Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015288.1 Kokia drynarioides strain JFW-HI SEQ_130333, 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: 637797
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 464 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:7231 original size:39 final size:40
Alignment explanation
Indices: 7187--7270 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 40
7177 TGGGACAAGT
*
7187 CTCTTCCAAGAGGT-AT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTGATCATCCAATATGAAAAGG-TTGTGA
* * *
7226 CTCTT-CAATAGGTGTTCATCCAATTTGAAAAGGTTGTGA
1 CTCTTCCAAGAGGTGATCATCCAATATGAAAAGGTTGTGA
7265 CTCTTC
1 CTCTTC
7271 ACAAAGTGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
38 7 0.18
39 17 0.45
40 14 0.37
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (40 bp):
CTCTTCCAAGAGGTGATCATCCAATATGAAAAGGTTGTGA
Found at i:11226 original size:18 final size:19
Alignment explanation
Indices: 11181--11226 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
11171 ATTTTTTTTT
* *
11181 TTTTCTGTTTTGTGGCACGC
1 TTTTC-GTTTTATGGCACGA
11201 TTTT-GTTTTATGGCAC-A
1 TTTTCGTTTTATGGCACGA
11218 TTTTCGTTT
1 TTTTCGTTT
11227 ATTTTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
20 4 0.17
ACGTcount: A:0.09, C:0.15, G:0.20, T:0.57
Consensus pattern (19 bp):
TTTTCGTTTTATGGCACGA
Found at i:27415 original size:24 final size:24
Alignment explanation
Indices: 27388--27434 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
27378 CCCACTCGAG
*
27388 CCTAGAATTATTAGCTCTTACGAA
1 CCTAGAATGATTAGCTCTTACGAA
* *
27412 CCTATAATGGTTAGCTCTTACGA
1 CCTAGAATGATTAGCTCTTACGA
27435 GCTCAGACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CCTAGAATGATTAGCTCTTACGAA
Found at i:39910 original size:19 final size:20
Alignment explanation
Indices: 39886--39924 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
39876 CACTTTCTTC
*
39886 CTTGTAATAATA-TTAGGTT
1 CTTGTAATAAGAGTTAGGTT
*
39905 CTTGTATTAAGAGTTAGGTT
1 CTTGTAATAAGAGTTAGGTT
39925 TTATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (20 bp):
CTTGTAATAAGAGTTAGGTT
Found at i:40600 original size:24 final size:25
Alignment explanation
Indices: 40562--40608 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
40552 CAAATTAAAT
*
40562 TTTATAAATAATTAATATTAATTGC
1 TTTATAAATAATTAATAATAATTGC
*
40587 TTTA-AAATATTTAATAATAATT
1 TTTATAAATAATTAATAATAATT
40609 TATATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTATAAATAATTAATAATAATTGC
Found at i:44911 original size:3 final size:3
Alignment explanation
Indices: 44905--44942 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44895 TATTTAAAAT
44905 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44943 TACGAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48441 original size:19 final size:19
Alignment explanation
Indices: 48417--48454 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48407 ATACAATCAA
48417 AATTCTGCATGAGGCACCT
1 AATTCTGCATGAGGCACCT
48436 AATTCTGCATGAGGCACCT
1 AATTCTGCATGAGGCACCT
48455 TTGCATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
AATTCTGCATGAGGCACCT
Found at i:51262 original size:13 final size:13
Alignment explanation
Indices: 51244--51269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51234 GGTAACTGAG
51244 CAAAACACAAATC
1 CAAAACACAAATC
51257 CAAAACACAAATC
1 CAAAACACAAATC
51270 AAGCCTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAACACAAATC
Found at i:51953 original size:3 final size:3
Alignment explanation
Indices: 51945--51980 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
51935 TGTTTTCTGG
51945 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51981 TGTTTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53331 original size:8 final size:8
Alignment explanation
Indices: 53315--53365 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
53305 AACAATATTT
53315 TTATAAAA
1 TTATAAAA
*
53323 TTTTAAAA
1 TTATAAAA
*
53331 -TATATAA
1 TTATAAAA
53338 TTATAAAA
1 TTATAAAA
*
53346 TTCTAAAAA
1 TTAT-AAAA
53355 TTAATAAAA
1 TT-ATAAAA
53364 TT
1 TT
53366 TCAAGTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
7 5 0.15
8 16 0.47
9 12 0.35
10 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:60206 original size:1 final size:1
Alignment explanation
Indices: 60200--60227 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
60190 NNNNNNNNNN
60200 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
60228 CCAGTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:63409 original size:13 final size:13
Alignment explanation
Indices: 63391--63425 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
63381 TAAAGAAATT
63391 GGCATTGCTCTTA
1 GGCATTGCTCTTA
63404 GGCATTGCTCTTA
1 GGCATTGCTCTTA
*
63417 TGCATTGCT
1 GGCATTGCT
63426 TCTGGCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (13 bp):
GGCATTGCTCTTA
Found at i:63953 original size:33 final size:31
Alignment explanation
Indices: 63895--63962 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 31
63885 CTTCTTATAA
*
63895 ATAATATGATTTTTGATAAAGATATAAATTT
1 ATAATATGATTTTTGATAAAAATATAAATTT
** *
63926 ATAATATGATGTTTTTTTAATAAATATATATTT
1 ATAATATGAT-TTTTGATAA-AAATATAAATTT
63959 ATAA
1 ATAA
63963 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 10 0.32
32 7 0.23
33 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (31 bp):
ATAATATGATTTTTGATAAAAATATAAATTT
Found at i:67239 original size:63 final size:63
Alignment explanation
Indices: 67131--67328 Score: 225
Period size: 63 Copynumber: 3.1 Consensus size: 63
67121 GACACACGAG
* * *
67131 CGTGTGTCATACAAATAAGAAATAGTGAGCTACACGGTCTGGGGCCACAAGCGTGTGTCTAGAT
1 CGTGTGTCATAC-AATAAGAAACAGTGAGTTACACGGTCTAGGGCCACAAGCGTGTGTCTAGAT
* * *** * *
67195 CGTGTGTCATACAATAAGAAACAATGAGTTACACGATCTAGGGCCATGTGCTTGTGTCTAGAC
1 CGTGTGTCATACAATAAGAAACAGTGAGTTACACGGTCTAGGGCCACAAGCGTGTGTCTAGAT
* * * * * *
67258 CGTGTGTCATATAAGTAAGAAACAGTGAGTCACACGGCCTAGGGACACAGGCGTGTGTGTTAGAT
1 CGTGTGTCATACAA-TAAGAAACAGTGAGTTACACGGTCTAGGGCCACAAGCGTGTGT-CTAGAT
67323 CGTGTG
1 CGTGTG
67329 AAGGTTTGAC
Statistics
Matches: 110, Mismatches: 22, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
63 54 0.49
64 46 0.42
65 10 0.09
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (63 bp):
CGTGTGTCATACAATAAGAAACAGTGAGTTACACGGTCTAGGGCCACAAGCGTGTGTCTAGAT
Found at i:67612 original size:39 final size:39
Alignment explanation
Indices: 67558--67736 Score: 144
Period size: 39 Copynumber: 4.6 Consensus size: 39
67548 ATTTCAACAC
*
67558 TGAACTGGCGGTGACACTGTAAACACCGTAATACTGTAT
1 TGAACTGGCAGTGACACTGTAAACACCGTAATACTGTAT
* * * *** * * *
67597 TGAACTGGTAATGACACTATAAACACTACAATGCAT-CAC
1 TGAACTGGCAGTGACACTGTAAACACCGTAATAC-TGTAT
* * * *
67636 TGAACTGACGGTGATACTGTAAACACCGTAATACAGTAT
1 TGAACTGGCAGTGACACTGTAAACACCGTAATACTGTAT
* * ** *
67675 TGAACTGGCAGTGACACTGCAAACACTGCGATACTATAT
1 TGAACTGGCAGTGACACTGTAAACACCGTAATACTGTAT
** *
67714 TGATTTGGCGGTGACACTGTAAA
1 TGAACTGGCAGTGACACTGTAAA
67737 TATCGTACGA
Statistics
Matches: 102, Mismatches: 36, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
39 101 0.99
40 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (39 bp):
TGAACTGGCAGTGACACTGTAAACACCGTAATACTGTAT
Found at i:67726 original size:78 final size:78
Alignment explanation
Indices: 67555--67736 Score: 231
Period size: 78 Copynumber: 2.3 Consensus size: 78
67545 TGGATTTCAA
* * *
67555 CACTGAACTGGCGGTGACACTGTAAACACCGTAATACTGTATTGAACTGGTAATGACACTATAAA
1 CACTGAACTGGCGGTGACACTGTAAACACCGTAATACAGTATTGAACTGGCAATGACACTACAAA
*
67620 CACTACAATGCAT
66 CACTACAATACAT
* * * *
67633 CACTGAACTGACGGTGATACTGTAAACACCGTAATACAGTATTGAACTGGCAGTGACACTGCAAA
1 CACTGAACTGGCGGTGACACTGTAAACACCGTAATACAGTATTGAACTGGCAATGACACTACAAA
* *
67698 CACTGCGATACTAT
66 CACTACAATAC-AT
* **
67712 -ATTGATTTGGCGGTGACACTGTAAA
1 CACTGAACTGGCGGTGACACTGTAAA
67737 TATCGTACGA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 86 0.98
79 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (78 bp):
CACTGAACTGGCGGTGACACTGTAAACACCGTAATACAGTATTGAACTGGCAATGACACTACAAA
CACTACAATACAT
Found at i:67767 original size:39 final size:39
Alignment explanation
Indices: 67724--67816 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
67714 TGATTTGGCG
* ** *
67724 GTGACACTGTAAATATCGTACGACTACAACTTAGTAGTA
1 GTGACACTGTAAACATCACACGACTACAACTCAGTAGTA
* * *
67763 GTGACACTATAAGCATCACACGACTATAACTCAGTAGTA
1 GTGACACTGTAAACATCACACGACTACAACTCAGTAGTA
* *
67802 GTAACATTGTAAACA
1 GTGACACTGTAAACA
