Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015776.1 Corchorus olitorius cultivar O-4 contig15809, 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: 23375
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:7311 original size:153 final size:153
Alignment explanation
Indices: 7090--7396 Score: 614
Period size: 153 Copynumber: 2.0 Consensus size: 153
7080 TTAAGTTGCA
7090 TATGTAACATTCATTAGCTTTCATTCCATAGAGGTATTTTTATAGCATTCAGTGTATTCCATCAT
1 TATGTAACATTCATTAGCTTTCATTCCATAGAGGTATTTTTATAGCATTCAGTGTATTCCATCAT
7155 GGTTTTAAGCTTTTCCAGTTTCAAATTGATTACATGGTCATAGTATTTAGGAATATAAGACAGGC
66 GGTTTTAAGCTTTTCCAGTTTCAAATTGATTACATGGTCATAGTATTTAGGAATATAAGACAGGC
7220 ACTACACCAAAATTGTCAATTAG
131 ACTACACCAAAATTGTCAATTAG
7243 TATGTAACATTCATTAGCTTTCATTCCATAGAGGTATTTTTATAGCATTCAGTGTATTCCATCAT
1 TATGTAACATTCATTAGCTTTCATTCCATAGAGGTATTTTTATAGCATTCAGTGTATTCCATCAT
7308 GGTTTTAAGCTTTTCCAGTTTCAAATTGATTACATGGTCATAGTATTTAGGAATATAAGACAGGC
66 GGTTTTAAGCTTTTCCAGTTTCAAATTGATTACATGGTCATAGTATTTAGGAATATAAGACAGGC
7373 ACTACACCAAAATTGTCAATTAG
131 ACTACACCAAAATTGTCAATTAG
7396 T
1 T
7397 GACACACGTA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (153 bp):
TATGTAACATTCATTAGCTTTCATTCCATAGAGGTATTTTTATAGCATTCAGTGTATTCCATCAT
GGTTTTAAGCTTTTCCAGTTTCAAATTGATTACATGGTCATAGTATTTAGGAATATAAGACAGGC
ACTACACCAAAATTGTCAATTAG
Found at i:11181 original size:46 final size:46
Alignment explanation
Indices: 11096--11229 Score: 195
Period size: 46 Copynumber: 3.0 Consensus size: 46
11086 ATTTTCAAAC
* *
11096 ATAATAGTTTTCTATTAAAGT-AATTCCAAAAGAAGATTTTGGAAA
1 ATAAAAGTTTTCTATTTAAGTAAATTCCAAAAGAAGATTTTGGAAA
* **
11141 GTAAAAGTTTTCTATTTAAGTAAATTCCAAAAGGGGATTTTGGAAA
1 ATAAAAGTTTTCTATTTAAGTAAATTCCAAAAGAAGATTTTGGAAA
11187 ATAAAAGTTTTCT-TTTAAG-AAA-TCCAAAAGAAGATTTTGGAAA
1 ATAAAAGTTTTCTATTTAAGTAAATTCCAAAAGAAGATTTTGGAAA
11230 TTAATAAAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 19 0.24
44 3 0.04
45 24 0.30
46 34 0.43
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (46 bp):
ATAAAAGTTTTCTATTTAAGTAAATTCCAAAAGAAGATTTTGGAAA
Found at i:13837 original size:31 final size:30
Alignment explanation
Indices: 13766--13838 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
13756 GACCATAATC
*
13766 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGC-TTAATTT
** *
13797 TAATGATTTGTTTAATTTAATGG-TTAATTT
1 TTTTAATTTGTTTAATTTAA-GGCTTAATTT
13827 GTTTTAATTTGT
1 -TTTTAATTTGT
13839 AATAATTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
30 6 0.18
31 25 0.76
32 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (30 bp):
TTTTAATTTGTTTAATTTAAGGCTTAATTT
Found at i:13841 original size:24 final size:21
Alignment explanation
Indices: 13802--13850 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
13792 CATTTTAATG
**
13802 ATTTGTTTAATTTAATGGTTA
1 ATTTGTTTAATTTAATAATTA
13823 ATTTGTTTTAATTTGTAATAATTA
1 ATTTG-TTTAA-TT-TAATAATTA
13847 ATTT
1 ATTT
13851 AAATTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 2 0.09
24 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
ATTTGTTTAATTTAATAATTA
Found at i:14117 original size:25 final size:23
Alignment explanation
Indices: 14080--14126 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
14070 TATTCAATCT
14080 TTATATATATATTGATA-ATTATG
1 TTATATATATATT-ATATATTATG
14103 TTATATTATTATATTATATATTAT
1 TTATA-TA-TATATTATATATTAT
14127 CAATAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATATATATATTATATATTATG
Found at i:14338 original size:16 final size:16
