Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015065.1 Kokia drynarioides strain JFW-HI SEQ_130109, 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: 941295
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 356 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1956 original size:23 final size:23
Alignment explanation
Indices: 1930--2029 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 23
1920 CCAAAGTACT
1930 AACAGAAAGCACACACAGTGCTA
1 AACAGAAAGCACACACAGTGCTA
* * * *
1953 AACAGAGAGTACACAAAGTACTA
1 AACAGAAAGCACACACAGTGCTA
* *
1976 ATCA-AAGAGCACACACAGCGCTAA
1 AACAGAA-AGCACACACAGTGCT-A
*
2000 TAACAGAGAA-CACGAGAC-GTGCTA
1 -AACAGA-AAGCAC-ACACAGTGCTA
2024 AACAGA
1 AACAGA
2030 GAGAGCGCTA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
22 1 0.02
23 39 0.67
24 2 0.03
25 10 0.17
26 5 0.09
27 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (23 bp):
AACAGAAAGCACACACAGTGCTA
Found at i:8847 original size:26 final size:24
Alignment explanation
Indices: 8794--8841 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
8784 CATTTTTTAG
8794 TAAATTATTTTTAGAAAAAACAGA
1 TAAATTATTTTTAGAAAAAACAGA
8818 TAAATTATTTTTAGAAAAAACAGA
1 TAAATTATTTTTAGAAAAAACAGA
8842 CATAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
TAAATTATTTTTAGAAAAAACAGA
Found at i:10400 original size:29 final size:30
Alignment explanation
Indices: 10340--10406 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
10330 ATAATTATTA
* *
10340 AAAATTAAACCAAATCAAAATTCCATTTAT
1 AAAATTAAACAAAATCAAAATTCCATATAT
* * *
10370 AAAATTACACAAAATTAAAATT-CGTATAT
1 AAAATTAAACAAAATCAAAATTCCATATAT
*
10399 AACATTAA
1 AAAATTAA
10407 CATTACATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (30 bp):
AAAATTAAACAAAATCAAAATTCCATATAT
Found at i:11930 original size:35 final size:36
Alignment explanation
Indices: 11883--11968 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
11873 AAAGAGAAAT
*
11883 TAAAAAAATAAAAGT-ATA-TATAAATTTTTAAATCA
1 TAAAAAAATAAAA-TAATATTAGAAATTTTTAAATCA
* *
11918 TAAAAAAGTAAAATAATATTAGAAATTTTTAAA-AA
1 TAAAAAAATAAAATAATATTAGAAATTTTTAAATCA
* *
11953 TTACAAAATAAAATAA
1 TAAAAAAATAAAATAA
11969 ACATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
34 1 0.02
35 29 0.67
36 13 0.30
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (36 bp):
TAAAAAAATAAAATAATATTAGAAATTTTTAAATCA
Found at i:13637 original size:39 final size:40
Alignment explanation
Indices: 13560--13635 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
13550 TTAATCTACC
*
13560 TAAAAATGATAAAAAAATTAATTTAATCCTTTAAAAATTA
1 TAAAAATGATAAAAAAATTAATTTAATCCCTTAAAAATTA
* * *
13600 TAAAAAT-ATAAATAATTTAATTTCGATCCCTTAAAA
1 TAAAAATGATAAAAAAATTAATTT-AATCCCTTAAAA
13636 TTTTTTTCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 14 0.45
40 17 0.55
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (40 bp):
TAAAAATGATAAAAAAATTAATTTAATCCCTTAAAAATTA
Found at i:23480 original size:5 final size:5
Alignment explanation
Indices: 23470--23494 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23460 TTCATGTACT
23470 GGGTC GGGTC GGGTC GGGTC GGGTC
1 GGGTC GGGTC GGGTC GGGTC GGGTC
23495 TAAGCATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GGGTC
Found at i:29044 original size:2 final size:2
Alignment explanation
Indices: 29039--29069 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29029 AAAAAAAAAA
29039 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29070 AATAATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31670 original size:21 final size:22
Alignment explanation
Indices: 31646--31693 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
31636 CGATATAAGG
31646 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
31667 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
31689 AAAAA
1 AAAAA
31694 ATAGAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:34039 original size:27 final size:28
Alignment explanation
Indices: 33996--34062 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
33986 AAACATCATT
*
33996 AAATATAATAGAAAATACAAATT-TA-AA
1 AAATATAATATAAAATA-AAATTATATAA
*
34023 AAATATAATATATAATAAAATTATATAA
1 AAATATAATATAAAATAAAATTATATAA
*
34051 ATAATTTAATAT
1 A-AATATAATAT
34063 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.15
27 17 0.50
28 3 0.09
29 9 0.26
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (28 bp):
AAATATAATATAAAATAAAATTATATAA
Found at i:34198 original size:14 final size:14
Alignment explanation
Indices: 34181--34208 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34171 AAGTTAAAAT
34181 TTAAAAATAAATAA
1 TTAAAAATAAATAA
34195 TTAAAAATAAATAA
1 TTAAAAATAAATAA
34209 AACACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAATAAATAA
Found at i:50288 original size:29 final size:30
Alignment explanation
Indices: 50208--50295 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 30
50198 CCCCGAGGAC
*
50208 TTTGAAAGGTTTGG-CTTTCATTTGAGCACT
1 TTTGAAAGGTTTGGCCTTT-ATATGAGCACT
** * *
50238 TTTGTAAAGGTTAAGCCCTTATATAAGCA-T
1 TTTG-AAAGGTTTGGCCTTTATATGAGCACT
50268 TTTGAAAGGTTTGGCCTTTATATGAGCA
1 TTTGAAAGGTTTGGCCTTTATATGAGCA
50296 ACCCCTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 20 0.43
30 9 0.19
31 15 0.32
32 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (30 bp):
TTTGAAAGGTTTGGCCTTTATATGAGCACT
Found at i:63457 original size:117 final size:115
Alignment explanation
Indices: 63253--63484 Score: 351
Period size: 117 Copynumber: 2.0 Consensus size: 115
63243 TTGATACAAA
** *
63253 CCCAACTAACGAATTAAATCAAATAAAGTTGATAAAAAAATTAAATAATGAATGATTCCAAAACA
1 CCCAACTAACGAAAAAAATCAAATAAAGTTGATAAAAAAATCAAATAATGAATGATTCCAAAACA
*
63318 CTAATGACTTTTTGGATGGAGGCGTGGCCCAAGTCATCCCCCGATTCCTT
66 CTAATGACTTTTTGGATGGAGGCGTGGCCCAAGTCATCCCCCAATTCCTT
63368 CCCAACTAACGAAAAAAATCAAATAAAGTTTGACTAAAAAAATCAAATAACT-AACTG-TTCCAA
1 CCCAACTAACGAAAAAAATCAAATAAAG-TTGA-TAAAAAAATCAAATAA-TGAA-TGATTCCAA
* * *
63431 AACACTAATGACTTTTTGGTTGGAGGCTTGGCCCAAGTCATCCCTCAATTCCTT
62 AACACTAATGACTTTTTGGATGGAGGCGTGGCCCAAGTCATCCCCCAATTCCTT
63485 GTATTTACGC
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
115 26 0.25
116 4 0.04
117 73 0.69
118 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (115 bp):
CCCAACTAACGAAAAAAATCAAATAAAGTTGATAAAAAAATCAAATAATGAATGATTCCAAAACA
CTAATGACTTTTTGGATGGAGGCGTGGCCCAAGTCATCCCCCAATTCCTT
Found at i:75823 original size:34 final size:34
Alignment explanation
Indices: 75780--75844 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
75770 TATAAAAGGT
* *
75780 TAAGGAAGATATAAGGTTAAAGGTCAAGGGAAGA
1 TAAGGAAGATAGAAGGTTAAAAGTCAAGGGAAGA
*
75814 TAAGGAAGATGGAAGGTTAAAAGTCAAGGGA
1 TAAGGAAGATAGAAGGTTAAAAGTCAAGGGA
75845 GGTTAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (34 bp):
TAAGGAAGATAGAAGGTTAAAAGTCAAGGGAAGA
Found at i:77360 original size:37 final size:37
Alignment explanation
Indices: 77311--77530 Score: 341
Period size: 37 Copynumber: 5.9 Consensus size: 37
77301 TGCTAAAGGT
*
77311 CACCGGCTCGAAGCCTACTAGGCACATAGCCTGAAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
* *
77348 CACCGGCACGAAGCCTACTAGGCACATAACCTGAAAC
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
** * *
77385 CACTAGTACGAAGCCTACTAGGCACATAGCCTAAAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
*
77422 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
* * *
77459 CACCAGCACGAAACCTACTAGGCACATAGCTTGAAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
77496 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAA
77531 TATTGTGCAA
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 162 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.13
Consensus pattern (37 bp):
CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
Found at i:83806 original size:26 final size:28
Alignment explanation
Indices: 83754--83806 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
83744 TATTTTAGAA
*
83754 AATTATTAAAATAATAAAATTGCATTTT
1 AATTATTAAAATAATAAAATTGAATTTT
* *
83782 AATT-TTAAAA-AATATAATTTAATTT
1 AATTATTAAAATAATAAAATTGAATTT
83807 CAAATTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 6 0.27
28 4 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
AATTATTAAAATAATAAAATTGAATTTT
Found at i:84211 original size:26 final size:26
Alignment explanation
Indices: 84175--84233 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
84165 CCCACTTTGA
84175 AAAATCCGTTAGTTAGCTGCTACTGT
1 AAAATCCGTTAGTTAGCTGCTACTGT
84201 AAAATCCGTTAGTTAGCTGCTACTGT
1 AAAATCCGTTAGTTAGCTGCTACTGT
84227 AAAATCC
1 AAAATCC