67817 CTACTAGAGC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (39 bp):
GTGACACTGTAAACATCACACGACTACAACTCAGTAGTA
Found at i:82312 original size:16 final size:16
Alignment explanation
Indices: 82291--82328 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
82281 AATTTATTTA
82291 GATTGAGTCTTAATTC
1 GATTGAGTCTTAATTC
82307 GATTGAGTCTTAATTC
1 GATTGAGTCTTAATTC
82323 GATTGA
1 GATTGA
82329 TATGGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (16 bp):
GATTGAGTCTTAATTC
Found at i:84295 original size:2 final size:2
Alignment explanation
Indices: 84288--84317 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84278 GTGTCTCAAG
84288 AT 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 AT
84318 GTCAGATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87261 original size:3 final size:3
Alignment explanation
Indices: 87253--87279 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
87243 TGTGACATTT
87253 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
87280 ACAACAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:87321 original size:12 final size:12
Alignment explanation
Indices: 87304--87330 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
87294 ATGTTGAGCG
87304 TTGTGTATGTTT
1 TTGTGTATGTTT
87316 TTGTGTATGTTT
1 TTGTGTATGTTT
87328 TTG
1 TTG
87331 GTGCACGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (12 bp):
TTGTGTATGTTT
Found at i:88613 original size:20 final size:20
Alignment explanation
Indices: 88590--88643 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 20
88580 TTAGGAATAT
88590 AAAACTAAATTGTATAAATG
1 AAAACTAAATTGTATAAATG
**
88610 AAAA--AAA-AAT-TAAATG
1 AAAACTAAATTGTATAAATG
88626 AAAACTAAATTGTATAAA
1 AAAACTAAATTGTATAAA
88644 AAAAATGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 6 0.23
19 1 0.04
20 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (20 bp):
AAAACTAAATTGTATAAATG
Found at i:97589 original size:19 final size:19
Alignment explanation
Indices: 97565--97602 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
97555 AAATATTTTA
97565 TGTCATATCGAT-TCGATTC
1 TGTCATATC-ATATCGATTC
*
97584 TGTCATTTCATATCGATTC
1 TGTCATATCATATCGATTC
97603 GATTTTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (19 bp):
TGTCATATCATATCGATTC
Found at i:97599 original size:24 final size:24
Alignment explanation
Indices: 97567--97612 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
97557 ATATTTTATG
97567 TCATATCGATTCGATTCTGTCATT
1 TCATATCGATTCGATTCTGTCATT
*
97591 TCATATCGATTCGATTTTGTCA
1 TCATATCGATTCGATTCTGTCA
97613 ATATTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (24 bp):
TCATATCGATTCGATTCTGTCATT
Found at i:100935 original size:17 final size:17
Alignment explanation
Indices: 100890--100943 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 17
100880 GAAATTTTGT
100890 ATTAAGAATTTGAGATAAA
1 ATTAA-AATTTG-GATAAA
100909 ATTATAAAATTTGGATAAA
1 A-T-TAAAATTTGGATAAA
*
100928 ATTAAAATTTGAATAA
1 ATTAAAATTTGGATAA
100944 TTTGATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.41
18 1 0.03
19 8 0.25
20 7 0.22
21 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
ATTAAAATTTGGATAAA
Found at i:104249 original size:31 final size:31
Alignment explanation
Indices: 104203--104295 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
104193 GTATTAATTT
*
104203 AAAA-AAATTCAAGTATTAAAATAAATATTA
1 AAAATAAACTCAAGTATTAAAATAAATATTA
* * *
104233 AAACTAAACTCAAGTATCAAATTAAATATTA
1 AAAATAAACTCAAGTATTAAAATAAATATTA
* *
104264 AAAATAAACTCATGTACT-AAATAATATATTA
1 AAAATAAACTCAAGTATTAAAATAA-ATATTA
104295 A
1 A
104296 CCTTTTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 8 0.15
31 44 0.85
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (31 bp):
AAAATAAACTCAAGTATTAAAATAAATATTA
Found at i:119820 original size:22 final size:21
Alignment explanation
Indices: 119786--119828 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
119776 TCGAAATCTA
*
119786 AAATAATTTAAATAATTAAAT
1 AAATAATTAAAATAATTAAAT
*
119807 AAATAATTCAAAATGATTAAAT
1 AAATAATT-AAAATAATTAAAT
119829 TCAAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATAATTAAAATAATTAAAT
Found at i:123387 original size:19 final size:18
Alignment explanation
Indices: 123347--123392 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
123337 ACTTAACAAT
*
123347 AAAAAAAAAACAACAACCA
1 AAAAAAAAAACAA-AAACA
* *
123366 AAAAGAAAAACAAAAATA
1 AAAAAAAAAACAAAAACA
123384 AAAAAAAAA
1 AAAAAAAAA
123393 CTTAACTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAACAAAAACA
Found at i:131055 original size:19 final size:20
Alignment explanation
Indices: 131018--131063 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
131008 TAATAATATT
131018 ATAATTTATTATATAAAATA
1 ATAATTTATTATATAAAATA
131038 ATAATTT-TTA-ATTAAAATA
1 ATAATTTATTATA-TAAAATA
131057 AT-ATTTA
1 ATAATTTA
131064 ATTAACTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATTTATTATATAAAATA
Found at i:131058 original size:16 final size:16
Alignment explanation
Indices: 131037--131068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
131027 TATATAAAAT
*
131037 AATAATTTTTAATTAA
1 AATAATATTTAATTAA
131053 AATAATATTTAATTAA
1 AATAATATTTAATTAA
131069 CTTGTAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAATATTTAATTAA
Found at i:132640 original size:30 final size:30
Alignment explanation
Indices: 132577--132648 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
132567 ATTTCCAATT
*
132577 AATAATAATAAAATTATATTTTAACTTCTAA
1 AATAATAA-AAAATTATATTTGAACTTCTAA
* *
132608 AATAATAAAAAATTAT-TTTGATCTTTTAAA
1 AATAATAAAAAATTATATTTGAACTTCT-AA
*
132638 AATTATAAAAA
1 AATAATAAAAA
132649 TATAAACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 8 0.22
30 20 0.56
31 8 0.22
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (30 bp):
AATAATAAAAAATTATATTTGAACTTCTAA
Found at i:135302 original size:17 final size:18
Alignment explanation
Indices: 135280--135317 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
135270 GATTTCAAAA
135280 TTAAATTCTTA-TTTTAT
1 TTAAATTCTTATTTTTAT
*
135297 TTAAATTTTTATTTTTAT
1 TTAAATTCTTATTTTTAT
135315 TTA
1 TTA
135318 TTTATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAAATTCTTATTTTTAT
Found at i:141603 original size:69 final size:69
Alignment explanation
Indices: 141524--141664 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
141514 TTTGATACTT
*
141524 GAATTTTTTAATTTAATTCCAATATTCATTTTGGTACTCAAATCAAACATTATAAGTACTTAATA
1 GAATTTTTTAATTTAATTCCAATATTCATTTTGGTACTCAAATCAAACATTATAAGTACTCAATA
141589 GAAA
66 GAAA
141593 GAATTTTTTAATTTAATTCCAATATTCATTTTGGTACTCAAATCAAACATTATAAGTACTCAATA
1 GAATTTTTTAATTTAATTCCAATATTCATTTTGGTACTCAAATCAAACATTATAAGTACTCAATA
141658 GAAA
66 GAAA
141662 GAA
1 GAA
141665 AAAAACCTTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (69 bp):
GAATTTTTTAATTTAATTCCAATATTCATTTTGGTACTCAAATCAAACATTATAAGTACTCAATA
GAAA
Found at i:145959 original size:18 final size:19
Alignment explanation
Indices: 145924--145961 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
145914 AATATATGCA
*
145924 ATTTAATTTAGCATAATTT
1 ATTTAATTTAGCACAATTT
*
145943 ATTTATTTTAG-ACAATTT
1 ATTTAATTTAGCACAATTT
145961 A
1 A
145962 ATTCATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTAATTTAGCACAATTT
Found at i:150462 original size:135 final size:135
Alignment explanation
Indices: 149742--150441 Score: 1134
Period size: 135 Copynumber: 5.2 Consensus size: 135
149732 ACCGTGCCTC
149742 CTGAAACCGGTCT-CCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTG
1 CTGAAACCGGT-TGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTG
*
149806 AGAACTATCACTACTAGATGATTCCAAAGGTTTATACTTTTTCAGCTCGCTATTAGTCGTATTAC
65 AGAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTAC
*
149871 TAGAAA
130 TAGAAG
149877 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* *
149942 GAATTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGCCGTATTACT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
150007 AGAAG
131 AGAAG
150012 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
*
150077 GAACTATCACTACTAGATGATTCGAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
150142 AGAAG
131 AGAAG
* *
150147 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGTTTGACAAGAATTCCGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* * * * * * * *
150212 TAAGTATCACTGCTGGATGATTGCAAAGGTTCT-TCCTTTTTCAGCTCTCTATTAGTTGTATTAG
66 GAACTATCACTACTAGATGATTCCAAAGGTT-TATCCTTTTTCAGCTCGCTATTAGTCGTATTAC
150276 TAGAAG
