Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014963.1 Kokia drynarioides strain JFW-HI SEQ_130007, 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: 411358
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 371 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1159 original size:40 final size:40
Alignment explanation
Indices: 1104--1183 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1094 TAAGAAGGTG
* * *
1104 ATTGATGAATGAGAAGAGTTGCAGAGAAAATGGATATTTA
1 ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
*
1144 ATTGACGAATGAGAAGAGTTACAGAGAAGATAGATATTTA
1 ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
1184 TAGTTTAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (40 bp):
ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
Found at i:36922 original size:18 final size:18
Alignment explanation
Indices: 36888--36923 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36878 TCATGACCCT
* *
36888 TGAACATAAATAGTAAAA
1 TGAACATAAAGAATAAAA
36906 TGAACATAAAGAATAAAA
1 TGAACATAAAGAATAAAA
36924 AAACTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (18 bp):
TGAACATAAAGAATAAAA
Found at i:38519 original size:6 final size:6
Alignment explanation
Indices: 38453--38517 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
38443 GCCTCACCTT
38453 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
38501 CATCAT CATCAT CATCA
1 CATCAC CATCAC CATCA
38518 TCTGAGTCTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (6 bp):
CATCAC
Found at i:43204 original size:2 final size:2
Alignment explanation
Indices: 43197--43223 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43187 CTCGCCGGTA
43197 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
43224 GCTATTTAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45552 original size:24 final size:22
Alignment explanation
Indices: 45519--45563 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
45509 TGTTTTGTTG
45519 TACTTCTATTCAACCATTCTATTT
1 TACTTCTATTCAA-C-TTCTATTT
*
45543 TACTTGTATTCAACTTCTATT
1 TACTTCTATTCAACTTCTATT
45564 CTACCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 12 0.60
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (22 bp):
TACTTCTATTCAACTTCTATTT
Found at i:46524 original size:141 final size:141
Alignment explanation
Indices: 46270--46550 Score: 544
Period size: 141 Copynumber: 2.0 Consensus size: 141
46260 TGTAAAAGCA
*
46270 AATTCTTTGCTGTTCCGGGGGGAAAATGCTTAACCCAGCGTGTTTGTTTGGTTTTCGAGTTAGAT
1 AATTCTTTGCTGTTCCAGGGGGAAAATGCTTAACCCAGCGTGTTTGTTTGGTTTTCGAGTTAGAT
46335 GCCATTTTACTGAAAATTTATTGATCCACATAAATTGTAGTTTCTTAGTCAATCTTTTGTTAGAT
66 GCCATTTTACTGAAAATTTATTGATCCACATAAATTGTAGTTTCTTAGTCAATCTTTTGTTAGAT
46400 TGTTGATGCTT
131 TGTTGATGCTT
46411 AATTCTTTGCTGTTCCAGGGGGAAAATGCTTAACCCAGCGTGTTTGTTTGGTTTTCGAGTTAGAT
1 AATTCTTTGCTGTTCCAGGGGGAAAATGCTTAACCCAGCGTGTTTGTTTGGTTTTCGAGTTAGAT
*
46476 GCCATTTTACTGAAAATTTATTGATCCACATAAATTTTAGTTTCTTAGTCAATCTTTTGTTAGAT
66 GCCATTTTACTGAAAATTTATTGATCCACATAAATTGTAGTTTCTTAGTCAATCTTTTGTTAGAT
46541 TGTTGATGCT
131 TGTTGATGCT
46551 CTATGTTTGC
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (141 bp):
AATTCTTTGCTGTTCCAGGGGGAAAATGCTTAACCCAGCGTGTTTGTTTGGTTTTCGAGTTAGAT
