Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014756.1 Corchorus olitorius cultivar O-4 contig14789, 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: 10674
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Found at i:383 original size:108 final size:106
Alignment explanation
Indices: 11--437 Score: 592
Period size: 108 Copynumber: 4.0 Consensus size: 106
1 ATCAATGTGA
** * *
11 AGATCAACTCTGATCATCGAAAACTTCTTAAAATAAGATCAACTTTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCAT--AGAAAACTTCT
* **
76 TGAAATGAGATCAACTCTGACCATTAAAAAAAAAACTTCTTGAAAT-G
64 TGAAATGAGATCAACTCTGATCA-T----CGAAAACTTCTTGAAATCG
*
123 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGGAGATCAACTCTGATCATA-AAAACTTCTT
1 AGATCAACTCTGATC-ATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAGAAAACTTCTT
* *
186 GAAATGAGATCAACACTGATCATTGAAAACTTCTTGAAA-CG
65 GAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAATCG
* *
227 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAGAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAGAAAACTTCTTG
292 AAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGCG
66 AAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAT-CG
* **
334 ATGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCACCGAAAACTTCTT
1 A-GATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAGAAAACTTCTT
*
399 GAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
65 GAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
438 CGACCGCATT
Statistics
Matches: 291, Mismatches: 17, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
103 1 0.00
104 63 0.22
105 47 0.16
107 3 0.01
108 99 0.34
109 30 0.10
110 1 0.00
112 46 0.16
113 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (106 bp):
AGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAGAAAACTTCTTG
AAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAATCG
Found at i:440 original size:35 final size:35
Alignment explanation
Indices: 11--437 Score: 570
Period size: 35 Copynumber: 11.9 Consensus size: 35
1 ATCAATGTGA
* *
11 AGATCAACTCTGATCATCGAAAACTTCTTAAAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* **
46 AGATCAACTTTGATCATAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAATG
* **
83 AGATCAACTCTGACCATTAAAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCA-T----CGAAAACTTCTTGAAATG
* * *
123 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGG
1 AGATCAACTCTGATC-ATCGAAAACTTCTTGAAATG
*
158 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* * *
192 AGATCAACACTGATCATTGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
227 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
262 AGATCAACTCTGATCATAGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
297 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGCG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAT--G
*
334 ATGATCAACTCTGATCATCGAAAACTTCTTGAAAGG
1 A-GATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
370 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
405 AGATCAACTCTGATCATCGAAAACTTCTTGAAA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAA
438 CGACCGCATT
Statistics
Matches: 356, Mismatches: 25, Indels: 22
0.88 0.06 0.05
Matches are distributed among these distances:
34 32 0.09
35 224 0.63
36 2 0.01
37 30 0.08
38 33 0.09
40 34 0.10
41 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:496 original size:52 final size:53
Alignment explanation
Indices: 424--561 Score: 170
Period size: 55 Copynumber: 2.6 Consensus size: 53
414 CTGATCATCG
* * ** *
424 AAAACTTCTTGAAACGACCGCATTGGATCATCT-TTTCAATTCTAATCATTAA
1 AAAACTTCTTGGAATGACCGCATTGGATCATCTGGGTCAACTCTAATCATTAA
* * *
476 AAAACTTCTTGGAATAACCGCACTGGATCATCTGAGGGTCAACTCTAATCCTTAA
1 AAAACTTCTTGGAATGACCGCATTGGATCATCT--GGGTCAACTCTAATCATTAA
*
531 AAAACTTCTTGGAATGACCGCATCGGATCAT
1 AAAACTTCTTGGAATGACCGCATTGGATCAT
562 TTGAGGATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
52 29 0.40
55 43 0.60
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (53 bp):
AAAACTTCTTGGAATGACCGCATTGGATCATCTGGGTCAACTCTAATCATTAA
Found at i:4991 original size:4 final size:4
Alignment explanation
Indices: 4984--5021 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
4974 TACCAAAGGA
4984 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5022 GTGAATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Done.