84234 AGACTAGCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (26 bp):
AAAATCCGTTAGTTAGCTGCTACTGT
Found at i:92199 original size:19 final size:20
Alignment explanation
Indices: 92172--92214 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
92162 TTTATAGAAA
*
92172 ATTTTATATTT-AAATTATT
1 ATTTCATATTTGAAATTATT
*
92191 ATTTCATATTTGTAATTATT
1 ATTTCATATTTGAAATTATT
92211 -TTTC
1 ATTTC
92215 TTTCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTCATATTTGAAATTATT
Found at i:95622 original size:3 final size:3
Alignment explanation
Indices: 95609--95638 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
95599 AGTAAATAAA
*
95609 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
95639 GGTTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:98785 original size:6 final size:6
Alignment explanation
Indices: 98774--98802 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
98764 CCTCTTCAAA
98774 TGTTGG TGTTGG TGTTGG TGTTGG TGTTG
1 TGTTGG TGTTGG TGTTGG TGTTGG TGTTG
98803 CATTTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGTTGG
Found at i:104506 original size:28 final size:29
Alignment explanation
Indices: 104473--104527 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
104463 TTTAATTCTT
*
104473 TTTAATAGTATAGGAATTAATT-AATCCA
1 TTTAATAGTATAGAAATTAATTCAATCCA
104501 TTTAATAGTATAGAAATTAATTCAATC
1 TTTAATAGTATAGAAATTAATTCAATC
104528 ATATCCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTAATAGTATAGAAATTAATTCAATCCA
Found at i:105024 original size:33 final size:33
Alignment explanation
Indices: 104982--105051 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
104972 TCGTTATATA
* *
104982 TTTTTTTAAATTTAAGTTTAA-CTATTAACATTT
1 TTTTTTTAAATTCAAGTTCAATCTATT-ACATTT
*
105015 TTTTTTTAAATTCAAGTTCAATTTATTACATTT
1 TTTTTTTAAATTCAAGTTCAATCTATTACATTT
105048 TTTT
1 TTTT
105052 AGTTACATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (33 bp):
TTTTTTTAAATTCAAGTTCAATCTATTACATTT
Found at i:122459 original size:30 final size:30
Alignment explanation
Indices: 122425--122486 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
122415 TGAAGACGAG
122425 TAGCTTTACCGTATATTTATATAAAAATAA
1 TAGCTTTACCGTATATTTATATAAAAATAA
122455 TAGCTTTACCGTATATTTATATAAAAATAA
1 TAGCTTTACCGTATATTTATATAAAAATAA
122485 TA
1 TA
122487 ACTTGCCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (30 bp):
TAGCTTTACCGTATATTTATATAAAAATAA
Found at i:130071 original size:29 final size:29
Alignment explanation
Indices: 130028--130107 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
130018 CATTTGAATC
*
130028 ATAATTAAAATTTCATGTATGT-AATTACACA
1 ATAA-TAAAAATTCATGTAT-TAAATTACA-A
130059 A-AATAAAAATTCATGTATTAAATTACAA
1 ATAATAAAAATTCATGTATTAAATTACAA
*
130087 ATTGATTAAAAATTCATGTAT
1 A-T-AATAAAAATTCATGTAT
130108 AATTTTAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 3 0.07
29 21 0.49
30 2 0.05
31 17 0.40
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (29 bp):
ATAATAAAAATTCATGTATTAAATTACAA
Found at i:134919 original size:4 final size:4
Alignment explanation
Indices: 134910--134938 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
134900 AAACGCTTTA
134910 TCCC TCCC TCCC TCCC TCCC TCCC -CCC TC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TC
134939 ACTGCCTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
TCCC
Found at i:159139 original size:18 final size:19
Alignment explanation
Indices: 159094--159140 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
159084 TGATTAAAAA
* *
159094 ATTATTAAAATATTTTTTC
1 ATTATTAAAATAATTTATC
*
159113 ATAATTAAAATAATTTAT-
1 ATTATTAAAATAATTTATC
159131 ATTATTAAAA
1 ATTATTAAAA
159141 AATATTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTAAAATAATTTATC
Found at i:165830 original size:1 final size:1
Alignment explanation
Indices: 165824--165855 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
165814 NNNNNNNNNN
*
165824 TTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
165856 CACAACCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:166530 original size:10 final size:10
Alignment explanation
Indices: 166515--166547 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
166505 TTACTAATTT
166515 AAAATTTTAA
1 AAAATTTTAA
166525 AAAATTTT-A
1 AAAATTTTAA
166534 AAAATTTTAA
1 AAAATTTTAA
166544 AAAA
1 AAAA
166548 CTTAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:166536 original size:9 final size:9
Alignment explanation
Indices: 166515--166546 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
166505 TTACTAATTT
166515 AAAATTTTAA
1 AAAATTTT-A
166525 AAAATTTTA
1 AAAATTTTA
166534 AAAATTTTA
1 AAAATTTTA
166543 AAAA
1 AAAA
166547 ACTTAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATTTTA
Found at i:170529 original size:14 final size:14
Alignment explanation
Indices: 170506--170579 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
170496 AAAAAAAAAA
*
170506 TTATTGTTTTATTG
1 TTATTTTTTTATTG
170520 TTATTTTTTTATTG
1 TTATTTTTTTATTG
*
170534 TT-TTGTTGTTATT-
1 TTATT-TTTTTATTG
* * *
170547 TAACTTTTATATTG
1 TTATTTTTTTATTG
* * *
170561 TTACTATTTTGTTG
1 TTATTTTTTTATTG
170575 TTATT
1 TTATT
170580 ATTTGAATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 9 0.20
14 37 0.80
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.70
Consensus pattern (14 bp):
TTATTTTTTTATTG
Found at i:170531 original size:22 final size:22
Alignment explanation
Indices: 170506--170547 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
170496 AAAAAAAAAA
170506 TTATTGTTTTATTGTTATTTTT
1 TTATTGTTTTATTGTTATTTTT
*
170528 TTATTGTTTTGTTGTTATTT
1 TTATTGTTTTATTGTTATTT
170548 AACTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (22 bp):
TTATTGTTTTATTGTTATTTTT
Found at i:170989 original size:20 final size:24
Alignment explanation
Indices: 170966--171021 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 24
170956 AAAAAAAAAA
170966 AAAATTGAT-AATAAAA-A-A-TT
1 AAAATTGATAAATAAAATATATTT
*
170986 AAAAAT-ATAAATAAAATATATTT
1 AAAATTGATAAATAAAATATATTT
171009 AAAATTGAGTAAA
1 AAAATTGA-TAAA
171022 ATAAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.07
20 12 0.43
21 1 0.04
22 1 0.04
23 7 0.25
24 1 0.04
25 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (24 bp):
AAAATTGATAAATAAAATATATTT
Found at i:174146 original size:62 final size:62
Alignment explanation
Indices: 174070--174191 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
174060 ATGAATTAAT
174070 AATTATTCATAATTAACTATTTTCTATGTCTACAATAAATGAGGAATCTGACTAAGGAAATA
1 AATTATTCATAATTAACTATTTTCTATGTCTACAATAAATGAGGAATCTGACTAAGGAAATA
174132 AATTATTCATAATTAACTATTTTCTATGTCTACAATAAATGAGGAATCTGACTAAGGAAA
1 AATTATTCATAATTAACTATTTTCTATGTCTACAATAAATGAGGAATCTGACTAAGGAAA
174192 AAAAAAATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (62 bp):
AATTATTCATAATTAACTATTTTCTATGTCTACAATAAATGAGGAATCTGACTAAGGAAATA
Found at i:176946 original size:60 final size:61
Alignment explanation
Indices: 176856--176988 Score: 232
Period size: 61 Copynumber: 2.2 Consensus size: 61
176846 TTGGTATCTG
* *
176856 AACTTGATATTTTTTTCTTAATTTGGTACCTAAA-TTTTTTTTTGGTCCAATTTGATACTCA
1 AACTTGATA-CTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTGGTCCAATTTGATACTCA
176917 AACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTGGTCCAATTTGATACTCA
1 AACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTGGTCCAATTTGATACTCA
176978 AACTTGATACT
1 AACTTGATACT
176989 CAAACTTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
60 22 0.32
61 47 0.68
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (61 bp):
AACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTTGGTCCAATTTGATACTCA
Found at i:176981 original size:30 final size:30
Alignment explanation
Indices: 176890--176982 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
176880 GGTACCTAAA
176890 TTTTTTTTTGGTCCAATTTGATACTCAAAC
1 TTTTTTTTTGGTCCAATTTGATACTCAAAC
** *
176920 TTGATACTTTT--TCCTAATTTGGTAC-CTAAAC
1 TT--TTTTTTTGGTCC-AATTTGATACTC-AAAC
176951 TTTTTTTTTGGTCCAATTTGATACTCAAAC
1 TTTTTTTTTGGTCCAATTTGATACTCAAAC
176981 TT
1 TT
176983 GATACTCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
29 5 0.10
30 21 0.42
31 19 0.38
32 5 0.10
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTTTTTTTGGTCCAATTTGATACTCAAAC
Found at i:176986 original size:13 final size:13
Alignment explanation
Indices: 176968--176995 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
176958 TTGGTCCAAT
176968 TTGATACTCAAAC
1 TTGATACTCAAAC
176981 TTGATACTCAAAC
1 TTGATACTCAAAC
176994 TT
1 TT
176996 TTTGGGGTCC
