Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013947.1 Kokia drynarioides strain JFW-HI SEQ_128977, 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: 265696
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:300 original size:43 final size:43
Alignment explanation
Indices: 218--302 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
208 ATTAACATGT
* *
218 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
261 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
303 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:943 original size:44 final size:45
Alignment explanation
Indices: 871--1006 Score: 184
Period size: 44 Copynumber: 3.0 Consensus size: 45
861 GCATAGCTCA
*
871 TCAAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
916 TCAA-CCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * * * *
960 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGTCATCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1005 TC
1 TC
1007 TATTCCTCCC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 42 0.52
45 38 0.47
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:4341 original size:4 final size:4
Alignment explanation
Indices: 4299--4384 Score: 52
Period size: 4 Copynumber: 21.2 Consensus size: 4
4289 AACACATTAC
* * * *
4299 CTTT CTTT CCTT C-TT CTTT ATTT CCTCT CCTT C-TT CTTT CTTT CTTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTT-T
* * *
4347 CCTT C-TT CCTT CTTTT CCTT CTTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT C-TTT CTTT C-TTT CTTT CTTT CTTT C
4385 CCGTTTATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
3 9 0.14
4 45 0.69
5 11 0.17
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:4359 original size:20 final size:20
Alignment explanation
Indices: 4299--4382 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
4289 AACACATTAC
4299 CTTTCTT-TCCTTCTTCTTT
1 CTTTCTTCTCCTTCTTCTTT
* *
4318 ATTTCCTCTCCTTCTTCTTT
1 CTTTCTTCTCCTTCTTCTTT
*
4338 CTTTCTTCTCCTTCTTCCTT
1 CTTTCTTCTCCTTCTTCTTT
* *
4358 CTTT-TCCTTCTT-TTCTTT
1 CTTTCTTCTCCTTCTTCTTT
4376 CTTTCTT
1 CTTTCTT
4383 TCCCGTTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
18 9 0.17
19 12 0.22
20 33 0.61
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTTCTCCTTCTTCTTT
Found at i:4370 original size:9 final size:9
Alignment explanation
Indices: 4331--4379 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
4321 TCCTCTCCTT
4331 CTTC-TTTC
1 CTTCTTTTC
* *
4339 TTTCTTCTC
1 CTTCTTTTC
4348 CTTC--TTC
1 CTTCTTTTC
4355 CTTCTTTTC
1 CTTCTTTTC
4364 CTTCTTTTC
1 CTTCTTTTC
*
4373 TTTCTTT
1 CTTCTTT
4380 CTTTCCCGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
7 6 0.18
8 3 0.09
9 24 0.73
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
CTTCTTTTC
Found at i:5653 original size:24 final size:24
Alignment explanation
Indices: 5626--5672 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5616 CAAAAGTTCA
5626 AATATAATATATTTAAAAAAAATT
1 AATATAATATATTTAAAAAAAATT
* *
5650 AATATAATATCTTTAAATAAAAT
1 AATATAATATATTTAAAAAAAAT
5673 AACATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATAATATATTTAAAAAAAATT
Found at i:5686 original size:23 final size:24
Alignment explanation
Indices: 5637--5686 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
5627 ATATAATATA
* * *
5637 TTTAAAAAAAATTAATATAATATC
1 TTTAAAAAAAATTAACATAAAAAC
*
5661 TTTAAATAAAA-TAACATAAAAAC
1 TTTAAAAAAAATTAACATAAAAAC
5684 TTT
1 TTT
5687 TTTTTAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
TTTAAAAAAAATTAACATAAAAAC
Found at i:7066 original size:23 final size:24
Alignment explanation
Indices: 7039--7087 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
7029 TAATTTACTA
* *
7039 TTTAATCTTTGAAT-TATATTTAT
1 TTTAATATTTCAATATATATTTAT
*
7062 TTTAATATTTCAATATATTTTTAT
1 TTTAATATTTCAATATATATTTAT
7086 TT
1 TT
7088 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTAATATTTCAATATATATTTAT
Found at i:7087 original size:24 final size:23
Alignment explanation
Indices: 7039--7111 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 23
7029 TAATTTACTA
* *
7039 TTTAATCTTTGAATTATATTTAT
1 TTTAATATTTCAATTATATTTAT
7062 TTTAATATTTCAATATATTTTTATTTAT
1 TTTAATATTTCAAT-TA----TATTTAT
*
7090 TTTAATATTTAAATTATTATTT
1 TTTAATATTTCAATTA-TATTT
7112 TATCTCGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
23 12 0.29
24 8 0.19
27 2 0.05
28 20 0.48
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (23 bp):
TTTAATATTTCAATTATATTTAT
Found at i:7087 original size:28 final size:27
Alignment explanation
Indices: 7055--7107 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
7045 CTTTGAATTA
*
7055 TATTTATTTTAATATTTCAATATATTTT
1 TATTTATTTTAATATTTAAAT-TATTTT
7083 TATTTATTTTAATATTTAAATTATT
1 TATTTATTTTAATATTTAAATTATT
7108 ATTTTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTATTTTAATATTTAAATTATTTT
Found at i:7405 original size:25 final size:25
Alignment explanation
Indices: 7351--7408 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
7341 CTATTTTTAA
*
7351 TTTATTTTAAAAATATTTATATTAT
1 TTTATTTTAAAAATATTAATATTAT
* * *
7376 ATTATTTTAATAAT-TTAATAATTCT
1 TTTATTTTAAAAATATTAAT-ATTAT
7401 TTTATTTT
1 TTTATTTT
7409 TGATAGTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTTTAAAAATATTAATATTAT
Found at i:7751 original size:13 final size:13
Alignment explanation
Indices: 7733--7757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7723 AAAATTGGTT
7733 AAAAAATTTAAAA
1 AAAAAATTTAAAA
7746 AAAAAATTTAAA
1 AAAAAATTTAAA
7758 TGTTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATTTAAAA
Found at i:12407 original size:3 final size:3
Alignment explanation
Indices: 12388--12460 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
12378 ATTTAAGAGG
* * *
12388 AGA AAA AGA AGA A-A AGA AGA AAA AGA AGA AG- AGG AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
12434 AGA AGA AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
12461 GAAAAAATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:14195 original size:19 final size:20
Alignment explanation
Indices: 14171--14223 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
14161 TTGATTGATA
*
14171 TTTTTTGCTGTTTT-GTGTT
1 TTTTTTACTGTTTTGGTGTT
*
14190 TTTTTTACTATTTTGGTGTT
1 TTTTTTACTGTTTTGGTGTT
14210 TTTTTTACTGTTTT
1 TTTTTTACTGTTTT
14224 AGTTGTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.74
Consensus pattern (20 bp):
TTTTTTACTGTTTTGGTGTT
Found at i:14233 original size:12 final size:12
Alignment explanation
Indices: 14218--14285 Score: 56
Period size: 12 Copynumber: 6.1 Consensus size: 12
14208 TTTTTTTTAC
14218 TGTTTTAGTTGT
1 TGTTTTAGTTGT
*
14230 TGTTTTCG-TGT
1 TGTTTTAGTTGT
* *
14241 TGTTTTTGCTGT
1 TGTTTTAGTTGT
* *
14253 TATTTTTGTTGT
1 TGTTTTAGTTGT
14265 T-TTTTA--TGT
1 TGTTTTAGTTGT
14274 TGTTTT-GTTGT
1 TGTTTTAGTTGT
14285 T
1 T
14286 AATTTTGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 4 0.09
10 4 0.09
11 18 0.38
12 21 0.45
ACGTcount: A:0.04, C:0.03, G:0.22, T:0.71
Consensus pattern (12 bp):
TGTTTTAGTTGT
Found at i:14241 original size:32 final size:32
Alignment explanation
Indices: 14200--14267 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
14190 TTTTTTACTA
* *
14200 TTTTGGTGTTTTTTTTACTGTT-TTAGTTGTTG
1 TTTTCGTGTTGTTTTTACTGTTATT-GTTGTTG
* *
14232 TTTTCGTGTTGTTTTTGCTGTTATTTTTGTTG
1 TTTTCGTGTTGTTTTTACTGTTATTGTTGTTG
14264 TTTT
1 TTTT
14268 TTATGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.04, C:0.04, G:0.21, T:0.71
Consensus pattern (32 bp):
TTTTCGTGTTGTTTTTACTGTTATTGTTGTTG
Found at i:14266 original size:44 final size:43
Alignment explanation
Indices: 14199--14322 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 43
14189 TTTTTTTACT
* * ** * *
14199 ATTTTGGTGTTTTTTTTACTGTTTTAGTTGTTGTTTTCG-TGTTG
1 ATTTTGCTGTTATTTTTGTTGTTTT-TTTGTTGTTTT-GTTGTTA
*
14243 TTTTTGCTGTTATTTTTGTTGTTTTTTATGTTGTTTTGTTGTTA