GCCATTTTACTGAAAATTTATTGATCCACATAAATTGTAGTTTCTTAGTCAATCTTTTGTTAGAT
TGTTGATGCTT
Found at i:48340 original size:72 final size:72
Alignment explanation
Indices: 48255--48400 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 72
48245 TTAACCTATA
*
48255 AATAATTTTAAATTCAAACAATTTTAACTTATGTCTATAATCTAAATACAATTTTACATTCAACT
1 AATAATTTTAAATTCAAACAATTTTAACTTATGTCTATAATCTAAAGACAATTTTACATTCAACT
48320 AAATCAC
66 AAATCAC
* *
48327 AATAATTTTAAATTTAAACAATTTTAACTTATTTCTATAATCTAAAGACAATTTTACATTCAACT
1 AATAATTTTAAATTCAAACAATTTTAACTTATGTCTATAATCTAAAGACAATTTTACATTCAACT
48392 AAATCAC
66 AAATCAC
48399 AA
1 AA
48401 ACTTAGATTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (72 bp):
AATAATTTTAAATTCAAACAATTTTAACTTATGTCTATAATCTAAAGACAATTTTACATTCAACT
AAATCAC
Found at i:48727 original size:10 final size:10
Alignment explanation
Indices: 48714--48761 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
48704 TAAAATGATT
48714 AAAAATCATA
1 AAAAATCATA
* *
48724 AAAAGTTATA
1 AAAAATCATA
48734 AAAAATCATAA
1 AAAAATCAT-A
*
48745 AAAAAT-ATT
1 AAAAATCATA
48754 AAAAATCA
1 AAAAATCA
48762 AAATAGTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 6 0.19
10 18 0.58
11 7 0.23
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAATCATA
Found at i:48739 original size:20 final size:20
Alignment explanation
Indices: 48714--48761 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
48704 TAAAATGATT
**
48714 AAAAATCATAAAAAGTTATA
1 AAAAATCATAAAAAAATATA
*
48734 AAAAATCATAAAAAAATATT
1 AAAAATCATAAAAAAATATA
48754 AAAAATCA
1 AAAAATCA
48762 AAATAGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATCATAAAAAAATATA
Found at i:48825 original size:9 final size:9
Alignment explanation
Indices: 48805--48951 Score: 50
Period size: 10 Copynumber: 15.6 Consensus size: 9
48795 TTGTTATTAA
48805 TTTATAATTT
1 TTTAT-ATTT
48815 TTTATA-TT
1 TTTATATTT
*
48823 TTTA-ATAT
1 TTTATATTT
*
48831 TATA-AGTTT
1 TTTATA-TTT
*
48840 TATAATATTT
1 T-TTATATTT
*
48850 TTTTTATATT
1 TTTATAT-TT
*
48860 TTTATAGTT
1 TTTATATTT
*
48869 TTAATATGTT
1 TTTATAT-TT
*
48879 TATATCATTT
1 TTTAT-ATTT
*
48889 TTAATATTT
1 TTTATATTT
**
48898 AATAT-TTT
1 TTTATATTT
48906 TTTATGATTTT
1 TTTAT-A-TTT
48917 TTTAATAATTT
1 TTT-AT-ATTT
*
48928 TGTATTATTT
1 TTTA-TATTT
* *
48938 TTAACATTT
1 TTTATATTT
48947 TTTAT
1 TTTAT
48952 GGGAAATATT
Statistics
Matches: 98, Mismatches: 27, Indels: 25
0.65 0.18 0.17
Matches are distributed among these distances:
7 1 0.01
8 17 0.17
9 28 0.29
10 34 0.35
11 15 0.15
12 3 0.03
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTATATTT
Found at i:48875 original size:17 final size:19
Alignment explanation
Indices: 48850--48902 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
48840 TATAATATTT
*
48850 TTTTTATATTTT-TAT-AG
1 TTTTAATATTTTATATCAG
*
48867 TTTTAATATGTTTATATCAT
1 TTTTAATAT-TTTATATCAG
*
48887 TTTTAATATTTAATAT
1 TTTTAATATTTTATAT
48903 TTTTTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.27
18 3 0.10
19 9 0.30
20 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTATATCAG
Found at i:48908 original size:19 final size:19
Alignment explanation
Indices: 48842--48909 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 19
48832 ATAAGTTTTA
