Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014701.1 Kokia drynarioides strain JFW-HI SEQ_129740, 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: 8565
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.27
Warning! 393 characters in sequence are not A, C, G, or T
Found at i:2105 original size:6 final size:6
Alignment explanation
Indices: 2094--2189 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
2084 ATTTGTTTGA
* * *
2094 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * *
2140 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAAATT -ACTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT
2186 AAAT
1 AAAT
2190 AAAGCTAAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
5 19 0.28
6 46 0.67
7 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:2113 original size:11 final size:11
Alignment explanation
Indices: 2114--2169 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
2104 TTATTTTAAA
2114 TTTAAATTTAT
1 TTTAAATTTAT
* *
2125 TTTGAATTTAAA
1 TTTAAATTT-AT
*
2137 TTT-AATTTAAG
1 TTTAAATTT-AT
2148 TTTAAATTTAT
1 TTTAAATTTAT
2159 TTTCAAATTTA
1 TTT-AAATTTA
2170 AAATTACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:2185 original size:17 final size:17
Alignment explanation
Indices: 2061--2189 Score: 150
Period size: 17 Copynumber: 7.4 Consensus size: 17
2051 CCGAACTCCC
2061 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
2079 ATTAAATTTGTTTGAAAA
1 TTTAAATTTATTT-TAAA
2097 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
2114 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
2131 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
2148 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
2166 TTTAAAATTACTATAAA
1 TTTAAATTTATTTTAAA
2183 TTTAAAT
1 TTTAAAT
2190 AAAGCTAAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
17 55 0.59
18 38 0.41
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2187 original size:35 final size:34
Alignment explanation
Indices: 2061--2189 Score: 141
Period size: 35 Copynumber: 3.7 Consensus size: 34
2051 CCGAACTCCC
* * * *
2061 TTTAAATTTATTTTAAAAATTAAATTTGTTTGAAAA
1 TTTAAATTTAATTT-AAATTTAAATTTATTT-TAAA
* *
2097 TTTAAATTTATTTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTTAAA
*
2131 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTT-AAA
* * *
2166 TTTAAAATTACTATAAATTTAAAT
1 TTTAAATTTAATTTAAATTTAAAT
2190 AAAGCTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
34 31 0.38
35 36 0.44
36 14 0.17
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTAATTTAAATTTAAATTTATTTTAAA
Found at i:5573 original size:23 final size:23
Alignment explanation
Indices: 5543--5587 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5533 CCTTCCTCCT
5543 AACTATAAATCGAAAAAACCTTC
1 AACTATAAATCGAAAAAACCTTC
5566 AACTATAAATCGAAAAAACCTT
1 AACTATAAATCGAAAAAACCTT
5588 TAAACTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (23 bp):
AACTATAAATCGAAAAAACCTTC
Found at i:5593 original size:24 final size:23
Alignment explanation
Indices: 5543--5594 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
5533 CCTTCCTCCT
*
5543 AACTATAAATCGAAAAAACCTTC
1 AACTATAAATCGAAAAAACCTTA
5566 AACTATAAATCGAAAAAACCTTTA
1 AACTATAAATCGAAAAAACC-TTA
5590 AACTA
1 AACTA
5595 ACGGATCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.23
Consensus pattern (23 bp):
AACTATAAATCGAAAAAACCTTA
Found at i:6111 original size:23 final size:23
Alignment explanation
Indices: 6055--6112 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6045 CGTCCATCCT
*
6055 TGCTGACTAGACCCTCTAGAAGC
1 TGCTGACTGGACCCTCTAGAAGC
*
6078 TGCTGACTGGACCTTCTAGAAGC
1 TGCTGACTGGACCCTCTAGAAGC
*
6101 TGCTGATTGGAC
1 TGCTGACTGGAC
6113 GTTACATGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCTGACTGGACCCTCTAGAAGC
Found at i:6877 original size:14 final size:13
Alignment explanation
Indices: 6857--6887 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6847 TTTTTTTTCA
6857 TTTTCTC-CTTTT
1 TTTTCTCTCTTTT
6869 TTTTCTCTCTTTT
1 TTTTCTCTCTTTT
6882 TTTTCT
1 TTTTCT
6888 TTTCAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTCTCTTTT
Found at i:6915 original size:13 final size:13
Alignment explanation
Indices: 6897--6926 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6887 TTTTCAAACC
6897 TTTTGCTCTTTTT
1 TTTTGCTCTTTTT
*
6910 TTTTGCTGTTTTT
1 TTTTGCTCTTTTT
6923 TTTT
1 TTTT
6927 CTTCTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (13 bp):
TTTTGCTCTTTTT
Done.