Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010432.1 Kokia drynarioides strain JFW-HI SEQ_125322, 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: 47799
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:357 original size:17 final size:17
Alignment explanation
Indices: 335--368 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
325 CTTACAATAA
*
335 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
352 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
369 GATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:3241 original size:74 final size:75
Alignment explanation
Indices: 3152--3292 Score: 212
Period size: 75 Copynumber: 1.9 Consensus size: 75
3142 ATTTTTCTTC
* * * * *
3152 ATTATGATATTAATTTTATTTCATCCG-AATGCGACGATATATATGATAGTTGAATCTTTAGATA
1 ATTATGATATCAATTTTATTTCATCCGAAATACGAAGATATATATAATAGTTGAATCATTAGATA
3216 TAGGAGTTTT
66 TAGGAGTTTT
* *
3226 ATTATGATATCAATTTTGTTTCATCCGAAATACGAAGATATATATAATAGTTGGATCATTAGATA
1 ATTATGATATCAATTTTATTTCATCCGAAATACGAAGATATATATAATAGTTGAATCATTAGATA
3291 TA
66 TA
3293 AAAAAAATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
74 25 0.42
75 34 0.58
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (75 bp):
ATTATGATATCAATTTTATTTCATCCGAAATACGAAGATATATATAATAGTTGAATCATTAGATA
TAGGAGTTTT
Found at i:8059 original size:24 final size:25
Alignment explanation
Indices: 8023--8069 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
8013 TGTTCGATCC
*
8023 TTTCATCTACCTT-GACTTTTCACA
1 TTTCATCTACCTTAAACTTTTCACA
*
8047 TTTCATCTTCCTTAAACTTTTCA
1 TTTCATCTACCTTAAACTTTTCA
8070 TATTCTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.21, C:0.28, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTCATCTACCTTAAACTTTTCACA
Found at i:15320 original size:39 final size:39
Alignment explanation
Indices: 15266--15345 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
15256 CTAACTTGTA
*
15266 AAATTAAGATTTTTAAAAGAGATTGTATTTATAATTACT
1 AAATTAAGATTTTTAAAAGAAATTGTATTTATAATTACT
15305 AAATTAAGATTTTTAAAAGAAATTGTATTTATAATTACT
1 AAATTAAGATTTTTAAAAGAAATTGTATTTATAATTACT
15344 AA
1 AA
15346 TTTATAAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (39 bp):
AAATTAAGATTTTTAAAAGAAATTGTATTTATAATTACT
Found at i:15954 original size:50 final size:52
Alignment explanation
Indices: 15893--15991 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 52
15883 CTAATTGCTA
*
15893 GATAAAATAAAAATTGAAGTGTT-AAAAATGAAGT-ATTAATTTTTATGTTT
1 GATAAAATAAAAATTGAAATGTTAAAAAATGAAGTGATTAATTTTTATGTTT
* * * * *
15943 GATAAATTAAAATTTTAAATGTTAGAAAAATTAAGTGCTTAATTTTTAT
1 GATAAAATAAAAATTGAAATGTTA-AAAAATGAAGTGATTAATTTTTAT
15992 TATTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 19 0.47
52 10 0.25
53 11 0.28
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.41
Consensus pattern (52 bp):
GATAAAATAAAAATTGAAATGTTAAAAAATGAAGTGATTAATTTTTATGTTT
Found at i:20335 original size:19 final size:20
Alignment explanation
Indices: 20299--20336 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20289 TCTTTGCTGC
*
20299 ATTTTTGTTCTTACCCCTTT
1 ATTTTAGTTCTTACCCCTTT
*
20319 ATTTTAGTT-TTATCCCTT
1 ATTTTAGTTCTTACCCCTT
20337 CCTTGGCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.13, C:0.21, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTAGTTCTTACCCCTTT
Found at i:28167 original size:16 final size:16
Alignment explanation
Indices: 28146--28177 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28136 TTATTTGGTA
*
28146 TTTAAATTTAGTATTT
1 TTTAAATATAGTATTT
28162 TTTAAATATAGTATTT
1 TTTAAATATAGTATTT
28178 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTAAATATAGTATTT
Found at i:33281 original size:17 final size:18
Alignment explanation
Indices: 33256--33292 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
33246 TCTTTTAAAA
33256 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
33274 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
33291 AT
1 AT
33293 ATCTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:35740 original size:23 final size:24
Alignment explanation
Indices: 35696--35740 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35686 TTAAAAAAAA
* *
35696 TTTTAATTCAATCAAATGCATACT
1 TTTTAATTAAATAAAATGCATACT
35720 TTTTAATTAAATAAAAT-CATA
1 TTTTAATTAAATAAAATGCATA
35741 GGCAGAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTTAATTAAATAAAATGCATACT
Found at i:35783 original size:4 final size:4
Alignment explanation
Indices: 35767--35799 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
35757 TTGTGCAAGG
*
35767 CCAA CCCA CCAA CCAA CCAA CCAA CCAA CCAA C
1 CCAA CCAA CCAA CCAA CCAA CCAA CCAA CCAA C
35800 AAAAAGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.45, C:0.55, G:0.00, T:0.00
Consensus pattern (4 bp):
CCAA
Found at i:36044 original size:15 final size:17
Alignment explanation
Indices: 36023--36063 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
36013 TAATTTTTTA
36023 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
36039 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
36055 AAAATTATA
1 AAAATTATA
36064 TATTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:47683 original size:17 final size:17
Alignment explanation
Indices: 47658--47690 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47648 AAATAAACGG
47658 GAAAAAAAGAAAGAAAA
1 GAAAAAAAGAAAGAAAA
*
47675 GAAATAAAGAAAGAAA
1 GAAAAAAAGAAAGAAA
47691 TAAGGAGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
GAAAAAAAGAAAGAAAA
Found at i:47687 original size:12 final size:13
Alignment explanation
Indices: 47658--47717 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
47648 AAATAAACGG
*
47658 GAAAA-AAAGAAA
1 GAAAAGAAATAAA
47670 GAAAAGAAATAAA
1 GAAAAGAAATAAA
*
47683 G-AAAGAAATAAG
1 GAAAAGAAATAAA
* * *
47695 GAGAGGAAAGAAA
1 GAAAAGAAATAAA
47708 GAATAAGAAA
1 GAA-AAGAAA
47718 AGAAAGGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 16 0.43
13 16 0.43
14 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (13 bp):
GAAAAGAAATAAA
Done.