*
48842 TAATATT-TTTTTTATATT
1 TAATATTATTTTTAATATT
* *
48860 T-TTA-TAGTTTTAATATGT
1 TAATATTATTTTTAATAT-T
* *
48878 TTATATCATTTTTAATATT
1 TAATATTATTTTTAATATT
48897 TAATATT-TTTTTA
1 TAATATTATTTTTA
48910 TGATTTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 9 0.24
19 8 0.21
20 10 0.26
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66
Consensus pattern (19 bp):
TAATATTATTTTTAATATT
Found at i:48922 original size:22 final size:22
Alignment explanation
Indices: 48895--48939 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48885 ATTTTTAATA
* *
48895 TTTAATATTTTTTTATGATTTT
1 TTTAATAATTTTGTATGATTTT
*
48917 TTTAATAATTTTGTATTATTTT
1 TTTAATAATTTTGTATGATTTT
48939 T
1 T
48940 AACATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTAATAATTTTGTATGATTTT
Found at i:49472 original size:22 final size:22
Alignment explanation
Indices: 49447--49493 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
49437 GGGACAAAAA
* * *
49447 GAAAAAGCTCATGTATCAAATT
1 GAAAAAGATCAAGTACCAAATT
49469 GAAAAAGATCAAGTACCAAATT
1 GAAAAAGATCAAGTACCAAATT
49491 GAA
1 GAA
49494 TATTGAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (22 bp):
GAAAAAGATCAAGTACCAAATT
Found at i:55453 original size:2 final size:2
Alignment explanation
Indices: 55416--55441 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55406 TTTACATTAC
55416 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
55442 GTTTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74961 original size:26 final size:27
Alignment explanation
Indices: 74923--74973 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
74913 ATTGGGTTTT
*
74923 ATTTTTTTATTGACATACTAA-TTTTAG
1 ATTTTATTATTGACATA-TAACTTTTAG
74950 ATTTTATT-TTGACATATAACTTTT
1 ATTTTATTATTGACATATAACTTTT
74974 GAATAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 12 0.55
27 7 0.32
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (27 bp):
ATTTTATTATTGACATATAACTTTTAG
Found at i:77654 original size:29 final size:31
Alignment explanation
Indices: 77600--77660 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 31
77590 TAATCTAAAG
77600 TTAAAATATAAAATATAAAAGGATTAAATTT
1 TTAAAATATAAAATATAAAAGGATTAAATTT
77631 TTAAAA-ATAAAA-ATACAAA-GATTAAATTT
1 TTAAAATATAAAATATA-AAAGGATTAAATTT
77660 T
1 T
77661 CAATTTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.48
30 9 0.31
31 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (31 bp):
TTAAAATATAAAATATAAAAGGATTAAATTT
Found at i:78604 original size:216 final size:221
Alignment explanation
Indices: 78181--78850 Score: 717
Period size: 238 Copynumber: 2.9 Consensus size: 221
78171 TGTATGAGGA
* * *
78181 GTAAAAACTTCTTTTCATCCATTTTCTCGGTAAACAAACGGGAATTTGATCTTAAAGATCCTTAC
1 GTAAAAACTTCTTTTCATCCGTTTTCTTGGTAAACAAACGGGAATTTGATCTTAAAGATCCTTAA
* * * * *
78246 GCTTACAAGATTATGGTA-TTGCAGAGTCAAAAGTTTCATCTGTTTTCCAATTTTTTTTTTGCTT
66 GCTTACATGATTAT-GTATTTGCAAAGTCAAAA-TTTCATATGTTTT-C------TTTTTCGTTT
* * *
78310 GATCTGTTG-TTGGTTGGTGAGAAAGTGACGGAAAACTTGCGGAAAATGAATTTGAATTTATTGA
122 GATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAATTGAATTTGAATTTATTGA
*
78374 TTGATGTAAAATTAAAATA-TA-A-GTTA-T-GAT
187 TTGATGTAAAATTAAAATATTACATGTTAGTACAT
* * * *
