Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013208.1 Kokia drynarioides strain JFW-HI SEQ_128227, 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, 804
Length: 1341
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:88 original size:29 final size:28
Alignment explanation
Indices: 56--114 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
46 TGAGACTTTC
**
56 GGATACCCAGGGGGTAAAATGGTAATTTT
1 GGATACCCA-GGGACAAAATGGTAATTTT
* *
85 GGATTCTCAGGGACAAAATGGTAATTTT
1 GGATACCCAGGGACAAAATGGTAATTTT
113 GG
1 GG
115 GAAATTCGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (28 bp):
GGATACCCAGGGACAAAATGGTAATTTT
Found at i:180 original size:29 final size:28
Alignment explanation
Indices: 65--192 Score: 91
Period size: 29 Copynumber: 4.4 Consensus size: 28
55 CGGATACCCA
65 GGGGGTAAAATGGTAATTTTG-GATTCTC
1 GGGGGTAAAATGGTAATTTTGAGATT-TC
* ** * *
93 AGGGACAAAATGGTAATTTTGGGAAATTC
1 GGGGGTAAAATGGTAATTTTGAG-ATTTC
* *
122 GGGGTTAAAAAT-GAAATTCTT-AGATATTC
1 GGGGGT-AAAATGGTAATT-TTGAGAT-TTC
*
151 GGGGGTAAAAGGGTAATTTTGAGAGTTTC
1 GGGGGTAAAATGGTAATTTTGAGA-TTTC
*
180 GAGGGTTAAAATG
1 G-GGGGTAAAATG
193 AAATTTTTGG
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
28 25 0.33
29 32 0.42
30 19 0.25
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.31
Consensus pattern (28 bp):
GGGGGTAAAATGGTAATTTTGAGATTTC
Found at i:197 original size:29 final size:28
Alignment explanation
Indices: 119--472 Score: 186
Period size: 30 Copynumber: 12.1 Consensus size: 28
109 TTTTGGGAAA
*
119 TTCGGGGTTAAAAATGAAATTCTTAG-A-T
1 TTCGGGGTT-AAAATGAAATT-TTGGAAGT
* * *
147 ATTCGGGGGTAAAAGGGTAATTTT-GAGAGT
1 -TTCGGGGTTAAAA-TGAAATTTTGGA-AGT
177 TTCGAGGGTTAAAATGAAATTTTTGGAAGT
1 TTCG-GGGTTAAAATGAAA-TTTTGGAAGT
* * * *
207 TT-GGGATAAAAATGGAATTTTTAGAAGT
1 TTCGGGGTTAAAAT-GAAATTTTGGAAGT
* *
235 TTCAGGGTTAAAAATGGAATTTTTGGAAG-
1 TTCGGGGTT-AAAAT-GAAATTTTGGAAGT
* *
264 TTCGAGGGTAAAAATGGAAGTTTTGGAAGT
1 TTCG-GGGTTAAAAT-GAAATTTTGGAAGT
* *
294 TTTGGGGTTAAAAATGGAATTTTTGGAAG-
1 TTCGGGGTT-AAAAT-GAAATTTTGGAAGT
* *
323 TTCGGGGGTATAAATGGAATTTTTGGAAGT
1 TTCGGGGTTA-AAAT-GAAATTTTGGAAGT
* *
353 TTCGAGGTTAATAATGGAATTTTTGGAAG-
1 TTCGGGGTTAA-AAT-GAAATTTTGGAAGT
** *
382 TTCGGGGGCAAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTTAAAAT-GAAATTTTGGAAGT
* * *
412 TTCGAGGTCAAAAATGGAATTTTTGGAAG-
1 TTCGGGGT-TAAAAT-GAAATTTTGGAAGT
* *
441 TTCTGGGG-AAAAATGGAATTTTTGGACAGT
1 TTC-GGGGTTAAAAT-GAAATTTTGGA-AGT
471 TT
1 TT
473 AGGGACCTCC
Statistics
Matches: 273, Mismatches: 30, Indels: 43
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.00
28 44 0.16
29 107 0.39
30 119 0.44
31 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (28 bp):
TTCGGGGTTAAAATGAAATTTTGGAAGT
Found at i:201 original size:30 final size:30
Alignment explanation
Indices: 174--472 Score: 327
Period size: 30 Copynumber: 10.2 Consensus size: 30
164 TAATTTTGAG
*
174 AGTTTCGAGGGTTAAAATGAAATTTTTGGA
1 AGTTTCGAGGGTTAAAATGGAATTTTTGGA
* * *
204 AGTTT-G-GGATAAAAATGGAATTTTTAGA
1 AGTTTCGAGGGTTAAAATGGAATTTTTGGA
232 AGTTTC-AGGGTTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGTT-AAAATGGAATTTTTGGA
* *
262 AG-TTCGAGGGTAAAAATGGAAGTTTTGGA
1 AGTTTCGAGGGTTAAAATGGAATTTTTGGA
*
291 AGTTTTG-GGGTTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGTT-AAAATGGAATTTTTGGA
*
321 AG-TTCG-GGGGTATAAATGGAATTTTTGGA
1 AGTTTCGAGGGTTA-AAATGGAATTTTTGGA
350 AGTTTCGA-GGTTAATAATGGAATTTTTGGA
1 AGTTTCGAGGGTTAA-AATGGAATTTTTGGA
* **
380 AG-TTCGGGGGCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGTTAAAATGGAATTTTTGGA
*
409 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGT-TAAAATGGAATTTTTGGA
*
439 AG-TTCTG-GGG-AAAAATGGAATTTTTGGA
1 AGTTTC-GAGGGTTAAAATGGAATTTTTGGA
467 CAGTTT
1 -AGTTT
473 AGGGACCTCC
Statistics
Matches: 232, Mismatches: 20, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
28 42 0.18
29 83 0.36
30 107 0.46
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
AGTTTCGAGGGTTAAAATGGAATTTTTGGA
Found at i:302 original size:59 final size:59
Alignment explanation
Indices: 99--472 Score: 449
Period size: 59 Copynumber: 6.4 Consensus size: 59
89 TCTCAGGGAC
* * * * *
99 AAAATGGTAATTTTGGGAA-ATTCGGGGTTAAAAATGAAATTCTTAGATA-TTCGGGGGT-
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGA-AGTTCGGGGGTA
* * * *
157 AAAAGGGTAA-TTTT-GAGAGTTTCGAGGGTT-AAAATGAAATTTTTGGAAGTT-TGGGATA
1 AAAATGG-AATTTTTGGA-AGTTTCG-GGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * *
215 AAAATGGAATTTTTAGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* *
274 AAAATGGAAGTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * * *
333 TAAATGGAATTTTTGGAAGTTTCGAGGTTAATAATGGAATTTTTGGAAGTTCGGGGGCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * *
392 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCTGGGG-A
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
450 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
473 AGGGACCTCC
Statistics
Matches: 278, Mismatches: 28, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
56 2 0.01
57 16 0.06
58 84 0.30
59 176 0.63
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTA
Done.