Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014076.1 Corchorus olitorius cultivar O-4 contig14109, 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: 27357
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Found at i:608 original size:15 final size:15
Alignment explanation
Indices: 588--616 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
578 ATTCTGCTTG
588 ATTGAAGAAAGAGAT
1 ATTGAAGAAAGAGAT
603 ATTGAAGAAAGAGA
1 ATTGAAGAAAGAGA
617 AAACAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (15 bp):
ATTGAAGAAAGAGAT
Found at i:1390 original size:29 final size:31
Alignment explanation
Indices: 1307--1390 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 31
1297 TCAATTAAAC
*
1307 GGAGGGACTAAATTGATCATTTTCCAATAGT
1 GGAGGGACTAAATTGATCATTTTTCAATAGT
* ** *
1338 AGAGGGACTAAATTGA-CAGATTTC-ATATT
1 GGAGGGACTAAATTGATCATTTTTCAATAGT
*
1367 GGAGGGACTAAAATGATC-TTTTTC
1 GGAGGGACTAAATTGATCATTTTTC
1391 TGATAGTACA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 22 0.51
30 6 0.14
31 15 0.35
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (31 bp):
GGAGGGACTAAATTGATCATTTTTCAATAGT
Found at i:3044 original size:105 final size:102
Alignment explanation
Indices: 2904--3109 Score: 326
Period size: 105 Copynumber: 2.0 Consensus size: 102
2894 CTTAAATTTT
*
2904 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTGTAAGTA-CT
1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC-T-T-A-TACCT
*
2968 ATTTTATTTTTACCATTTTACT-ATTTTAATTAAAATACTTC
62 ATTTTATTTTTACCATTTTACTAATTTT-ATTAAAAAACTTC
3009 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
*
3074 TATTTTTATCATTTTACTAATTTTATTAAAAAACTT
66 TATTTTTACCATTTTACTAATTTTATTAAAAAACTT
3110 AGATATATTA
Statistics
Matches: 96, Mismatches: 3, Indels: 7
0.91 0.03 0.07
Matches are distributed among these distances:
101 2 0.02
102 35 0.36
103 6 0.06
104 1 0.01
105 52 0.54
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.50
Consensus pattern (102 bp):
TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
TATTTTTACCATTTTACTAATTTTATTAAAAAACTTC
Found at i:3051 original size:23 final size:26
Alignment explanation
Indices: 2992--3051 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 26
2982 ATTTTACTAT
2992 TTTAATTAAAATACTTCTATAGTTTTA
1 TTTAATTAAAATACTTCTATA-TTTTA
* * *
3019 CTCAACTAAAA-AC-TCTAT-TTTTA
1 TTTAATTAAAATACTTCTATATTTTA
3042 TTTAATTAAA
1 TTTAATTAAA
3052 TCTAATATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 12 0.44
25 5 0.19
26 2 0.07
27 8 0.30
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTAATTAAAATACTTCTATATTTTA
Found at i:3083 original size:23 final size:23
Alignment explanation
Indices: 3057--3100 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3047 TTAAATCTAA
*
3057 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
3080 TATCATTTTACTAATTTTATT
1 TATCATTATACTAATTTTATT
3101 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:8317 original size:95 final size:99
Alignment explanation
Indices: 8135--8322 Score: 303
Period size: 95 Copynumber: 1.9 Consensus size: 99
8125 CCCTGGTCTG
8135 GTTTTCACCTCTTACTTAGCGCTTTACTCAGGAGGTAAAAAAGAACGAAATAGCTTCATGCCACT
1 GTTTTCACCTCTTACTTAGCGCTTTACTCAGGAGGT-AAAAAGAACGAAATAGCTTCATGCCACT
8200 GATATGTTAAAGATGATAGGATAATTCATTCGAAT
65 GATATGTTAAAGATGATAGGATAATTCATTCGAAT
* *
8235 GTTTTCACCTCTTATTTAGTGCTTTACTCAGGAGGT-AAAA-AA-G-AATAGCTTCATGCCACTG
1 GTTTTCACCTCTTACTTAGCGCTTTACTCAGGAGGTAAAAAGAACGAAATAGCTTCATGCCACTG
* *
8296 ATATGTTAAAGCTGATAGGATATTTCA
66 ATATGTTAAAGATGATAGGATAATTCA
8323 CTTGAATCTT
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
95 43 0.51
96 1 0.01
97 2 0.02
98 4 0.05
100 34 0.40
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (99 bp):
GTTTTCACCTCTTACTTAGCGCTTTACTCAGGAGGTAAAAAGAACGAAATAGCTTCATGCCACTG
ATATGTTAAAGATGATAGGATAATTCATTCGAAT