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:0.21, G:0.07, T:0.36
Consensus pattern (13 bp):
TTGATACTCAAAC
Found at i:177274 original size:31 final size:31
Alignment explanation
Indices: 177208--177281 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
177198 AAAAAAGCTT
* * * * *
177208 AGGTACCAAATTAGGAAAAGATGCCAAGTTT
1 AGGTACTAAATTAGGAAAAAAAGCCAACTTC
*
177239 AGGTACTAAATTAGGAAAAAAAGTCAACTTC
1 AGGTACTAAATTAGGAAAAAAAGCCAACTTC
177270 AGGTACTAAATT
1 AGGTACTAAATT
177282 GAGTCAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (31 bp):
AGGTACTAAATTAGGAAAAAAAGCCAACTTC
Found at i:183718 original size:6 final size:6
Alignment explanation
Indices: 183707--183737 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
183697 TTATAAAGGG
183707 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G
183738 GTAAGAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (6 bp):
GTTTTT
Found at i:191418 original size:55 final size:52
Alignment explanation
Indices: 191298--191441 Score: 150
Period size: 55 Copynumber: 2.8 Consensus size: 52
191288 AACGTGCTAT
* * *
191298 ATAATAA-CTATTTAAACATATAAACAATAGATTAAAAAATAATATTTTAAC
1 ATAATAATCAATTTAAACATATAAACAATAGATTAAAAAACAATATTTCAAC
* * *
191349 ATAACAATCAATTTAAACATATAAATAGTTA-ATTCAAAATAAACAATATTTCAAC
1 ATAATAATCAATTTAAACATATAAACA-ATAGATT--AAA-AAACAATATTTCAAC
* * *
191404 ATAATAATCGATTTAAACATATAAA-AATCGATTCAAAA
1 ATAATAATCAATTTAAACATATAAACAATAGATTAAAAA
191442 GAAGAAGAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
51 8 0.11
52 22 0.29
53 3 0.04
54 7 0.09
55 36 0.47
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (52 bp):
ATAATAATCAATTTAAACATATAAACAATAGATTAAAAAACAATATTTCAAC
Found at i:191528 original size:61 final size:60
Alignment explanation
Indices: 191393--191552 Score: 225
Period size: 61 Copynumber: 2.6 Consensus size: 60
191383 CAAAATAAAC
* *
191393 AATATTTCAACATAATAATCGATTTAAACATATAAA-AATCGATTCAAAAGAAGAAGAAA
1 AATATTTCAACATAACAATCGATTTAAAAATATAAACAATCGATTCAAAAGAAGAAGAAA
* *
191452 AAGTA-TCCGAACATAACAATCGATTTAAAAATATAAACAATCGATTCAAAAGAAGAAGAAGT
1 AA-TATTTC-AACATAACAATCGATTTAAAAATATAAACAATCGATTCAAAAGAAGAAGAA-A
* *
191514 AATATTTCACCATAACAATCGATTTAAATATATAAACAA
1 AATATTTCAACATAACAATCGATTTAAAAATATAAACAA
191553 ACAATTATTG
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
59 4 0.04
60 28 0.31
61 53 0.60
62 4 0.04
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (60 bp):
AATATTTCAACATAACAATCGATTTAAAAATATAAACAATCGATTCAAAAGAAGAAGAAA
Found at i:191952 original size:15 final size:15
Alignment explanation
Indices: 191930--191971 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
191920 TTTAATCGTT
191930 TAAAATTATAAA-AA
1 TAAAATTATAAATAA
191944 TATAAATTATTTAAATAA
1 TA-AAATTA--TAAATAA
191962 TAAAATTATA
1 TAAAATTATA
191972 TTTTTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
17 10 0.42
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATTATAAATAA
Found at i:193491 original size:131 final size:132
Alignment explanation
Indices: 193256--193520 Score: 514
Period size: 131 Copynumber: 2.0 Consensus size: 132
193246 TTTCTATGTA
193256 GTTGTTCAGATGTAAGGCAACGGCAAAGGTATTTACTTCATATAGTTGTCAGTAATTAATTCACA
1 GTTGTTCAGATGTAAGGCAACGGCAAAGGTATTTACTTCATATAGTTGTCAGTAATTAATTCACA
193321 CTCTCCTTTTACCCTGTCTAATAAGTTGCGATATATGGATGATGTATTTCAGTTAATGAATAAAA
66 CTCTCCTTTTACCCTGTCTAATAAGTTGCGATATATGGATGATGTATTTCAGTTAATGAATAAAA
193386 TG
131 TG
*
193388 GTTGTTCAGATGTCAGGCAACGGCAAAGGTATTTAC-TCATATAGTTGTCAGTAATTAATTCACA
1 GTTGTTCAGATGTAAGGCAACGGCAAAGGTATTTACTTCATATAGTTGTCAGTAATTAATTCACA
193452 CTCTCCTTTTACCCTGTCTAATAAGTTGCGATATATGGATGATGTATTTCAGTTAATGAATAAAA
66 CTCTCCTTTTACCCTGTCTAATAAGTTGCGATATATGGATGATGTATTTCAGTTAATGAATAAAA
193517 TG
131 TG
193519 GT
1 GT
193521 CATTGGTTCC
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
131 97 0.73
132 35 0.27
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (132 bp):
GTTGTTCAGATGTAAGGCAACGGCAAAGGTATTTACTTCATATAGTTGTCAGTAATTAATTCACA
CTCTCCTTTTACCCTGTCTAATAAGTTGCGATATATGGATGATGTATTTCAGTTAATGAATAAAA
TG
Found at i:198038 original size:35 final size:36
Alignment explanation
Indices: 197984--198075 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 36
197974 TAATAATCTC
197984 TATACTAAAATTTTAAAATTA-AAATTAATCTTTTTCT-
1 TATAC-AAAA-TTTAAAATTATAAATTAAT-TTTTTCTA
* * *
198021 TATACAAAATTTAAAATTATTAATTAGTTTTTTTTA
1 TATACAAAATTTAAAATTATAAATTAATTTTTTCTA
*
198057 TATACAAAATTTAGAATTA
1 TATACAAAATTTAAAATTA
198076 CCTATAATCT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 16 0.33
36 28 0.57
37 5 0.10
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (36 bp):
TATACAAAATTTAAAATTATAAATTAATTTTTTCTA
Found at i:198089 original size:36 final size:36
Alignment explanation
Indices: 197984--198089 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 36
197974 TAATAATCTC
*
197984 TATACTAAAATTTTAAAATTA-AAATTAATCTTTTTCT
1 TATAC-AAAA-TTTAAAATTACTAATTAATCTTTTTCT
* * *
198021 TATACAAAATTTAAAATTATTAATTAGT-TTTTTTT
1 TATACAAAATTTAAAATTACTAATTAATCTTTTTCT
*
198056 ATATACAAAATTTAGAATTACCT-A-TAATCTTTTT
1 -TATACAAAATTTAAAATTA-CTAATTAATCTTTTT
198090 AATTCATAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
35 19 0.32
36 34 0.58
37 6 0.10
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (36 bp):
TATACAAAATTTAAAATTACTAATTAATCTTTTTCT
Found at i:210801 original size:2 final size:2
Alignment explanation
Indices: 210794--210822 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
210784 ATTTTACTTC
210794 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 A
210823 AATAAGATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:214609 original size:14 final size:14
Alignment explanation
Indices: 214590--214619 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
214580 AGAAATGTAA
214590 GCTCATATATATAG
1 GCTCATATATATAG
214604 GCTCATATATATAG
1 GCTCATATATATAG
214618 GC
1 GC
214620 CCCGAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (14 bp):
GCTCATATATATAG
Found at i:224118 original size:3 final size:3
Alignment explanation
Indices: 224110--224138 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
224100 ACACTTTCAT
224110 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
224139 TCAAGCTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:226629 original size:2 final size:2
Alignment explanation
Indices: 226624--226654 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
226614 ATGCGCGCGC
226624 AT AT AT AT -T 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 AT AT
226655 TGTGATCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:228102 original size:6 final size:6
Alignment explanation
Indices: 228091--228115 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
228081 CTCATCTCTT
228091 GTTGGC GTTGGC GTTGGC GTTGGC G
1 GTTGGC GTTGGC GTTGGC GTTGGC G
228116 GTGCCGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GTTGGC
Found at i:232140 original size:2 final size:2
Alignment explanation
Indices: 232133--232173 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
232123 CAGAAATCAG
232133 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
232174 CAAAACACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:233521 original size:59 final size:57
Alignment explanation
Indices: 233415--233537 Score: 201
Period size: 59 Copynumber: 2.1 Consensus size: 57
233405 GGATGATTAA
*
233415 AACTATTGCAGCACCTAATATTGTAGTTTTCTCAAGATCCAAGTGAATCGTGATTCT
1 AACTATTGCAGCACCTAATATTGTAGTTTTCTCAAGATCCAAGTGAATCATGATTCT
*
233472 AACTATTGCAGCACCTAATATCGTGTAGTTTTCTCGAGATCCAAGTGAATCATGATTCT
1 AACTATTGCAGCACCTAATAT--TGTAGTTTTCTCAAGATCCAAGTGAATCATGATTCT
*
233531 AGCTATT
1 AACTATT
233538 AGGAAATAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 21 0.34
59 40 0.66
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (57 bp):
AACTATTGCAGCACCTAATATTGTAGTTTTCTCAAGATCCAAGTGAATCATGATTCT
Found at i:236197 original size:21 final size:21
Alignment explanation
Indices: 236180--236224 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
236170 TAATTTTATT
*
236180 TTTATTTTTTTAACTTTTAAA
1 TTTATGTTTTTAACTTTTAAA
*
236201 TTTGTGTTTTTAACTTTTAAA
1 TTTATGTTTTTAACTTTTAAA
236222 TTT
1 TTT
236225 TTCAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATGTTTTTAACTTTTAAA
Found at i:244343 original size:26 final size:26
Alignment explanation
Indices: 244314--244366 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
244304 AAAAAAATAC
244314 TATACTAGAATT-TAAATATTTAAAAA
1 TATACTA-AATTGTAAATATTTAAAAA
* **