1 ATTTTGCTGTTATTTTTGTTGTTTTTT-TGTTGTTTTGTTGTTA
* *
14287 ATTTTGCTGCTATTTTGGTTGTTATTTTTGTTGTTT
1 ATTTTGCTGTTATTTTTGTTGTT-TTTTTGTTGTTT
14323 GAATGTTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.03
44 61 0.91
45 4 0.06
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (43 bp):
ATTTTGCTGTTATTTTTGTTGTTTTTTTGTTGTTTTGTTGTTA
Found at i:14280 original size:32 final size:35
Alignment explanation
Indices: 14220--14292 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 35
14210 TTTTTTACTG
* *
14220 TTTTAGTTGTTGTTTTCGTGTTGTTTTTGCTGTTA
1 TTTTTGTTGTTGTTTTCATGTTGTTTTTGCTGTTA
*
14255 TTTTTGTTGTT-TTTT-ATGTTG-TTTTGTTGTTA
1 TTTTTGTTGTTGTTTTCATGTTGTTTTTGCTGTTA
*
14287 ATTTTG
1 TTTTTG
14293 CTGCTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 15 0.44
33 5 0.15
34 4 0.12
35 10 0.29
ACGTcount: A:0.07, C:0.03, G:0.21, T:0.70
Consensus pattern (35 bp):
TTTTTGTTGTTGTTTTCATGTTGTTTTTGCTGTTA
Found at i:14330 original size:44 final size:44
Alignment explanation
Indices: 14227--14335 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
14217 CTGTTTTAGT
** * *
14227 TGTTGTTTTCG-TGTTGTTTTTGCTGTTATTTTTGTTGTTTTTTA
1 TGTTGTTTT-GATGTTAATTTTGCTGCTATTTTGGTTGTTTTTTA
*
14271 TGTTGTTTTGTTGTTAATTTTGCTGCTATTTTGGTTGTTATTTT-
1 TGTTGTTTTGATGTTAATTTTGCTGCTATTTTGGTTGTT-TTTTA
*
14315 TGTTG-TTTGAATGTTATTTTT
1 TGTTGTTTTG-ATGTTAATTTT
14336 ATGCGTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 5 0.09
44 47 0.84
45 4 0.07
ACGTcount: A:0.08, C:0.04, G:0.20, T:0.68
Consensus pattern (44 bp):
TGTTGTTTTGATGTTAATTTTGCTGCTATTTTGGTTGTTTTTTA
Found at i:14486 original size:25 final size:26
Alignment explanation
Indices: 14447--14496 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
14437 TAATATAACT
* *
14447 TTTTTAATGTATTTTAAATTTATTTA
1 TTTTTAATATATTTTAAATGTATTTA
14473 TTTTTAATAT-TTTTAAATGTATTT
1 TTTTTAATATATTTTAAATGTATTT
14497 GGTATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTTAATATATTTTAAATGTATTTA
Found at i:16401 original size:36 final size:37
Alignment explanation
Indices: 16326--16410 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 37
16316 AACAAAACAT
*
16326 TAAAAAAAT-TAAGATGATTATATATGAAACTAATGAA
1 TAAAAAAATATAAAATGATTATATATGAAACTAA-GAA
* * * *
16363 TAAAAAAATATAAAATTATTATATGTTAAATTAA-AA
1 TAAAAAAATATAAAATGATTATATATGAAACTAAGAA
*
16399 TAAATAAATATA
1 TAAAAAAATATA
16411 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 13 0.32
37 9 0.22
38 19 0.46
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (37 bp):
TAAAAAAATATAAAATGATTATATATGAAACTAAGAA
Found at i:18265 original size:2 final size:2
Alignment explanation
Indices: 18258--18285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18248 ACAAGTAGTA
18258 AT 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 AT
18286 GAATTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23793 original size:59 final size:59
Alignment explanation
Indices: 23727--24008 Score: 196
Period size: 59 Copynumber: 4.6 Consensus size: 59
23717 TTCCTTGAAC
* * *
23727 TAAAAGTAGGAGGATTAAATTTCAAAAATTGAAAAGAACAG-GGACTAAATTTGTCAAAA
1 TAAAAGTAGAAGGATTAAATTTCAAAAATTGAAAAAAACAGAGG-CTAAATTTCTCAAAA
* * * * * *
23786 TAAAAGTAGAATGATTAAATTTTAAAATTTGAAAGAAAACGAAGTGAAGGGTAAAATTACTCAAC
1 TAAAAGTAGAAGGATTAAATTTCAAAAATTGAAA-AAAAC--A--G-AGGCT-AAATTTCTCAAA
*
23851 T
59 A
* * *
23852 TAAAAGTAGGAGGATTAAATTTCAAAAA-TGAAAAATAATAGAGGCTAAA-TTCTCAAAG
1 TAAAAGTAGAAGGATTAAATTTCAAAAATTGAAAAA-AACAGAGGCTAAATTTCTCAAAA
* * * *
23910 TAAAAGTAGAATGG-CTAAATTTCAAAAATTGAAAGAAAACAAGTGAAGGGTTAAATTCCTCGAA
1 TAAAAGTAGAA-GGATTAAATTTCAAAAATTGAAA-AAAAC-A--G-A-GGCTAAATTTCTCAAA
*
23974 C
59 A
* *
23975 TAAAAGTA-AGAGAATTAAATTTTAAAAATTGAAA
1 TAAAAGTAGA-AGGATTAAATTTCAAAAATTGAAA
24009 CGAACAAGGA
Statistics
Matches: 174, Mismatches: 29, Indels: 34
0.73 0.12 0.14
Matches are distributed among these distances:
58 29 0.17
59 42 0.24
60 11 0.06
61 1 0.01
62 2 0.01
63 2 0.01
64 11 0.06
65 41 0.24
66 35 0.20