130 TAGAAG
* *
150282 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGTTTGACAAGAATTCCGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* * * * * * *
150347 TAACTATCACTGCTGGATGATTCTAAAGGTTCATCCTTTTTCAGCTCGCTATTAGTTGTATTAGT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
150412 AGAAG
131 AGAAG
* *
150417 CTGAAACCGGTCGCCATATTTGCTT
1 CTGAAACCGGTTGCCATTTTTGCTT
150442 AGGGGCTGTA
Statistics
Matches: 537, Mismatches: 25, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
134 1 0.00
135 535 1.00
136 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (135 bp):
CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
AGAAG
Found at i:151494 original size:11 final size:11
Alignment explanation
Indices: 151478--151502 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
151468 TTAATAATTG
151478 AAAAGGAAAAA
1 AAAAGGAAAAA
151489 AAAAGGAAAAA
1 AAAAGGAAAAA
151500 AAA
1 AAA
151503 GGATTTTGGC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGGAAAAA
Found at i:151738 original size:25 final size:24
Alignment explanation
Indices: 151693--151739 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
151683 ATTTTTCCTC
* *
151693 TTTTTATTTATTTATTTAGTTTAT
1 TTTTTATTTATTTACTCAGTTTAT
*
151717 TTTTTATATTATTTCCTCAGTTT
1 TTTTTAT-TTATTTACTCAGTTT
151740 CGAGAAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTATTTATTTACTCAGTTTAT
Found at i:164251 original size:20 final size:20
Alignment explanation
Indices: 164223--164260 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
164213 TAATCAACTA
164223 CGATATTCA-AGTTATGTTAC
1 CGATATTCATAGTT-TGTTAC
*
164243 CGATTTTCATAGTTTGTT
1 CGATATTCATAGTTTGTT
164261 CATTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (20 bp):
CGATATTCATAGTTTGTTAC
Found at i:171831 original size:32 final size:30
Alignment explanation
Indices: 171795--171875 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
171785 TTTTAAATCC
* *
171795 TCAAAGTTGAGCGATGAAATTTAATTAAAAAA
1 TCAAAATTG-GCGATAAAATTTAA-TAAAAAA
* *
171827 TCAAAATTGGTGATAAAATTTAAT-AAAAT
1 TCAAAATTGGCGATAAAATTTAATAAAAAA
**
171856 TCAAAATTGATGATAAAATT
1 TCAAAATTGGCGATAAAATT
171876 CAGTGGCATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 23 0.52
30 1 0.02
31 12 0.27
32 8 0.18
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (30 bp):
TCAAAATTGGCGATAAAATTTAATAAAAAA
Found at i:171860 original size:29 final size:31
Alignment explanation
Indices: 171811--171875 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
171801 TTGAGCGATG
*
171811 AAATTTAATTAAAAAATCAAAATTGGTGATA
1 AAATTTAATTAAAAAATCAAAATTGATGATA
*
171842 AAATTTAA-T-AAAATTCAAAATTGATGATA
1 AAATTTAATTAAAAAATCAAAATTGATGATA
171871 AAATT
1 AAATT
171876 CAGTGGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 23 0.72
30 1 0.03
31 8 0.25
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (31 bp):
AAATTTAATTAAAAAATCAAAATTGATGATA
Found at i:184906 original size:25 final size:25
Alignment explanation
Indices: 184872--184921 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
184862 CAAGTTGTTG
184872 AGCATATTCCTTTGAAACATTCTTT
1 AGCATATTCCTTTGAAACATTCTTT
184897 AGCATATTCCTTTGAAACATTCTTT
1 AGCATATTCCTTTGAAACATTCTTT
184922 TTTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (25 bp):
AGCATATTCCTTTGAAACATTCTTT
Found at i:185077 original size:37 final size:37
Alignment explanation
Indices: 185036--185106 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
185026 AATAATGAAA
*
185036 AAATTACA-TTTTAATCCCTCAAAAATGATAAAAAATT
1 AAATTA-ATTTTTAACCCCTCAAAAATGATAAAAAATT
* * *
185073 AAATTAATTTTTAACCCCTTAAAAGTTATAAAAA
1 AAATTAATTTTTAACCCCTCAAAAATGATAAAAA
185107 TATAAACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 28 0.97
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.34
Consensus pattern (37 bp):
AAATTAATTTTTAACCCCTCAAAAATGATAAAAAATT
Found at i:188152 original size:40 final size:41
Alignment explanation
Indices: 188097--188175 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
188087 ACATGGACTA
*
188097 ATTTGTTTATTTTTAAAAT-AAAAAGGGTAAAATATAATGT
1 ATTTGTTTATTTTTAAAATAAAAAAAGGTAAAATATAATGT
*
188137 ATTTGTTTATTTTTAAACTAAAAAAAGGTAAAATATAAT
1 ATTTGTTTATTTTTAAAATAAAAAAAGGTAAAATATAAT
188176 TTGACTCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 18 0.50
41 18 0.50
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.42
Consensus pattern (41 bp):
ATTTGTTTATTTTTAAAATAAAAAAAGGTAAAATATAATGT
Found at i:193608 original size:24 final size:23
Alignment explanation
Indices: 193563--193608 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
193553 TAGAAAATTA
*
193563 TTTAAATTTTAAAGATATTTTTC
1 TTTAAATTTTAAAGATAATTTTC
193586 TTTAATATTTT-AAGTATAATTTT
1 TTTAA-ATTTTAAAG-ATAATTTT
193609 ATTAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTAAATTTTAAAGATAATTTTC
Found at i:193675 original size:14 final size:13
Alignment explanation
Indices: 193631--193679 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
193621 CAAAACACTC
*
193631 TTATTTATATAAA
1 TTATTTAAATAAA
*
193644 TTATTTAAA-AGA
1 TTATTTAAATAAA
193656 -TATTTAAATTAAA
1 TTATTTAAA-TAAA
193669 TTATTTAAATA
1 TTATTTAAATA
193680 TTTTATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 12 0.40
14 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TTATTTAAATAAA
Found at i:196163 original size:18 final size:19
Alignment explanation
Indices: 196140--196176 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
196130 TAATTTTTTC
196140 GATAAATTAT-AATAATAA
1 GATAAATTATAAATAATAA
*
196158 GATAAATTTTAAATAATAA
1 GATAAATTATAAATAATAA
196177 AAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
GATAAATTATAAATAATAA
Found at i:201126 original size:12 final size:12
Alignment explanation
Indices: 201109--201134 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
201099 TTTTAGTTAA
201109 AAAATCAAATAG
1 AAAATCAAATAG
201121 AAAATCAAATAG
1 AAAATCAAATAG
201133 AA
1 AA
201135 CTTGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATCAAATAG
Found at i:214563 original size:39 final size:39
Alignment explanation
Indices: 214520--214594 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
214510 CAAAGTCGAT
214520 TCAACAAGCAAAATAAAACGATCACAGTTGACGTCCAAC
1 TCAACAAGCAAAATAAAACGATCACAGTTGACGTCCAAC
214559 TCAACAAGCAAAATAAAACGATCACAGTTGACGTCC
1 TCAACAAGCAAAATAAAACGATCACAGTTGACGTCC
214595 GACCTCATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.16
Consensus pattern (39 bp):
TCAACAAGCAAAATAAAACGATCACAGTTGACGTCCAAC
Found at i:214978 original size:18 final size:18
Alignment explanation
Indices: 214952--214990 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
214942 TTTCGAGTCT
*
214952 TTTCGATCTTTAGCATCC
1 TTTCCATCTTTAGCATCC
*
214970 TTTCCATCTTTAGCGTCC
1 TTTCCATCTTTAGCATCC
214988 TTT
1 TTT
214991 GCTGGAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.28, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTCCATCTTTAGCATCC
Found at i:227813 original size:17 final size:18
Alignment explanation
Indices: 227788--227822 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
227778 TATAAATTCG
227788 TCATAATATTGAATTTTA
1 TCATAATATTGAATTTTA
*
227806 TCAT-ATATTTAATTTTA
1 TCATAATATTGAATTTTA
227823 ATTGATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
TCATAATATTGAATTTTA
Found at i:228479 original size:2 final size:2
Alignment explanation
Indices: 228474--228500 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
228464 AAAAATAATT
228474 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
228501 TAAATCTTAA
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:232416 original size:49 final size:49
Alignment explanation
Indices: 232344--232445 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
232334 TAGGAAAAAA
232344 TTGTTACTTTCAGGACTAAATATGAACCCTCTTTATCCAAGAACCCTAT
1 TTGTTACTTTCAGGACTAAATATGAACCCTCTTTATCCAAGAACCCTAT
*
232393 TTGTTACTTTCAGGACTAAATATGAACCCTCTTTATCCGAGAACCCTAT
1 TTGTTACTTTCAGGACTAAATATGAACCCTCTTTATCCAAGAACCCTAT
232442 TTGT
1 TTGT
232446 GTTTATACCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (49 bp):
TTGTTACTTTCAGGACTAAATATGAACCCTCTTTATCCAAGAACCCTAT
Found at i:232852 original size:29 final size:30
Alignment explanation
Indices: 232797--232862 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
232787 GTTTAACGTA
*
232797 TAATTATATACATGAATTTCAATTTTG-TG
1 TAATTTTATACATGAATTTCAATTTTGATG
* *
232826 TAATTTTATACATGAAATTTTAA-TTTGATT
1 TAATTTTATACATG-AATTTCAATTTTGATG
232856 TAATTTT
1 TAATTTT