244340 TATATTAAATTGTTTATATTTAAAAA
1 TATACTAAATTGTAAATATTTAAAAA
244366 T
1 T
244367 TTAATAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
TATACTAAATTGTAAATATTTAAAAA
Found at i:244451 original size:3 final size:3
Alignment explanation
Indices: 244443--244470 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
244433 TTATATTTAA
244443 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
244471 TGAGTTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:246024 original size:22 final size:23
Alignment explanation
Indices: 245999--246044 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
245989 TTTTAAGTGG
* *
245999 ACGA-AATAAAATTGTAATTTTT
1 ACGATAATAAAAATATAATTTTT
*
246021 ACGATAGTAAAAATATAATTTTT
1 ACGATAATAAAAATATAATTTTT
246044 A
1 A
246045 AAATATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
ACGATAATAAAAATATAATTTTT
Found at i:251396 original size:2 final size:2
Alignment explanation
Indices: 251389--251415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
251379 ATTAGGATTT
251389 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 T
251416 GATTGGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:254164 original size:68 final size:68
Alignment explanation
Indices: 254086--254221 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
254076 ATTAATGCAT
*
254086 TGTTAACTTTAATAAAAATATTAAGATTAAAATATGTCGTAAGTACGTATGCTCTTCATAATTTT
1 TGTTAACTTTAATAAAAATATTAAGATTAAAATATGTCGTAAGTACCTATGCTCTTCATAATTTT
254151 CGC
66 CGC
*
254154 TGTTAACTTTAATAAAAATATTAAGGTTAAAATATGTCGTAAGTACCTATGCTCTTCATAATTTT
1 TGTTAACTTTAATAAAAATATTAAGATTAAAATATGTCGTAAGTACCTATGCTCTTCATAATTTT
254219 CGC
66 CGC
254222 ATTTAATCCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (68 bp):
TGTTAACTTTAATAAAAATATTAAGATTAAAATATGTCGTAAGTACCTATGCTCTTCATAATTTT
CGC
Found at i:258329 original size:11 final size:11
Alignment explanation
Indices: 258315--258339 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
258305 TCCTTTTTCT
258315 TTTTTTTTTTA
1 TTTTTTTTTTA
258326 TTTTTTTTTTA
1 TTTTTTTTTTA
258337 TTT
1 TTT
258340 CTCTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:260399 original size:11 final size:11
Alignment explanation
Indices: 260383--260439 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
260373 GGGGACCAAC
* *
260383 GAAAAATGAAG
1 GAAAAAAGAAA
260394 GAAAAAAGAAA
1 GAAAAAAGAAA
260405 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
260418 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
260430 GAAAGAAGAA
1 GAAAAAAGAA
260440 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.38
12 17 0.43
13 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:260407 original size:4 final size:4
Alignment explanation
Indices: 260394--260436 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
260384 AAAAATGAAG
*
260394 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
260437 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:260409 original size:21 final size:21
Alignment explanation
Indices: 260394--260435 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
260384 AAAAATGAAG
260394 GAAA-AAAGAAAGAAAAAAGA
1 GAAAGAAAGAAAGAAAAAAGA
260414 GAAAGAAAGAAAGAAAGAAAGA
1 GAAAGAAAGAAAGAAA-AAAGA
260436 AGAAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAGA
Found at i:260455 original size:9 final size:9
Alignment explanation
Indices: 260433--260469 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
260423 AAAGAAAGAA
260433 AGAAGAA-G
1 AGAAGAAGG
260441 -GAAGAAGG
1 AGAAGAAGG
260449 AGAAGAAGG
1 AGAAGAAGG
*
260458 GGAAGAAGG
1 AGAAGAAGG
260467 AGA
1 AGA
260470 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:261030 original size:16 final size:16
Alignment explanation
Indices: 260985--261034 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
260975 TAAACCTAAC
*
260985 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
261001 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
261015 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
261031 TAAT
1 TAAT
261035 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:262363 original size:43 final size:43
Alignment explanation
Indices: 262281--262365 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
262271 ATTAACATGT
* * *
262281 TAAATTATATTACTTGACTTGTGTTAATATGGTTTCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
*
262324 TAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTT-ACATGTTA
262366 TTAACTGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 33 0.92
44 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
Found at i:262997 original size:45 final size:46
Alignment explanation
Indices: 262933--263040 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 46
262923 GCATAGCTCA
*
262933 TCAAGCCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATAC-
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACT
*
262978 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGTAATACT
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACT
* *
263024 TAAAG-GAAGGATATCAG
1 TCAAGCCAAGGATATCAG
263041 GATGAGTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 54 0.93
46 4 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (46 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACT
Found at i:263051 original size:45 final size:45
Alignment explanation
Indices: 262935--263055 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 45
262925 ATAGCTCATC
* * *
262935 AAGCCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATACTC
1 AAGCCAAGGATATCAGCATCAATTTGACGAGCCACCGCAATACTA
* *
262980 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGTAATACTTA
1 AAGCCAAGGATATCAGCATCAATTTGACGAGCCACCGCAATAC-TA
* * * *
263026 AAG-GAAGGATATCAGGATGAGTTTGACGAG
1 AAGCCAAGGATATCAGCATCAATTTGACGAG
263056 TCATCGCGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 63 0.94
46 4 0.06
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCATCAATTTGACGAGCCACCGCAATACTA
Found at i:263376 original size:28 final size:28
Alignment explanation
Indices: 263345--263409 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
263335 ACCTAAATTA
*
263345 TAAACCCTAAACTTAAAACACTAAACCG
1 TAAACACTAAACTTAAAACACTAAACCG
** * *
263373 TAAACACTAGGCTTGAAACTCTAAACCG
1 TAAACACTAAACTTAAAACACTAAACCG
263401 TAAACACTA
1 TAAACACTA
263410 GATTGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.46, C:0.26, G:0.08, T:0.20
Consensus pattern (28 bp):
TAAACACTAAACTTAAAACACTAAACCG
Found at i:266560 original size:4 final size:4
Alignment explanation
Indices: 266540--266606 Score: 57
Period size: 4 Copynumber: 17.0 Consensus size: 4
266530 ACACATTACA
* * * * *
266540 TTTC TTTC CTTC -GTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
*
266587 TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC
266607 CCGTTTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 5 0.10
4 42 0.84
5 3 0.06
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:270030 original size:6 final size:7
Alignment explanation
Indices: 270012--270037 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
270002 AAATATACAA
270012 TAAAAAT
1 TAAAAAT
270019 TAAAAAT
1 TAAAAAT
270026 TAAAAAT
1 TAAAAAT
270033 TAAAA
1 TAAAA
270038 GATAAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:270043 original size:14 final size:13
Alignment explanation
Indices: 270010--270043 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
270000 ACAAATATAC
270010 AATAAAAATTAAA
1 AATAAAAATTAAA
270023 AATTAAAAATTAAA
1 AA-TAAAAATTAAA
270037 AGATAAA
1 A-ATAAA
270044 TTCCACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.84
15 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AATAAAAATTAAA
Found at i:274498 original size:61 final size:61
Alignment explanation
Indices: 274403--274528 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
274393 CGCGGTCTAT
274403 TTTTTATTTATTTGTATGACACTTTTGTTAGGGACGTGTCTGAGTGCCGGACACAGTATGG
1 TTTTTATTTATTTGTATGACACTTTTGTTAGGGACGTGTCTGAGTGCCGGACACAGTATGG
274464 TTTTTATTTATTTGTATGACACTTTTGTTAGGGACGTGTCTGAGTGCCGGACACAGTATGG
1 TTTTTATTTATTTGTATGACACTTTTGTTAGGGACGTGTCTGAGTGCCGGACACAGTATGG
274525 TTTT
1 TTTT
274529 GACATAGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (61 bp):
TTTTTATTTATTTGTATGACACTTTTGTTAGGGACGTGTCTGAGTGCCGGACACAGTATGG
Found at i:275895 original size:20 final size:19
Alignment explanation
Indices: 275847--275896 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
275837 AATATTCCCT
* *
275847 TTTGTTTATTGAAATTGGGT
1 TTTGTTT-TTGAAATTGAGA
