Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018422.1 Corchorus olitorius cultivar O-4 contig18455, 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: 11362
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:152 original size:30 final size:30
Alignment explanation
Indices: 116--182 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
106 GAAATCATTC
*
116 TGAAAAAAGAAATTTGCTTATGATCCTCTT
1 TGAAAAAAGAAATTTGCTTATGAACCTCTT
146 TGAAAAAAGAAATTTGCTTATGAACCTCTT
1 TGAAAAAAGAAATTTGCTTATGAACCTCTT
176 TGAAAAA
1 TGAAAAA
183 TAATTGATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (30 bp):
TGAAAAAAGAAATTTGCTTATGAACCTCTT
Found at i:653 original size:14 final size:15
Alignment explanation
Indices: 643--671 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
633 TACTACAGAT
643 TACAA-AGTACAAAA
1 TACAATAGTACAAAA
657 TACAATAGTACAAAA
1 TACAATAGTACAAAA
672 CGTGTCCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
TACAATAGTACAAAA
Found at i:2730 original size:102 final size:102
Alignment explanation
Indices: 2554--2760 Score: 405
Period size: 102 Copynumber: 2.0 Consensus size: 102
2544 CTCTATCATT
2554 TGAAATAGAGTTATGCATTTTCCCTAAAATCAAAACGATCATTAGACACATTGACATACTCTGCA
1 TGAAATAGAGTTATGCATTTTCCCTAAAATCAAAACGATCATTAGACACATTGACATACTCTGCA
2619 TCAGATTCAATACATGTTTTAGTGCATTCTAGTAATA
66 TCAGATTCAATACATGTTTTAGTGCATTCTAGTAATA
*
2656 TGAAATAGAGTTATGCATTTTCCCTAACATCAAAACGATCATTAGACACATTGACATACTCTGCA
1 TGAAATAGAGTTATGCATTTTCCCTAAAATCAAAACGATCATTAGACACATTGACATACTCTGCA
2721 TCAGATTCAATACATGTTTTAGTGCATTCTAGTAATA
66 TCAGATTCAATACATGTTTTAGTGCATTCTAGTAATA
2758 TGA
1 TGA
2761 TGTCTCTAGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (102 bp):
TGAAATAGAGTTATGCATTTTCCCTAAAATCAAAACGATCATTAGACACATTGACATACTCTGCA
TCAGATTCAATACATGTTTTAGTGCATTCTAGTAATA
Found at i:9687 original size:44 final size:44
Alignment explanation
Indices: 9639--9778 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 44
9629 AAATACATTT
* * * *
9639 TGAAAATTTGATAGCCTCATTATGAAATTTCGATAACTTTCCTA
1 TGAAAATTTGATAACCTCAATATGAAATTTTGATAACTTACCTA
* * * *
9683 TGAAAATTTGATAACCACACTATGAAATTTTGGTAAC-CACACTA
1 TGAAAATTTGATAACCTCAATATGAAATTTTGATAACTTAC-CTA
* * *
9727 TGAAATTTTGATAACCTCAATGTGAAATTTTGATAA-TCTGCCTA
1 TGAAAATTTGATAACCTCAATATGAAATTTTGATAACT-TACCTA
9771 T-AAAATTT
1 TGAAAATTT
9779 TAATAATCAC
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
43 7 0.09
44 70 0.90
45 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (44 bp):
TGAAAATTTGATAACCTCAATATGAAATTTTGATAACTTACCTA
Found at i:9705 original size:22 final size:22
Alignment explanation
Indices: 9639--9778 Score: 117
Period size: 22 Copynumber: 6.4 Consensus size: 22
9629 AAATACATTT
* *
9639 TGAAAATTTGATAGCCTCATTA
1 TGAAAATTTGATAACCTCACTA
*
9661 TG-AAATTTCGATAACTTTC-CTA
1 TGAAAATTT-GATAAC-CTCACTA
*
9683 TGAAAATTTGATAACCACACTA
1 TGAAAATTTGATAACCTCACTA
* * *
9705 TGAAATTTTGGTAACCACACTA
1 TGAAAATTTGATAACCTCACTA
* * *
9727 TGAAATTTTGATAACCTCAATG
1 TGAAAATTTGATAACCTCACTA
* *
9749 TGAAATTTTGATAATCTGC-CTA
1 TGAAAATTTGATAACCT-CACTA
9771 T-AAAATTT
1 TGAAAATTT
9779 TAATAATCAC
