Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002455.1 Kokia drynarioides strain JFW-HI SEQ_114573, 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: 38132
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:2344 original size:18 final size:18
Alignment explanation
Indices: 2321--2376 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2311 TTACACTTTA
2321 TTTAATATTTTTATAAAT
1 TTTAATATTTTTATAAAT
*
2339 TTTAATAATATTTTACAAAT
1 TTTAAT-AT-TTTTATAAAT
*
2359 TTATAA-ATTTTTTTAAAT
1 TT-TAATATTTTTATAAAT
2377 AAATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 14 0.44
19 4 0.12
20 11 0.34
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATATTTTTATAAAT
Found at i:2372 original size:20 final size:20
Alignment explanation
Indices: 2297--2373 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
2287 ATTAATTTTT
*
2297 ATTTTTAAATTTTTTTAC-A
1 ATTTATAAATTTTTTTACAA
* * * *
2316 CTTTATTTAATATTTTTATAA
1 ATTTA-TAAATTTTTTTACAA
* *
2337 ATTT-TAATAATATTTTACAA
1 ATTTATAA-ATTTTTTTACAA
2357 ATTTATAAATTTTTTTA
1 ATTTATAAATTTTTTTA
2374 AATAAATTAT
Statistics
Matches: 41, Mismatches: 13, Indels: 7
0.67 0.21 0.11
Matches are distributed among these distances:
19 5 0.12
20 29 0.71
21 7 0.17
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATAAATTTTTTTACAA
Found at i:2380 original size:14 final size:14
Alignment explanation
Indices: 2361--2393 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2351 TTACAAATTT
*
2361 ATAAATTTTTTTAA
1 ATAAATTATTTTAA
2375 ATAAATTATTTTAA
1 ATAAATTATTTTAA
2389 A-AAAT
1 ATAAAT
2394 AAATACGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATTATTTTAA
Found at i:11727 original size:17 final size:17
Alignment explanation
Indices: 11707--11746 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
11697 TTATTAATTT
**
11707 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
11724 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
11741 TATTTA
1 T-TTTA
11747 TTTACATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:12987 original size:23 final size:24
Alignment explanation
Indices: 12952--13000 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
12942 TAAAGGTGAT
* *
12952 TTAATAAATAAATAAATTAAAAAA
1 TTAATAAAAAAATAAACTAAAAAA
*
12976 TTAA-AAAAAAATAAACTAAAGAA
1 TTAATAAAAAAATAAACTAAAAAA
12999 TT
1 TT
13001 TTTTTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
TTAATAAAAAAATAAACTAAAAAA
Found at i:22176 original size:15 final size:17
Alignment explanation
Indices: 22141--22180 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
22131 TTAATAAAAA
22141 TATAATTTCATTATTTG
1 TATAATTTCATTATTTG
*
22158 TATAATTT-A-TATTTT
1 TATAATTTCATTATTTG
22173 TATAATTT
1 TATAATTT
22181 TTCGAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATAATTTCATTATTTG
Found at i:31417 original size:12 final size:12
Alignment explanation
Indices: 31393--31437 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
31383 GCTCACAACG
31393 TCTTTTCCTTTTT
1 TCTTTTCC-TTTT
* *
31406 TTTTTTTCTTTT
1 TCTTTTCCTTTT
31418 TCTTTTCCTTTT
1 TCTTTTCCTTTT
*
31430 CCTTTTCC
1 TCTTTTCC
31438 AATTTTCACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTCCTTTT
Found at i:31418 original size:14 final size:15
Alignment explanation
Indices: 31395--31436 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
31385 TCACAACGTC
31395 TTTTCCTTTT-TTTT
1 TTTTCCTTTTCTTTT
*
31409 TTTTCTTTTTCTTTT
1 TTTTCCTTTTCTTTT
31424 CCTTTTCCTTTTC
1 --TTTTCCTTTTC
31437 CAATTTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
17 10 0.43
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCCTTTTCTTTT
Found at i:32809 original size:2 final size:2
Alignment explanation
Indices: 32797--32831 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32787 TATCACAACC
*
32797 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32832 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32837 original size:2 final size:2
Alignment explanation
Indices: 32832--32866 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
32822 TATATATATA
32832 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
32867 AATTTACTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Done.