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAAAGTAGAAGGATTAAATTTCAAAAATTGAAAAAAACAGAGGCTAAATTTCTCAAAA
Found at i:24008 original size:124 final size:125
Alignment explanation
Indices: 23697--24008 Score: 418
Period size: 125 Copynumber: 2.5 Consensus size: 125
23687 TTTTAAAATC
* *
23697 AAACAAGTGTAGGGGTTAAATTCCTTGAACTAAAAGTAGGAGGATTAAATTTCAAAAATTG-AAA
1 AAACAAGTG-AAGGGTTAAATTCCTCGAACTAAAAGTAGGAGGATTAAATTTCAAAAATTGAAAA
* * * *
23761 AGAACAGGGACTAAATTTGTCAAAATAAAAGTAGAATGATTAAATTTTAAAATTTGAAAGA
65 AGAACAGGGACTAAATTTCTCAAAATAAAAGTAGAATGACTAAATTTCAAAAATTGAAAGA
* *
23822 AAACGAAGTGAAGGGTAAAATTACTC-AACTTAAAAGTAGGAGGATTAAATTTCAAAAA-TGAAA
1 AAAC-AAGTGAAGGGTTAAATTCCTCGAAC-TAAAAGTAGGAGGATTAAATTTCAAAAATTGAAA
* * * *
23885 AATAATAGAGG-CTAAA-TTCTCAAAGTAAAAGTAGAATGGCTAAATTTCAAAAATTGAAAGA
64 AAGAACAG-GGACTAAATTTCTCAAAATAAAAGTAGAATGACTAAATTTCAAAAATTGAAAGA
* * *
23946 AAACAAGTGAAGGGTTAAATTCCTCGAACTAAAAGTAAGAGAATTAAATTTTAAAAATTGAAA
1 AAACAAGTGAAGGGTTAAATTCCTCGAACTAAAAGTAGGAGGATTAAATTTCAAAAATTGAAA
24009 CGAACAAGGA
Statistics
Matches: 164, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
123 44 0.27
124 56 0.34
125 57 0.35
126 7 0.04
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (125 bp):
AAACAAGTGAAGGGTTAAATTCCTCGAACTAAAAGTAGGAGGATTAAATTTCAAAAATTGAAAAA
GAACAGGGACTAAATTTCTCAAAATAAAAGTAGAATGACTAAATTTCAAAAATTGAAAGA
Found at i:26242 original size:10 final size:11
Alignment explanation
Indices: 26217--26242 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26207 CCTTCCACCT
26217 TTTTTCTATAA
1 TTTTTCTATAA
26228 TTTTTCTATAA
1 TTTTTCTATAA
26239 TTTT
1 TTTT
26243 AATTATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTCTATAA
Found at i:32827 original size:61 final size:60
Alignment explanation
Indices: 32728--32854 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 60
32718 TTAAATCGAA
32728 ATTT-GATTAAAAATGATATTCAATTTGAGAATTATGTGAAAAAAAATAAAGAT-TTC-ATTT
1 ATTTGGATTAAAAATGATATTCAATTTGAGAATTATGTG-AAAAAAAT--AGATATTCGATTT
* * *
32788 ATTTGGATTAAAAATGATATTCTATTTGGGAATTATGTGAAAGAAATAGATATTCGATTT
1 ATTTGGATTAAAAATGATATTCAATTTGAGAATTATGTGAAAAAAATAGATATTCGATTT
32848 ATTTGGA
1 ATTTGGA
32855 AGATTATGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
58 4 0.07
59 3 0.05
60 22 0.36
61 32 0.52
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (60 bp):
ATTTGGATTAAAAATGATATTCAATTTGAGAATTATGTGAAAAAAATAGATATTCGATTT
Found at i:36576 original size:4 final size:4
Alignment explanation
Indices: 36567--36591 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
36557 TATTGCAGAA
36567 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
36592 ATGGAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:40456 original size:22 final size:22
Alignment explanation
Indices: 40421--40473 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
40411 AAAAATATAT
* *
40421 ATTTAAA-AGTTTTATATTTAA
1 ATTTAAATAATTTTATAATTAA
*
40442 ATTTATATAATTTTATAATTAA
1 ATTTAAATAATTTTATAATTAA
40464 ATTTAAATAA
1 ATTTAAATAA
40474 AATAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTAAATAATTTTATAATTAA
Found at i:42418 original size:19 final size:17
Alignment explanation
Indices: 42394--42428 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
42384 NNNNNNNAAA
42394 AAAAGAAAGAAAAGAAATT
1 AAAAG-AAGAAAA-AAATT
42413 AAAAGAAGAAAAAAAT
1 AAAAGAAGAAAAAAAT
42429 GAGTTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAAGAAGAAAAAAATT
Found at i:43986 original size:3 final size:3
Alignment explanation
Indices: 43978--44044 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
43968 TACGCAACAT
43978 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
44026 TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
44045 CTCAAAGGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:47713 original size:3 final size:3
Alignment explanation
Indices: 47705--47738 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
47695 CACATGGATC