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.13
22 76 0.78
23 9 0.09
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCACTA
Found at i:9950 original size:22 final size:22
Alignment explanation
Indices: 9895--9957 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
9885 CTCTCTATGT
*
9895 ATTTTCAATAAACTCTCC-ATAAA
1 ATTTTC-ATAACCTC-CCTATAAA
9918 ATTTTCATAACCTCCCTATAAA
1 ATTTTCATAACCTCCCTATAAA
**
9940 ATTTTGTTAACCTCCCTA
1 ATTTTCATAACCTCCCTA
9958 GGAACTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.06
22 28 0.78
23 6 0.17
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTTCATAACCTCCCTATAAA
Found at i:9966 original size:22 final size:22
Alignment explanation
Indices: 9915--9967 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
9905 AACTCTCCAT
** *
9915 AAAATTTTCATAACCTCCCTAT
1 AAAATTTTGTTAACCTCCCTAG
9937 AAAATTTTGTTAACCTCCCTAG
1 AAAATTTTGTTAACCTCCCTAG
* *
9959 GAACTTTTG
1 AAAATTTTG
9968 ATAAGCACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (22 bp):
AAAATTTTGTTAACCTCCCTAG
Found at i:10029 original size:22 final size:22
Alignment explanation
Indices: 10001--10080 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
9991 CCCTTCCTAT
10001 GAAATTTTGTTAACTTTCATAA
1 GAAATTTTGTTAACTTTCATAA
* * * * *
10023 GAAATTTTATTTACATCCCTAA
1 GAAATTTTGTTAACTTTCATAA
* * *
10045 GAAATTTTGATAACCTTT-TTAT
1 GAAATTTTGTTAA-CTTTCATAA
*
10067 GAAATTTTGGTAAC
1 GAAATTTTGTTAAC
10081 CTCTGTATGA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 2 0.05
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (22 bp):
GAAATTTTGTTAACTTTCATAA
Found at i:10081 original size:22 final size:22
Alignment explanation
Indices: 10045--10184 Score: 122
Period size: 22 Copynumber: 6.4 Consensus size: 22
10035 ACATCCCTAA
* *
10045 GAAATTTTGATAACCTTTTTAT
1 GAAATTTTGATAACCTCTGTAT
*
10067 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCTCTGTAT
**
10089 GAAA-TTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CTGTAT
* *
10110 GAAGTTTTGATAACCTCTATAT
1 GAAATTTTGATAACCTCTGTAT
* **
10132 GAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCTCTGTAT
* * * *
10154 GAAAATTTGATAATCTTTCTAT
1 GAAATTTTGATAACCTCTGTAT
*
10176 GTAATTTTG
1 GAAATTTTG
10185 GTTTGATTGT
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
20 2 0.02
21 14 0.15
22 77 0.81
23 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTGTAT
Found at i:10156 original size:44 final size:44
Alignment explanation
Indices: 10045--10184 Score: 156
Period size: 44 Copynumber: 3.2 Consensus size: 44
10035 ACATCCCTAA
**** * *
10045 GAAATTTTGATAACCTTTTTATGAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAACCTCTATAT
* *
10089 GAAA-TTTGATAACTACACTATGAAGTTTTGATAACCTCTATAT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAACCTCTATAT
* * * *
10132 GAAATTTTGATAACCACACTATGAAAATTTGATAATCTTTCTAT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAACCTCTATAT
*
10176 GTAATTTTG
1 GAAATTTTG
10185 GTTTGATTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
43 35 0.44
44 45 0.56
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAATTTTGATAACCTCTATAT
Done.