Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021186.1 Corchorus olitorius cultivar O-4 contig21219, 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: 14938
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1570 original size:76 final size:76
Alignment explanation
Indices: 1472--1616 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
1462 CTATGACGCA
* * * *
1472 GCCCATCTGGGTGATCAGGCAAAACACATGGTTCTTC-AGACAAATCATGTGGGCACCCAGCTGG
1 GCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGAC-AACCATGTGGGCACCCAGCTGG
1536 AGTCGTGACACT
65 AGTCGTGACACT
** * * * * *
1548 GCCCACCTGGGTTCTCAAGCAAACCACATGGGTGTTCAAGGCAACCATGTGGGCGCCCAGGTGGA
1 GCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGACAACCATGTGGGCACCCAGCTGGA
1613 GTCG
66 GTCG
1617 GGGTCCTTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 54 0.95
77 3 0.05
ACGTcount: A:0.24, C:0.28, G:0.29, T:0.19
Consensus pattern (76 bp):
GCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGACAACCATGTGGGCACCCAGCTGGA
GTCGTGACACT
Found at i:4465 original size:2 final size:2
Alignment explanation
Indices: 4458--4488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4448 AGAGACTGTT
4458 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4489 CCGGTAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6124 original size:76 final size:76
Alignment explanation
Indices: 6032--6262 Score: 376
Period size: 76 Copynumber: 3.0 Consensus size: 76
6022 TAAATGAATC
* *
6032 TGAACTAT-AAGAAATGCAGAAATGCCAAAGGTGCCTATCAAGATTTTTTT-GGTTTTTCTTCAA
1 TGAACTATGAA-AAATGCGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTCGGTTTTT-TTCAA
*
6095 AATGCAAATTAGA
64 AATGCAATTTAGA
6108 TGAACTATGAAAAATGCGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTCGGTTTTTTTCAAAA
1 TGAACTATGAAAAATGCGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTCGGTTTTTTTCAAAA
6173 TGCAATTTAGA
66 TGCAATTTAGA
** *
6184 TGAACTATGAAAAATTTGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTGGGTTTTTTTCAAAA
1 TGAACTATGAAAAATGCGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTCGGTTTTTTTCAAAA
6249 TGCAATTTAGA
66 TGCAATTTAGA
6260 TGA
1 TGA
6263 CTAAATATGA
Statistics
Matches: 147, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
76 138 0.94
77 9 0.06
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (76 bp):
TGAACTATGAAAAATGCGGAAATGCCAAAGGTGCTTATCAAGATTTTTTTCGGTTTTTTTCAAAA
TGCAATTTAGA
Found at i:6355 original size:27 final size:27
Alignment explanation
Indices: 6302--6484 Score: 222
Period size: 27 Copynumber: 6.7 Consensus size: 27
6292 AGTGAGCTTA
* **
6302 AAATGACCAAAATGCCCCTTGGATGTGC
1 AAATGACCAAAATGCCCC-TGAACATGC
* * * **