275867 TTTGATTTTTGAAATCTGAGA
1 TTTG-TTTTTGAAAT-TGAGA
275888 TTTGTTTTT
1 TTTGTTTTT
275897 TTTTAGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.58
Consensus pattern (19 bp):
TTTGTTTTTGAAATTGAGA
Found at i:280656 original size:29 final size:29
Alignment explanation
Indices: 280614--280681 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
280604 CAAGGAGAGT
*
280614 CTAATTTGATCCATTTAATAGTA-AAGGGA
1 CTAATTTGATCCATTTAATAATAGAA-GGA
*
280643 CTAAATTGATCCATTTAATAATAGAAGGA
1 CTAATTTGATCCATTTAATAATAGAAGGA
280672 CTAATTTGAT
1 CTAATTTGAT
280682 AAAGTTTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 33 0.94
30 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (29 bp):
CTAATTTGATCCATTTAATAATAGAAGGA
Found at i:282561 original size:231 final size:231
Alignment explanation
Indices: 282153--282841 Score: 1103
Period size: 231 Copynumber: 3.0 Consensus size: 231
282143 AGACTTGGCT
* * ** * * * * * * *
282153 TAGAGGACGATGATGAGGGTTTCGGAGGCAGTGTTGTTGGTTTAGATGGTTTCAGTCCTTCAGGT
1 TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCAGTGCTTTAGGT
* *
282218 GATGGAGATGGTTTTTGGGCCGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGAGGAA-ATT
66 GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGA-GAATATA
* *
282282 GAACCGGCTTGACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGC
130 GATCCGGCTTAACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGC
282347 CATTCATTTCCAGGTGATGAACTCAGGGATGAAGTTG
195 CATTCATTTCCAGGTGATGAACTCAGGGATGAAGTTG
282384 TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCAGTGCTTTAGGT
1 TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCAGTGCTTTAGGT
*
282449 GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGAGAATATGG
66 GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGAGAATATAG
282514 ATCCGGCTTAACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGCC
131 ATCCGGCTTAACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGCC
282579 ATTCATTTCCAGGTGATGAACTCAGGGATGAAGTTG
196 ATTCATTTCCAGGTGATGAACTCAGGGATGAAGTTG
*
282615 TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCGGTGCTTTAGGT
1 TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCAGTGCTTTAGGT
* ** *
282680 GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATAATGGCAGTGGACTAGGAGGATATAG
66 GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGAGAATATAG
* *
282745 ATCCGGCATAAAC-GAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATTGC
131 ATCCGGC-TTAACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGC
* ** *
282809 CACTCATTTCTGGGAGATGAACTCAGGGATGAA
195 CATTCATTTCCAGGTGATGAACTCAGGGATGAA
282842 CTTGGGTAAC
Statistics
Matches: 429, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
230 3 0.01
231 422 0.98
232 4 0.01
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.30
Consensus pattern (231 bp):
TAGAAGACGATGAAGAGGGTTTCAAAGACGGTGTGGTTGGTTTAGGTGGTGTCAGTGCTTTAGGT
GATGGAGATGGTTTTTGGGCTGTGAATGACGTTTTAAATGATGGCAGCAGACTAGGAGAATATAG
ATCCGGCTTAACTGAGGACTGAGGTGGTTTGGTTGAAGTTGTAGATGAATGAATGTTATATAGCC
ATTCATTTCCAGGTGATGAACTCAGGGATGAAGTTG
Found at i:300282 original size:31 final size:29
Alignment explanation
Indices: 300247--300321 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
300237 AATTTTAAAA
300247 TTATACATAAATATTAAGTTAATGTGTAATT
1 TTATACATAAAT-TTAA-TTAATGTGTAATT
* ** *
300278 TTATACATAAATTTTATTTTTTTGTAATT
1 TTATACATAAATTTAATTAATGTGTAATT
300307 TTATACATGAAATTT
1 TTATACAT-AAATTT
300322 TGATTTGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 18 0.46
30 9 0.23
31 12 0.31
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (29 bp):
TTATACATAAATTTAATTAATGTGTAATT
Found at i:300322 original size:30 final size:30
Alignment explanation
Indices: 300271--300327 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
300261 TAAGTTAATG
300271 TGTAATTTTATACATAAATTTT-ATTTTTT
1 TGTAATTTTATACATAAATTTTGATTTTTT
300300 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTTTATACAT-AAATTTTGATTT
300328 GATCTAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 15 0.58
30 7 0.27
31 4 0.15
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (30 bp):
TGTAATTTTATACATAAATTTTGATTTTTT
Found at i:305892 original size:51 final size:52
Alignment explanation
Indices: 305820--305922 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 52
305810 GAGCAGGCTG
305820 CTGAATTAAGAAAAGAAGTTGGAA-TA-TCGGACAGAAGTTTGG-AGCAAGTCA
1 CTGAATTAAGAAAAGAAGTTGGAATTACT-GGA-AGAAGTTTGGAAGCAAGTCA
* * *
305871 CTGAATCT-AGAAGAGATGTTGGAATTACTGGAAGAAGTTTGGAATCAAGTCA
1 CTGAAT-TAAGAAAAGAAGTTGGAATTACTGGAAGAAGTTTGGAAGCAAGTCA
305923 GTCGGCTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 30 0.67
52 14 0.31
53 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (52 bp):
CTGAATTAAGAAAAGAAGTTGGAATTACTGGAAGAAGTTTGGAAGCAAGTCA
Found at i:320477 original size:21 final size:22
Alignment explanation
Indices: 320435--320485 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
320425 GTAAAAAAAT
*
320435 ATAAATATTATTAGAATTTATA
1 ATAAATATTATTAGAATATATA
320457 ATAAA-ATTATTTA-AATATAT-
1 ATAAATATTA-TTAGAATATATA
*
320477 ATAATTATT
1 ATAAATATT
320486 TTTTAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAATATTATTAGAATATATA
Found at i:326095 original size:51 final size:51
Alignment explanation
Indices: 326019--326127 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
326009 TGATTCTAGG
* *
326019 TTGGATCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATATCTGAG-AGAAGT
1 TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACT-AGCAGAAGT
* *
326070 TTGGAGCAGGCTGCTGATTCAAGAAACGAAGTTGGAATAACTAGCAGAAGT
1 TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTAGCAGAAGT
*
326121 TTAGAGC
1 TTGGAGC
326128 CAAGTCAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 2 0.04
51 50 0.96
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (51 bp):
TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTAGCAGAAGT
Found at i:326182 original size:60 final size:60
Alignment explanation
Indices: 326078--326235 Score: 192
Period size: 60 Copynumber: 2.6 Consensus size: 60
326068 GTTTGGAGCA
* * * * * * * * *
326078 GGCTGCTGATTCAAGAAACGAAGTTGGAATAACT-AGCAGAAGTTTAGAGCCAAGTCAAGT
1 GGCTGCTGAATCTAGAAAAGAAGCTGGAATAGCTGGGAAG-AGTTTAGAGCCAAGCCAACT
*
326138 GGCTGCTGAATCTAGAAAAGAATCTGGAATAGCTGGGAAGAGTTTAGAGCCAAGCCAACT
1 GGCTGCTGAATCTAGAAAAGAAGCTGGAATAGCTGGGAAGAGTTTAGAGCCAAGCCAACT
* *
326198 GGCTGCTGAGTCTAGAAAAGAAGCTGGAATAGTTGGGA
1 GGCTGCTGAATCTAGAAAAGAAGCTGGAATAGCTGGGA
326236 GAACTTTGGA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 81 0.96
61 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.21
Consensus pattern (60 bp):
GGCTGCTGAATCTAGAAAAGAAGCTGGAATAGCTGGGAAGAGTTTAGAGCCAAGCCAACT
Found at i:330968 original size:14 final size:15
Alignment explanation
Indices: 330938--330970 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
330928 ATTAATTTAT
330938 AATATATTTAAATAA
1 AATATATTTAAATAA
*
330953 AATATATTT-TATAA
1 AATATATTTAAATAA
330967 AATA
1 AATA
330971 GCATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTTAAATAA
Found at i:331887 original size:110 final size:109
Alignment explanation
Indices: 331564--331888 Score: 415
Period size: 109 Copynumber: 3.0 Consensus size: 109
331554 ACTATAGAAT
* * * *
331564 AGAAAGGGAGTGATAGCTTTTGATTGGTGC-AGACAATGCGAAC-AAGAAGGCCACACAACAACA
1 AGAAAGAGAGTGAAAGCATTTGATTGGTGCAAG-CAATGC-AACAAAGAAGGCCATACAACAACA
* * *
331627 ATTTTAACAGTCCAATGACTTAAATGAGAACTTATGAATAATTCAC
64 ATTTTAACAGTCCAATGACTTAAATGAAAACTTATGAATAGTTAAC
* * *
331673 AGAAAGAGAGTGAAAGCATTTGATTGGTGCAGGCAATGCAAACAAA-TACGCCATACAACAACAA
1 AGAAAGAGAGTGAAAGCATTTGATTGGTGCAAGCAATGC-AACAAAGAAGGCCATACAACAACAA
* * *
331737 TTTTAACAATTCAATGACTTAAATGAAAACTTATAAATAGTTAAC
65 TTTTAACAGTCCAATGACTTAAATGAAAACTTATGAATAGTTAAC
*
331782 AGAAAGAGAGTGAGAGCATTTGATTGGTGCAAGCAATGCAAGCAAAGAAGGCCATACAACAAC-A
1 AGAAAGAGAGTGAAAGCATTTGATTGGTGCAAGCAATGCAA-CAAAGAAGGCCATACAACAACAA
* * * *
331846 TATTTAATAGCCCAGTGATTTAAATGAAAACTTATGAATAGTT
65 T-TTTAACAGTCCAATGACTTAAATGAAAACTTATGAATAGTT
331889 CTATAACGAT
Statistics
Matches: 186, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
108 2 0.01
109 133 0.72
110 51 0.27
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (109 bp):
AGAAAGAGAGTGAAAGCATTTGATTGGTGCAAGCAATGCAACAAAGAAGGCCATACAACAACAAT
TTTAACAGTCCAATGACTTAAATGAAAACTTATGAATAGTTAAC
Found at i:338836 original size:20 final size:18
Alignment explanation
Indices: 338808--338855 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
338798 TCACATTAAT
*