Found at i:10761 original size:15 final size:15
Alignment explanation
Indices: 10741--10770 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10731 ACAGTCGGGA
*
10741 TTTTTTCTTTTCTTT
1 TTTTTTCTTCTCTTT
10756 TTTTTTCTTCTCTTT
1 TTTTTTCTTCTCTTT
10771 AAAGACAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTCTCTTT
Found at i:12655 original size:20 final size:19
Alignment explanation
Indices: 12632--12747 Score: 115
Period size: 20 Copynumber: 5.6 Consensus size: 19
12622 ACATGTTCAA
12632 ACATAAGAACACATGCACTC
1 ACATAA-AACACATGCACTC
* *
12652 ACATAAAACACACTCCATTC
1 ACATAAAACACA-TGCACTC
12672 ATACATAAGAACACATGCACTC
1 --ACATAA-AACACATGCACTC
* *
12694 ACATAAAACACACTCCATTC
1 ACATAAAACACA-TGCACTC
12714 ATACATAAGAACACATGCACTC
1 --ACATAA-AACACATGCACTC
12736 ACATAAAACACA
1 ACATAAAACACA
12748 CTCCATTCAT
Statistics
Matches: 80, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
19 18 0.22
20 28 0.35
22 22 0.28
23 12 0.15
ACGTcount: A:0.47, C:0.30, G:0.05, T:0.17
Consensus pattern (19 bp):
ACATAAAACACATGCACTC
Found at i:12691 original size:42 final size:42
Alignment explanation
Indices: 12627--12758 Score: 255
Period size: 42 Copynumber: 3.1 Consensus size: 42
12617 CTTTAACATG
*
12627 TTCAAACATAAGAACACATGCACTCACATAAAACACACTCCA
1 TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
12669 TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
1 TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
12711 TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
1 TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
12753 TTCATA
1 TTCATA
12759 AGTCGTTGCT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (42 bp):
TTCATACATAAGAACACATGCACTCACATAAAACACACTCCA
Found at i:16892 original size:199 final size:201
Alignment explanation
Indices: 16543--16942 Score: 687
Period size: 199 Copynumber: 2.0 Consensus size: 201
16533 GATAAACTAG
* *
16543 GCATAACAAATTTATGTTAATGAGTGTAAAAATTTTCCAAGAAATCTGGTGTCGTATGATGGCAT
1 GCATAACAAATTTATGTTAATGAGTGCAAAAATTTTCCAAGAAATCTGGTATCGTATGATGGCAT
* * * *
16608 TGATGGAAAGTGTCCCACTTCATACTCCACGAAGATTACAGTTCTAGTTAAAAACTTCTTTGTCA
66 TGATCGAAAGAGGCCCACTTCATACTCCACGAAGATTACAGTTCTAGTTAAAAACCTCTTTGTCA
*
16673 ATTTATTTTCTTGAAACTATGTTCTGTTTTATTTATTTAATGATTTATTTACTATTTATTATGTA
131 ATTTATTTTCTTGAAACTATGTTATGTTTTATTTATTTAATGATTTATTTACTATTTATTATGTA
*
16738 GTACTT
196 ATACTT
16744 GCATAACAAATTTATGTT-A-GAGTGCAAAAATTTTCCAAGAAATCTGGTATCGTATGATGGCAT
1 GCATAACAAATTTATGTTAATGAGTGCAAAAATTTTCCAAGAAATCTGGTATCGTATGATGGCAT
* *
16807 TGATCGAAAGAGGCCCACTTCATACTCCATGAAGATTACAGTTCTTGTTAAAAACCTCTTTGTCA
66 TGATCGAAAGAGGCCCACTTCATACTCCACGAAGATTACAGTTCTAGTTAAAAACCTCTTTGTCA
*
16872 ATTTATTTTCTTGGAACTATGTTATGTTTTATTTATTTAATGATTTATTTACTATTTATTATGTA
131 ATTTATTTTCTTGAAACTATGTTATGTTTTATTTATTTAATGATTTATTTACTATTTATTATGTA
16937 ATACTT
196 ATACTT
16943 CGCAAATTCA
Statistics
Matches: 188, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
199 169 0.90
200 1 0.01
201 18 0.10
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (201 bp):
GCATAACAAATTTATGTTAATGAGTGCAAAAATTTTCCAAGAAATCTGGTATCGTATGATGGCAT
TGATCGAAAGAGGCCCACTTCATACTCCACGAAGATTACAGTTCTAGTTAAAAACCTCTTTGTCA
ATTTATTTTCTTGAAACTATGTTATGTTTTATTTATTTAATGATTTATTTACTATTTATTATGTA
ATACTT
Found at i:17834 original size:45 final size:45
Alignment explanation
Indices: 17761--17851 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
17751 TTTTGATTTG
*
17761 AATCATTCATCTAATCTTTCTTATGCATCTACTTCATTTCCTTTC
1 AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
* * * *
17806 AATCTTTCCTCTAATGTTTCATATGCATCTCCTTCATTTCCTTTC
1 AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
17851 A
1 A
17852 CCAACTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.21, C:0.27, G:0.03, T:0.48
Consensus pattern (45 bp):
AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
Done.