78404 GTAAAAACTTATTTTCATCCGTTTTCTTGGTAAACAAGCGGGAATTTGATCTTAAAGGTCTTTAA
1 GTAAAAACTTCTTTTCATCCGTTTTCTTGGTAAACAAACGGGAATTTGATCTTAAAGATCCTTAA
* * *
78469 GCTTACATGATTATGTATTTGCAAAGTCACAATTTCATTTGTTTTCTTTTTGGTTTGATCTGTTG
66 GCTTACATGATTATGTATTTGCAAAGTCAAAATTTCATATGTTTTCTTTTTCGTTTGATCTGTTG
*
78534 TTTGGTTGGTGAGAAAGTGAAGGGAAAGTTGCGGAAATTGAATTTGAATTTATTGATTGATGTAA
131 TTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAATTGAATTTGAATTTATTGATTGATGTAA
78599 AATTAAAATAGGAATTACGATGTTAGGTTTACAT
196 AATTAAAAT----ATTAC-ATGTTA-G--TACAT
* * * * * *
78633 GTATGAGCCGTAAATACTTCTTGTCATCTGTTTCCGTGGTCAACAAACGGGAATTTGATCTTAGA
1 G--T-A-----AAA-ACTTCTTTTCATCCGTTTTCTTGGTAAACAAACGGGAATTTGATCTTAAA
* * * *
78698 GATCCTTAAGCTTGCATGATCATGTTTTTGTAAAGTCAAAATTTCATATGTTTTTCTTTTTCGTT
57 GATCCTTAAGCTTACATGATTATGTATTTGCAAAGTCAAAATTTCATATG-TTTTCTTTTTCGTT
*
78763 TGATCTGTTGTTTGGTTGGTGAG-AAGTGAAGGAAAAGTTGCTGAAATTGAATTGAATTGAATTT
121 TGATCTGTTGTTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAATTGAA-T---TTGAATTT
*
78827 GTTGATTGATGTAAAATTAAAATA
182 ATTGATTGATGTAAAATTAAAATA
78851 CGAGTGAAGT
Statistics
Matches: 380, Mismatches: 38, Indels: 43
0.82 0.08 0.09
Matches are distributed among these distances:
215 17 0.04
216 69 0.18
220 1 0.00
221 3 0.01
222 15 0.04
223 84 0.22
224 4 0.01
228 1 0.00
229 3 0.01
231 1 0.00
232 1 0.00
237 3 0.01
238 111 0.29
239 37 0.10
242 30 0.08
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (221 bp):
GTAAAAACTTCTTTTCATCCGTTTTCTTGGTAAACAAACGGGAATTTGATCTTAAAGATCCTTAA
GCTTACATGATTATGTATTTGCAAAGTCAAAATTTCATATGTTTTCTTTTTCGTTTGATCTGTTG
TTTGGTTGGTGAGAAAGTGAAGGAAAAGTTGCGGAAATTGAATTTGAATTTATTGATTGATGTAA
AATTAAAATATTACATGTTAGTACAT
Found at i:81517 original size:17 final size:17
Alignment explanation
Indices: 81495--81527 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
81485 TTGCGAGCAC
81495 CAATGTCTAATTTACAT
1 CAATGTCTAATTTACAT
*
81512 CAATGTCTTATTTACA
1 CAATGTCTAATTTACA
81528 CTAGCAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (17 bp):
CAATGTCTAATTTACAT
Found at i:83805 original size:3 final size:3
Alignment explanation
Indices: 83797--83844 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
83787 AAGTTCAAGT
* * * * *
83797 GAA GAA GAA AAA GAA GAA AAA CAA AAA GAA GAA GAA GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
83845 TAATAAAGAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:84356 original size:99 final size:99
Alignment explanation
Indices: 84038--85830 Score: 1545
Period size: 93 Copynumber: 18.1 Consensus size: 99
84028 AACTAATAAT
* * *
84038 AAGAAGAGCAATGAGAATGAAGATGCTATTGAGGCTATTGCTGTAGCTGTTGTTGATGGTGCAAT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
* * * *
84103 TGATGTTGAGAGTGATGAAACT----GG-A-AAG
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* * *
84131 AAGAAGAGCAATGAAAATGAGGATGCTATTGAAGCTATTGCTGTTGCTGTTGTTGATGGTGGAGT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
84196 TGATGTAGGGAGTGATGAAATTG-AA--AAG--A
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* *
84225 AAG-AGAGCAATGAAAATGAGGATGCTACTGAGGCAATTGCTGTTGCTGTTGTTGATGGTGCAAT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
*
84289 TGACGTAGGGAGTGATGAAATTGAAAGGAAGAAA
