Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014037.1 Kokia drynarioides strain JFW-HI SEQ_129068, 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: 6652
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1972 original size:27 final size:27
Alignment explanation
Indices: 1942--2013 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
1932 ACCTGTGAGC
1942 AAAGAGAGAGGAGAGAGAAAG-GAGGAA-
1 AAAGAGAGAGGAGAGAGAAAGTGA--AAG
* * *
1969 AAAGA-ACTATGACAGAGAAAGTGAAAG
1 AAAGAGA-GAGGAGAGAGAAAGTGAAAG
1996 AAAGAGAGAGGAGAGAGA
1 AAAGAGAGAGGAGAGAGA
2014 GAAAAGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.38, T:0.04
Consensus pattern (27 bp):
AAAGAGAGAGGAGAGAGAAAGTGAAAG
Found at i:2246 original size:16 final size:14
Alignment explanation
Indices: 2219--2263 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2209 ATAAGAAAGT
2219 TTTTATTTAAATTA
1 TTTTATTTAAATTA
*
2233 TGTATTA-TTAAAATA
1 T-T-TTATTTAAATTA
2248 TTTTATTTAAATTA
1 TTTTATTTAAATTA
2262 TT
1 TT
2264 AGGTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 9 0.35
16 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTTATTTAAATTA
Found at i:2273 original size:30 final size:28
Alignment explanation
Indices: 2219--2288 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
2209 ATAAGAAAGT
2219 TTTTATTTAAATTATGTATTATTAAAATA
1 TTTTATTTAAATTATGTATTATT-AAATA
*
2248 TTTTATTTAAATTAT-TAGGTTATTAAATT
1 TTTTATTTAAATTATGTA--TTATTAAATA
2277 TTTTATTATAAA
1 TTTTATT-TAAA
2289 AAGTTCAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 2 0.05
29 26 0.70
30 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTATTTAAATTATGTATTATTAAATA
Found at i:3217 original size:10 final size:10
Alignment explanation
Indices: 3204--3331 Score: 59
Period size: 10 Copynumber: 12.7 Consensus size: 10
3194 TAAATAGATT
3204 AAAATTATTAA
1 AAAATTATT-A
*
3215 AAAAGTTTTTA
1 AAAA-TTATTA
*
3226 AAAATTATTT
1 AAAATTATTA
* *
3236 AAAGTTATAA
1 AAAATTATTA
* *
3246 AAAATAAATA
1 AAAATTATTA
* *
3256 AATTTAAATAATA
1 AA---AATTATTA
3269 AAAA--ATTA
1 AAAATTATTA
*
3277 AAAATTA-AA
1 AAAATTATTA
**
3286 AAAAGAATTA
1 AAAATTATTA
*
3296 AAAATTGTT-
1 AAAATTATTA
3305 AAAATTA-TA
1 AAAATTATTA
3314 AATAATTATTA
1 AA-AATTATTA
3325 AAAATTA
1 AAAATTA
3332 CAAAAATCAT
Statistics
Matches: 86, Mismatches: 21, Indels: 21
0.67 0.16 0.16
Matches are distributed among these distances:
8 8 0.09
9 14 0.16
10 39 0.45
11 13 0.15
12 4 0.05
13 8 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAATTATTA
Found at i:3268 original size:17 final size:16
Alignment explanation
Indices: 3243--3288 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
3233 TTTAAAGTTA
3243 TAAAAAATAAATAAATT
1 TAAAAAATAAA-AAATT
*
3260 TAAATAATAAAAAA-T
1 TAAAAAATAAAAAATT
*
3275 TAAAAATTAAAAAA
1 TAAAAAATAAAAAA
3289 AGAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 3 0.12
