Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010059.1 Kokia drynarioides strain JFW-HI SEQ_124833, 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: 76671
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:2390 original size:31 final size:31
Alignment explanation
Indices: 2355--2448 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
2345 CATTAGTTAT
* **
2355 TAAATTATGGGTAAGTTTTTATTTTGGTCAC
1 TAAATTATGGGAAAGTTTTTATTTAAGTCAC
**
2386 TAAATTATTTGAAAGTTTTTATTTAAGTCAC
1 TAAATTATGGGAAAGTTTTTATTTAAGTCAC
* *** **
2417 TAACTTATTCAAAAGTTTTCGTTTAAGTCAC
1 TAAATTATGGGAAAGTTTTTATTTAAGTCAC
2448 T
1 T
2449 GGGCTATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (31 bp):
TAAATTATGGGAAAGTTTTTATTTAAGTCAC
Found at i:11457 original size:21 final size:21
Alignment explanation
Indices: 11411--11460 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
11401 CAATCAGCAC
* *
11411 AACTACAAGCTTTAGTCCGGG
1 AACTACAAGCTTTACTCCAGG
*
11432 AACTACAAGCTTTTCTCCAGG
1 AACTACAAGCTTTACTCCAGG
*
11453 CACTACAA
1 AACTACAA
11461 CCATGAGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (21 bp):
AACTACAAGCTTTACTCCAGG
Found at i:39418 original size:62 final size:62
Alignment explanation
Indices: 39325--39446 Score: 235
Period size: 62 Copynumber: 2.0 Consensus size: 62
39315 CAGTTCATAT
*
39325 ATACATATATAATGAAGTGTTGCCTTTGCTATTGCAGTTTGTGGTATAGGGACAATGAATAC
1 ATACATATATAATGAAGTGTTGCCTTTGCTATTGCAGTTTGTGGCATAGGGACAATGAATAC
39387 ATACATATATAATGAAGTGTTGCCTTTGCTATTGCAGTTTGTGGCATAGGGACAATGAAT
1 ATACATATATAATGAAGTGTTGCCTTTGCTATTGCAGTTTGTGGCATAGGGACAATGAAT
39447 CTTGGATGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (62 bp):
ATACATATATAATGAAGTGTTGCCTTTGCTATTGCAGTTTGTGGCATAGGGACAATGAATAC
Found at i:40861 original size:7 final size:8
Alignment explanation
Indices: 40839--40865 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40829 TTATAAAAAC
40839 TAATTTTT
1 TAATTTTT
40847 TAATTTTT
1 TAATTTTT
40855 TAATTTTT
1 TAATTTTT
40863 TAA
1 TAA
40866 ATATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TAATTTTT
Found at i:47450 original size:2 final size:2
Alignment explanation
Indices: 47443--47473 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47433 CCTTGAGAAT
*
47443 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47474 TTTTCCGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:49565 original size:6 final size:6
Alignment explanation
Indices: 49554--49588 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
49544 ATGGGATCAT
49554 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
49589 TCTGAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:60391 original size:145 final size:147
Alignment explanation
Indices: 60107--60407 Score: 561
Period size: 145 Copynumber: 2.0 Consensus size: 147
60097 AAGACAAACT
60107 AATTCAACTATCATGGCAAAAGAATAATCAAATTCAATTACATATATCAAAACCTATCTTAAGGC
1 AATTCAACTATCATGGCAAAAGAATAATCAAATTCAATTACATATATCAAAACCTATCTTAAGGC
60172 CTTTAGCTATCAATACCAATTCACAATTTAAAACATTCAAAATCCATTCATTATGACATTCAATA
66 C-TTA--TATCAATACCAATTCACAATTTAAAACATTCAAAATCCATTCATTATGACATTCAATA
60237 TCAAACTCATTTCACATAAA
128 TCAAACTCATTTCACATAAA
60257 AATTCAACTATCATGGCAAAAGAATAATCAAATTCAATTACATATATCAAAACCTATCTTAAGGC
1 AATTCAACTATCATGGCAAAAGAATAATCAAATTCAATTACATATATCAAAACCTATCTTAAGGC
60322 C-T-TATCAATACCAATTCACAATTTAAAACATTCAAAATCCATTCATTATGACATTCAATATCA
66 CTTATATCAATACCAATTCACAATTTAAAACATTCAAAATCCATTCATTATGACATTCAATATCA
60385 AACTCATTTCACATAAA
131 AACTCATTTCACATAAA
60402 AATTCA
1 AATTCA
60408 TTTAATATAT
Statistics
Matches: 151, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
145 84 0.56
148 1 0.01
150 66 0.44
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.31
Consensus pattern (147 bp):
AATTCAACTATCATGGCAAAAGAATAATCAAATTCAATTACATATATCAAAACCTATCTTAAGGC
CTTATATCAATACCAATTCACAATTTAAAACATTCAAAATCCATTCATTATGACATTCAATATCA
AACTCATTTCACATAAA
Found at i:75637 original size:13 final size:13
Alignment explanation
Indices: 75619--75644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75609 AAATTCTTTA
75619 CCATATTATTGAT
1 CCATATTATTGAT
75632 CCATATTATTGAT
1 CCATATTATTGAT
75645 ACGGAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CCATATTATTGAT
Done.