Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012135.1 Corchorus olitorius cultivar O-4 contig12168, 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: 34108
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9017 original size:18 final size:19
Alignment explanation
Indices: 8994--9031 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
8984 GTGCATGGGT
*
8994 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
9012 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
9031 T
1 T
9032 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:10402 original size:30 final size:30
Alignment explanation
Indices: 10344--10402 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
10334 CAAGGGGGAA
*
10344 GGAATGATGCGCCCAAGGCTTATCATGGAG
1 GGAATGATGCGCCCAAGGCTAATCATGGAG
*
10374 GGAATGATGCG-CCAAGGACTAATGATGGA
1 GGAATGATGCGCCCAAGG-CTAATCATGGA
10403 CTTGAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.34, T:0.19
Consensus pattern (30 bp):
GGAATGATGCGCCCAAGGCTAATCATGGAG
Found at i:10469 original size:18 final size:19
Alignment explanation
Indices: 10446--10483 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
10436 GTGCATGGAT
*
10446 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
10464 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
10483 T
1 T
10484 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:13006 original size:45 final size:45
Alignment explanation
Indices: 12938--13073 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
12928 GGCAAAATTA
* *
12938 GTTTCAAAATTGGGATTTATGGTTTGGGATTGGGTTTCAACGTTG
1 GTTTCAAAAATGGGATTTATGGTTTGGGATTGGGTTTCAAAGTTG
*
12983 GTTTCAAAAATGGGATTTTTGGTTTGGGATTGGGTTTCAAAGTTG
1 GTTTCAAAAATGGGATTTATGGTTTGGGATTGGGTTTCAAAGTTG
* *
13028 GTTTAAAAAATGGGATTTATGGTTTGGGATTGGGTTTCAAAATTG
1 GTTTCAAAAATGGGATTTATGGTTTGGGATTGGGTTTCAAAGTTG
13073 G
1 G
13074 GATTTACTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (45 bp):
GTTTCAAAAATGGGATTTATGGTTTGGGATTGGGTTTCAAAGTTG
Found at i:15514 original size:17 final size:16
Alignment explanation
Indices: 15494--15544 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
15484 TATTTAAAAG
*
15494 TAAATATACGATAAATA
1 TAAATATA-AATAAATA
15511 TAAATAATAAATAAATA
1 TAAAT-ATAAATAAATA
15528 TAAATAATAAATAAATA
1 TAAAT-ATAAATAAATA
15545 AATAAAAGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 29 0.91
18 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAATATAAATAAATA
Found at i:15523 original size:4 final size:4
Alignment explanation
Indices: 15510--15550 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
15500 TACGATAAAT
15510 ATAA AT-A ATAA ATAA AT-- ATAA AT-A ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
15551 AGGCCACTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.06
3 6 0.18
4 25 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:19519 original size:178 final size:177
Alignment explanation
Indices: 19230--19553 Score: 465
Period size: 178 Copynumber: 1.8 Consensus size: 177
19220 CCGATTAAGG
* * *
19230 TGATTTAAGTGTTTATTAAAAGATTGTTCCATTATCTACAACTTTCATGAGGACTCGAAAACTAA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAGGACTCGAAAACTAA
* * *
19295 ATTTAATGTTTCAAGTATCAAAAATGCTTCTGAAAAATTTGTTGTTTCGGTTAACGGGAATAGAC
66 ATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCGGTTAACGGAAATAGAC
*
19360 GGTCGACTTACTATTATATAACTTTTGCTCCGGATGTGTGATTGAGA
131 GGTCGACTTAATATTATATAACTTTTGCTCCGGATGTGTGATTGAGA
* * * * *
19407 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAATTTTCATGAAGGACTCGAAAAGTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATG-AGGACTCGAAAACTA
*
19472 AATTTATTG-TTCAAGGTAT-AAACAATGCTTC-CAAAGAATTAGTTGTTTCGGTTAACGGAAAT
65 AATTTAATGTTTCAA-GTATCAAA-AATGCTTCTCAAA-AATTAGTTGTTTCGGTTAACGGAAAT
*
19534 AGACGGTCTACTTAATATTA
127 AGACGGTCGACTTAATATTA
19554 CGTAATTTGT
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
177 53 0.41
178 76 0.59
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (177 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAGGACTCGAAAACTAA
ATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCGGTTAACGGAAATAGAC
GGTCGACTTAATATTATATAACTTTTGCTCCGGATGTGTGATTGAGA
Found at i:25182 original size:22 final size:22
Alignment explanation
Indices: 25133--25188 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
25123 GTTTGTGGCG
25133 TTTTGTTCATAAAACGCCACTA
1 TTTTGTTCATAAAACGCCACTA
**
25155 CATTGTTCATAAAACGCC-CTGA
1 TTTTGTTCATAAAACGCCACT-A
25177 TTTTGTTACATA
1 TTTTGTT-CATA
25189 TTAGTTATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTTGTTCATAAAACGCCACTA
Found at i:31014 original size:16 final size:15
Alignment explanation
Indices: 30989--31018 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30979 AGTAGCTAAT
30989 AATAGAAATTACTAC
1 AATAGAAATTACTAC
31004 AATATGAAATTACTA
1 AATA-GAAATTACTA
31019 GTATCATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
AATAGAAATTACTAC
Found at i:33693 original size:16 final size:15
Alignment explanation
Indices: 33655--33696 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
33645 ACAGAGGTTG
*
33655 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
33670 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
33685 ACTAGAAAACAA
1 AC-AGAAAACAA
33697 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.