAGTTGG
1 TTCAAGCTCATCAGAGTTGG
*
366 TTCAAGCTCATCGGAGTTG
1 TTCAAGCTCATCAGAGTTG
385 CCTAAGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (20 bp):
TTCAAGCTCATCAGAGTTGG
Found at i:1705 original size:155 final size:156
Alignment explanation
Indices: 1182--3461 Score: 2993
Period size: 156 Copynumber: 14.8 Consensus size: 156
1172 TCGTATCAAG
* *
1182 TCTTACCAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
*
1247 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* * *
1312 GAACTAAGAACTTCACAATGGAGTAG
131 GAGCTAAGAACTTCACAATGGACTAA
* * *
1338 TCTTACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAAC
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
**
1403 CGAAGACGATTTTTAAAACTTAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* *
1468 GAGCTACGAACTTTACAATGGACTAA
131 GAGCTAAGAACTTCACAATGGACTAA
* * *
1494 TCTTACCAAAGTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * ** * * *
1559 CAAAGACTATTTTTAAAATAGAACTAAAGGGCCCCGAATGGTCCAAAATAACAAGTGTT-TAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* * *
1623 GAGCTAAAAACTTCACATTGGACTAG
131 GAGCTAAGAACTTCACAATGGACTAA
*
1649 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * * *
1714 CGAAGACGA--TTCAAAACCGAACTAATAGACCCCGAAAGGCCCAAAATAACAAGTGTTCAAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* **
1777 GAGCTAAGAACTTCACAGTAAAC-ATA
131 GAGCTAAGAACTTCACAATGGACTA-A
* * *
1803 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATG-AAAGCATTGAGG-TTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * ** * *
1866 CGAAGACGA--TTCAAAA--GTCACTAATGGGCTGCG-ATAGGCCAAAAATAACAAGTGTTCCAA
66 CGAAGACGATTTTTAAAACCG-AACTAATGGGCCCCGAAT-GGCCCAAAATAACAAGTGTTCAAA
* *
1926 ATGAGCTAAAAACTTCACAGTGGACTAA
129 ATGAGCTAAGAACTTCACAATGGACTAA
* * * * *
1954 TCTCACGAAAATGATTAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * *
2019 CGAAGACGA--TTCAAAA-CGAAACTAATGGGCCTCG-ATAGGCCCAAAATAACAAGTGTTCCAA
66 CGAAGACGATTTTTAAAACCG-AACTAATGGGCCCCGAAT-GGCCCAAAATAACAAGTGTTCAAA
*
2080 ATGAGCTAAGAACTTCACAGTGGACTAA
129 ATGAGCTAAGAACTTCACAATGGACTAA
* * * * * * *
2108 TCTCATCAAAATGATTATACTTAGGACATAAACAATGGAAGGAAAAGCCTTGCGGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * * * *
2173 CGAAGACGA--TTCAAAA-CGTCACT-AT------CG--CGGCCCAAAATAACAAGTGTTCCAAT
66 CGAAGACGATTTTTAAAACCG-AACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAA
* *
2226 TGAGCTAA-ATACTTCACAGTAGACTAA
130 TGAGCTAAGA-ACTTCACAATGGACTAA
* * * * * *
2253 TCTCACCAAAATGTTTATACTTAGGCCATAAACAATGGAAGGAAAAGCCTTGAGGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * * *
2318 CGAAGACGA--TTCAAAA-CGTCAGTAATGGGCCGCG-ATAGGCCCAAAATAACAAGTGTTCAAA
66 CGAAGACGATTTTTAAAACCG-AACTAATGGGCCCCGAAT-GGCCCAAAATAACAAGTGTTCAAA
2379 ATGAGCTAAGAACTTCACAATGGACTAA
129 ATGAGCTAAGAACTTCACAATGGACTAA
*
2407 TCTTACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * * *
2472 CGAAGACAATTTTTCAAACCGAACTAATGGGCCCCGAATGACCCAAAATAACAAGTGTTCAAAAC
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* * * *
2537 GAGCTAAAAACGTCATAGTGGACTAA
131 GAGCTAAGAACTTCACAATGGACTAA
* * *
2563 TCTTACCAAAATAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTATGGTTTGCCA
1 TCTTACC--AA-AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCA
* * * * *
2628 AATCGAAGACCATTTTTAAAACCGAACTAACGGGCCCTGAATGGTCCAAAATGACAAGTGTTCAA
63 AATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAA
*
2693 AATGAGCTAAAAACTTCACAATGGACTAA
128 AATGAGCTAAGAACTTCACAATGGACTAA
2722 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * *
2787 CGAAGACGA--TTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATTAACAAGTGTTCAAAC
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAA-TAACAAGTGTTCAAAA
*
2850 TGAGCTAAAAACTTCACAATGGACTAA
130 TGAGCTAAGAACTTCACAATGGACTAA
* * * *
2877 TCTAACCAAAATGATTATAGTTAGGCCAGAAACAATGGAAAGAAAAGCATTATGGTTTTCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * * * *
2942 CGGAGACTATTTTTAAAACCGAACTAATGGGCCCTGAATGGTCCAAAATATCAAGTGTTCAAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* *
3007 GAGCTAAGAACTTCACATTGGACTAG
131 GAGCTAAGAACTTCACAATGGACTAA
* *
3033 TCTTACCAAAATGATTATAGTTAGGCCATAAAC-ATAGGAAAGAAAAGCATTGTGGTCTGTCAAA
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGTGGTTTGCCAAA
* * *
3097 TCGAAGACGA--TTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAA
65 TCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAA
*
3160 TGACCTAAGAACTTCACAATGGACTAA
130 TGAGCTAAGAACTTCACAATGGACTAA
*
3187 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT-GTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * **
3251 CGAAGACCATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTTTAAAT
66 CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
* *
3316 GAGCTAAGAACTTTACAATGGACTAG
131 GAGCTAAGAACTTCACAATGGACTAA
* * *
3342 TCTTACCAAAATGACTATAGTTAGGCCATAAATAATGG-AAGAAAAGCATTGTTGTTTGCCAAAT
1 TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
*
3406 CGAAGACGATTTTTAAAACCGAACTAATGGGTCCCCGAATGGTCCAAAAT-ACAAGT
66 CGAAGACGATTTTTAAAACCGAACTAATGGG-CCCCGAATGGCCCAAAATAACAAGT
Statistics
Matches: 1896, Mismatches: 193, Indels: 71
0.88 0.09 0.03
Matches are distributed among these distances:
144 1 0.00
145 131 0.07
146 2 0.00
147 2 0.00
150 2 0.00
151 94 0.05
152 39 0.02
153 95 0.05
154 483 0.25
155 361 0.19
156 506 0.27
157 39 0.02
158 2 0.00
159 139 0.07
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (156 bp):
TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
CGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAAT
GAGCTAAGAACTTCACAATGGACTAA
Done.