*
47705 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47739 CTTATATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51022 original size:20 final size:21
Alignment explanation
Indices: 50987--51026 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
50977 TCAAAACGAC
*
50987 ATAGTTTTGCCTTTTAACTTA
1 ATAGTTTTGACTTTTAACTTA
51008 ATAGTTTT-ACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
51027 TAGAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTA
Found at i:52713 original size:16 final size:16
Alignment explanation
Indices: 52692--52724 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52682 TGCTCTGCAT
52692 TCATACACAT-AAAAAA
1 TCATACAC-TCAAAAAA
52708 TCATACACTCAAAAAA
1 TCATACACTCAAAAAA
52724 T
1 T
52725 TGGTCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (16 bp):
TCATACACTCAAAAAA
Found at i:53876 original size:4 final size:4
Alignment explanation
Indices: 53869--53895 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53859 CGTGTATATA
53869 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
53896 ATGCATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:53908 original size:12 final size:12
Alignment explanation
Indices: 53865--53909 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
53855 CTCTCGTGTA
53865 TATATATGTATG
1 TATATATGTATG
*
53877 TATGTATGTATG
1 TATATATGTATG
*
53889 TATGTATATGCATG
1 TA--TATATGTATG
53903 TATATAT
1 TATATAT
53910 CAATGTGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 18 0.64
14 10 0.36
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (12 bp):
TATATATGTATG
Found at i:62750 original size:24 final size:24
Alignment explanation
Indices: 62707--62755 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
62697 GAAAATAATT
* *
62707 ATTTTATTTTAATTTGATTTTTTA
1 ATTTTATTTTAATTTAATTTGTTA
62731 ATTTT-TTTTAATGTTAATTTGTTA
1 ATTTTATTTTAAT-TTAATTTGTTA
62755 A
1 A
62756 GATAACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
ATTTTATTTTAATTTAATTTGTTA
Found at i:65520 original size:155 final size:154
Alignment explanation
Indices: 65097--65646 Score: 779
Period size: 155 Copynumber: 3.6 Consensus size: 154
65087 ATTTTTTTTA
* * * * *
65097 AAGCTTCTTGTAAACAAGTCTTATTTTTTTAT-A---A-TTTACGATTAGTTTTTTTCGCTTTGG
1 AAGCTTCTTATAAACGAGTCTTTTTTTTTTATAATTCAGTTTACGATTCG-TTTTCTCGCTTTGG
65157 TGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGT
65 TGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGT
*
65222 TGTGCGAATTACATTTGTTTTGATT
130 TGTGAGAATTACATTTGTTTTGATT
* *
65247 AAGCTTCTTATAAACGAGTC-TTGTTTTTTATAATTCAGTTTACTATTCGTTTTCTCGCTTTGGT
1 AAGCTTCTTATAAACGAGTCTTTTTTTTTTATAATTCAGTTTACGATTCGTTTTCTCGCTTTGGT
*
65311 GATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGTT
66 GATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGTT
*
65376 GTGAGAATTACATTTGTTTTTATT
131 GTGAGAATTACATTTGTTTTGATT
*
65400 AAGCTTCTTATAAACGAGTCTTTTTTTTTTTATAATTCAGTTTACGATTCGTTTTCTCGCTTTGT
1 AAGCTTCTTATAAACGAGTC-TTTTTTTTTTATAATTCAGTTTACGATTCGTTTTCTCGCTTTGG
* *
65465 TGATTTGGTAGATTGGCTGGTTTTTGGAATTTGAATTTAGTGTTTTGTGTTGATTTTCAGTGACT
65 TGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGT
* *
65530 TGTAAGAATTACATTTCATTTTGATT
130 TGTGAGAATTACATTT-GTTTTGATT
* ** * * * * *
65556 AAACTTCTTATAAACGTTTCTTGTTTTTTTATAATTCAGTTTAGGATTCACTTTTTTTTGCTTTG
1 AAGCTTCTTATAAACGAGTCTTTTTTTTTTATAATTCAGTTTACGATT--CGTTTTCTCGCTTTG
* * *
65621 GTGGTTTGGTCGATTGGCTGTTTTTT
64 GTGATTTGGTAGATTGGCTGGTTTTT
65647 TAAAAACGTG
Statistics
Matches: 359, Mismatches: 31, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
149 9 0.03
150 19 0.05
153 121 0.34
154 9 0.03
155 143 0.40
156 24 0.07
157 34 0.09
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (154 bp):
AAGCTTCTTATAAACGAGTCTTTTTTTTTTATAATTCAGTTTACGATTCGTTTTCTCGCTTTGGT
GATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGTGTTTTGTGTTGATTTTCAGTGAGTT
GTGAGAATTACATTTGTTTTGATT
Found at i:75723 original size:14 final size:14
