Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003519.1 Kokia drynarioides strain JFW-HI SEQ_116361, 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: 28714
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:11855 original size:23 final size:23
Alignment explanation
Indices: 11829--12000 Score: 186
Period size: 23 Copynumber: 7.5 Consensus size: 23
11819 ACATTAGCGC
*
11829 GCTTACTGTTTAGCATTGTGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* *
11852 GCTTATTGTTCAGCACTGTGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* *
11875 GCTTATTGTTCAGCACTGTGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* * * *
11898 GCTTACTGATTCGCACTATATGT
1 GCTTACTGTTTAGCACTGTGTGT
*
11921 GTTTACTGATTTA-CACTGTGTGT
1 GCTTACTG-TTTAGCACTGTGTGT
* *
11944 GCTTACTATTTTGCACTGTGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* *
11967 GCCTATTGATTT-GCACTGTGTGT
1 GCTTACTG-TTTAGCACTGTGTGT
11990 GCTTACTGTTT
1 GCTTACTGTTT
12001 CCCCAACACT
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
22 6 0.05
23 113 0.91
24 5 0.04
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTTAGCACTGTGTGT
Found at i:12743 original size:20 final size:20
Alignment explanation
Indices: 12718--12771 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
12708 AGTCTTCAAG
*
12718 GTATCGATAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
*
12738 GTATCGGTAGGAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* *
12758 CTATTGGTAGAAGT
1 GTATCGGTAGAAGT
12772 CTCACTGGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.06, G:0.37, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Found at i:14485 original size:10 final size:9
Alignment explanation
Indices: 14442--14492 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
14432 AAAATTAATA
*
14442 AATAAATTT
1 AATAATTTT
14451 AATAATTTT
1 AATAATTTT
*
14460 AAAAATTTTT
1 AATAA-TTTT
14470 AA-AATTTT
1 AATAATTTT
14478 AATTAATTATT
1 AA-TAATT-TT
14489 AATA
1 AATA
14493 TGATATCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 6 0.17
9 14 0.39
10 12 0.33
11 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATAATTTT
Found at i:14490 original size:19 final size:19
Alignment explanation
Indices: 14449--14492 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
14439 ATAAATAAAT
*
14449 TTAATAATTTTAAAAATTT
1 TTAATAATTTTAAAAATTA
*
14468 TTAA-AATTTTAATTAATTA
1 TTAATAATTTTAA-AAATTA
14487 TTAATA
1 TTAATA
14493 TGATATCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 12 0.57
20 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATAATTTTAAAAATTA
Found at i:15520 original size:33 final size:32
Alignment explanation
Indices: 15478--15540 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 32
15468 GCCTGACCCA
15478 AATCCACAAAAGGAAAAAAAACTGCTATTTTCG
1 AATCCACAAAAGGAAAAAAAA-TGCTATTTTCG
*
15511 AATCCACAAAAGGAACAAAAATGCTATTTT
1 AATCCACAAAAGGAAAAAAAATGCTATTTT
15541 TTTTTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.22
Consensus pattern (32 bp):
AATCCACAAAAGGAAAAAAAATGCTATTTTCG
Found at i:15562 original size:24 final size:24
Alignment explanation
Indices: 15530--15575 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15520 AAGGAACAAA
* *
15530 AATGCTATTTTTTTTTTGTTTTTT
1 AATGCTATTTTCTTGTTGTTTTTT
15554 AATGCTATTTTCTTGTTGTTTT
1 AATGCTATTTTCTTGTTGTTTT
15576 CTCTCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.70
Consensus pattern (24 bp):
AATGCTATTTTCTTGTTGTTTTTT
Found at i:27239 original size:2 final size:2
Alignment explanation
Indices: 27232--27257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27222 CATCAATGAA
27232 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27258 GAAAATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28252 original size:14 final size:15
Alignment explanation
Indices: 28233--28278 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
28223 TAATGTGTAA
28233 TTTAATATATA-AAT
1 TTTAATATATATAAT
*
28247 TTTAATTTGATATAAT
1 TTTAATAT-ATATAAT
*
28263 TAT-ATATATATAAT
1 TTTAATATATATAAT
28277 TT
1 TT
28279 GAATTATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 15 0.58
15 6 0.23
16 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTAATATATATAAT
Found at i:28669 original size:2 final size:2
Alignment explanation
Indices: 28664--28692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28654 CCGAATTATC
28664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28693 TAAAAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.