Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002417.1 Kokia drynarioides strain JFW-HI SEQ_114514, 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: 9112
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Found at i:162 original size:29 final size:28
Alignment explanation
Indices: 111--454 Score: 257
Period size: 29 Copynumber: 11.8 Consensus size: 28
101 CACGGGGGGC
* * **
111 AAAATGGTAGTTTTGGAAGGTTCGGAATCA
1 AAAATGGGATTTTTGGAA-GTTCGGGGT-A
*
141 AAAATGGGATTTTTGGAAGTTCAAGGGT-
1 AAAATGGGATTTTTGGAAGTTC-GGGGTA
* * * *
169 AAAATGGTAATTTTCGAAAGGTTCGAGGTCA
1 AAAATGG-GATTTTTGGAA-GTTCGGGGT-A
*
200 AAAATGGGATTTTTGGAAGTTTGTGGGT-
1 AAAATGGGATTTTTGGAAGTTCG-GGGTA
* * *
228 AAAATGGTAATTTTTGGAGAATTTGGGGTCA
1 AAAATGG-GATTTTTGGA-AGTTCGGGGT-A
* * *
259 AAAATGGGATTTTTTGAAATTCGAGGTTA
1 AAAATGGGATTTTTGGAAGTTCG-GGGTA
*
288 AAAATGAGATTTTTGGAAGTTCGGAGGT-
1 AAAATGGGATTTTTGGAAGTTCGG-GGTA
* *
316 AAAATGGTAATTTTTGGAGAGTTTGGGGTCA
1 AAAATGG-GATTTTTGGA-AGTTCGGGGT-A
347 AAAATGGGATTTTTGGAAGTTCGGGGT-
1 AAAATGGGATTTTTGGAAGTTCGGGGTA
* *
374 AAAATGGTAATTTTGGAGAGTTCGGGGTGA
1 AAAATGGGATTTTTGGA-AGTTCGGGGT-A
* *
404 AAAATGAGATTTTTGGATGTTCGAGGGT-
1 AAAATGGGATTTTTGGAAGTTCG-GGGTA
*
432 AAAATGGTAATTTTTGGAGAGTT
1 AAAATGG-GATTTTTGGA-AGTT
455 TCAGGACCTC
Statistics
Matches: 253, Mismatches: 39, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
27 15 0.06
28 37 0.15
29 95 0.38
30 85 0.34
31 21 0.08
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (28 bp):
AAAATGGGATTTTTGGAAGTTCGGGGTA
Found at i:241 original size:88 final size:85
Alignment explanation
Indices: 141--447 Score: 270
Period size: 88 Copynumber: 3.5 Consensus size: 85
131 TTCGGAATCA
* * *
141 AAAATGGGATTTTTGGA-AGTTCAAGGGT-AAAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAA
1 AAAATGGAATTTTTGGAGAGTT-TAGGGTAAAAATGGTAATTTTTGAAA-GTTCGAGGT-AAAAA
*
204 TGGGATTTTTGGAAGTTTGTGGGT
63 TGGGATTTTTGGAAGTTCG-GGGT
* * * *
228 AAAATGGTAATTTTTGGAGAATTTGGGGTCAAAAATGGGATTTTTTGAAA-TTCGAGGTTAAAAA
1 AAAATGG-AATTTTTGGAGAGTTTAGGGT-AAAAATGGTAATTTTTGAAAGTTCGAGG-TAAAAA
*
292 TGAGATTTTTGGAAGTTCGGAGGT
63 TGGGATTTTTGGAAGTTCGG-GGT
* * * *
316 AAAATGGTAATTTTTGGAGAGTTTGGGGTCAAAAATGG-GATTTTTGGAAGTTCGGGGT-AAAAT
1 AAAATGG-AATTTTTGGAGAGTTTAGGGT-AAAAATGGTAATTTTTGAAAGTTCGAGGTAAAAAT
* *
379 GGTAATTTTGGAGAGTTCGGGGT
64 GGGATTTTTGGA-AGTTCGGGGT
* *
402 GAAAAAT-GAGATTTTTGGA-TGTTCGAGGGT-AAAATGGTAATTTTTG
1 --AAAATGGA-ATTTTTGGAGAGTT-TAGGGTAAAAATGGTAATTTTTG
448 GAGAGTTTCA
Statistics
Matches: 186, Mismatches: 21, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
85 7 0.04
86 28 0.15
87 38 0.20
88 93 0.50
89 4 0.02
90 16 0.09
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (85 bp):
AAAATGGAATTTTTGGAGAGTTTAGGGTAAAAATGGTAATTTTTGAAAGTTCGAGGTAAAAATGG
GATTTTTGGAAGTTCGGGGT
Found at i:258 original size:59 final size:58
Alignment explanation
Indices: 111--290 Score: 184
Period size: 59 Copynumber: 3.1 Consensus size: 58
101 CACGGGGGGC
* * * *
111 AAAATGGTAGTTTTGGAAGGTTCG-GAATCAAAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAATGGTAATTTTCGAAAGTTCGAG-GTCAAAAATGGGATTTTTGGAAGTTCAAGGGT
***
169 AAAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGTGGGT
1 AAAATGGTAATTTTCGAAA-GTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGT
* * * * * * *
228 AAAATGGTAATTTTTGGAGAA-TTTGGGGTCAAAAATGGGATTTTTTGAAATTCGAGGTT
1 AAAATGGTAA-TTTTCGA-AAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGT
287 AAAA
1 AAAA
291 ATGAGATTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 16 0.16
59 78 0.76
60 7 0.07
61 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTCGAAAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGT
Found at i:300 original size:59 final size:57
Alignment explanation
Indices: 141--454 Score: 250
Period size: 59 Copynumber: 5.4 Consensus size: 57
131 TTCGGAATCA
* * * *
141 AAAATGGGATTTTTGGA-AGTTCAAGGG-T-AAAATG-GTAATTTTCGAAAGGTTCGAGGT
1 AAAATGGGATTTTTGGAGAGTTC-GGGGTTAAAAATGAG--ATTTTTGGAA-GTTCGGGGT
* * *
198 CAAAAATGGGATTTTTGGA-AGTTTGTGGG-T-AAAATG-GTAATTTTTGGAGAATTTGGGGT
1 --AAAATGGGATTTTTGGAGAGTTCG-GGGTTAAAAATGAG--ATTTTTGGA-AGTTCGGGGT
* * *
257 CAAAAATGGGATTTTTTGA-AATTCGAGGTTAAAAATGAGATTTTTGGAAGTTCGGAGGT
1 --AAAATGGGATTTTTGGAGAGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCGG-GGT
* * * *
316 AAAATGGTAATTTTTGGAGAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT
1 AAAATGG-GATTTTTGGAGAGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGT
* * * *
374 AAAATGGTAATTTTGGAGAGTTCGGGGTGAAAAATGAGATTTTTGGATGTTCGAGGGT
1 AAAATGGGATTTTTGGAGAGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCG-GGGT
*
432 AAAATGGTAATTTTTGGAGAGTT
1 AAAATGG-GATTTTTGGAGAGTT
455 TCAGGACCTC
Statistics
Matches: 217, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
57 47 0.22
58 36 0.17
59 126 0.58
60 7 0.03
61 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (57 bp):
AAAATGGGATTTTTGGAGAGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGT
Done.