232863 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.53
Consensus pattern (30 bp):
TAATTTTATACATGAATTTCAATTTTGATG
Found at i:233907 original size:20 final size:19
Alignment explanation
Indices: 233882--233934 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
233872 TTCAAATTAA
233882 TTAATTGAATTATTTTAAAT
1 TTAATT-AATTATTTTAAAT
* *
233902 TTAATTATTTAATTTTATAT
1 TTAATTAATT-ATTTTAAAT
233922 TTAGATTTAATTA
1 TTA-A-TTAATTA
233935 ATTAATTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.11
20 17 0.63
21 2 0.07
22 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTAATTAATTATTTTAAAT
Found at i:233931 original size:26 final size:25
Alignment explanation
Indices: 233876--233941 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
233866 TATTTATTCA
233876 AATTAATTAATTGAATTATTTTAAATTT
1 AATTAATTAATT---TTATTTTAAATTT
* *
233904 AATTATTTAATTTTATATTTAGATTT
1 AATTAATTAATTTTAT-TTTAAATTT
233930 AATTAATTAATT
1 AATTAATTAATT
233942 GAGTTGAGTT
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
28 11 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
AATTAATTAATTTTATTTTAAATTT
Found at i:234829 original size:3 final size:3
Alignment explanation
Indices: 234801--234857 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
234791 TCATTTATTC
* * *
234801 TCT TCT CCT TCT TGT TCT TGT TCT TCT TCT TCT TCT T-T TCT TCAT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
*
234846 TTT TCT T-T TCT T
1 TCT TCT TCT TCT T
234858 AAACCCTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.04, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:242673 original size:25 final size:25
Alignment explanation
Indices: 242645--242696 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
242635 TATTGAAAAT
242645 AATTTTATTT-TGAAAAATTAATTTG
1 AATTTT-TTTGTGAAAAATTAATTTG
*
242670 AATTTTTTTGTGACAAATTAATTTG
1 AATTTTTTTGTGAAAAATTAATTTG
242695 AA
1 AA
242697 AATTCTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (25 bp):
AATTTTTTTGTGAAAAATTAATTTG
Found at i:244314 original size:28 final size:28
Alignment explanation
Indices: 244273--244340 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
244263 ATCTTGAATT
* **
244273 TTAAATCTTGAATCTTAAA-CTTCAAACA
1 TTAAATCTTAAATCCCAAATCTT-AAACA
*
244301 TTAAATTTTAAATCCCAAATCTTAAACA
1 TTAAATCTTAAATCCCAAATCTTAAACA
*
244329 CTAAATCTTAAA
1 TTAAATCTTAAA
244341 CTTTAAATCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (28 bp):
TTAAATCTTAAATCCCAAATCTTAAACA
Found at i:245120 original size:21 final size:22
Alignment explanation
Indices: 245095--245140 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
245085 AATTTAATTT
245095 TTTAATTT-T-TATTTTCAAGAA
1 TTTAATTTATATATTTTCAA-AA
*
245116 TTTAATTTATATATTTTTAAAA
1 TTTAATTTATATATTTTCAAAA
245138 TTT
1 TTT
245141 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTAATTTATATATTTTCAAAA
Found at i:245142 original size:23 final size:22
Alignment explanation
Indices: 245094--245143 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
245084 AAATTTAATT
245094 TTTTAATTTTTATTTTCAAGAA
1 TTTTAATTTTTATTTTCAAGAA
*
245116 -TTTAATTTATATATTTTTAA-AA
1 TTTTAATTT-T-TATTTTCAAGAA
245138 TTTTAA
1 TTTTAA
245144 AATTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATTTTTATTTTCAAGAA
Found at i:253818 original size:8 final size:9
Alignment explanation
Indices: 253780--253876 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 9
253770 CATGTGATAG
253780 AAAAATTAT
1 AAAAATTAT
253789 AAAAA--AT
1 AAAAATTAT
* *
253796 GAAAATCAAT
1 AAAAAT-TAT
253806 AAAAATTAT
1 AAAAATTAT
253815 AAAAATTATT
1 AAAAATTA-T
**
253825 AAATTTTAAT
1 AAAAATT-AT
253835 AAAAA-TATT
1 AAAAATTA-T
*
253844 AAAAATTAG
1 AAAAATTAT
*
253853 AAAAA-AAT
1 AAAAATTAT
253861 ATAAAATGTAT
1 A-AAAAT-TAT
253872 AAAAA
1 AAAAA
253877 AACCTTTAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
7 6 0.09
8 3 0.04
9 31 0.46
10 23 0.34
11 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:253827 original size:19 final size:19
Alignment explanation
Indices: 253780--253857 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
253770 CATGTGATAG
253780 AAAAATTA-TAAAAA--AT
1 AAAAATTATTAAAAATTAT
* * *
253796 GAAAATCAATAAAAATTAT
1 AAAAATTATTAAAAATTAT
**
253815 AAAAATTATTAAATTTTAAT
1 AAAAATTATTAAAAATT-AT
*
253835 AAAAA-TATTAAAAATTAG
1 AAAAATTATTAAAAATTAT
253853 AAAAA
1 AAAAA
253858 AATATAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 6 0.12
19 23 0.48
20 7 0.15
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:253878 original size:19 final size:20
Alignment explanation
Indices: 253805--253866 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
253795 TGAAAATCAA
* *
253805 TAAAAATTA-TAAAAATTAT
1 TAAAAATTAGAAAAAAATAT
** *
253824 TAAATTTTA-ATAAAAATAT
1 TAAAAATTAGAAAAAAATAT
253843 TAAAAATTAGAAAAAAATA-
1 TAAAAATTAGAAAAAAATAT
253862 TAAAA
1 TAAAA
253867 TGTATAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATTAGAAAAAAATAT
Found at i:254158 original size:26 final size:25
Alignment explanation
Indices: 254129--254185 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
254119 TTTAATTTCG
*
254129 TTTAACATAATATTTGAATTCTTTTT
1 TTTAACATAATATTTAAATT-TTTTT
** *
254155 TTTAAGTTGATATTTAAATTTTTTT
1 TTTAACATAATATTTAAATTTTTTT
254180 TATTAA
1 T-TTAA
254186 AATTAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTAACATAATATTTAAATTTTTTT
Found at i:258887 original size:2 final size:2
Alignment explanation
Indices: 258880--258915 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
258870 TGTGATTATC
258880 AT AT AT AT 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 AT AT AT AT
258916 CCAATCCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:260968 original size:69 final size:69
Alignment explanation
Indices: 260857--260995 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
260847 ATGTCCTTTG
*
260857 TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGATTGATTTAGCATGCTTCTCGACATCTTCT
1 TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGAATGATTTAGCATGCTTCTCGACATCTTCT
260922 TCAA
66 TCAA
260926 TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGAATGATTTAGCATGCTTCTCGACATCTTCT
1 TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGAATGATTTAGCATGCTTCTCGACATCTTCT
260991 TCAA
66 TCAA
260995 T
1 T
260996 TTGTTGGAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.43
Consensus pattern (69 bp):
TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGAATGATTTAGCATGCTTCTCGACATCTTCT
TCAA
Found at i:262039 original size:12 final size:12
Alignment explanation
Indices: 262024--262053 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
262014 ATGTTGATAG
262024 TGGTGATGACAA
1 TGGTGATGACAA
*
262036 TGGTGATGGCAA
1 TGGTGATGACAA
262048 TGGTGA
1 TGGTGA
262054 CGATGACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.40, T:0.27
Consensus pattern (12 bp):
TGGTGATGACAA
Found at i:264241 original size:111 final size:111
Alignment explanation
Indices: 264047--264275 Score: 440
Period size: 111 Copynumber: 2.1 Consensus size: 111
264037 TATATAAAGC
264047 CGAATTTTGATCTTTATACTATATTCATGTCAACATTTAATTTGAATATCTAGTCGTGTTAATCA
1 CGAATTTTGATCTTTATACTATATTCATGTCAACATTTAATTTGAATATCTAGTCGTGTTAATCA
264112 TTTTGATTAACTAATTATATTATAAAAGTAAATGAATCAAATAATT
66 TTTTGATTAACTAATTATATTATAAAAGTAAATGAATCAAATAATT
264158 CGAATTTTGATCTTTATACTATATTCATGTCAACATTTAATTTGAATATCTAGTCGTGTTAATCA
1 CGAATTTTGATCTTTATACTATATTCATGTCAACATTTAATTTGAATATCTAGTCGTGTTAATCA
*
264223 TTTTGATTAACTAATTATATTATAAAAGTAACTGAATCAAATAATT
66 TTTTGATTAACTAATTATATTATAAAAGTAAATGAATCAAATAATT
*
264269 CAAATTT
1 CGAATTT
264276 AGTTATAAGT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 116 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (111 bp):
CGAATTTTGATCTTTATACTATATTCATGTCAACATTTAATTTGAATATCTAGTCGTGTTAATCA
TTTTGATTAACTAATTATATTATAAAAGTAAATGAATCAAATAATT
Found at i:266669 original size:20 final size:21
Alignment explanation
Indices: 266620--266670 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
266610 TTTTGAATTT
* *
266620 TTTATTTATATTTTTAAAATG
1 TTTATTTTTATTTTTAAAAAG
266641 TTT-TGTTTTA-TTTTAAAAAG
1 TTTAT-TTTTATTTTTAAAAAG
266661 TTTATTTTTA
1 TTTATTTTTA
266671 AAGGGACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTATTTTTATTTTTAAAAAG
Found at i:266716 original size:22 final size:21
Alignment explanation
Indices: 266685--266727 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
266675 GACTAAATTC
*
266685 TTTAAATTAAAAATATAAAAA
1 TTTAAATTAAAAATAAAAAAA
*
