Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013715.1 Kokia drynarioides strain JFW-HI SEQ_128743, 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: 6978
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:270 original size:29 final size:29
Alignment explanation
Indices: 238--437 Score: 133
Period size: 30 Copynumber: 6.8 Consensus size: 29
228 ACCTAAGGAC
* *
238 AAAATGATAATTTTAGGAAGTTCGGGGTT
1 AAAATGATAATTTTTGGAAGTTTGGGGTT
* * *
267 AAAAAATG-GAATTTTTGGATGTTTGGGGGT
1 --AAAATGATAATTTTTGGAAGTTTGGGGTT
* * * *
297 -AAATGGTAATATTTGGAAGTTTTAGGGTCA
1 AAAATGATAATTTTTGGAAG-TTTGGGGT-T
*
327 AAAATG-GAATTTTTGGAAGTTTGAGGG-T
1 AAAATGATAATTTTTGGAAGTTTG-GGGTT
* * *
355 AAAATGGTAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGATAATTTTTGGAAG-TTTGGGGT-T
* *
386 AAAAT-ATAATTTTGAGGAAGTTTGGGGTC
1 AAAATGATAATTTT-TGGAAGTTTGGGGTT
*
415 GAAAT-ATAATTTTTGGATAGTTT
1 AAAATGATAATTTTTGGA-AGTTT
438 AAAGATCTTT
Statistics
Matches: 134, Mismatches: 24, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
27 5 0.04
28 19 0.14
29 40 0.30
30 49 0.37
31 21 0.16
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAATGATAATTTTTGGAAGTTTGGGGTT
Found at i:330 original size:59 final size:59
Alignment explanation
Indices: 238--413 Score: 193
Period size: 58 Copynumber: 3.0 Consensus size: 59
228 ACCTAAGGAC
* ** * * *
238 AAAATGATAAT-TTTAGGAAGTTCGGGGTTAAAAAATGGAATTTTTGGATGTTTGGGGGT
1 AAAATGGTAATATTT-GGAAGTTTTGGGTCAAAAAATGGAATTTTTGGAAGTTTGAGGGT
297 -AAATGGTAATATTTGGAAGTTTTAGGGTC-AAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATATTTGGAAGTTTT-GGGTCAAAAAATGGAATTTTTGGAAGTTTGAGGGT
* *
355 AAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAAATAT--AATTTTGAGGAAGTTTG-GGGT
1 AAAATGGTAATATTTGGAAGTTTTG-GGTCAAAAA-ATGGAATTTT-TGGAAGTTTGAGGGT
414 CGAAATATAA
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
58 44 0.43
59 43 0.42
60 13 0.13
61 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (59 bp):
AAAATGGTAATATTTGGAAGTTTTGGGTCAAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:425 original size:59 final size:59
Alignment explanation
Indices: 238--437 Score: 185
Period size: 59 Copynumber: 3.4 Consensus size: 59
228 ACCTAAGGAC
* ** * * * * *
238 AAAATGATAATTTTAGGAAG-TTCGGGGTTAAAAAATGGAATTTTTGGATGTTTGGGGGT
1 AAAATGATAATTTTTGGAAGTTTTAGGG-TCAAAAATAGAATTTTAGGAAGTTTGAGGGT
* * * *
297 -AAATGGTAATATTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAATGATAATTTTTGGAAGTTTTAGGGTCAAAAATAGAATTTTAGGAAGTTTGAGGGT
* *
355 AAAATGGTAATTTTTGGAAGTTTT-GAGGTCAAAAATATAATTTTGAGGAAGTTTG-GGGT
1 AAAATGATAATTTTTGGAAGTTTTAG-GGTCAAAAATAGAATTTT-AGGAAGTTTGAGGGT
*
414 CGAAAT-ATAATTTTTGGATAGTTT
1 -AAAATGATAATTTTTGGA-AGTTT
438 AAAGATCTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
58 45 0.37
59 58 0.48
60 18 0.15
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (59 bp):
AAAATGATAATTTTTGGAAGTTTTAGGGTCAAAAATAGAATTTTAGGAAGTTTGAGGGT
Found at i:1329 original size:3 final size:3
Alignment explanation
Indices: 1233--1309 Score: 82
Period size: 3 Copynumber: 24.7 Consensus size: 3
1223 TTACTTAAAA
** * * *
1233 TAT TAT TAT TAAT TAT TAAT GGT TAT TAT TAA TGT CATT TAT TAT TAT
1 TAT TAT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
1281 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1310 AAACAGTCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
3 54 0.89
4 7 0.11
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4489 original size:20 final size:18
Alignment explanation
Indices: 4449--4491 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
4439 ATTTTACATA
* *
4449 TAATTATATTAGATTATT
1 TAATTATATTAAATTAAT
4467 TAATTATTATCTAAATTAAT
1 TAATTA-TAT-TAAATTAAT
4487 TAATT
1 TAATT
4492 TTTTATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATATTAAATTAAT
Found at i:5298 original size:18 final size:16
Alignment explanation
Indices: 5267--5310 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
5257 AGTTTAAAGT
*
5267 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
5284 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
5298 TTAAAAATTTATT
1 TTAAAAATTTATT
5311 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Done.