17 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAATAAAAAATT
Found at i:3269 original size:24 final size:24
Alignment explanation
Indices: 3232--3282 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3222 TTTAAAAATT
*
3232 ATTTAAAGTTATAAAAAATAAATAA
1 ATTTAAAGTAATAAAAAATAAA-AA
*
3257 ATTTAAA-TAATAAAAAATTAAAA
1 ATTTAAAGTAATAAAAAATAAAAA
3280 ATT
1 ATT
3283 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTAAAGTAATAAAAAATAAAAA
Found at i:3308 original size:19 final size:18
Alignment explanation
Indices: 3264--3301 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3254 TAAATTTAAA
3264 TAATAAAAAATTAAAAAT
1 TAATAAAAAATTAAAAAT
*
3282 TAAAAAAAGAATTAAAAAT
1 TAATAAAA-AATTAAAAAT
3301 T
1 T
3302 GTTAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
TAATAAAAAATTAAAAAT
Found at i:4438 original size:59 final size:60
Alignment explanation
Indices: 4312--4652 Score: 387
Period size: 59 Copynumber: 5.8 Consensus size: 60
4302 ACTCGAGAGT
* * * * * * *
4312 AAAATGGTAATTTT-GGAAGT-TCGGGGATAAAA-TGTAATTTTTGGAAGATTCGGAGTTA
1 AAAATGGGATTTTTGGGAAGTCT-GGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
* *
4370 AAAATGGGATTTTT-GGAAGTCTGGGGGTAAGATGGTAA-TTTTGGAAGCTTCGGGGTCAA
1 AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTC-A
* * *
4429 AAAATGGGATTTTTGGGAATTC-GAGGGTAAAACGGTAA-TTTTGGAAGCTTCGGGGTTA
1 AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
* * * *
4487 AAAATGAGATTTTTGGAAATTC-GGGAGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
1 AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
* * * *
4546 AAAATGGGATTTTTGGGAA-TTTAGAGGTAAAACGGTAATTTTTGGAAGCTTCGAGGTCA
1 AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
* * *
4605 AAATTGGGATTTTTGGGAATTC-GAGGGTAAAACGGTAATTTTTGGAAG
1 AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAG
4653 GTTCAGGGAC
Statistics
Matches: 246, Mismatches: 30, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
58 78 0.32
59 161 0.65
60 7 0.03
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (60 bp):
AAAATGGGATTTTTGGGAAGTCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
Found at i:4443 original size:117 final size:117
Alignment explanation
Indices: 4312--4652 Score: 417
Period size: 117 Copynumber: 2.9 Consensus size: 117
4302 ACTCGAGAGT
* * * *
4312 AAAATGGTAATTTT-GGAAGTTCGGGGATAAAA-TGTAATTTTTGGAAGATTCGGAGTTAAAAAT
1 AAAATGGGATTTTTGGGAA-TTCGGGG-TAAAACGGTAATTTTTGGAAGCTTCGGAGTTAAAAAT
* * *
4375 GGGATTTTTGGAAGTCTGGGGGTAAGATGGTAA-TTTTGGAAGCTTCGGGGTCAA
64 GGGATTTTTGGAAATCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTC-A
*
4429 AAAATGGGATTTTTGGGAATTCGAGGGTAAAACGGTAA-TTTTGGAAGCTTCGGGGTTAAAAATG
1 AAAATGGGATTTTTGGGAATTCG-GGGTAAAACGGTAATTTTTGGAAGCTTCGGAGTTAAAAATG
* *
4493 AGATTTTTGGAAAT-TCGGGAGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
65 GGATTTTTGGAAATCT-GGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
* * * *
