Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010754.1 Kokia drynarioides strain JFW-HI SEQ_125712, 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: 23475
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:3224 original size:26 final size:27
Alignment explanation
Indices: 3186--3250 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
3176 ATTAAAAAAT
*
3186 ATTTTTAATAATA-TTTAATTA-TTTT-A
1 ATTTTTAAAAATAGTTT--TTATTTTTCA
3212 ATTTTTAAAAATAGTTTTTATTTTTCA
1 ATTTTTAAAAATAGTTTTTATTTTTCA
*
3239 AATTTTAAAAAT
1 ATTTTTAAAAAT
3251 TAATTAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.09
26 16 0.47
27 15 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTTTAAAAATAGTTTTTATTTTTCA
Found at i:5035 original size:59 final size:58
Alignment explanation
Indices: 4961--5308 Score: 334
Period size: 59 Copynumber: 5.9 Consensus size: 58
4951 AGGAACATTT
* *
4961 GGGTTAAAATGTGATTTTGGAGAAGTTT-GGGGTCAAATATGATTTTGAGAAGGTTTAGG
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTCAAATATGATTTT-AGAAAGTTTA-G
5020 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTCAAA-ATGTAATTTTAGAAAAGTTTTA-
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTCAAATATG--ATTTTAG-AAAG-TTTAG
* * * *
5080 GGGTTAAAATGTGATTTTGG-GAAGTTTATGGGTCAAAATGTGATTTTAGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTC-AAATATGATTTTA-GAAAGTTTAG
* * *
5139 GGGTTAAAATTTGATTTTAGAAAAGTTTAGGGGTGAAAATATGATTTTAGAAAAGTTT-G
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGT-CAAATATGATTTTAG-AAAGTTTAG
* * * *
5198 GGGTTAAAATGTGATTTTAGAAAAATTT-GAGGTGAATATATGATTTTAGAAAAGTTTA-
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTCAA-ATATGATTTTAG-AAAGTTTAG
* ** ** * *
5256 AGGTTAAAATGCAATTTTAAAAAAGTTT-GAGGATCAAAATATAATTTTAGAAA
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAG-GGGTC-AAATATGATTTTAGAAA
5309 AATTTGAAGG
Statistics
Matches: 248, Mismatches: 25, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
57 2 0.01
58 55 0.22
59 110 0.44
60 67 0.27
61 10 0.04
62 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTCAAATATGATTTTAGAAAGTTTAG
Found at i:5059 original size:30 final size:30
Alignment explanation
Indices: 4961--5309 Score: 329
Period size: 30 Copynumber: 11.8 Consensus size: 30
4951 AGGAACATTT
* *
4961 GGGTTAAAATGTGATTTTGGAGAAGTTT-G
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * *
4990 GGG-TCAAATATGATTTT-GAGAAGGTTTAGG
1 GGGTTAAAATGTGATTTTAGA-AAAGTTTA-G
*
5020 GGGTTAAAATGTGATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* *
5050 GGGTCAAAATGTAATTTTAGAAAAGTTTTA-
1 GGGTTAAAATGTGATTTTAGAAAAG-TTTAG
** *
5080 GGGTTAAAATGTGATTTT-GGGAAGTTTAT
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * *
5109 GGGTCAAAATGTGATTTTAGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
*
5139 GGGTTAAAATTTGATTTTAGAAAAGTTTAG
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* *
5169 GGGTGAAAATATGATTTTAGAAAAGTTT-G
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
*
5198 GGGTTAAAATGTGATTTTAGAAAAATTT-G
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * * *
5227 AGGTGAATATATGATTTTAGAAAAGTTTA-
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* ** *
5256 AGGTTAAAATGCAATTTTAAAAAAGTTT-G
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * * *
5285 AGGATCAAAATATAATTTTAGAAAA
1 -GGGTTAAAATGTGATTTTAGAAAA
5310 ATTTGAAGGT
Statistics
Matches: 266, Mismatches: 43, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.01
28 21 0.08
29 96 0.36
30 122 0.46
31 23 0.09
32 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTAGAAAAGTTTAG
Found at i:5067 original size:89 final size:88
Alignment explanation
Indices: 4961--5265 Score: 339
Period size: 89 Copynumber: 3.4 Consensus size: 88
4951 AGGAACATTT
* * *
4961 GGGTTAAAATGTGATTTTGGAGAAGTTT-GGGGTCAAATATGATTTTGAGAAGGTTTAGGGGGTT
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTAAAATATGATTTTGAGAA-GTTTA-GGGGTT
*
5025 AAAATGTGATTTTGGAAAAGTTTAG
64 AAAATGTGATTTTGGAAAAGTTTAA
* * * * * * *
5050 GGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTTAAAATGTGATTTTGGGAAGTTTATGGGTCA
1 GGGTTAAAATGTGATTTTAGAAAAG-TTTAGGGGTAAAATATGATTTTGAGAAGTTTAGGGGTTA
5115 AAATGTGATTTTAGG-AAAGTTTAA
65 AAATGTGATTTT-GGAAAAGTTTAA
* *
5139 GGGTTAAAATTTGATTTTAGAAAAGTTTAGGGGTGAAAATATGATTTTAGAAAAGTTT-GGGGTT
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGT-AAAATATGATTTT-GAGAAGTTTAGGGGTT
* * *
5203 AAAATGTGATTTTAGAAAAATTTGA
64 AAAATGTGATTTTGGAAAAGTTTAA
* * * * *
5228 -GGTGAATATATGATTTTAGAAAAGTTTAAGGTTAAAAT
1 GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTAAAAT
5266 GCAATTTTAA
Statistics
Matches: 182, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
87 5 0.03
88 37 0.20
89 104 0.57
90 17 0.09
91 19 0.10
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (88 bp):
GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTAAAATATGATTTTGAGAAGTTTAGGGGTTAA
AATGTGATTTTGGAAAAGTTTAA
Found at i:8314 original size:2 final size:2
Alignment explanation
Indices: 8307--8332 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8297 TTAAAAATTA
8307 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
8333 CGGGGGTTTT
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:12477 original size:18 final size:17
Alignment explanation
Indices: 12451--12486 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
12441 AATATGTTCT
*
12451 AAATTACATAATATAAAA
1 AAATAACATAATA-AAAA
12469 AAATAACATAATAAAAA
1 AAATAACATAATAAAAA
12486 A
1 A
12487 TATTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAACATAATAAAAA
Found at i:19363 original size:2 final size:2
Alignment explanation
Indices: 19358--19388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19348 GCGATCGGAG
19358 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
19389 GGAGGGGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.