Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013112.1 Kokia drynarioides strain JFW-HI SEQ_128131, 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: 13069
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:55 original size:29 final size:29
Alignment explanation
Indices: 23--113 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
13 AAAATTACCA
23 TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
* * * * *
52 TTTTGACCTCGGATCTTCTAAAAATTACCA-
1 TTTT-ACCCCCGAACTTCCAAAAA-TCCCAT
* *
82 TTTTACCCTCGAACTTCC-AAAATCCTAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
110 TTTT
1 TTTT
114 GATTCCGAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
27 3 0.06
28 8 0.17
29 13 0.28
30 19 0.40
31 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTTACCCCCGAACTTCCAAAAATCCCAT
Found at i:92 original size:30 final size:30
Alignment explanation
Indices: 5--92 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
1 TCGA
*
5 ATCTTCTAAAAATTACCATTTTACCC-CCG
1 ATCTTCTAAAAATTACCATTTTACCCTCGG
* * *
34 AACTTCCAAAAA-TCCCATTTTTGA-CCTCGG
1 ATCTTCTAAAAATTACCA-TTTT-ACCCTCGG
64 ATCTTCTAAAAATTACCATTTTACCCTCG
1 ATCTTCTAAAAATTACCATTTTACCCTCG
93 AACTTCCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.09
29 17 0.36
30 22 0.47
31 4 0.09
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.34
Consensus pattern (30 bp):
ATCTTCTAAAAATTACCATTTTACCCTCGG
Found at i:97 original size:59 final size:58
Alignment explanation
Indices: 5--115 Score: 195
Period size: 59 Copynumber: 1.9 Consensus size: 58
1 TCGA
5 ATCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGG
1 ATCTTCTAAAAATTACCATTTTACCCCCGAACTTCC-AAAATCCCATTTTTGACCTCGG
* *
64 ATCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAATCCTATTTTTGA
1 ATCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAATCCCATTTTTGA
116 TTCCGAACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
58 15 0.30
59 35 0.70
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
ATCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAATCCCATTTTTGACCTCGG
Found at i:12155 original size:139 final size:140
Alignment explanation
Indices: 11736--12155 Score: 625
Period size: 139 Copynumber: 3.0 Consensus size: 140
11726 AAATGGTTAG
* *
11736 CTTCCTGATGA-GATACTGAGAAGTGAACCAAAATTCGTCTTCCTGATGAGATACAAAGAAGCGG
1 CTTCCAGATGAGGATACTGAGAAGTGAACC-AAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
* * * *
11800 ATTGAAACGGTGATGGGGTCATCTTCTTGATGAA-ACACTGAG-AGAAGACCCAAACGAGGCTTG
65 ATTGAAACAGTGATGGGATCATCTTCCTGAT-AAGACACTGAGAAGAAGACCCAAACGAGGCTCG
11863 AAACGAGCAGAT
129 AAACGAGCAGAT
* * * * *
11875 CTTCTAGATGAGG-TATTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCAGA
1 CTTCCAGATGAGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
* *
11939 TTGAAACAGTGATGGGATCATCTTTCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
66 TTGAAACAGTGATGGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
*
12004 ACGAGCAAAT
131 ACGAGCAGAT
*
12014 CTTCCATATG-GGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
1 CTTCCAGATGAGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
* *
12078 TGGAAACAGTGATAGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
66 TTGAAACAGTGATGGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
*
12143 ACGAGCCGAT
131 ACGAGCAGAT
12153 CTT
1 CTT
12156 NNNNNNNNNN
Statistics
Matches: 251, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
137 1 0.00
138 68 0.27
139 181 0.72
140 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (140 bp):
CTTCCAGATGAGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
TTGAAACAGTGATGGGATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
ACGAGCAGAT
Found at i:12760 original size:17 final size:17
Alignment explanation
Indices: 12736--12792 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
12726 TTGGAAATTG
12736 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
12753 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
12770 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
12787 AATTTA
1 AATTTA
12793 GAAAAGTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.