Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012104.1 Kokia drynarioides strain JFW-HI SEQ_127103, 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: 12721
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1033 original size:27 final size:27
Alignment explanation
Indices: 995--1050 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
985 AGAATAATGC
*
995 TCATAACTTTTTGTATGATTTATTAGT
1 TCATAAATTTTTGTATGATTTATTAGT
1022 TCATAAATTTTTGTATGATTTATTAGT
1 TCATAAATTTTTGTATGATTTATTAGT
1049 TC
1 TC
1051 TTTACCCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (27 bp):
TCATAAATTTTTGTATGATTTATTAGT
Found at i:11545 original size:97 final size:96
Alignment explanation
Indices: 11375--11563 Score: 238
Period size: 97 Copynumber: 2.0 Consensus size: 96
11365 AGGAAAAGGA
**
11375 TATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGCAAGTTAAGGAGCAATATTTCAAAATC
1 TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGCAAGTTAAGGAGCAATATTTCAAAATC
*
11440 GAATATAAAGAAAACATTGCCTCGATTTAGGG
66 GAATATAAA-AAAACATTACCTCGATTTAGGG
* * * * * *
11472 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTATGTTAAGGCA-CAAATTTTTGAAAC
1 TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGCAAGTTAAGG-AGC-AATATTTCAAAA
* *
11536 TCGAA-ATAAAAGAATATTACCTCGATTT
64 TCGAATATAAAAAAACATTACCTCGATTT
11564 TAAAGTCTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
96 15 0.19
97 49 0.62
98 15 0.19
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGCAAGTTAAGGAGCAATATTTCAAAATC
GAATATAAAAAAACATTACCTCGATTTAGGG
Found at i:11962 original size:29 final size:30
Alignment explanation
Indices: 11917--12232 Score: 235
Period size: 29 Copynumber: 10.7 Consensus size: 30
11907 TTCGAGGTTT
*
11917 AAAATAGAATTTTTGGAAGTTTTAGGGG-C
1 AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* *
11946 -AAATGGTAATTTTTGGATG-TTTCGGGGTC
1 AAAATGG-AATTTTTGGAAGTTTTAGGGGTC
* *
11975 AAAATGGAATTTTTAGAAGTTTT-GAGGTC
1 AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* * * * *
12004 AAAAATAGAATTTTTGGAAG--CTCGAGGTT
1 -AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* *
12033 AAAATGGAATTTTTGGAAG-TTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* *
12062 AAAAATAGAATTTTTGGAAG-TTTGGGGGT-
1 -AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* *
12091 AAGAATGAAATTTTTGGAAGTTTT-GGGGTTA
1 AA-AATGGAATTTTTGGAAGTTTTAGGGG-TC
* * ** * *
12122 AAAATGGGATTTTAGGAAGTTCGA-GCGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGGTC
12151 AAAATGGAATTTTTGGAAGTTTTA-GGGTC
1 AAAATGGAATTTTTGGAAGTTTTAGGGGTC
* ** *
12180 AAAATTGGAATTTTAGGAAG-TTCGGGGGTA
1 AAAA-TGGAATTTTTGGAAGTTTTAGGGGTC
*
12210 AAAATAGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
12233 AGAGACCTCC
Statistics
Matches: 234, Mismatches: 36, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
28 33 0.14
29 100 0.43
30 97 0.41
31 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGGTC
Found at i:12038 original size:88 final size:87
Alignment explanation
Indices: 11881--12232 Score: 293
Period size: 88 Copynumber: 4.0 Consensus size: 87
11871 CAAACATTCG
* * ** ** *
11881 GGGGT-AAAAGGGTAATTTTGAG-AGTTTTCGAGGTTTAAAATAGAATTTTTGGAAGTTTTAGGG
1 GGGGTCAAAATGG-AATTTTTAGAAGTTTT-GAGGTCAAAAATAGAATTTTTGGAAGTTCGAGGT
** *
11944 GCAAATGGTAATTTTTGGATGTTTC
64 TAAAATGG-AATTTTTGGAAGTTTC
*
11969 GGGGTCAAAATGGAATTTTTAGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGCTCGAGGTTA
1 GGGGTCAAAATGGAATTTTTAGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGAGGTTA
12034 AAATGGAATTTTTGGAAGTTTC
66 AAATGGAATTTTTGGAAGTTTC
* * * * * * * *
12056 GAGGTCAAAAATAGAATTTTTGGAAGTTTGGGGGT-AAGAAT-GAAATTTTTGGAAGTTTTGGGG
1 GGGGTC-AAAATGGAATTTTTAGAAGTTTTGAGGTCAAAAATAG-AATTTTTGGAAG-TTCGAGG
* *
12119 TTAAAAATGGGATTTTAGGAAG-TTC
63 TT-AAAATGGAATTTTTGGAAGTTTC
* * * * * * *
12144 GAGCGTAAAAATGGAATTTTTGGAAGTTTT-AGGGTCAAAATTGGAATTTTAGGAAGTTCGGGGG
1 G-GGGTCAAAATGGAATTTTTAGAAGTTTTGA-GGTCAAAAATAGAATTTTTGGAAGTTC-GAGG
* *
12208 TAAAAATAGAATTTTTGGACAGTTT
63 TTAAAATGGAATTTTTGGA-AGTTT
12233 AGAGACCTCC
Statistics
Matches: 215, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
86 1 0.00
87 37 0.17
88 121 0.56
89 53 0.25
90 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (87 bp):
GGGGTCAAAATGGAATTTTTAGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGAGGTTA
AAATGGAATTTTTGGAAGTTTC
Found at i:12234 original size:59 final size:59
Alignment explanation
Indices: 11917--12232 Score: 338
Period size: 59 Copynumber: 5.4 Consensus size: 59
11907 TTCGAGGTTT
* * * *
11917 AAAATAGAATTTTTGGAAGTTTTAGGGGC--AAATGGTAATTTTTGGATGTTTC-GGGGTC
1 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGG-AATTTTTGGAAG-TTCGGGGGTA
* * * * *
11975 AAAATGGAATTTTTAGAAGTTTT-GAGGTCAAAAATAGAATTTTTGGAAGCTC-GAGGTT
1 AAAATGGAATTTTTGGAAGTTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * *
12033 AAAATGGAATTTTTGGAAG-TTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * * * * * * *
12092 AGAATGAAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTAGGAAGTTCGAGCGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* *
12151 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAATTGGAATTTTAGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
*
12210 AAAATAGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
12233 AGAGACCTCC
Statistics
Matches: 219, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
57 4 0.02
58 75 0.34
59 126 0.58
60 14 0.06
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
Done.