338808 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
338828 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
338848 AAATTATT
1 AAATTATT
338856 AAATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:339569 original size:22 final size:22
Alignment explanation
Indices: 339526--339569 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
339516 AAAATTATTT
*
339526 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
339548 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
339570 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:352262 original size:17 final size:17
Alignment explanation
Indices: 352219--352264 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
352209 GTTTATTTTG
352219 TTGTT-ATTGTTTGTATA
1 TTGTTAATT-TTTGTATA
*
352236 TTGTTTAATTTTTGTTTA
1 TTG-TTAATTTTTGTATA
352254 TTGTTAATTTT
1 TTGTTAATTTT
352265 GCAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 12 0.46
19 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (17 bp):
TTGTTAATTTTTGTATA
Found at i:353570 original size:17 final size:17
Alignment explanation
Indices: 353539--353585 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
353529 AAAAATTATA
*
353539 TAAAATTATTAAATA-T
1 TAAAATAATTAAATATT
353555 TAAAATAATATAAATATT
1 TAAAATAAT-TAAATATT
*
353573 TAAAAAAATTAAA
1 TAAAATAATTAAA
353586 AATAATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATAATTAAATATT
Found at i:358310 original size:168 final size:166
Alignment explanation
Indices: 358027--358344 Score: 532
Period size: 168 Copynumber: 1.9 Consensus size: 166
358017 ATTTCCAAAA
*
358027 TTCCAAATTTTATATTTTTTAAAAAAATTATAATTTTTTAAATTTTTTTAAAGGATATATAAAAA
1 TTCCAAATTTTATATTTTTTAAAAAAATTATAATTTTTTAAATTTTTTTAAAGAATATATAAAAA
*
358092 AGTTAAAAGTTTAAAATGTTTCTAAAATAATAATTTTGAAGAACTAAATAAGTTAATTAATGATT
66 AGTTAAAAGTTTAAAATGTTCCTAAAATAATAATTTTGAAGAACTAAATAAGTTAATTAATGATT
*
358157 TAAATTTATCATACTAAAATTTTTTTTTTCCTTATT
131 TAAATTTATCACACTAAAATTTTTTTTTTCCTTATT
358193 TTCCAAATTTTATATTTTTT-AAAAAATTATAATTTTTTTTTAAA-TTTTTTAAAGAATATATAA
1 TTCCAAATTTTATATTTTTTAAAAAAATTATAA---TTTTTTAAATTTTTTTAAAGAATATAT-A
* *
358256 AAAAATTTAAAAGTTTAAAATGTTCCTAAAATAATAATTTTGAAGAATTAAATAAGTTAATTAAT
62 AAAAAGTTAAAAGTTTAAAATGTTCCTAAAATAATAATTTTGAAGAACTAAATAAGTTAATTAAT
*
358321 GATTTAAGTTTATCACACTAAAAT
127 GATTTAAATTTATCACACTAAAAT
358345 ATATATATAT
Statistics
Matches: 142, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
165 12 0.08
166 20 0.14
167 16 0.11
168 94 0.66
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (166 bp):
TTCCAAATTTTATATTTTTTAAAAAAATTATAATTTTTTAAATTTTTTTAAAGAATATATAAAAA
AGTTAAAAGTTTAAAATGTTCCTAAAATAATAATTTTGAAGAACTAAATAAGTTAATTAATGATT
TAAATTTATCACACTAAAATTTTTTTTTTCCTTATT
Found at i:360577 original size:28 final size:28
Alignment explanation
Indices: 360527--360584 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
360517 ATTCTTTCTC
360527 AATTGATCACACCAAGAAGTCCACAATA
1 AATTGATCACACCAAGAAGTCCACAATA
*** *
360555 AATTGATCACACTGGGAATTCCACAATA
1 AATTGATCACACCAAGAAGTCCACAATA
360583 AA
1 AA
360585 ATGGTATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (28 bp):
AATTGATCACACCAAGAAGTCCACAATA
Found at i:373070 original size:16 final size:15
Alignment explanation
Indices: 373049--373078 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
373039 TATACTAAAT
373049 TTTAATTCAATAATTA
1 TTTAATTCAA-AATTA
373065 TTTAATTCAAAATT
1 TTTAATTCAAAATT
373079 CCATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATTCAAAATTA
Found at i:376492 original size:38 final size:38
Alignment explanation
Indices: 376408--376492 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
376398 TGAGTCTATT
* * * *
376408 CAGAATTGCGCCCAGAATTGTCACTGCATGACGATGTC
1 CAGAATTGTGCCCAAAATTATCACTGCATGACGATGCC
376446 CAGAATTGTGCCCAAAATTATCACTGCATGA-GTATGCC
1 CAGAATTGTGCCCAAAATTATCACTGCATGACG-ATGCC
376484 CAGAATTGT
1 CAGAATTGT
376493 CGTTGCAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.02
38 41 0.98
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (38 bp):
CAGAATTGTGCCCAAAATTATCACTGCATGACGATGCC
Found at i:377696 original size:20 final size:20
Alignment explanation
Indices: 377673--377712 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
377663 CTATCGGTAG
*
377673 AACTCCACCTCTACCGATAC
1 AACTACACCTCTACCGATAC
**
377693 AACTACAGTTCTACCGATAC
1 AACTACACCTCTACCGATAC
377713 CTTGAAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.38, G:0.07, T:0.23
Consensus pattern (20 bp):
AACTACACCTCTACCGATAC
Found at i:383036 original size:16 final size:17
Alignment explanation
Indices: 383015--383051 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
383005 TTTATACTAA
383015 AATTC-ATACTTTAAC-C
1 AATTCAATA-TTTAACTC
383031 AATTCAATATTTAACTC
1 AATTCAATATTTAACTC
383048 AATT
1 AATT
383052 TCCTCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTCAATATTTAACTC
Found at i:384418 original size:22 final size:22
Alignment explanation
Indices: 384393--384465 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
384383 AACGAACCAA
*
384393 ACAAATTAAACATAACAATTTC
1 ACAACTTAAACATAACAATTTC
* *
384415 ACAACTTAAATATACCTAA---C
1 ACAACTTAAACATAAC-AATTTC
384435 A-AACTTAAACATAACAATTTC
1 ACAACTTAAACATAACAATTTC
384456 ACAACTTAAA
1 ACAACTTAAA
384466 TACACCTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 2 0.05
19 12 0.29
20 2 0.05
21 2 0.05
22 21 0.51
23 2 0.05
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (22 bp):
ACAACTTAAACATAACAATTTC
Found at i:384441 original size:19 final size:19
Alignment explanation
Indices: 384417--384484 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
384407 ACAATTTCAC
384417 AACTTAAATATACCTAACA
1 AACTTAAATATACCTAACA
* *
384436 AACTTAAACATAAC-AATTTCA
1 AACTTAAATATACCTAA---CA
* *
384457 CAACTTAAATACACCTAATA
1 -AACTTAAATATACCTAACA
384477 AACTTAAA
1 AACTTAAA
384485 CATAACAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 1 0.03
21 2 0.05
22 11 0.29
23 2 0.05
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (19 bp):
AACTTAAATATACCTAACA
Found at i:384443 original size:41 final size:41
Alignment explanation
Indices: 384392--384494 Score: 181
Period size: 41 Copynumber: 2.5 Consensus size: 41
384382 TAACGAACCA
*
384392 AACAAA-TTAAACATAACAATTTCACAACTTAAATATACCT
1 AACAAACTTAAACATAACAATTTCACAACTTAAATACACCT
384432 AACAAACTTAAACATAACAATTTCACAACTTAAATACACCT
1 AACAAACTTAAACATAACAATTTCACAACTTAAATACACCT
*
384473 AATAAACTTAAACATAACAATT
1 AACAAACTTAAACATAACAATT
384495 CCAAACAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 6 0.10
41 54 0.90
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.26
Consensus pattern (41 bp):
AACAAACTTAAACATAACAATTTCACAACTTAAATACACCT
Found at i:393011 original size:29 final size:30
Alignment explanation
Indices: 392979--393035 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
392969 TTGTCTAATA
*
392979 TGTAATCTTATATATTAACTTT-GATTTTG
1 TGTAATCTTATATATTAAATTTCGATTTTG
* *
393008 TGTATTTTTATATATTAAATTTCGATTT
1 TGTAATCTTATATATTAAATTTCGATTT
393036 GATCCTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (30 bp):
TGTAATCTTATATATTAAATTTCGATTTTG
Found at i:393622 original size:21 final size:23
Alignment explanation
Indices: 393578--393622 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
393568 ATTTTTTTAA
*
393578 TTTTTAAATTCAAAATATATATT
1 TTTTTAAATTCAAAATATAAATT
*
393601 TTTTTAAATT-AAGAT-TAAATT
1 TTTTTAAATTCAAAATATAAATT
393622 T
1 T
393623 AAAATGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTAAATTCAAAATATAAATT
Found at i:410725 original size:21 final size:21
Alignment explanation
Indices: 410687--410726 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
410677 GCTTGCTGTT
** *
410687 GAGGAGGAAATTCTTGTTGGA
1 GAGGAGGAAACCCATGTTGGA
410708 GAGGAGGAAACCCATGTTG
1 GAGGAGGAAACCCATGTTG
410727 ATGATGTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.38, T:0.23
Consensus pattern (21 bp):
GAGGAGGAAACCCATGTTGGA
Found at i:414005 original size:27 final size:27
Alignment explanation
Indices: 413987--414039 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
413977 CATTCCTTTG
*
413987 GAGTTCATCTTGAAAACCATACCTTCA
1 GAGTTCATCATGAAAACCATACCTTCA
*
414014 GAGTTCGTCATGAAAACCATACCTTC
1 GAGTTCATCATGAAAACCATACCTTC
414040 GGAACTCGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (27 bp):
GAGTTCATCATGAAAACCATACCTTCA
Found at i:414048 original size:27 final size:27
Alignment explanation
Indices: 413997--414050 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
413987 GAGTTCATCT