Alignment explanation
Indices: 75704--75730 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
75694 ATGTGGTCCA
75704 TTTTTTTTTATTTT
1 TTTTTTTTTATTTT
75718 TTTTTTTTTATTT
1 TTTTTTTTTATTT
75731 ATCTTTTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTTTATTTT
Found at i:75731 original size:18 final size:18
Alignment explanation
Indices: 75704--75738 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
75694 ATGTGGTCCA
75704 TTTTTTTTTAT-TTTTTT
1 TTTTTTTTTATCTTTTTT
75721 TTTTTTATTTATCTTTTT
1 TTTTTT-TTTATCTTTTT
75739 CCTTGCTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTATCTTTTTT
Found at i:86575 original size:25 final size:25
Alignment explanation
Indices: 86527--86575 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
86517 AAAATTACTT
*
86527 AATATTAATTTGTTAAATATAATTC
1 AATATTAATTTGTTAAACATAATTC
*
86552 AATATTTATTT-TTAAACATGAATT
1 AATATTAATTTGTTAAACAT-AATT
86576 TTTTAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
AATATTAATTTGTTAAACATAATTC
Found at i:86724 original size:26 final size:26
Alignment explanation
Indices: 86689--86738 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
86679 ATACTCTCGA
86689 AAAAAATTTAAATATTAAATTAAACT
1 AAAAAATTTAAATATTAAATTAAACT
*
86715 AAAATATTTAAATATTAAATTAAA
1 AAAAAATTTAAATATTAAATTAAA
86739 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAAAATTTAAATATTAAATTAAACT
Found at i:86733 original size:21 final size:22
Alignment explanation
Indices: 86707--86755 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
86697 TAAATATTAA
86707 ATTAAACTAAAAT-ATTTAAAT
1 ATTAAACTAAAATAATTTAAAT
*
86728 ATTAAATTAAAATAATTTAAAT
1 ATTAAACTAAAATAATTTAAAT
86750 -TTAAAC
1 ATTAAAC
86756 ACCAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAACTAAAATAATTTAAAT
Found at i:107344 original size:75 final size:75
Alignment explanation
Indices: 107249--107397 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
107239 ACTATTAGCA
* * *
107249 TTGTAATAGTTGTTGTTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCTCAGTGAATATGGCCTC
1 TTGTAATAGTTGTTGCTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCTCAGTGAACAAGGCCTC
107314 ATTGTTACCG
66 ATTGTTACCG
107324 TTGTAATAGTTGTTGCTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCTCAGTGAACAAGGCCTC
1 TTGTAATAGTTGTTGCTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCTCAGTGAACAAGGCCTC
107389 ATTGTTACC
66 ATTGTTACC
107398 ATCGTAGTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (75 bp):
TTGTAATAGTTGTTGCTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCTCAGTGAACAAGGCCTC
ATTGTTACCG
Found at i:113293 original size:17 final size:16
Alignment explanation
Indices: 113259--113314 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
113249 AATTTAAATT
*
113259 TTTTAATTCAATTTAA
1 TTTTAAATCAATTTAA
*
113275 TTTTAAATCATTTTAA
1 TTTTAAATCAATTTAA
* * *
113291 ATTTAAATTAATATTAT
1 TTTTAAATCAAT-TTAA
113308 TTTTAAA
1 TTTTAAA
113315 ATAAATTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 23 0.72
17 9 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAAATCAATTTAA
Found at i:130811 original size:13 final size:13
Alignment explanation
Indices: 130793--130821 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
130783 CGTTGTTTTG
130793 TTTTTTTT-TTTA
1 TTTTTTTTATTTA
130805 TTTTTTTTATTTA
1 TTTTTTTTATTTA
130818 TTTT
1 TTTT
130822 GTATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTATTTA
Found at i:131902 original size:11 final size:11
Alignment explanation
Indices: 131886--131917 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
131876 TGAGCCACTA
131886 TCTTTTCTTTT
1 TCTTTTCTTTT
131897 TCTTTTCTTTT
1 TCTTTTCTTTT
131908 T-TTTT-TTTT
1 TCTTTTCTTTT
131917 T
1 T
131918 GCAGACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.24
10 4 0.19
11 12 0.57
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:132870 original size:23 final size:23
Alignment explanation