6330 AAATGACTAAAATGCCCTTGGATGTGC
1 AAATGACCAAAATGCCCCTGAACATGC
* **
6357 AAATGACTAAAATGCCCCCAAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
6384 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
6411 AAATGACCAAAAAGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
6438 AAATGACAAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
6465 AAATGACCCAAAACGCCCCT
1 AAATGA-CCAAAATGCCCCT
6485 AAATGACCCT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
27 111 0.80
28 27 0.20
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:8087 original size:791 final size:791
Alignment explanation
Indices: 6566--8156 Score: 2993
Period size: 791 Copynumber: 2.0 Consensus size: 791
6556 TCAAGACGCT
6566 TCCATGTGCTCCCATCATAGAGGAGATCCCATGAGTACACAACCTAGAGAGGTTGTGTTGGCCAA
1 TCCATGTGCTCCCATCATAGAGGAGATCCCATGAGTACACAACCTAGAGAGGTTGTGTTGGCCAA
6631 CGACACCTTGAAAAAGTTGTCGACATTGGCCTTAGAGATGAAGCTCCAAAGCTTAGAGGACTCAG
66 CGACACCTTGAAAAAGTTGTCGACATTGGCCTTAGAGATGAAGCTCCAAAGCTTAGAGGACTCAG
6696 CTGCCCCATCAGCTGATGCGGCTTATCAAAGTGTAGAAGATTCACAAGACGAGATCACCGTGGAG
131 CTGCCCCATCAGCTGATGCGGCTTATCAAAGTGTAGAAGATTCACAAGACGAGATCACCGTGGAG
*
6761 GAACTTGACTTTGCTCCCATGAATTTAGATGATCTCAAGGCTGAAGTACAAGATCCTTTACTTGA
196 GAACTTGACTTTGCTCCCATGAAGTTAGATGATCTCAAGGCTGAAGTACAAGATCCTTTACTTGA
* * *
6826 AGTGAATCTTGGTATTGAAGAAGAGCCTAGGCCGACCTATATAAGTCAGTTGTTGGCCGAAGAAG
261 AGTGAATCTTGGTACTGAAAAAGAGCCTAGGCCGACCTATATAACTCAGTTGTTGGCCGAAGAAG
* *
6891 ACAAGCCATGCTTTGTAGCCTTGTTAAAGGAGTACAAAGATTGTTTCGCCTAGGACTATGACGAA
326 ACAAGCCACGCATTGTAGCCTTGTTAAAGGAGTACAAAGATTGTTTCGCCTAGGACTATGACGAA
*
6956 ATGCCTGGCTTAAATCGTGACTTGGTGGAGCACCGCCTACCAATAATTGAAGGTTACCATCCCTA
391 ATGCCTGGCTTAAATCGTGACTTGGTGGAGCACCACCTACCAATAATTGAAGGTTACCATCCCTA
*
7021 TCAACAACCTCCTAGAAGAATGGCTAATGATGTCATCCTTAAAGTTAAAGAGGAAGTTGAAAAGC
456 TCAACAACCTCCTAGAAGAATGACTAATGATGTCATCCTTAAAGTTAAAGAGGAAGTTGAAAAGC
*
7086 TTCTTAAAGCAGGATTCATCCGTACCGCAAGGTATGTAGAATGGATTTCAAACATTGTTCCTGTG
521 TTCTTAAAGCAGGATTCATCCGTACCGCAAGGTATGTAGAATGGATTTCAAACATAGTTCCTGTG
7151 ATTAAAAAGAATGGTAAGATCAGGGTGTGTGTTGACTTTCGAAACTTGAATTCAGCCACCCCTAA
586 ATTAAAAAGAATGGTAAGATCAGGGTGTGTGTTGACTTTCGAAACTTGAATTCAGCCACCCCTAA
7216 AGATGAATATCCTATGCCTGTTGCAGACTTACTGGTAGATGGAGCCACCCAACATCAAGTGTTGT
651 AGATGAATATCCTATGCCTGTTGCAGACTTACTGGTAGATGGAGCCACCCAACATCAAGTGTTGT
7281 CCTTCATGGATGGACACAGTGGCTACAATCAGATCTACATAGCAGAGGAGGATGTTCCAAAGACA
716 CCTTCATGGATGGACACAGTGGCTACAATCAGATCTACATAGCAGAGGAGGATGTTCCAAAGACA
7346 GCTTTTCGCAG
781 GCTTTTCGCAG
* *
7357 TCCATGTGCTCCCATCATAGAGGAGATCCCATTAGTACACAACCTAGAGTGGTTGTGTTGGCCAA
1 TCCATGTGCTCCCATCATAGAGGAGATCCCATGAGTACACAACCTAGAGAGGTTGTGTTGGCCAA