266706 TTTAAATTTAAATATAAAAAAA
1 TTTAAA-TTAAAAATAAAAAAA
266728 CAACAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTAAATTAAAAATAAAAAAA
Found at i:266726 original size:21 final size:21
Alignment explanation
Indices: 266685--266725 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
266675 GACTAAATTC
266685 TTTAAATTAAAAATATAAAAA
1 TTTAAATTAAAAATATAAAAA
*
266706 TTTAAATT-TAAATATAAAAA
1 TTTAAATTAAAAATATAAAAA
266726 AACAACAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAAATTAAAAATATAAAAA
Found at i:266797 original size:11 final size:11
Alignment explanation
Indices: 266781--266871 Score: 67
Period size: 11 Copynumber: 8.0 Consensus size: 11
266771 CTAAATATCT
266781 TTTTAAATTTA
1 TTTTAAATTTA
*
266792 TTTTAAGATTAA
1 TTTTAA-ATTTA
* *
266804 ATTT-ATTTTAA
1 TTTTAAATTT-A
* *
266815 ATTTAAATTTG
1 TTTTAAATTTA
*
266826 CTTTAAATTTAA
1 TTTTAAATTT-A
*
266838 TTTTAAATTAA
1 TTTTAAATTTA
*
266849 GTTTAAATTTA
1 TTTTAAATTTA
266860 CTTTTAAATTTA
1 -TTTTAAATTTA
266872 AAATTCATTA
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
10 2 0.03
11 31 0.50
12 29 0.47
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:266803 original size:17 final size:17
Alignment explanation
Indices: 266782--266873 Score: 105
Period size: 17 Copynumber: 5.4 Consensus size: 17
266772 TAAATATCTT
266782 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
266800 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
266816 TTTAAATTTGCTTTAAA
1 TTTAAATTTATTTTAAA
* ** *
266833 TTTAATTTTAAATTAAG
1 TTTAAATTTATTTTAAA
266850 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
266868 TTTAAA
1 TTTAAA
266874 ATTCATTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
16 1 0.02
17 50 0.82
18 10 0.16
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:266819 original size:6 final size:6
Alignment explanation
Indices: 266782--266873 Score: 68
Period size: 6 Copynumber: 16.0 Consensus size: 6
266772 TAAATATCTT
* * **
266782 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * **
266827 TTTAAA TTTAAT TTTAAA -TTAAG TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
266874 ATTCATTAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
5 16 0.25
6 48 0.75
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:266867 original size:23 final size:23
Alignment explanation
Indices: 266782--266869 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
266772 TAAATATCTT
*
266782 TTTAAATTT-ATTTTAAGATTAAA
1 TTTAAATTTAATTTTAA-ATTAAG
* * *
266805 TTT-ATTTTAAATTTAAATT-TG
1 TTTAAATTTAATTTTAAATTAAG
266826 CTTTAAATTTAATTTTAAATTAAG
1 -TTTAAATTTAATTTTAAATTAAG
*
266850 TTTAAATTTACTTTTAAATT
1 TTTAAATTTAATTTTAAATT
266870 TAAAATTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
22 10 0.19
23 42 0.79
24 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAATTTTAAATTAAG
Found at i:267574 original size:3 final size:3
Alignment explanation
Indices: 267520--267556 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
267510 ATTAAATGAT
267520 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
267557 TTTAATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:267871 original size:21 final size:20
Alignment explanation
Indices: 267847--267885 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
267837 TTGGAGTTTT
267847 AAAACAAAAGCATTTAAAGAA
1 AAAACAAAAGCA-TTAAAGAA
* *
267868 AAAAGAAAAGGATTAAAG
1 AAAACAAAAGCATTAAAG
267886 CTTTTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAACAAAAGCATTAAAGAA
Found at i:268689 original size:30 final size:30
Alignment explanation
Indices: 268615--268911 Score: 228
Period size: 30 Copynumber: 10.1 Consensus size: 30
268605 GCCAGAAGGT
* *
268615 CCTTAAACTATCCAAAAA-T-CATATTTGAC
1 CCTTAAACTTTCCAAAAATTACAT-TTTAAC
**
268644 CCCAAAACTTTCCAAAAATTACA-TTTATAC
1 CCTTAAACTTTCCAAAAATTACATTTTA-AC
*
268674 CCTTAAACCTTCCAAAAATTACATTTTAAC
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
268704 CCTTAAACTTTCCAAAAATTACAATTTTAAC
1 CCTTAAACTTTCCAAAAATTAC-ATTTTAAC
*
268735 CC-TAAAC-TTCTCAAAAATTACATTTTCAC
1 CCTTAAACTTTC-CAAAAATTACATTTTAAC
* * * *
268764 CCCTAAAC-TTCTAAAAATTATAATTCT-AC
1 CCTTAAACTTTCCAAAAATTA-CATTTTAAC
268793 CC-TAAACTTTCC-AAAATTACCATTTT-AC
1 CCTTAAACTTTCCAAAAATTA-CATTTTAAC
** ** * *
268821 CCCAAAACTTTAAAAAAAATCACATTTTTGAC
1 CCTTAAACTTT-CCAAAAATTACA-TTTTAAC
268853 CCTTAAACTTTCC-AAAATTACCA-TTT-AC
1 CCTTAAACTTTCCAAAAATTA-CATTTTAAC
* * * *
268881 CCCT-AA-TGTCTAAAAATTACATTTTTAC
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
268909 CCT
1 CCT
268912 CGAGTTTCCA
Statistics
Matches: 221, Mismatches: 29, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.02
27 12 0.05
28 29 0.13
29 55 0.25
30 81 0.37
31 28 0.13
32 11 0.05
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.34
Consensus pattern (30 bp):
CCTTAAACTTTCCAAAAATTACATTTTAAC
Found at i:268724 original size:60 final size:59
Alignment explanation
Indices: 268615--268911 Score: 272
Period size: 60 Copynumber: 5.1 Consensus size: 59
268605 GCCAGAAGGT
* * * * *
268615 CCTTAAA-CTATCCAAAAATCATATTTGACCCCAAAACTTTCCAAAAATTACATTTATAC
1 CCTTAAACCT-TCCAAAAATTACATTTTACCCCTAAACTTTCCAAAAATTACATTTTTAC
* *
268674 CCTTAAACCTTCCAAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTACAATTTTAAC
1 CCTTAAACCTTCCAAAAATTACATTTT-ACCCCTAAACTTTCCAAAAATTAC-ATTTTTAC
* * * *
268735 CC-TAAA-CTTCTCAAAAATTACATTTTCACCCCTAAAC-TTCTAAAAATTATAATTCTAC
1 CCTTAAACCTTC-CAAAAATTACATTTT-ACCCCTAAACTTTCCAAAAATTACATTTTTAC
* * ** *
268793 CC-TAAACTTTCC-AAAATTACCATTTTACCCCAAAACTTTAAAAAAAATCACATTTTTGAC
1 CCTTAAACCTTCCAAAAATTA-CATTTTACCCCTAAACTTT-CCAAAAATTACATTTTT-AC
* * *
268853 CCTTAAACTTTCC-AAAATTACCA-TTTACCCCT-AA-TGTCTAAAAATTACATTTTTAC
1 CCTTAAACCTTCCAAAAATTA-CATTTTACCCCTAAACTTTCCAAAAATTACATTTTTAC
268909 CCT
1 CCT
268912 CGAGTTTCCA
Statistics
Matches: 201, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.02
57 30 0.15
58 22 0.11
59 52 0.26
60 64 0.32
61 28 0.14
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.34
Consensus pattern (59 bp):
CCTTAAACCTTCCAAAAATTACATTTTACCCCTAAACTTTCCAAAAATTACATTTTTAC
Found at i:268955 original size:29 final size:30
Alignment explanation
Indices: 268866--268958 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 30
268856 TAAACTTTCC
* * *
268866 AAAATTACCA--TTTACCC-CTAATGTCTA
1 AAAATTACCATTTTTACCCTCGAATGCCCA
* **
268893 AAAATTA-CATTTTTACCCTCGAGTTTCCA
1 AAAATTACCATTTTTACCCTCGAATGCCCA
* *
268922 TAAATTACCATTTTT-CTCTCGAATGCCCA
1 AAAATTACCATTTTTACCCTCGAATGCCCA
268951 AAAATTAC
1 AAAATTAC
268959 ATTGTCTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.04
27 7 0.13
28 7 0.13
29 29 0.56
30 7 0.13
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCTCGAATGCCCA
Found at i:274549 original size:20 final size:20
Alignment explanation
Indices: 274524--274564 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
274514 TGAGATAAGC
* *
274524 AAAAGTGAAAGGACTAAATT
1 AAAAGTAAAAGAACTAAATT
274544 AAAAGTAAAAGAACTAAATT
1 AAAAGTAAAAGAACTAAATT
274564 A
1 A
274565 TAAATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAAGTAAAAGAACTAAATT
Found at i:277054 original size:22 final size:22
Alignment explanation
Indices: 277018--277116 Score: 128
Period size: 22 Copynumber: 4.4 Consensus size: 22
277008 ACGCTAGTGC
277018 GCTTACTGTTCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
*
277041 GCTTCTAGTT-AGCAGTGTGTGT
1 GCTTCT-GTTCAGCACTGTGTGT
*
277063 GCTTCTGTTCAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
277085 GCTTATGTTCAGCATTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
277107 GCTTACTGTT
1 GCTT-CTGTT
277117 TCCCAGCACT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
21 3 0.05
22 52 0.79
23 11 0.17
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:277086 original size:44 final size:45
Alignment explanation
Indices: 277018--277116 Score: 148
Period size: 44 Copynumber: 2.2 Consensus size: 45
277008 ACGCTAGTGC
* *
277018 GCTTACTGTTCAGCACTGTGTGTGCTTCTAGTT-AGCAGTGTGTGT
1 GCTTACTGTTCAGCACTATGTGTGCTTAT-GTTCAGCAGTGTGTGT
*
277063 GCTT-CTGTTCAGCACTATGTGTGCTTATGTTCAGCATTGTGTGT
1 GCTTACTGTTCAGCACTATGTGTGCTTATGTTCAGCAGTGTGTGT
277107 GCTTACTGTT
1 GCTTACTGTT
277117 TCCCAGCACT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 3 0.06
44 37 0.76
45 9 0.18
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (45 bp):
GCTTACTGTTCAGCACTATGTGTGCTTATGTTCAGCAGTGTGTGT
Found at i:277133 original size:25 final size:25
Alignment explanation
Indices: 277104--277215 Score: 172