4546 AAAATGGGATTTTTGGGAATTTAGAGGTAAAACGGTAATTTTTGGAAGCTTC-GAGGTCAAAATT
1 AAAATGGGATTTTTGGGAA-TTCGGGGTAAAACGGTAATTTTTGGAAGCTTCGGA-GTTAAAAAT
* *
4610 GGGATTTTTGGGAAT-TCGAGGGTAAAACGGTAATTTTTGGAAG
64 GGGATTTTTGGAAATCT-GGGGGTAAAACGGTAATTTTTGGAAG
4653 GTTCAGGGAC
Statistics
Matches: 197, Mismatches: 19, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
116 1 0.01
117 104 0.53
118 92 0.47
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (117 bp):
AAAATGGGATTTTTGGGAATTCGGGGTAAAACGGTAATTTTTGGAAGCTTCGGAGTTAAAAATGG
GATTTTTGGAAATCTGGGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCA
Found at i:4626 original size:118 final size:117
Alignment explanation
Indices: 4345--4652 Score: 428
Period size: 118 Copynumber: 2.6 Consensus size: 117
4335 GGGATAAAAT
* * * *
4345 GTAATTTTTGGAAGATTCGGAGTTAAAAATGGGATTTTT-GGAAGTCTGGGGGTAAGATGGTAA-
1 GTAATTTTTGGAAGCTTCGG-GTTAAAAATGGGATTTTTGGGAA-T-TCGGGGTAAAACGGTAAT
*
4408 TTTTGGAAGCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTCGAGGGTAAAACG
63 TTTTGGAAGCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTAGAGGGTAAAACG
* *
4463 GTAA-TTTTGGAAGCTTCGGGGTTAAAAATGAGATTTTTGGAAATTCGGGAGTAAAACGGTAATT
1 GTAATTTTTGGAAGCTTC-GGGTTAAAAATGGGATTTTTGGGAATTCGGG-GTAAAACGGTAATT
4527 TTTGGAAGCTTCGGGGTC-AAAAATGGGATTTTTGGGAATTTAGA-GGTAAAACG
64 TTTGGAAGCTTCGGGGTCAAAAAATGGGATTTTTGGGAA-TTAGAGGGTAAAACG
* *
4580 GTAATTTTTGGAAGCTTCGAGGTCAAAATTGGGATTTTTGGGAATTCGAGGGTAAAACGGTAATT
1 GTAATTTTTGGAAGCTTCG-GGTTAAAAATGGGATTTTTGGGAATTCG-GGGTAAAACGGTAATT
4645 TTTGGAAG
64 TTTGGAAG
4653 GTTCAGGGAC
Statistics
Matches: 171, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
116 4 0.02
117 74 0.43
118 91 0.53
119 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.32
Consensus pattern (117 bp):
GTAATTTTTGGAAGCTTCGGGTTAAAAATGGGATTTTTGGGAATTCGGGGTAAAACGGTAATTTT
TGGAAGCTTCGGGGTCAAAAAATGGGATTTTTGGGAATTAGAGGGTAAAACG
Found at i:4645 original size:29 final size:29
Alignment explanation
Indices: 4437--4649 Score: 144
Period size: 29 Copynumber: 7.3 Consensus size: 29
4427 AAAAAATGGG
4437 ATTTTTGGGAATTCGAGGGTAAAACGGTA
1 ATTTTTGGGAATTCGAGGGTAAAACGGTA
**
4466 A-TTTT-GGAAGCTTCG-GGGTTAAAAATG-A
1 ATTTTTGGGAA--TTCGAGGG-TAAAACGGTA
*
4494 GATTTTTGGAAATTCG-GGAGTAAAACGGTA
1 -ATTTTTGGGAATTCGAGG-GTAAAACGGTA
* *
4524 ATTTTT-GGAAGCTTCG-GGGTCAAAAATGG-G
1 ATTTTTGGGAA--TTCGAGGGT--AAAACGGTA
*
4554 ATTTTTGGGAATT-TAGAGGTAAAACGGTA
1 ATTTTTGGGAATTCGAG-GGTAAAACGGTA
* *
4583 ATTTTT-GGAAGCTTCGA-GGTCAAAATTGG-G
1 ATTTTTGGGAA--TTCGAGGGT-AAAA-CGGTA
4613 ATTTTTGGGAATTCGAGGGTAAAACGGTA
1 ATTTTTGGGAATTCGAGGGTAAAACGGTA
4642 ATTTTTGG
1 ATTTTTGG
4650 AAGGTTCAGG
Statistics
Matches: 144, Mismatches: 16, Indels: 48
0.69 0.08 0.23
Matches are distributed among these distances:
27 4 0.03
28 23 0.16
29 61 0.42
30 36 0.25
31 20 0.14
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (29 bp):
ATTTTTGGGAATTCGAGGGTAAAACGGTA