Indices: 132839--132889 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
132829 TATATCTTAC
*
132839 ATTACATCCAACACTCGTTAACT
1 ATTATATCCAACACTCGTTAACT
132862 ATTATATCCAACACTCGTTAACT
1 ATTATATCCAACACTCGTTAACT
132885 ATTAT
1 ATTAT
132890 TCTTCTCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTATATCCAACACTCGTTAACT
Found at i:137926 original size:7 final size:7
Alignment explanation
Indices: 137910--137946 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
137900 GGTGGGTAAA
*
137910 GCAGTTG
1 GCAGTGG
137917 GCAGTGG
1 GCAGTGG
137924 GCAGTGG
1 GCAGTGG
137931 GCAGTGG
1 GCAGTGG
137938 GCAGTGG
1 GCAGTGG
137945 GC
1 GC
137947 TGCAACATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.16, G:0.54, T:0.16
Consensus pattern (7 bp):
GCAGTGG
Found at i:140159 original size:31 final size:31
Alignment explanation
Indices: 140095--140159 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
140085 GATTAGTGAA
* *
140095 ATATGAAAAATAACCAATATTAAAATTTAAT
1 ATATGAAAAATAACCAATATCAAAATTCAAT
140126 ATAT-AAAAATATACCAA-ATCAAAATTCATAT
1 ATATGAAAAATA-ACCAATATCAAAATTCA-AT
140157 ATA
1 ATA
140160 ACATTACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (31 bp):
ATATGAAAAATAACCAATATCAAAATTCAAT
Found at i:143386 original size:18 final size:18
Alignment explanation
Indices: 143358--143401 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
143348 GCCGTTAGCT
*
143358 GTTAG-TCTGTTAGTTTG
1 GTTAGTTCTGTTAGTTTA
*
143375 GTTAGTTCTGTTATTTTA
1 GTTAGTTCTGTTAGTTTA
143393 GTTAGTTCT
1 GTTAGTTCT
143402 TTAATGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.14, C:0.07, G:0.23, T:0.57
Consensus pattern (18 bp):
GTTAGTTCTGTTAGTTTA
Found at i:149291 original size:3 final size:3
Alignment explanation
Indices: 149274--149306 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
149264 TTTATCGCAG
*
149274 ATT AAT ATT -TT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
149307 AAGTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:165683 original size:73 final size:73
Alignment explanation
Indices: 165575--165721 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
165565 CTCAACTGAA
* * * * *
165575 AATTATATTTAATTGGATGAACTGATTAATAATGGAAATGGATTGAGTGTTTATGTTAATCTCTG
1 AATTATATTTAATTGGATGAACTAACTAACAATGGAAATGGATTGAATGTTTATGCTAATCTCTG
165640 AATTTTTG
66 AATTTTTG
*
165648 AATTATATTTAATTGGATGAATTAACTAACAATGGAAATGGATTGAATGTTTATGCTAATCTCTG
1 AATTATATTTAATTGGATGAACTAACTAACAATGGAAATGGATTGAATGTTTATGCTAATCTCTG
165713 AATTTTTG
66 AATTTTTG
165721 A
1 A
165722 TCATGTGGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (73 bp):
AATTATATTTAATTGGATGAACTAACTAACAATGGAAATGGATTGAATGTTTATGCTAATCTCTG
AATTTTTG
Found at i:183855 original size:16 final size:16
Alignment explanation
Indices: 183834--183865 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
183824 TTTATTGACT
183834 TAATAAATTTTTTTAA
1 TAATAAATTTTTTTAA
183850 TAATAAATTTTTTTAA
1 TAATAAATTTTTTTAA
183866 AAAAATCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATAAATTTTTTTAA
Found at i:197252 original size:29 final size:29
Alignment explanation
Indices: 197193--197251 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
197183 TATGGTTTAA
*
197193 TGTGCAATTGTATACATTAACTTTGATTT
1 TGTGCAATTGTATACATAAACTTTGATTT
* *
197222 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACAT-AAACTTTGATTT
197252 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAACTTTGATTT
Found at i:199907 original size:37 final size:37
Alignment explanation
Indices: 199846--199919 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
199836 TAAAATCTAA
199846 AAAGATGAAAATTAAATTCAT-AAAAATAAAAAATAT
1 AAAGATGAAAATTAAATTCATAAAAAATAAAAAATAT
* *
199882 AAAGATTAAAATTTAAATTCATAAAAAATAAAACATAT
1 AAAGATGAAAA-TTAAATTCATAAAAAATAAAAAATAT
199920 TTTAATTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 10 0.29
37 10 0.29
38 14 0.41
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (37 bp):