Period size: 25 Copynumber: 4.5 Consensus size: 25
277094 CAGCATTGTG
277104 TGTGCTTACTGTTTC-CCAGCACTTA
1 TGTGCTT-CTGTTTCTCCAGCACTTA
*
277129 TGTGCTACTGTTTCTCCAGCACTTA
1 TGTGCTTCTGTTTCTCCAGCACTTA
277154 TGTGCTTCTGTTTCTCCAGCACTTA
1 TGTGCTTCTGTTTCTCCAGCACTTA
*
277179 TGTGCTTCTGTTTCCCCAGCACTTA
1 TGTGCTTCTGTTTCTCCAGCACTTA
* *
277204 TGCGATTCTGTT
1 TGTGCTTCTGTT
277216 AAGTATTTCG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
24 7 0.09
25 74 0.91
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.42
Consensus pattern (25 bp):
TGTGCTTCTGTTTCTCCAGCACTTA
Found at i:283219 original size:22 final size:22
Alignment explanation
Indices: 283189--283311 Score: 131
Period size: 22 Copynumber: 5.4 Consensus size: 22
283179 GAACACTAGC
283189 GCTTACTGTTCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
*
283212 GCTTCTGTTTAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* * *
283234 GCTTCTGTTCAACATTGTATGT
1 GCTTCTGTTCAGCACTGTGTGT
*
283256 GCTTCTGTTCAGCACTTTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
283278 GCCTACTGTTTCGCAGCACT-TATGT
1 G-CTTCTG-TT--CAGCACTGTGTGT
283303 GCTTCTGTT
1 GCTTCTGTT
283312 TCCCCAGTAC
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
22 54 0.64
23 11 0.13
24 7 0.08
25 5 0.06
26 7 0.08
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:284496 original size:10 final size:10
Alignment explanation
Indices: 284476--284520 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
284466 AAAATTATTA
284476 AATACTAAAAT
1 AATA-TAAAAT
284487 AATATAAAAT
1 AATATAAAAT
*
284497 AATTTAAAA-
1 AATATAAAAT
*
284506 AATAAAAAAT
1 AATATAAAAT
284516 AATAT
1 AATAT
284521 GAAGGGTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 7 0.24
10 18 0.62
11 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AATATAAAAT
Found at i:284514 original size:19 final size:20
Alignment explanation
Indices: 284481--284518 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
284471 TATTAAATAC
*
284481 TAAAATAATATAAAATAATT
1 TAAAATAATAAAAAATAATT
284501 TAAAA-AATAAAAAATAAT
1 TAAAATAATAAAAAATAAT
284519 ATGAAGGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAATAATAAAAAATAATT
Found at i:284516 original size:26 final size:25
Alignment explanation
Indices: 284434--284516 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 25
284424 TAAGATAACT
*
284434 ATATAAAAATTTTCAATAAATAAAAA
1 ATATAAAAATTTT-AAAAAATAAAAA
* *
284460 ATATATAAAATTATTAAATACTAAAATA
1 ATATA-AAAATT-TTAAAAAATAAAA-A
*
284488 ATATAAAATAATTTAAAAAATAAAAA
1 ATATAAAA-ATTTTAAAAAATAAAAA
284514 ATA
1 ATA
284517 ATATGAAGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 9 0.19
27 28 0.60
28 10 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
ATATAAAAATTTTAAAAAATAAAAA
Found at i:284777 original size:26 final size:27
Alignment explanation
Indices: 284742--284792 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
284732 ATAATATATC
*
284742 AAATACATTTAAAA-ACATTAAAAAAT
1 AAATAAATTTAAAATACATTAAAAAAT
284768 AAATAAATTTAAAATACATTAAAAA
1 AAATAAATTTAAAATACATTAAAAA
284793 TTTATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (27 bp):
AAATAAATTTAAAATACATTAAAAAAT
Found at i:284945 original size:21 final size:20
Alignment explanation
Indices: 284908--284946 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
284898 AAAACGCATA
* *
284908 AAAAATAACATCCAAACAAC
1 AAAAATAACAACAAAACAAC
284928 AAAAATAACAACTAAAACA
1 AAAAATAACAAC-AAAACA
284947 GTAGCAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:284961 original size:32 final size:32
Alignment explanation
Indices: 284921--285061 Score: 140
Period size: 32 Copynumber: 4.2 Consensus size: 32
284911 AATAACATCC
* **
284921 AAACAACAAAAATAACAACTAAAACAGTAGCA
1 AAACAACAAAAATAACAACCAAAACAGTAAAA
* * *
284953 AAACAACAAAAATAGCAACAAAAGCAACAGCAAAA
1 AAACAACAAAAATAACAAC-CAA--AACAGTAAAA
* *
284988 ATAAC-ACGAAAACAACAACCAAAACAGTAAAA
1 A-AACAACAAAAATAACAACCAAAACAGTAAAA
*
285020 AAACAACACAAAAATAGCAACCAAAACAGTAAAA
1 AAAC-A-ACAAAAATAACAACCAAAACAGTAAAA
285054 AAACAACA
1 AAACAACA
285062 CCAAAACAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
32 31 0.35
33 3 0.03
34 30 0.34
35 19 0.21
36 3 0.03
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (32 bp):
AAACAACAAAAATAACAACCAAAACAGTAAAA
Found at i:285011 original size:23 final size:24
Alignment explanation
Indices: 284954--285045 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
284944 ACAGTAGCAA
*
284954 AACAACAAAAATAGCAACAAAAGC
1 AACAACAAAAATAACAACAAAAGC
*
284978 AACAGCAAAAATAAC-ACGAAAA-C
1 AACAACAAAAATAACAAC-AAAAGC
* * ** *
285001 AACAACCAAAACAGTAA-AAAAAC
1 AACAACAAAAATAACAACAAAAGC
*
285024 AAC-ACAAAAATAGCAACCAAAA
1 AACAACAAAAATAACAA-CAAAA
285046 CAGTAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
22 14 0.26
23 17 0.32
24 22 0.42
ACGTcount: A:0.67, C:0.22, G:0.07, T:0.04
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAGC
Found at i:285028 original size:34 final size:34
Alignment explanation
Indices: 284926--285070 Score: 129
Period size: 34 Copynumber: 4.3 Consensus size: 34
284916 CATCCAAACA
* * **
284926 ACAAAAATAACAACTAAAACAGTAGCAAAACAAC
1 ACAAAAACAACAACCAAAACAGTAAAAAAACAAC
* *
284960 A-AAAATAGCAACAA--AAGCAACAG--CAAAAATAAC
1 ACAAAA-A-CAACAACCAA--AACAGTAAAAAAACAAC
*
284993 ACGAAAACAACAACCAAAACAGTAAAAAAACAAC
1 ACAAAAACAACAACCAAAACAGTAAAAAAACAAC
* *
285027 ACAAAAATAGCAACCAAAACAGTAAAAAAACAAC
1 ACAAAAACAACAACCAAAACAGTAAAAAAACAAC
*
285061 ACCAAAACAA
1 ACAAAAACAA
285071 TAAAATAATT
Statistics
Matches: 89, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
32 11 0.12
33 15 0.17
34 53 0.60
35 10 0.11
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (34 bp):
ACAAAAACAACAACCAAAACAGTAAAAAAACAAC
Found at i:285046 original size:23 final size:22
Alignment explanation
Indices: 284951--285047 Score: 83
Period size: 23 Copynumber: 4.3 Consensus size: 22
284941 AAAACAGTAG
284951 CAAAAC-A-ACAAAAATAGCAA
1 CAAAACAACACAAAAATAGCAA
*
284971 CAAAAGCAACAGCAAAAATAAC-A
1 CAAAA-CAACA-CAAAAATAGCAA
* * *
284994 CGAAAACAACAACCAAAACAGTAA
1 C-AAAACAAC-ACAAAAATAGCAA
*
285018 AAAAACAACACAAAAATAGCAA
1 CAAAACAACACAAAAATAGCAA
285040 CCAAAACA
1 -CAAAACA
285048 GTAAAAAAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.08
21 1 0.02
22 11 0.19
23 27 0.46
24 15 0.25
ACGTcount: A:0.67, C:0.23, G:0.06, T:0.04
Consensus pattern (22 bp):
CAAAACAACACAAAAATAGCAA
Found at i:289165 original size:29 final size:30
Alignment explanation
Indices: 289120--289290 Score: 115
Period size: 30 Copynumber: 5.8 Consensus size: 30
289110 TAAAATGGTA
289120 ATTTTTGGAAGTTTCGGGGTCAAAAACGAG
1 ATTTTTGGAAGTTTCGGGGTCAAAAACGAG
* *
289150 ATTTTTGGAAG-TTCGGGGT-AAAATC-ATA
1 ATTTTTGGAAGTTTCGGGGTCAAAAACGA-G
* * * *
289178 ATTTTTGCAAGTTTCGAGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGTCAAAAACGAG
* * **
289208 ATTTTTTGAAG-TTCGAGTGT-AAAATGGTA-
1 ATTTTTGGAAGTTTCG-GGGTCAAAAACG-AG
* ** *
289237 ATTTTTAGAAGTTTTAGGGTCAAAAA-TATG
1 ATTTTTGGAAGTTTCGGGGTCAAAAACGA-G
*
289267 ATTTTTGGAAGTTTAGGGGT-AAAA
1 ATTTTTGGAAGTTTCGGGGTCAAAA
289291 TGGTAATTTT
Statistics
Matches: 107, Mismatches: 24, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
27 1 0.01
28 16 0.15
29 41 0.38
30 49 0.46
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (30 bp):
ATTTTTGGAAGTTTCGGGGTCAAAAACGAG
Found at i:289183 original size:58 final size:57
Alignment explanation
Indices: 289110--289302 Score: 233
Period size: 59 Copynumber: 3.3 Consensus size: 57
289100 CATCCGGGAT
289110 TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAACGAGATTTTTGGAAGTTCGGGG
1 TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAA-GAGATTTTTGGAAGTTCGGGG
** * * * * *
289168 TAAAATCATAATTTTTGCAAGTTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGAGTG
1 TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAA-GAGATTTTTGGAAGTTCG-GGG
* ** * *
289227 TAAAATGGTAATTTTTAGAAGTTTTAGGGTCAAAAATATGATTTTTGGAAGTTTAGGGG
1 TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAAGA-GATTTTTGGAAG-TTCGGGG
289286 TAAAATGGTAATTTTTG
1 TAAAATGGTAATTTTTG
289303 AATAGTTTAG
Statistics
Matches: 111, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
58 48 0.43
59 60 0.54
60 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.37
Consensus pattern (57 bp):
TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAAGAGATTTTTGGAAGTTCGGGG
Found at i:289312 original size:30 final size:29
Alignment explanation
Indices: 289110--289314 Score: 109
Period size: 30 Copynumber: 7.0 Consensus size: 29