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
*
84323 AAGAAGTGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGC------TGATGGTGCAAT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
*
84382 TGATGTAGGGAGTGATGAAATTGAAAAGAAGAAA
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* * * * ** * * *
84416 AAGAAGA-AAAAGAAGAGGAAGAGCAATGAAAATGAGGAGGCTATAGAGGCTATTGCTGTTGTTG
1 AAGAAGAGCAATGAA-A--ATGAG-GATG-CTAT--TGAGGCTAT---TGCTGTTGCTGTTGTTG
*
84480 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGGAAGGAAGCAAAA
56 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAG--AAA
* * *
84526 GAAGGAGAGCAATGAAAATGAGGATGCTATTGAAGCAATTGCTGTTGCTGTTGTTGATGGTGCAA
1 -AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAA
*
84591 TTGATGTAGGGAGTGGTGAAATTGAAAGGAAGAAAAAGA
65 TTGATGTAGGGAGTGATGAAATTGAAAGGAAG---AA-A
* *
84630 AGGAGAAGAGCAACGAAAATGAGGATGCTATTGAAGCTATTGCTGTTGCTGTTGTTGATGGTGCA
1 A--AGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCA
* *
84695 ATTGATGTAGGGATTAATGAAATTG-AA--AAG---
64 ATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* *
84725 AAGGAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGGGCAAT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
84790 TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAAAA
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAG--AAA
84826 GAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGC------TGATGGTGCAA
1 -AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAA
* *
84885 TTGATGTAGGAAGTGATGAAATTGAAAAGAAGAAA
65 TTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* * * * ** * * *
84920 AAGAAGA-AAAAGAAGAGGAAGAGCAATGAAAATGAGGAGGCTATAGAGGCTATTGCTGTTGTTG
1 AAGAAGAGCAATGAA-A--ATGAG-GATG-CTAT--TGAGGCTAT---TGCTGTTGCTGTTGTTG
84984 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAAAAGA
56 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAG---AA-A
*
85032 AGGAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGCTGATGGTGCA
1 A--AGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCA
* *
85097 ATTGATGTAGGGAGTAATGAAATTGAAAAGAAGAAA
64 ATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* ** * *
85133 AAGAAGAAG-AA-GAAGAATAAGAGCAATGAAAATGAGGAGGCTATTGAGGCTATTGCTGTTGTT
1 AAGAAG-AGCAATGAA-AAT--GAG-GATG-CTAT--TGAGGCTATT---GCTGTTGCTGTTGTT
85196 GATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAAAAAA
55 GATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAG----AAA
*
85245 AGAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTA--G-T-TT--TGTTGATGATGGTGCA
1 A-A-GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCA
* * *
85304 ATTGATGTAGGAAGTCATGAAATTGAAAAGAAGAAAAA
64 ATTGATGTAGGGAGTGATGAAATTGAAAGGAAG--AAA
* * * * * *** **
85342 GAAGAAGAGCAATGAAAATGAGGAGGCTATT---GCTGTTGTTGATGGTGCAATTGAT-GTAGGG
1 -AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGT-GCA
* * *** ** ** *
85403 AGTGATGAAATTAAAAAGATGAAAAAG-AA-GAAGAAG
64 ATTGATG-TA-GGGAGTGATGAAATTGAAAGGAAGAAA
*
85439 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTA------TTGCTGTTGTTGATGGCGCAAT
1 AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
85498 TGATGTAGGGAGTGATG---TTGAAAGGAAGAAAAAGAA
66 TGATGTAGGGAGTGATGAAATTGAAAGGAAG----A-AA
*