**
413997 TGAAAACCATACCTTCAGAGTTCGTCA
1 TGAAAACCATACCTTCAGAACTCGTCA
*
414024 TGAAAACCATACCTTCGGAACTCGTCA
1 TGAAAACCATACCTTCAGAACTCGTCA
414051 CAAAGGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (27 bp):
TGAAAACCATACCTTCAGAACTCGTCA
Found at i:414105 original size:27 final size:27
Alignment explanation
Indices: 414075--414140 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
414065 TTAGATGGCT
*
414075 GCCACAAGGGCTTTCCTTT-CAAGATTC
1 GCCACAAAGGCTTT-CTTTACAAGATTC
*
414102 GCCACAAAGGC-TTCTTTACAAGATTT
1 GCCACAAAGGCTTTCTTTACAAGATTC
*
414128 TCCACAAAGGCTT
1 GCCACAAAGGCTT
414141 CATTATTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.12
26 19 0.56
27 11 0.32
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (27 bp):
GCCACAAAGGCTTTCTTTACAAGATTC
Found at i:419427 original size:30 final size:30
Alignment explanation
Indices: 419387--419542 Score: 127
Period size: 30 Copynumber: 5.1 Consensus size: 30
419377 AAACTTAAAA
* *
419387 TTTTGGAAAGTTTG-GAGGTTAAAATGTAAT
1 TTTTAGAAAGTTTGAG-GGTTAAAATGAAAT
**
419417 TTTTAGAAAGTTTTG-GAGGTTAAAATGTGAT
1 TTTTAGAAAG-TTTGAG-GGTTAAAATGAAAT
* * * * *
419448 TTTCAAAAAACTTTAAGGGTCAAAATGAAAT
1 TTT-TAGAAAGTTTGAGGGTTAAAATGAAAT
* * * *
419479 TTTCAAAAAGTTTGAGGGTCAAAATGAAAC
1 TTTTAGAAAGTTTGAGGGTTAAAATGAAAT
* *
419509 TTTTAGAAAGTTTAAGGGTTAAAATGAATT
1 TTTTAGAAAGTTTGAGGGTTAAAATGAAAT
419539 TTTT
1 TTTT
419543 TTAAAATTCA
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
30 60 0.58
31 39 0.38
32 5 0.05
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (30 bp):
TTTTAGAAAGTTTGAGGGTTAAAATGAAAT
Found at i:420778 original size:24 final size:25
Alignment explanation
Indices: 420739--420785 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
420729 TGGGCTTTAG
420739 TTGTAATGGGTAATTGGGTTAGGGT
1 TTGTAATGGGTAATTGGGTTAGGGT
*
420764 TTGTATTGGGT-ATTGGGTTAGG
1 TTGTAATGGGTAATTGGGTTAGG
420786 ATTGGGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (25 bp):
TTGTAATGGGTAATTGGGTTAGGGT
Found at i:420918 original size:18 final size:17
Alignment explanation
Indices: 420884--420933 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
420874 TTTTGAATGT
*
420884 TTTTTATTATTTATTTTTG
1 TTTTT-TTATTT-TTTTGG
420903 TTTTTTTAGTTTTTTTGG
1 TTTTTTTA-TTTTTTTGG
420921 TTTGTTTTATTTT
1 TTT-TTTTATTTT
420934 GGGTCGGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTTTTTTGG
Found at i:421507 original size:46 final size:45
Alignment explanation
Indices: 421366--421524 Score: 219
Period size: 46 Copynumber: 3.5 Consensus size: 45
421356 TGAGATAGTA
* * *
421366 GCTTCAATTTGCCCCTCTTAATTTAGGGGTAAAAGATTGGACGGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTG
* * * ** *
421412 GCTTCAATGTGCCCTTCTTGATTACGACTAAAAGATTGGATGATG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
421457 GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTG
421503 GCTTCAATCTGCCCCTCTTGAT
1 GCTTCAATCTGCCCCTCTTGAT
421525 GGTGATGTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 39 0.40
46 59 0.60
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (45 bp):
GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
Found at i:421887 original size:49 final size:48
Alignment explanation
Indices: 421802--422225 Score: 362
Period size: 49 Copynumber: 8.7 Consensus size: 48
421792 TACAGCTTTG
* * * *
421802 AGATTCACCTTTGCGGCTTCAATCTTTCCCATCATATCTCTAAGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCATATCTCCAAGGTACA
* * * * * * *
421851 AGGTTTGTCATTGCGGCTTCAACCTTTCCCTCCATATCTCCATGTTATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCT-CATATCTCCAAGGTACA
* * * * ** *
421900 AGATTCACCGTTGCAGCTTTAATCTTTCCCATCACGTCTCTAAGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCATATCTCCAAGGTACA
* * * *
421949 AGGTTCGCCATTGCGGCTTCAACCTTTCCCTCTATATCTCCATGATACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTC-ATATCTCCAAGGTACA
* * *
421998 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTTTATATCTCCATGATACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCATATCTCCAAGGTACA
* * * * * * * *
422047 AGATTCGCCGTTGCGGCTTCAATCTTTCTCATTATTTTTCTAAGGCATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTC-CCTCATATCTCCAAGGTACA
* * * *
422096 AGGTTCGCCGTTGCGACTTCAACCTTTCCCTCCATATCTCCACGGTACT
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCT-CATATCTCCAAGGTACA
* * * * * * *
422145 AGATTTGTCGTTACAGCTTCAATCTTTCCCATCACATCTCTAAGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCATATCTCCAAGGTACA
* *
422194 AGGTTCGCCATTGCGGCTTCAACCTTTCCCTC
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTC
422226 CAAACTTGTA
Statistics
Matches: 291, Mismatches: 77, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
48 7 0.02
49 280 0.96
50 4 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.35
Consensus pattern (48 bp):
AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCATATCTCCAAGGTACA
Found at i:421986 original size:147 final size:146
Alignment explanation
Indices: 421812--422223 Score: 439
Period size: 147 Copynumber: 2.8 Consensus size: 146
421802 AGATTCACCT
* * * *
421812 TTGCGGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTTGTCATTGCGGCTTCAACCTT
1 TTGCGGCTTCAACCTTTCCC-TCATATCTCCAAGGTACAAGATTTGTCGTTGCGGCTTCAACCTT
* * *
421877 TCCCTCCATATCTCCATGTTATAAGATTCACCGTTGCAGCTTTAATCTTTCCCATCACGTCTCTA
65 TCCCTCCATATCTCCATGATACAAGATTCACCGTTGCAGCTTCAATCTTTCCCATCACGTCTCTA
*
421942 AGGTACAAGGTTCGCCA
130 AGGCACAAGGTTCGCCA
* * * *
421959 TTGCGGCTTCAACCTTTCCCTCTATATCTCCATGATACAAGATTCGCCGTTGCGGCTTCAACCTT
1 TTGCGGCTTCAACCTTTCCCTC-ATATCTCCAAGGTACAAGATTTGTCGTTGCGGCTTCAACCTT
** * * * * ** *
422024 TCCCTTTATATCTCCATGATACAAGATTCGCCGTTGCGGCTTCAATCTTTCTCATTATTTTTCTA
65 TCCCTCCATATCTCCATGATACAAGATTCACCGTTGCAGCTTCAATCTTTCCCATCACGTCTCTA
* *
422089 AGGCATAAGGTTCGCCG
130 AGGCACAAGGTTCGCCA
* * * * * *
422106 TTGCGACTTCAACCTTTCCCTCCATATCTCCACGGTACTAGATTTGTCGTTACAGCTTCAATCTT
1 TTGCGGCTTCAACCTTTCCCT-CATATCTCCAAGGTACAAGATTTGTCGTTGCGGCTTCAACCTT
* * * * * * * * *
422171 TCCCAT-CACATCTCTAAGGTACAAGGTTCGCCATTGCGGCTTCAACCTTTCCC
65 TCCC-TCCATATCTCCATGATACAAGATTCACCGTTGCAGCTTCAATCTTTCCC
422224 TCCAAACTTG
Statistics
Matches: 221, Mismatches: 41, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
146 2 0.01
147 217 0.98
148 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.35
Consensus pattern (146 bp):
TTGCGGCTTCAACCTTTCCCTCATATCTCCAAGGTACAAGATTTGTCGTTGCGGCTTCAACCTTT
CCCTCCATATCTCCATGATACAAGATTCACCGTTGCAGCTTCAATCTTTCCCATCACGTCTCTAA
GGCACAAGGTTCGCCA
Found at i:425197 original size:81 final size:81
Alignment explanation
Indices: 425062--425225 Score: 292
Period size: 81 Copynumber: 2.0 Consensus size: 81
425052 CTTTTATTCC
* *
425062 TTATATCGTTAGACCACTAACCGTTATTTCAATGCAAAAATGCTTGAATAGGGTTGTAAGGTAGA
1 TTATATCGTTAGACCACTAACCGTTATTTCAATGCAAAAATGCTTCAACAGGGTTGTAAGGTAGA
425127 TGAAATTAAATTTTAT
66 TGAAATTAAATTTTAT
*
425143 TTATATCGTTAGACCACTAACCGTTATTTCAATGCAAAAATGCTTCAACAGGGTTGTAAGGTGGA
1 TTATATCGTTAGACCACTAACCGTTATTTCAATGCAAAAATGCTTCAACAGGGTTGTAAGGTAGA
*
425208 TGAAATTGAATTTTAT
66 TGAAATTAAATTTTAT
425224 TT
1 TT
425226 GAGGCAAAGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (81 bp):
TTATATCGTTAGACCACTAACCGTTATTTCAATGCAAAAATGCTTCAACAGGGTTGTAAGGTAGA
TGAAATTAAATTTTAT
Found at i:425361 original size:112 final size:112
Alignment explanation
Indices: 425156--425372 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 112
425146 TATCGTTAGA
* * ** *
425156 CCACTAACCGTTATTTCAATGCAAAAATGCTTCAACAGGGTTGTAAGGTGGATGAAATTGAATTT
1 CCACTAACCGTCATTTCAATGCAAAAATGCTTAAACAGGGTTGTAAGGTGGAAAAAATTGAATAT
* * *
425221 TATTTGAGGCAAAGCTCGGATGATTGAAAAGATTAAAAATCATTACT
66 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTACT
* * * *
425268 CCACTAACCGTCATTTTAATGCAAGAATGCTTAAATAGGGTTTTAAGGTGGAAAAAATTGAATAT
1 CCACTAACCGTCATTTCAATGCAAAAATGCTTAAACAGGGTTGTAAGGTGGAAAAAATTGAATAT
425333 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
66 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
425373 GGCAAACATT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 93 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (112 bp):
CCACTAACCGTCATTTCAATGCAAAAATGCTTAAACAGGGTTGTAAGGTGGAAAAAATTGAATAT
TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTACT
Found at i:425731 original size:7 final size:7
Alignment explanation
Indices: 425684--425732 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
425674 CAACCTCTCC
425684 TTTTTCTT
1 TTTTTC-T
425692 TTTCTTCT
1 TTT-TTCT
*
425700 CTTTTCT
1 TTTTTCT
425707 TTTTTCT
1 TTTTTCT
*
425714 TTTTTTT
1 TTTTTCT