7422 CGACACCTTGAAAAAGTTGTCGACATTGGCCTTAGAGATGAAGCTCCAAAGCTTAGAGGACTCAG
66 CGACACCTTGAAAAAGTTGTCGACATTGGCCTTAGAGATGAAGCTCCAAAGCTTAGAGGACTCAG
*
7487 CTGTCCCATCAGCTGATGCGGCTTATCAAAGTGTAGAAGATTCACAAGACGAGATCACCGTGGAG
131 CTGCCCCATCAGCTGATGCGGCTTATCAAAGTGTAGAAGATTCACAAGACGAGATCACCGTGGAG
7552 GAACTTGACTTTGCTCCCATGAAGTTAGATGATCTCAAGGCTGAAGTACAAGATCCTTTACTTGA
196 GAACTTGACTTTGCTCCCATGAAGTTAGATGATCTCAAGGCTGAAGTACAAGATCCTTTACTTGA
*
7617 AGTGAATCTTGGTACTGAAAAAGTGCCTAGGCCGACCTATATAACTCAGTTGTTGGCCGAAGAAG
261 AGTGAATCTTGGTACTGAAAAAGAGCCTAGGCCGACCTATATAACTCAGTTGTTGGCCGAAGAAG
* *
7682 ACAAGCCACGCATTGTAGCCTTGTTAAAGGAGTACAATGATTGTTTCGCCTTGGACTATGACGAA
326 ACAAGCCACGCATTGTAGCCTTGTTAAAGGAGTACAAAGATTGTTTCGCCTAGGACTATGACGAA
*
7747 ATGCCTGGCTTAAATCGTGACTTGGTGGAGCACCACCTACCAATCATTGAAGGTTACCATCCCTA
391 ATGCCTGGCTTAAATCGTGACTTGGTGGAGCACCACCTACCAATAATTGAAGGTTACCATCCCTA
*
7812 TCAACAACCTCCTAGAAGAATGACTAATGATGTCATCCTTGAAGTTAAAGAGGAAGTTGAAAAGC
456 TCAACAACCTCCTAGAAGAATGACTAATGATGTCATCCTTAAAGTTAAAGAGGAAGTTGAAAAGC
*
7877 TTCTTAAAGCAGGATTCATCCGTACCGCAAGGTATGTAGAATGGATTTCAAACATAGTTCTTGTG
521 TTCTTAAAGCAGGATTCATCCGTACCGCAAGGTATGTAGAATGGATTTCAAACATAGTTCCTGTG
*
7942 ATTAAAAAGAATGGTAAGATCAGGGTGTGTGTTGACTTTCGTAACTTGAATTCAGCCACCCCTAA
586 ATTAAAAAGAATGGTAAGATCAGGGTGTGTGTTGACTTTCGAAACTTGAATTCAGCCACCCCTAA
*
8007 AGATGAATATCCTATGCCTGTTGCAGACTTACTGGTAGATGGAGCCGCCCAACATCAAGTGTTGT
651 AGATGAATATCCTATGCCTGTTGCAGACTTACTGGTAGATGGAGCCACCCAACATCAAGTGTTGT
8072 CCTTCATGGATGGACACAGTGGCTACAATCAGATCTACATAGCAGAGGAGGATGTTCCAAAGACA
716 CCTTCATGGATGGACACAGTGGCTACAATCAGATCTACATAGCAGAGGAGGATGTTCCAAAGACA
8137 GCTTTTCGCAG
781 GCTTTTCGCAG
*
8148 TCCAGGTGC
1 TCCATGTGC
8157 AATCGGTACT
Statistics
Matches: 779, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
791 779 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (791 bp):
TCCATGTGCTCCCATCATAGAGGAGATCCCATGAGTACACAACCTAGAGAGGTTGTGTTGGCCAA
CGACACCTTGAAAAAGTTGTCGACATTGGCCTTAGAGATGAAGCTCCAAAGCTTAGAGGACTCAG
CTGCCCCATCAGCTGATGCGGCTTATCAAAGTGTAGAAGATTCACAAGACGAGATCACCGTGGAG
GAACTTGACTTTGCTCCCATGAAGTTAGATGATCTCAAGGCTGAAGTACAAGATCCTTTACTTGA
AGTGAATCTTGGTACTGAAAAAGAGCCTAGGCCGACCTATATAACTCAGTTGTTGGCCGAAGAAG
ACAAGCCACGCATTGTAGCCTTGTTAAAGGAGTACAAAGATTGTTTCGCCTAGGACTATGACGAA
ATGCCTGGCTTAAATCGTGACTTGGTGGAGCACCACCTACCAATAATTGAAGGTTACCATCCCTA
TCAACAACCTCCTAGAAGAATGACTAATGATGTCATCCTTAAAGTTAAAGAGGAAGTTGAAAAGC
TTCTTAAAGCAGGATTCATCCGTACCGCAAGGTATGTAGAATGGATTTCAAACATAGTTCCTGTG
ATTAAAAAGAATGGTAAGATCAGGGTGTGTGTTGACTTTCGAAACTTGAATTCAGCCACCCCTAA
AGATGAATATCCTATGCCTGTTGCAGACTTACTGGTAGATGGAGCCACCCAACATCAAGTGTTGT
CCTTCATGGATGGACACAGTGGCTACAATCAGATCTACATAGCAGAGGAGGATGTTCCAAAGACA
GCTTTTCGCAG
Done.