85534 GAAGAAGAGCAATAAAAATGAGGATGCTATTGAGGCTA------TTGCTGTTGTTGATGGTG---
1 -AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAA
*
85590 TTGATGTAGGGAGTGATGAAATTGAAAAGAAGAAA
65 TTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
* * * * * * *
85625 AAGAAGAAGAAGAAGAACAAAGAGAATG--A-GGAGGCTATTGAGGCTATTGCTGTTGTTGACGG
1 AAGAAG-AGCA-ATGAA-AATGAGGATGCTATTGAGGCTATT---GCTGTTGCTGTTGTTGATGG
85687 TGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAAAAGA
60 TGCAATTGATGTAGGGAGTGATGAAATTGAAAGGAAG---AA-A
*
85731 AGAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTA------ATGCTGTTGTTGATGGTGCA
1 A-A-GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCA
* *
85790 ATTGATGTAGGGAGTGATGAAATTGAAAAGAAGAAG
64 ATTGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
85826 AAGAA
1 AAGAA
85831 CAAAGAGAAT
Statistics
Matches: 1403, Mismatches: 162, Indels: 270
0.76 0.09 0.15
Matches are distributed among these distances:
88 1 0.00
89 2 0.00
90 17 0.01
91 11 0.01
92 15 0.01
93 344 0.25
94 13 0.01
95 13 0.01
96 174 0.12
97 13 0.01
98 10 0.01
99 198 0.14
100 5 0.00
101 16 0.01
102 154 0.11
103 7 0.00
104 3 0.00
105 159 0.11
106 6 0.00
107 7 0.00
108 164 0.12
109 4 0.00
110 7 0.00
111 15 0.01
112 18 0.01
113 3 0.00
114 16 0.01
115 8 0.01
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.24
Consensus pattern (99 bp):
AAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTTGATGGTGCAAT
TGATGTAGGGAGTGATGAAATTGAAAGGAAGAAA
Found at i:84419 original size:9 final size:9
Alignment explanation
Indices: 84405--84431 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
84395 GATGAAATTG
84405 AAAAGAAGA
1 AAAAGAAGA
84414 AAAAGAAGA
1 AAAAGAAGA
84423 AAAAGAAGA
1 AAAAGAAGA
84432 GGAAGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:84535 original size:96 final size:97
Alignment explanation
Indices: 84418--85830 Score: 1651
Period size: 99 Copynumber: 14.1 Consensus size: 97
84408 AGAAGAAAAA
* *
84418 GAAGAAAAAGAAGAGGAAGAGCAATGAAAATGAGGAGGCTATAGAGGCTATTGCTGTTGTTGATG
1 GAAGAAAAAG-A-AGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATG
*
84483 GTGCAATTGATGTAGGGAGTGATGAAATTGGAAG
64 GTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
* *
84517 GAAGCAAAAGAAGG-AGAGCAATGAAAATGAGGATGCTATTGAAGCAATTGCTGTTGCTGTTGTT
1 GAAGAAAAAGAAGGAAGAGCAATGAAAATGAGGATGCTATTG-AG-----GCTATTGCTGTTGTT
*
84581 GATGGTGCAATTGATGTAGGGAGTGGTGAAATTGAAAG
60 GATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
* *
84619 GAAGAAAAAGAAGGAGAAGAGCAACGAAAATGAGGATGCTATTGAAGCTATTGCTGTTGCTGTTG
1 GAAGAAAAAGAA-G-GAAGAGCAATGAAAATGAGGATGCTATTG-AG-----GCTATTGCTGTTG
84684 TTGATGGTGCAATTGATGTAGGGA-T--T--AA-TGAAA-
58 TTGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
**
84717 -TTG-AAAAGAAGG-AGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTGTT
1 GAAGAAAAAGAAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTA------TTGCTGTTGTT
*
84779 GATGGGGCAATTGATGTAGGGAGTGATGAAATTGAAAG
60 GATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
*
84817 GAAGAAAAAGAA-GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGATGGT
1 GAAGAAAAAGAAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGT
*
84881 GCAATTGATGTAGGAAGTGATGAAATTGAAAAGAAG