Found at i:4660 original size:29 final size:29
Alignment explanation
Indices: 4310--4660 Score: 139
Period size: 29 Copynumber: 12.0 Consensus size: 29
4300 CAACTCGAGA
* *
4310 GTAAAATGGTAA-TTTTGGAAG-TTCGGG
1 GTAAAACGGTAATTTTTGGAAGCTTCAGG
* *
4337 GATAAAA-TGTAATTTTTGGAAGATTC-GG
1 G-TAAAACGGTAATTTTTGGAAGCTTCAGG
* * **
4365 AGTTAAAAATGG-GATTTTTGGAAG-TCTGGGG
1 -G-T-AAAACGGTAATTTTTGGAAGCT-TCAGG
* * *
4396 GTAAGATGGTAA-TTTTGGAAGCTTCGGG
1 GTAAAACGGTAATTTTTGGAAGCTTCAGG
* *
4424 GTCAAAAAATGG-GATTTTTGGGAA--TTCGAGG
1 GT---AAAACGGTAATTTTT-GGAAGCTTC-AGG
*
4455 GTAAAACGGTAA-TTTTGGAAGCTTCGGG
1 GTAAAACGGTAATTTTTGGAAGCTTCAGG
** * *
4483 GTTAAAAATG-AGATTTTTGGAA-ATTCGGG
1 G-TAAAACGGTA-ATTTTTGGAAGCTTCAGG
*
4512 AGTAAAACGGTAATTTTTGGAAGCTTCGGG
1 -GTAAAACGGTAATTTTTGGAAGCTTCAGG
* * *
4542 GTCAAAAATGG-GATTTTTGGGAA--TTTAGAG
1 GT--AAAACGGTAATTTTT-GGAAGCTTCAG-G
4572 GTAAAACGGTAATTTTTGGAAGCTTC-GAG
1 GTAAAACGGTAATTTTTGGAAGCTTCAG-G
* *
4601 GTCAAAATTGG-GATTTTTGGGAA--TTCGAGG
1 GT-AAAA-CGGTAATTTTT-GGAAGCTTC-AGG
*
4631 GTAAAACGGTAATTTTTGGAAGGTTCAGG
1 GTAAAACGGTAATTTTTGGAAGCTTCAGG
4660 G
1 G
4661 ACGTCCGAGG
Statistics
Matches: 253, Mismatches: 31, Indels: 78
0.70 0.09 0.22
Matches are distributed among these distances:
27 9 0.04
28 67 0.26
29 75 0.30
30 64 0.25
31 34 0.13
32 4 0.02
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.32
Consensus pattern (29 bp):
GTAAAACGGTAATTTTTGGAAGCTTCAGG
Found at i:5113 original size:29 final size:30
Alignment explanation
Indices: 5053--5416 Score: 234
Period size: 29 Copynumber: 12.7 Consensus size: 30
5043 AAATGGTAAA
* *
5053 TTTGGAAG-TTCGGGGAT-AAAATGGTAATT
1 TTTGGAAGATTCGGGGTTAAAAATGG-GATT
5082 TTTGGAAGATTCGGGGTTAAAAATGGGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
*
5112 TTTGGAAG-TTCGGGGGT---AA---GA--
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* *
5133 --TGGTAGCTTCGGGGTTAAAAATGGGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* * * *
5161 TTTGGAAG-TCCGGGGGT-AAGATGGTAATT
1 TTTGGAAGATTCGGGGTTAAAAATGG-GATT
* *
5190 TTTGGAAGCTTCGGGGTCAAAAATGGGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* * * *
5220 TTTGGGA-ATTCGGGGGT-AAAATGGTAAT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
*
5248 TTTGGAAGGTTCGGGGTTAAAAATGGGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* * * *
5278 TTTGGGA-ATTCGAGGG-T-AAAACGGTAAT
1 TTTGGAAGATTCG-GGGTTAAAAATGGGATT
* *
5306 TTTGGAAGGTTCGGAGTTAAAAATGGGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* * **
5336 TTTGGGAA-A-TCGGGGGTAAAATTGTAATTT
1 TTT-GGAAGATTCGGGGTTAAAAATGGGA-TT
* * **
5366 TTTGGAAGGTTCGGAGTTAAAAATAAGATT
1 TTTGGAAGATTCGGGGTTAAAAATGGGATT
* *
5396 TTTGGGA-ATTCGGGGGTAAAA
1 TTTGGAAGATTCGGGGTTAAAA
5417 CGATAATTTT
Statistics
Matches: 255, Mismatches: 54, Indels: 52
0.71 0.15 0.14
Matches are distributed among these distances:
19 5 0.02
20 8 0.03
23 4 0.02
26 4 0.02