AAAGATGAAAATTAAATTCATAAAAAATAAAAAATAT
Found at i:200120 original size:3 final size:3
Alignment explanation
Indices: 200100--200139 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
200090 TTACGCGAGT
* *
200100 TGC TGT TGC TGT TGC TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
200140 TCCCCCCACC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.28, G:0.33, T:0.40
Consensus pattern (3 bp):
TGC
Found at i:216730 original size:20 final size:19
Alignment explanation
Indices: 216696--216740 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
216686 TCTATTTGTG
*
216696 TTTTATAATGATTAATTCTA
1 TTTT-TAATGATTAAATCTA
*
216716 TTTTTAATGATTTAAATGTA
1 TTTTTAATGA-TTAAATCTA
216736 TTTTT
1 TTTTT
216741 TAAAAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTAATGATTAAATCTA
Found at i:240454 original size:69 final size:69
Alignment explanation
Indices: 240329--240466 Score: 181
Period size: 69 Copynumber: 2.0 Consensus size: 69
240319 ACATTATTAG
* * *
240329 TATTTTCTACCAAAATTTGTCATGACATGTTGATTAGATTGTCTCATATAGCATTGCATATGAAT
1 TATTTTCTACCAAAATTTGACATGACATGTTGATTAGACTGTCTCATAGAGCATTGCATATGAAT
240394 AACA
66 AACA
* * *
240398 TATTTTCTGCCAAAATTTGACATGACATGTTGAATT-GACTGTCTCAT-GCGATATTGCATATGA
1 TATTTTCTACCAAAATTTGACATGACATGTTG-ATTAGACTGTCTCATAGAG-CATTGCATATGA
*
240461 TTAACA
64 ATAACA
240467 AAAATAAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
68 1 0.02
69 56 0.93
70 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (69 bp):
TATTTTCTACCAAAATTTGACATGACATGTTGATTAGACTGTCTCATAGAGCATTGCATATGAAT
AACA
Found at i:250998 original size:20 final size:20
Alignment explanation
Indices: 250973--251012 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
250963 TTAAATTCTA
250973 AGTTAGGTGCAATGGTTATC
1 AGTTAGGTGCAATGGTTATC
250993 AGTTAGGTGCAATGGTTATC
1 AGTTAGGTGCAATGGTTATC
251013 TTGATGACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (20 bp):
AGTTAGGTGCAATGGTTATC
Found at i:259795 original size:8 final size:8
Alignment explanation
Indices: 259779--259820 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
259769 GTCACGTCAA
*
259779 TAAATAAT
1 TAAAAAAT
259787 TAAAAAAT
1 TAAAAAAT
259795 TAAAAATAT
1 TAAAAA-AT
*
259804 TTAAAAA-
1 TAAAAAAT
259811 TAAAAAAT
1 TAAAAAAT
259819 TA
1 TA
259821 TAAAGTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.21
8 16 0.55
9 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAAAAAT
Found at i:260773 original size:24 final size:24
Alignment explanation
Indices: 260745--260807 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
260735 AGAAATAATC
260745 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* * *
260769 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
260793 TTTTAGTCAAACTCT
1 TTTCAGTTAAACTCT
260808 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:262765 original size:24 final size:24
Alignment explanation
Indices: 262737--262799 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
262727 AGAAATAATC
*
262737 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTCAATTG
* * *
262761 TTTCAATTAAACTTTGTTCATTTG
1 TTTCAGTTAAACTCTGTTCAATTG
* *
262785 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
262800 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTCAATTG
Found at i:264440 original size:13 final size:13
Alignment explanation
Indices: 264422--264449 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
264412 AACTTTATTT
264422 TTTAGGATTAATA
1 TTTAGGATTAATA
264435 TTTAGGATTAATA
1 TTTAGGATTAATA
264448 TT
1 TT
264450 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:264556 original size:25 final size:23
Alignment explanation
Indices: 264515--264560 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
264505 TCAATTAGGG
264515 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
264538 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
264561 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Done.