425721 TTTTTCT
1 TTTTTCT
425728 TTTTT
1 TTTTT
425733 TCCCTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 27 0.75
8 6 0.17
9 3 0.08
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:425733 original size:23 final size:22
Alignment explanation
Indices: 425684--425732 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
425674 CAACCTCTCC
425684 TTTTTCTTTTTCTTCTCTTTTCT
1 TTTTTCTTTTT-TTCTCTTTTCT
*
425707 TTTTTCTTTTTTT-TTTTTTCT
1 TTTTTCTTTTTTTCTCTTTTCT
425728 TTTTT
1 TTTTT
425733 TCCCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTCTTTTCT
Found at i:431324 original size:31 final size:30
Alignment explanation
Indices: 431233--431426 Score: 162
Period size: 30 Copynumber: 6.4 Consensus size: 30
431223 AAAATTAATA
* *
431233 TTTTGGAAAGTTT-GGGGTTAAAATGTAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATGAAAT
* * * *
431262 TTTCAAAAAGTTTAGAGGTTAAAATGTAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATGAAAT
*
431292 TTTTAGAAAGTTTAAGGGGTCAAAATGAAAT
1 TTTTAGAAAGTTT-AGGGGTTAAAATGAAAT
* * *
431323 TTTTAGAAAGTTT-GAGGGTGAAAAAAGAAAC
1 TTTTAGAAAGTTTAG-GGGT-TAAAATGAAAT
* *
431354 TTTTAGAATGTTT-GAGGGCTAAAATGAAAT
1 TTTTAGAAAGTTTAG-GGGTTAAAATGAAAT
* * * *
431384 TTCTAGAAAATTTAAGGGTTAAATTTG-AAT
1 TTTTAGAAAGTTTAGGGGTTAAA-ATGAAAT
*
431414 TTTTGGAAAGTTT
1 TTTTAGAAAGTTT
431427 GGGAGCTGAA
Statistics
Matches: 133, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
29 11 0.08
30 68 0.51
31 54 0.41
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.37
Consensus pattern (30 bp):
TTTTAGAAAGTTTAGGGGTTAAAATGAAAT
Found at i:431324 original size:61 final size:60
Alignment explanation
Indices: 431222--431426 Score: 165
Period size: 61 Copynumber: 3.4 Consensus size: 60
431212 AAAAATGGGG
* *
431222 TAAAAT-TAATATTTTGGAAAGTTT-GGGGTTAAAATGTAATTTTCAAAAAGTTTAGA-GGT
1 TAAAATGTAAT-TTTTAGAAAGTTTAGGGG-TAAAATGAAATTTTCAAAAAGTTTAGAGGGT
* *
431281 TAAAATGTAATTTTTAGAAAGTTTAAGGGGTCAAAATGAAATTTTTAGAAAGTTT-GAGGGT
1 TAAAATGTAATTTTTAGAAAGTTT-AGGGGT-AAAATGAAATTTTCAAAAAGTTTAGAGGGT
* * * * * *
431342 GAAAAAAGAAACTTTTAGAATGTTTGAGGGCTAAAATGAAA-TTTCTAGAAAA-TTTA-AGGGT
1 -TAAAATGTAATTTTTAGAAAGTTT-AGGGGTAAAATGAAATTTTC-A-AAAAGTTTAGAGGGT
* *
431403 T-AAATTTGAATTTTTGGAAAGTTT
1 TAAAATGT-AATTTTTAGAAAGTTT
431427 GGGAGCTGAA
Statistics
Matches: 116, Mismatches: 20, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
59 21 0.18
60 23 0.20
61 45 0.39
62 27 0.23
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (60 bp):
TAAAATGTAATTTTTAGAAAGTTTAGGGGTAAAATGAAATTTTCAAAAAGTTTAGAGGGT
Found at i:433184 original size:42 final size:42
Alignment explanation
Indices: 433125--433352 Score: 174
Period size: 42 Copynumber: 5.4 Consensus size: 42
433115 CATATAACAA
* * * * * *
433125 CCGAGTCATAAGTCTTCCTTTAAACGTAATTTTATGTTCGTC
1 CCGAGTCATGAGTCTTCCTTAAAACATAATCTTATGCTCCTC
* *
433167 CCGAGTCATGAGTCTTCCTTAAAATATAATCTTATGCTCCTT
1 CCGAGTCATGAGTCTTCCTTAAAACATAATCTTATGCTCCTC
* * * * * *
433209 CTGAGTCACGAGTCTTCCTTAAAACATAATCTCATTCTCTTT
1 CCGAGTCATGAGTCTTCCTTAAAACATAATCTTATGCTCCTC
* ** * * *
433251 CTGAGTCACAAGTCTTCCTTTTAAACATAATCTCATGCTCATC
1 CCGAGTCATGAGTCTTCC-TTAAAACATAATCTTATGCTCCTC
* * * * *
433294 CCGAGAT-ATGAGTCTTCTTTTAATAC--ACTCTCATGCTCATC
1 CCGAG-TCATGAGTCTTC-CTTAAAACATAATCTTATGCTCCTC
*
433335 CCGAGACATGAGTCTTCC
1 CCGAGTCATGAGTCTTCC
433353 ATTTATACAT
Statistics
Matches: 154, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
41 29 0.19
42 87 0.56
43 37 0.24
44 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (42 bp):
CCGAGTCATGAGTCTTCCTTAAAACATAATCTTATGCTCCTC
Found at i:433361 original size:41 final size:41
Alignment explanation
Indices: 433281--433361 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
433271 TTAAACATAA
* *
433281 TCTCATGCTCATCCCGAGATATGAGTCTTCTTTTAATACAC
1 TCTCATGCTCATCCCGAGACATGAGTCTTCATTTAATACAC
433322 TCTCATGCTCATCCCGAGACATGAGTCTTCCATTT-ATACA
1 TCTCATGCTCATCCCGAGACATGAGTCTT-CATTTAATACA
433362 TCAAATGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (41 bp):
TCTCATGCTCATCCCGAGACATGAGTCTTCATTTAATACAC
Found at i:434496 original size:3 final size:3
Alignment explanation
Indices: 434488--434515 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
434478 TTATTGTTAC
434488 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
434516 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:435019 original size:51 final size:50
Alignment explanation
Indices: 434964--435178 Score: 152
Period size: 51 Copynumber: 4.2 Consensus size: 50
434954 GGAAAAGTTT
*
434964 TGATTTTTTTAACAATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAATAG
1 TGATTTTTTTAACAATTTCAAAATAAAAGTTTAGATTTTTAA-AAAAATAG
* ** * * *
435015 TGATTTTCATTAA-AA--AAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAA
1 TGATTTT-TTTAACAATTTCAAAATA-AAAGTTTAGATTTTTAAAAA-AATAG
* *** * * * * **
435065 T-ATGTTTTTAGTTATTTTAAAGAAAAAATTTTA-ATTTTTAAATAAAGTTT
1 TGATTTTTTTAACAATTTCAAA-ATAAAAGTTTAGATTTTTAAA-AAAATAG
* *
435115 TGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAAATAG
1 TGATTTTTTTAACAATTTCAAAATAAAAGTTTAGATTTTTAA-AAAAATAG
435166 TGATTTTCTTTAA
1 TGATTTT-TTTAA
435179 AAAAAAAAGA
Statistics
Matches: 124, Mismatches: 28, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
48 3 0.02
49 13 0.10
50 40 0.32
51 55 0.44
52 13 0.10
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (50 bp):
TGATTTTTTTAACAATTTCAAAATAAAAGTTTAGATTTTTAAAAAAATAG
Found at i:435242 original size:151 final size:148
Alignment explanation
Indices: 434957--435362 Score: 565
Period size: 151 Copynumber: 2.7 Consensus size: 148
434947 GATCTTGGGA
*
434957 AAAGTTTTGATTTTTTTAACAATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTT
* * * * *
435022 CATTAAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAG
66 C-TT-TAAAAAAAAAAGAAAGTTTA-AATTTTAAAAATAAAAATCTATTTTTAGTCATTTTAAAG
** *
435087 AAAAAATTTTAATTTTTAAAT
128 AAAAAATTCAAATTTTTAAAC
* *
435108 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTT
435173 CTTTAAAAAAAAAAGAAAGTTTAAATTTTAAAAAATAAAAATCTATTTTTCAGTCATTTTAAAGA
66 CTTTAAAAAAAAAAGAAAGTTTAAATTTT-AAAAATAAAAATCTATTTTT-AGTCATTTTAAAGA
435238 AAAAATTCAAATTTTTAAAC
129 AAAAATTCAAATTTTTAAAC
* *
435258 AAAGTTTTGA-TTTTTTAACAATTTTGAAATAAAAAAGTTTTGATTTTTTTTA-AAAAATAGTGA
1 AAAGTTTTGATTTTTTTAACAATTTCGAAAT--AAAAGTTTTGA--TTTTTAAGAAAAATAGTGA
435321 TTTTCTTT---AAAAAAA-AAAGTTTAAATTTT-AAAATAAAAATCT
62 TTTTCTTTAAAAAAAAAAGAAAGTTTAAATTTTAAAAATAAAAATCT
435363 GTTATAAAAA
Statistics
Matches: 234, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
146 13 0.06
148 19 0.08
149 62 0.26
150 42 0.18
151 73 0.31
152 19 0.08
153 6 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (148 bp):
AAAGTTTTGATTTTTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTT
CTTTAAAAAAAAAAGAAAGTTTAAATTTTAAAAATAAAAATCTATTTTTAGTCATTTTAAAGAAA
AAATTCAAATTTTTAAAC
Found at i:435282 original size:30 final size:30
Alignment explanation
Indices: 435247--435306 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
435237 AAAAAATTCA
435247 AATTTT-TAAACAAAGTTTTGATTTTTTAAC
1 AATTTTATAAA-AAAGTTTTGATTTTTTAAC
435277 AATTTTGAAATAAAAAAGTTTTGATTTTTT
1 AATTTT---ATAAAAAAGTTTTGATTTTTT
435307 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.23
33 16 0.62
34 4 0.15
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (30 bp):
AATTTTATAAAAAAGTTTTGATTTTTTAAC
Found at i:435284 original size:17 final size:19
Alignment explanation
Indices: 435248--435305 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
435238 AAAAATTCAA
435248 ATTTTTAAACAAAGTTTTG
1 ATTTTTAAACAAAGTTTTG
*
435267 ATTTTTTAAC-AA-TTTTG
1 ATTTTTAAACAAAGTTTTG
**
435284 A--AATAAA-AAAGTTTTG
1 ATTTTTAAACAAAGTTTTG
435300 ATTTTT
1 ATTTTT
435306 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 9
0.66 0.14 0.20
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 6 0.21
18 3 0.10
19 9 0.31
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTTTTAAACAAAGTTTTG
Found at i:435394 original size:40 final size:38
Alignment explanation
Indices: 435330--435405 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 38
435320 ATTTTCTTTA
*
435330 AAAAAAAAAGTTTAAATTTTAAAATAAAAATCTGTTAT
1 AAAAAAAAAGTTTAAATTTTAAAATAAAAATATGTTAT
* *
435368 AAAAAAAAAGTTTAGATTTTTAAAAATTAAAATATGTT
1 AAAAAAAAAGTTTA-AATTTT-AAAATAAAAATATGTT
435406 TTTTTAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 14 0.42
39 5 0.15
40 14 0.42
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.36
Consensus pattern (38 bp):
AAAAAAAAAGTTTAAATTTTAAAATAAAAATATGTTAT
Done.