Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014739.1 Kokia drynarioides strain JFW-HI SEQ_129778, 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: 17490
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:4559 original size:15 final size:15
Alignment explanation
Indices: 4522--4560 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4512 TTATGTGTGC
*
4522 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
4537 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
4551 TTAATTCTTG
1 TTAATTCTTG
4561 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:5263 original size:20 final size:22
Alignment explanation
Indices: 5219--5269 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
5209 TATTATTATT
*
5219 TATTTTT-ATTTTATTATTTGC
1 TATTTTTAATTTAATTATTTGC
5240 -ATTTTTAATTTAATT-TTT-C
1 TATTTTTAATTTAATTATTTGC
5259 TA-TTTTAATTT
1 TATTTTTAATTT
5270 TTTTTCCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATTTAATTATTTGC
Found at i:8095 original size:12 final size:12
Alignment explanation
Indices: 8078--8116 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8068 ACATGTCTTT
8078 AAAAAATTGAAA
1 AAAAAATTGAAA
* *
8090 AAAAAATTTATTA
1 AAAAAATTGA-AA
8103 AAAAAATTGAAA
1 AAAAAATTGAAA
8115 AA
1 AA
8117 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
AAAAAATTGAAA
Found at i:8166 original size:12 final size:11
Alignment explanation
Indices: 8136--8189 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 11
8126 ATTTAGTATA
*
8136 TTTATTTTCAT
1 TTTATTTTTAT
8147 TTTCATTTTTAGT
1 TTT-ATTTTTA-T
8160 TTTA-TTTTAT
1 TTTATTTTTAT
8170 TTTATTTTTAAT
1 TTTATTTTT-AT
8182 TTTATTTT
1 TTTATTTT
8190 AACTATGCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.13
11 12 0.32
12 17 0.45
13 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:8169 original size:5 final size:5
Alignment explanation
Indices: 8136--8190 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 5
8126 ATTTAGTATA
8136 TTTAT TTTCAT TTTCATT TTTAGT TTTAT TTTAT TTTATT TTTAAT TTTAT
1 TTTAT TTT-AT TTT-A-T TTTA-T TTTAT TTTAT TTTA-T TTT-AT TTTAT
8187 TTTA
1 TTTA
8191 ACTATGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 19 0.42
6 21 0.47
7 5 0.11
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:8183 original size:17 final size:16
Alignment explanation
Indices: 8153--8190 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
8143 TCATTTTCAT
8153 TTTTAGTTTTATTTTA
1 TTTTAGTTTTATTTTA
*
8169 TTTTATTTTTAATTTTA
1 TTTTAGTTTT-ATTTTA
8186 TTTTA
1 TTTTA
8191 ACTATGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTAGTTTTATTTTA
Found at i:12397 original size:30 final size:31
Alignment explanation
Indices: 12340--12406 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
12330 AAAAGGATTG
*
12340 TTTTGTCACTTTTCGATAAGTTTAGTGACTA
1 TTTTGTCACTTTTCGATAAGTTGAGTGACTA
*
12371 TTTTGTCACATTTTC-A-AAGTTGAGTGACTG
1 TTTTGTCAC-TTTTCGATAAGTTGAGTGACTA
12401 TTTTGT
1 TTTTGT
12407 TAAATGGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 18 0.55
31 10 0.30
32 5 0.15
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (31 bp):
TTTTGTCACTTTTCGATAAGTTGAGTGACTA
Found at i:16944 original size:27 final size:27
Alignment explanation
Indices: 16924--16987 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
16914 CGGCGGCGGC
16924 TGCGGTTGCATGAAAAGCGGCTGCGTT
1 TGCGGTTGCATGAAAAGCGGCTGCGTT
16951 TGCGGTTGCATGAAAAGCGGCTGCGTT
1 TGCGGTTGCATGAAAAGCGGCTGCGTT
16978 TGCGGTTGCA
1 TGCGGTTGCA
16988 GCTGCTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.38, T:0.27
Consensus pattern (27 bp):
TGCGGTTGCATGAAAAGCGGCTGCGTT
Found at i:16949 original size:42 final size:39
Alignment explanation
Indices: 16863--16951 Score: 97
Period size: 42 Copynumber: 2.2 Consensus size: 39
16853 TAACTTGCGC
* * * * *
16863 CTGCGTTTCTTTCTGTGGCGGCGTTTGCATGAACAGCGT
1 CTGCGTTTCTTTCGGCGGCGGCGGTTGCATGAAAAGCGG
*
16902 TTGCGTTTCTTTCGGCGGCGGCTGCGGTTGCATGAAAAGCGG
1 CTGCGTTTCTTTCGGCGGC-G--GCGGTTGCATGAAAAGCGG
16944 CTGCGTTT
1 CTGCGTTT
16952 GCGGTTGCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 16 0.40
40 1 0.03
42 23 0.57
ACGTcount: A:0.10, C:0.22, G:0.34, T:0.34
Consensus pattern (39 bp):
CTGCGTTTCTTTCGGCGGCGGCGGTTGCATGAAAAGCGG
Done.