28 37 0.15
29 87 0.34
30 81 0.32
31 29 0.11
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (30 bp):
TTTGGAAGATTCGGGGTTAAAAATGGGATT
Found at i:5116 original size:59 final size:59
Alignment explanation
Indices: 5056--5436 Score: 466
Period size: 58 Copynumber: 6.6 Consensus size: 59
5046 TGGTAAATTT
* *
5056 GGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGATTCGGGGTTAAAAATGGGATTTTT-
1 GGAA-TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
* *
5115 GGAAGTTCGGGGGT--AA--G--A----TGGTAGCTTCGGGGTTAAAAATGGGATTTTT-
1 GGAA-TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
* * * *
5164 GGAAGTCCGGGGGTAAGATGGTAATTTTTGGAAGCTTCGGGGTCAAAAATGGGATTTTTG
1 GGAA-TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
5224 GGAATTCGGGGGTAAAATGGTAA-TTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
1 GGAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
* * *
5282 GGAATTCGAGGGTAAAACGGTAA-TTTTGGAAGGTTCGGAGTTAAAAATGGGATTTTTG
1 GGAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
* * * **
5340 GGAAATCGGGGGTAAAATTGTAATTTTTTGGAAGGTTCGGAGTTAAAAATAAGATTTTTG
1 GGAATTCGGGGGTAAAATGGTAA-TTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
* *
5400 GGAATTCGGGGGTAAAACGATAATTTTTGGAAGGTTC
1 GGAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC
5437 AGGGACCTCC
Statistics
Matches: 285, Mismatches: 24, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
49 42 0.15
51 1 0.00
53 2 0.01
55 2 0.01
57 2 0.01
58 107 0.38
59 73 0.26
60 56 0.20
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (59 bp):
GGAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTG
Found at i:5149 original size:49 final size:49
Alignment explanation
Indices: 5091--5186 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
5081 TTTTGGAAGA
*
5091 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAGATGGTAGC
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTAGC
5140 TTCGGGGTTAAAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTA
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTA
5187 ATTTTTGGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.25, C:0.06, G:0.39, T:0.30
Consensus pattern (49 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGTCCGGGGGTAAGATGGTAGC
Found at i:5397 original size:31 final size:31
Alignment explanation
Indices: 5305--5403 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
5295 AAAACGGTAA
**
5305 TTTT-GGAAGGTTCGGAGTTAAAAATGGGAT
1 TTTTGGGAAGGTTCGGAGTTAAAAATAAGAT
* * * * *
5335 TTTTGGGAA--ATCGGGGGTAAAATTGTA-AT
1 TTTTGGGAAGGTTCGGAGTTAAAAAT-AAGAT
*
5364 TTTTTGGAAGGTTCGGAGTTAAAAATAAGAT
1 TTTTGGGAAGGTTCGGAGTTAAAAATAAGAT
5395 TTTTGGGAA
1 TTTTGGGAA
5404 TTCGGGGGTA
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
29 21 0.41
30 5 0.10
31 25 0.49
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (31 bp):
TTTTGGGAAGGTTCGGAGTTAAAAATAAGAT
Done.