289100 CATCCGGGAT
* *
289110 TAAAATGGTAATTTTTGGAAGTTTCGGGG
1 TAAAATGGTAATTTTTGAAAGTTTAGGGG
** * *
289139 TCAAAAACG-AGATTTTTGGAAG-TTCGGGG
1 T-AAAATGGTA-ATTTTTGAAAGTTTAGGGG
** * * *
289168 TAAAATCATAATTTTTGCAAGTTTCGAGG
1 TAAAATGGTAATTTTTGAAAGTTTAGGGG
* * * *
289197 TCAAAAATGGGATTTTTTG-AAG-TTCGAGTG
1 T--AAAATGGTAATTTTTGAAAGTTTAG-GGG
289227 TAAAATGGTAATTTTT-AGAAGTTTTA-GGG
1 TAAAATGGTAATTTTTGA-AAG-TTTAGGGG
* * *
289256 TCAAAAAT-ATGATTTTTGGAAGTTTAGGGG
1 T--AAAATGGTAATTTTTGAAAGTTTAGGGG
289286 TAAAATGGTAATTTTTGAATAGTTTAGGG
1 TAAAATGGTAATTTTTGAA-AGTTTAGGG
289315 ACCTTCGGGG
Statistics
Matches: 137, Mismatches: 22, Indels: 33
0.71 0.11 0.17
Matches are distributed among these distances:
28 33 0.24
29 41 0.30
30 44 0.32
31 19 0.14
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGAAAGTTTAGGGG
Found at i:290364 original size:26 final size:27
Alignment explanation
Indices: 290328--290384 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
290318 TATCCTTTTT
*
290328 TTATTATTATTAATTAAATA-TTATTA
1 TTATTATTATTAATTAAACATTTATTA
*
290354 TTATTATTATTATTTAAACATTTATTA
1 TTATTATTATTAATTAAACATTTATTA
290381 TTAT
1 TTAT
290385 AAAAAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATTATTAATTAAACATTTATTA
Found at i:290384 original size:3 final size:3
Alignment explanation
Indices: 290328--290367 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
290318 TATCCTTTTT
*
290328 TTA TTA TTA TTAA TTAA ATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA TTA TT
290368 TAAACATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:291098 original size:6 final size:6
Alignment explanation
Indices: 291089--291125 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
291079 TTTTGATATC
*
291089 AAATTT AAATTT AAATTT AGA-TT -AATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
291126 ATAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 1 0.04
5 4 0.15
6 22 0.81
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:292855 original size:6 final size:6
Alignment explanation
Indices: 292844--292927 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
292834 TTAAATGAAT
* *
292844 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
292890 TTTAGAA --TAAA CTTAAT TTTAAA -ATAAA TTTAAG TTTA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
292928 TTGGGCCCAG
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
4 4 0.07
5 11 0.18
6 41 0.68
7 4 0.07
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:292866 original size:17 final size:17
Alignment explanation
Indices: 292846--292928 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 17
292836 AAATGAATTT
292846 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
292863 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
*
292880 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
292897 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
292914 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
292929 TGGGCCCAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.02
17 54 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:292884 original size:34 final size:34
Alignment explanation
Indices: 292846--292928 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
292836 AAATGAATTT
* * *
292846 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
* *
292880 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
292914 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
292929 TGGGCCCAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:293441 original size:84 final size:83
Alignment explanation
Indices: 293287--293476 Score: 281
Period size: 84 Copynumber: 2.3 Consensus size: 83
293277 TTTTGATCCA
* * * * * * *
293287 CTTCTCTGTGTTTCATCAGGAAGATGATTTTGGTTACTTCCCCGTATCTTATCAGGAAGCTAATC
1 CTTCTCGGTGTCTCATCAGGAAGACGAATTTGGTTACTTCCCAGTATCTCATCAGGAAGCTAACC
293352 ATTTATTGCTTCGACCTG
66 ATTTATTGCTTCGACCTG
*
293370 CTTCTCGGTGTCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCGGTGTCTCATCAGGAAGACGAATTTGGTT-ACTTCCCAGTATCTCATCAGGAAGCTAAC
* *
293435 CGTTTATTGCTTCGACTTG
65 CATTTATTGCTTCGACCTG
293454 CTTCTCGGTGTCTCATCAGGAAG
1 CTTCTCGGTGTCTCATCAGGAAG
293477 CTGGGGTTCG
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 31 0.32
84 65 0.68
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (83 bp):
CTTCTCGGTGTCTCATCAGGAAGACGAATTTGGTTACTTCCCAGTATCTCATCAGGAAGCTAACC
ATTTATTGCTTCGACCTG
Found at i:293926 original size:207 final size:206
Alignment explanation
Indices: 293367--293967 Score: 963
Period size: 207 Copynumber: 2.9 Consensus size: 206
293357 TTGCTTCGAC
* * *
293367 CTGCTTCTCGGTGTCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCT
1 CTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAAGCT
* * * *
293432 AACC-GTTTATTGCTTCGACTTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGC
66 AACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCCTCAGGAAGCTGGGGTTCGAAGATTTGC
* * * * *
293496 TCACATCGAGCGTGGGTTTCATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCA
131 TCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGCCA
293561 TTTGTTTCAAT
196 TTTGTTTCAAT
* * * * *
293572 CTACTTCTCTGTATCTCATCAAGAAGATGAATTTGATTCACTTCT-AATATCTCATCATGAAGCT
1 CTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAAGCT
* * *
293636 AACTATTTTATTGCTTCGACCTGCTTCTCAGTATCTCCTCAAGAAGCTGGGGTTCGAAGATTTTG
66 AACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCCTCAGGAAGCTGGGGTTCGAAGA-TTTG
*
293701 CTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCACGCC
130 CTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGCC
293766 ATTTGTTTCAAT
195 ATTTGTTTCAAT
*
293778 CTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATATCTCATTAGGAAGCT
1 CTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAAGCT
*
293843 AACCATTTTATTGCTTCGACTTGCTTCTTAGTATCTCCTCAGGAAGCTGGGGTTCGAAGATCTTG
66 AACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCCTCAGGAAGCTGGGGTTCGAAGAT-TTG
293908 CTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC
130 CTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC
293968 GCATTGCTGT
Statistics
Matches: 360, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
204 20 0.06
205 88 0.24
206 117 0.32
207 135 0.38
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
CTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAAGCT
AACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCCTCAGGAAGCTGGGGTTCGAAGATTTGC
TCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGCCA
TTTGTTTCAAT
Found at i:305729 original size:29 final size:29
Alignment explanation
Indices: 305688--306187 Score: 361
Period size: 29 Copynumber: 17.1 Consensus size: 29
305678 TTTGGGAAAA
* * *
305688 TTCGAGGTTAAAAATGGAATTTTTAGACA-
1 TTCGGGGTCAAAAATGGAATTTTTGGA-AG
* *
305717 TTCGGGG-CCAAAAGGGTAA-TTTT-GAGAG
1 TTCGGGGTCAAAAATGG-AATTTTTGGA-AG
* * * *
305745 TTTCGAGGTCGAAAATGGAGTCTTTGGACA-
1 -TTCGGGGTCAAAAATGGAATTTTTGGA-AG
305775 TTCGGGGGT--AAAATGGTAATTTTTGGAAG
1 TTC-GGGGTCAAAAATGG-AATTTTTGGAAG
*
305804 TTTCGGGGTC-AAAATGGGATTTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
*
305833 TTCGGGGGT-AAAAATGGAACTTTTGGAAG
1 TTC-GGGGTCAAAAATGGAATTTTTGGAAG
*
305862 TTTCGGGGTC-AAAATGGGATTTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
*
305891 TTCGGGGGT-AAAAATGGAACTTTTGGAAG
1 TTC-GGGGTCAAAAATGGAATTTTTGGAAG
*
305920 TTTCGGGGTCAAAAATGGGATTTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
*
305950 TTCGGGGGT-AAAAATGGAACTTTTAGG-AG
1 TTC-GGGGTCAAAAATGGAA-TTTTTGGAAG
* *
305979 TTTCGAGGTCAAAAAT-GAGATTTTTAGAAG
1 -TTCGGGGTCAAAAATGGA-ATTTTTGGAAG
* * * * *
306009 GTAGAGGGT-AAAAACGTAACTTTTGGAAG
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAG
* *
306038 TTTTGGGGTCAAAAATGGGA-TTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
* *
306067 TTTGAGGGT-AAAAATGGAATTTTTAGAAG
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAG
* ***
306096 TTTTGGGGTCAAAAACAAAATTTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
** * *
306126 TTTCAAGGTTAAAAATGAAATTTTTGGAAG
1 -TTCGGGGTCAAAAATGGAATTTTTGGAAG
306156 TTCGAGGGT-AAAAATGGAATTTTTGGACAG
1 TTCG-GGGTCAAAAATGGAATTTTTGGA-AG
306186 TT
1 TT
306188 TAGGGACCTC
Statistics
Matches: 381, Mismatches: 55, Indels: 69
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 37 0.10
29 203 0.53
30 135 0.35
31 3 0.01
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (29 bp):
TTCGGGGTCAAAAATGGAATTTTTGGAAG
Found at i:305849 original size:59 final size:59
Alignment explanation