Alignment explanation
Indices: 14319--14351 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
14309 CGACATAGCT
14319 CGAACCTGAATGAACC
1 CGAACCTGAATGAACC
14335 CGAACCTGAATGAACC
1 CGAACCTGAATGAACC
14351 C
1 C
14352 AAACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.12
Consensus pattern (16 bp):
CGAACCTGAATGAACC
Found at i:14818 original size:23 final size:23
Alignment explanation
Indices: 14786--14832 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
14776 TGGAGGAAGA
* *
14786 GGGTTGGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTATTGAT
14809 GGGTTAGTGGTGACTGTATTGAT
1 GGGTTAGTGGTGACTGTATTGAT
14832 G
1 G
14833 CAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.04, G:0.43, T:0.40
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTATTGAT
Found at i:17695 original size:39 final size:39
Alignment explanation
Indices: 17641--17731 Score: 182
Period size: 39 Copynumber: 2.3 Consensus size: 39
17631 GGGAAGAGGA
17641 AAGATGTTTTCTTAAGAGGAAACGTAAGTTTGGATTCTT
1 AAGATGTTTTCTTAAGAGGAAACGTAAGTTTGGATTCTT
17680 AAGATGTTTTCTTAAGAGGAAACGTAAGTTTGGATTCTT
1 AAGATGTTTTCTTAAGAGGAAACGTAAGTTTGGATTCTT
17719 AAGATGTTTTCTT
1 AAGATGTTTTCTT
17732 TCATGAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (39 bp):
AAGATGTTTTCTTAAGAGGAAACGTAAGTTTGGATTCTT
Found at i:18781 original size:22 final size:23
Alignment explanation
Indices: 18733--18775 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
18723 ATTATAATAT
*
18733 ATATTAATATATGGATAACTTTA
1 ATATTAATATATGAATAACTTTA
*
18756 ATATTAATA-ATTAATAACTT
1 ATATTAATATATGAATAACTT
18776 ACATATAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATTAATATATGAATAACTTTA
Found at i:21290 original size:148 final size:146
Alignment explanation
Indices: 21014--21303 Score: 377
Period size: 148 Copynumber: 2.0 Consensus size: 146
21004 TTATATATTT
* * * *
21014 TGGTTTCCCTCTCTTTTTTTTCGCGCAAAATTGGAAACTTAGCTGAAAATTAACTATAACGACGC
1 TGGTTTCCCTCTCTCTTTTTCCGCGCAAAATTGGAAAATTAGCTAAAAATTAACTATAACGACGC
* * * * *
21079 TTTTTATTGGAAACACCGTAATAGTTGTTAGTGTGGTGGCTTTTGTACTTCAAAACGCCGCCATC
66 TTTTTATTGAAAACACCGTAATAGTTGTTAGTGTGGCGGCGTCTGTACTTAAAAACGCCGCCATC
*
21144 CTTAAGGCAAAACTTA
131 CTTAACGCAAAACTTA
* *
21160 TGGTTTCTCTCTCTCTCTTTTTCCTCGCAAAATTGGAAAATTAGCTAAAAATTGACTATAAC-A-
1 TGGTTTC-C-CTCTCTCTTTTTCCGCGCAAAATTGGAAAATTAGCTAAAAATTAACTATAACGAC
*** * *
21223 GCGTTTGTTATTGAAAATGTCGTAATATTTGTTAGTGTGGCGGCGTCTGTACTTAAAAATGCCGC
64 GC-TTT-TTATTGAAAACACCGTAATAGTTGTTAGTGTGGCGGCGTCTGTACTTAAAAACGCCGC
21288 CATCCTTAACGCAAAA
127 CATCCTTAACGCAAAA
21304 TTTAGGCAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
146 9 0.07
147 5 0.04
148 109 0.89
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (146 bp):
TGGTTTCCCTCTCTCTTTTTCCGCGCAAAATTGGAAAATTAGCTAAAAATTAACTATAACGACGC
TTTTTATTGAAAACACCGTAATAGTTGTTAGTGTGGCGGCGTCTGTACTTAAAAACGCCGCCATC
CTTAACGCAAAACTTA
Found at i:22337 original size:21 final size:21
Alignment explanation
Indices: 22311--22423 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
22301 TGCTAGAAGT
22311 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
22332 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
22353 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
22374 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
22395 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
22416 TCATTGGA
1 TCATTGGA
22424 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.