Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020512.1 Corchorus olitorius cultivar O-4 contig20545, 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: 17593
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:91 original size:2 final size:2
Alignment explanation
Indices: 84--109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74 TTTAAATTGA
84 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
110 TAAACATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1623 original size:14 final size:14
Alignment explanation
Indices: 1604--1633 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1594 ATTCAAATCG
1604 TAGGAAAAGAATAA
1 TAGGAAAAGAATAA
1618 TAGGAAAAGAATAA
1 TAGGAAAAGAATAA
1632 TA
1 TA
1634 CGAACCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (14 bp):
TAGGAAAAGAATAA
Found at i:1863 original size:40 final size:40
Alignment explanation
Indices: 1808--1883 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
1798 GCAACATGAA
*
1808 TTACATGGCAAACCCACTACCTCACACATCCCCATTAATT
1 TTACATGACAAACCCACTACCTCACACATCCCCATTAATT
1848 TTACATGACAAACCCACTACCTCACACATCCCCATT
1 TTACATGACAAACCCACTACCTCACACATCCCCATT
1884 CATATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.39, G:0.04, T:0.24
Consensus pattern (40 bp):
TTACATGACAAACCCACTACCTCACACATCCCCATTAATT
Found at i:3905 original size:18 final size:19
Alignment explanation
Indices: 3884--3924 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3874 AAATATTATA
*
3884 TTTTAACATATAAAACTT-
1 TTTTAAAATATAAAACTTG
3902 TTTTAAAATATAAAACTTG
1 TTTTAAAATATAAAACTTG
3921 TTTT
1 TTTT
3925 TGGCTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTTAAAATATAAAACTTG
Found at i:4115 original size:31 final size:32
Alignment explanation
Indices: 4052--4121 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
4042 TCCTTTAATT
* *
4052 CTAAATAGTGGCGTTTTCCTAAATAAAACGCCA
1 CTAAATAGTGGCGTTTT-CGAAAGAAAACGCCA
*
4085 CTAAATAGTGGCGTTTT-GAAAGGAAACGCCA
1 CTAAATAGTGGCGTTTTCGAAAGAAAACGCCA
*
4116 ATAAAT
1 CTAAAT
4122 TTAGTCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 16 0.48
33 17 0.52
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (32 bp):
CTAAATAGTGGCGTTTTCGAAAGAAAACGCCA
Found at i:8277 original size:21 final size:21
Alignment explanation
Indices: 8253--8309 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
8243 ATCCAACATC
8253 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * *
8274 TGAGACATTCGCAAGAAGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
8295 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
8310 GTGTTATAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.33, T:0.09
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Found at i:14657 original size:10 final size:10
Alignment explanation
Indices: 14642--14668 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
14632 GTAACACAAA
14642 TCACATACCT
1 TCACATACCT
14652 TCACATACCT
1 TCACATACCT
14662 TCACATA
1 TCACATA
14669 ATTCTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (10 bp):
TCACATACCT
Found at i:15489 original size:15 final size:16
Alignment explanation
Indices: 15456--15495 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
15446 TTACTTTGCT
15456 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
15472 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
15487 TTGCTTTCT
1 TTGTTTTCT
15496 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.