Indices: 305743--306187 Score: 503
Period size: 58 Copynumber: 7.6 Consensus size: 59
305733 TAATTTTGAG
* * *
305743 AGTTTCGAGGTCGAAAAT-GGAGTCTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGA-TTTTTGGA-AGTTCGGGGGTAAAAATGG-AATTTTTGGA
*
305802 AGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
*
305860 AGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
*
305918 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTAGG-
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAA-TTTTTGGA
* * * * * * * * *
305977 AGTTTCGAGGTCAAAAATGAGATTTTTAGAAGGTAGAGGGTAAAAACGTAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * * *
306036 AGTTTTGGGGTCAAAAATGGGA-TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTAGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* **** ** * *
306094 AGTTTTGGGGTCAAAAACAAAATTTTTGGAAGTTTCAAGGTTAAAAATGAAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGA
*
306154 AG-TTCGAGGGT-AAAAATGGAATTTTTGGACAGTT
1 AGTTTCG-GGGTCAAAAATGGGATTTTTGGA-AGTT
306188 TAGGGACCTC
Statistics
Matches: 338, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
57 1 0.00
58 152 0.45
59 150 0.44
60 35 0.10
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (59 bp):
AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
Found at i:306099 original size:58 final size:59
Alignment explanation
Indices: 305743--306187 Score: 503
Period size: 59 Copynumber: 7.6 Consensus size: 59
305733 TAATTTTGAG
* * * * *
305743 AGTTTCGAGGTCGAAAAT-GGAGTCTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGA-TTTTTGGA-AGTTCGAGGGTAAAAATGG-AACTTTTGGA
*
305802 AGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTTGGA
*
305860 AGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTTGGA
*
305918 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAACTTTTAGG-
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTT-GGA
* * * * * * *
305977 AGTTTCGAGGTCAAAAATGAGATTTTTAGAAGGTAGAGGGTAAAAACGTAACTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTTGGA
* * * *
306036 AGTTTTGGGGTCAAAAATGGGA-TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTAGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTTGGA
* **** * * * *
306094 AGTTTTGGGGTCAAAAACAAAATTTTTGGAAGTTTCAAGGTTAAAAATGAAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAACTTTTGGA
*
306154 AG-TTCGAGGGT-AAAAATGGAATTTTTGGACAGTT
1 AGTTTCG-GGGTCAAAAATGGGATTTTTGGA-AGTT
306188 TAGGGACCTC
Statistics
Matches: 342, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.00
58 149 0.44
59 160 0.47
60 32 0.09
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (59 bp):
AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAACTTTTGGA
Found at i:307215 original size:3 final size:3
Alignment explanation
Indices: 307207--307249 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
307197 CAATTGTCAC
307207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
307250 GAGCATTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:307905 original size:17 final size:17
Alignment explanation
Indices: 307856--307932 Score: 65
Period size: 17 Copynumber: 4.8 Consensus size: 17
307846 AAATGAATTT
307856 TAAATTTAAATTT---A
1 TAAATTTAAATTTAAAA
* *
307870 TAAA--TAAATTTCAAC
1 TAAATTTAAATTTAAAA
*
307885 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
307902 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
307919 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
307933 TTGGGCCCAG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
12 7 0.14
14 4 0.08
15 4 0.08
17 34 0.69
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:307917 original size:29 final size:31
Alignment explanation
Indices: 307851--307926 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
307841 TATTTAAATG
*
307851 AATTTTAAATTTAAATTTATAAATAAATTTC
1 AATTTTAAATTTAAATTTATAAATAAACTTC
* *
307882 AA--CTAAATTTAAATTTA-GAATAAACTT-
1 AATTTTAAATTTAAATTTATAAATAAACTTC
*
307909 AATTTTAAA-ATAAATTTA
1 AATTTTAAATTTAAATTTA
307927 AGTTTATTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.05
28 16 0.42
29 18 0.47
31 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (31 bp):
AATTTTAAATTTAAATTTATAAATAAACTTC
Found at i:310856 original size:26 final size:25
Alignment explanation
Indices: 310792--310858 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
310782 TATTCCAAAC
*
310792 ACTGGCTCGTAAGAGCGATGTTCTG
1 ACTGGCTCGTAAGAGCGATATTCTG
*
310817 ACTGGCTCATAAGAGCGATATTCTG
1 ACTGGCTCGTAAGAGCGATATTCTG
*
310842 TCTGGGCTCGTAAGAGC
1 ACT-GGCTCGTAAGAGC
310859 TAAATTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 25 0.68
26 12 0.32
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (25 bp):
ACTGGCTCGTAAGAGCGATATTCTG
Found at i:313906 original size:9 final size:9
Alignment explanation
Indices: 313892--313971 Score: 55
Period size: 9 Copynumber: 9.2 Consensus size: 9
313882 TTTAATCTTT
313892 TAAAAATTA
1 TAAAAATTA
313901 TAAAAA-TA
1 TAAAAATTA
*
313909 T--AGATTA
1 TAAAAATTA
313916 TTAAAAA-T-
1 -TAAAAATTA
*
313924 TAAAATTTA
1 TAAAAATTA
*
313933 TTAAAAATTG
1 -TAAAAATTA
*
313943 TAAAAACTA
1 TAAAAATTA
313952 TTAAAAA-TA
1 -TAAAAATTA
313961 TAAAAATTA
1 TAAAAATTA
313970 TA
1 TA
313972 TGTTATAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
6 2 0.04
7 7 0.13
8 11 0.20
9 20 0.36
10 15 0.27
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:313925 original size:10 final size:10
Alignment explanation
Indices: 313922--313970 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
313912 ATTATTAAAA
*
313922 ATTAAAATTT
1 ATTAAAAATT
313932 ATTAAAAATT
1 ATTAAAAATT
* *
313942 -GTAAAAACT
1 ATTAAAAATT
313951 ATTAAAAA-T
1 ATTAAAAATT
313960 A-TAAAAATT
1 ATTAAAAATT
313969 AT
1 AT
313971 ATGTTATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
8 6 0.19
9 11 0.34
10 15 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:313933 original size:17 final size:18
Alignment explanation
Indices: 313892--313970 Score: 85
Period size: 19 Copynumber: 4.6 Consensus size: 18
313882 TTTAATCTTT
313892 TAAAAATTA-TAAAAATA
1 TAAAAATTATTAAAAATA
*
313909 T--AGATTATTAAAAAT-
1 TAAAAATTATTAAAAATA
* *
313924 TAAAATTTATTAAAAATTG
1 TAAAAATTATTAAAAA-TA
*
313943 TAAAAACTATTAAAAATA
1 TAAAAATTATTAAAAATA
313961 TAAAAATTAT
1 TAAAAATTAT
313971 ATGTTATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
15 6 0.12
16 7 0.14
17 12 0.24
18 11 0.22
19 14 0.28
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAAATTATTAAAAATA
Found at i:314140 original size:11 final size:11
Alignment explanation
Indices: 314108--314157 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
314098 GAGCTTCTTA
314108 AAATAATTTTT
1 AAATAATTTTT
*
314119 --ATAA-ATTT
1 AAATAATTTTT
*
314127 AAATACTTTTT
1 AAATAATTTTT
314138 AAATAATTTTT
1 AAATAATTTTT
*
314149 AAAGAATTT
1 AAATAATTT
314158 AAAGGAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
10 3 0.10
11 21 0.68
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:315618 original size:20 final size:18
Alignment explanation
Indices: 315576--315620 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
315566 CAAAATTTAA
315576 TAAATATATAATGATAAT
1 TAAATATATAATGATAAT
* *
315594 AAAATATATAATTATTAAAT
1 TAAATATATAATGA-T-AAT
315614 TAAATAT
1 TAAATAT
315621 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 12 0.55
19 1 0.05
20 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATATATAATGATAAT
Found at i:317783 original size:11 final size:11
Alignment explanation
Indices: 317767--317794 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
317757 TATCCATCTG
317767 ATATTGCTTCT
1 ATATTGCTTCT
317778 ATATTGCTTCT
1 ATATTGCTTCT
317789 ATATTG
1 ATATTG
317795 GTTGACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (11 bp):
ATATTGCTTCT
Found at i:327331 original size:14 final size:15
Alignment explanation
Indices: 327312--327340 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
327302 TGTTTCATCT
327312 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
327326 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
327341 CATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:334203 original size:20 final size:21
Alignment explanation
Indices: 334180--334219 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
334170 TCAAAAAGTC
*
334180 GAGAAAAA-AAAGAAAAATAT
1 GAGAAAAATAAAAAAAAATAT
334200 GAGAAAAATAAAAAAAAATA
1 GAGAAAAATAAAAAAAAATA
334220 AAAAATATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (21 bp):
GAGAAAAATAAAAAAAAATAT
Done.