66 GCAATTGATGTAGGGAGTGATGAAATTG---A-AAG
* *
84917 AAAAAGAAGAAAAAGAAGAGGAAGAGCAATGAAAATGAGGAGGCTATAGAGGCTATTGCTGTTGT
1 -----GAAGAAAAAG-A-AGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGT
84982 TGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
59 TGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
85021 GAAGAAAAAGAAGGAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGCTGTTG
1 GAAGAAAAAGAA-G-GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTG-T--TG-T-
*
85086 CTGATGGTGCAATTGATGTAGGGAGTAATGAAATTGAAAAG
59 -TGATGGTGCAATTGATGTAGGGAGTGATGAAATTG-AAAG
* *
85127 AAGAAAAAGAAGAAGAAGAAGAATAAGAGCAATGAAAATGAGGAGGCTATTGAGGCTATTGCTGT
1 --G---AAG-A-AA-AAGAAG--GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGT
85192 TGTTGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
56 TGTTGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
* * *
85234 GAAGAAAAAAAAGAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTAGTT-TTGTTGATGAT
1 GAAG-AAAAAGA-AGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTA-TTGCTGTTGTTGAT
* * *
85298 GGTGCAATTGATGTAGGAAGTCATGAAATTGAAAA
63 GGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
85333 GAAGAAAAAGAA-GAAGAGCAATGAAAAT---GA-G-----GAGGCTATTGCTGTTGTTGATGGT
1 GAAGAAAAAGAAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGT
*
85388 GCAATTGATGTAGGGAGTGATGAAATTAAAAAG
66 GCAATTGATGTAGGGAGTGATGAAATT-GAAAG
*
85421 ATGAAAAAGAAGAAGAAGAAGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGT
1 --G---AAGAAAAAGAAG--GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGT
*
85486 TGATGGCGCAATTGATGTAGGGAGTGATG---TTGAAAG
59 TGATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
*
85522 GAAGAAAAAGAAGAAGAAGAGCAATAAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATG
1 GAAGAAAAAGAAG--GAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATG
*
85587 GTG---TTGATGTAGGGAGTGATGAAATTGAAAA
64 GTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
* * *
85618 GAAGAAAAAGAAGAAGAAGAAGAACAAAGAGAATGAGGAGGCTATTGAGGCTATTGCTGTTGTTG
1 GAAGAAAAAGAAG--GAAG-AG--CAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTG
*
85683 ACGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
61 ATGGTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
*
85720 GAAGAAAAAGAAGAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTAATGCTGTTGTTGATG
1 GAAGAAAAAG-A-AGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATG
*
85785 GTGCAATTGATGTAGGGAGTGATGAAATTGAAAA
64 GTGCAATTGATGTAGGGAGTGATGAAATTGAAAG
*
85819 GAAGAAGAAGAA
1 GAAGAAAAAGAA
85831 CAAAGAGAAT
Statistics
Matches: 1163, Mismatches: 64, Indels: 176
0.83 0.05 0.13
Matches are distributed among these distances:
86 2 0.00
87 47 0.04
88 3 0.00
90 1 0.00
92 3 0.00
93 88 0.08
94 2 0.00
95 1 0.00
96 196 0.17
97 11 0.01
98 12 0.01
99 273 0.23
100 12 0.01
101 12 0.01
102 152 0.13
103 3 0.00
104 7 0.01
105 161 0.14
106 5 0.00
107 5 0.00
108 111 0.10
110 1 0.00
111 5 0.00
112 1 0.00
113 4 0.00
114 45 0.04
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (97 bp):
GAAGAAAAAGAAGGAAGAGCAATGAAAATGAGGATGCTATTGAGGCTATTGCTGTTGTTGATGGT
GCAATTGATGTAGGGAGTGATGAAATTGAAAG
Found at i:84923 original size:9 final size:9
Alignment explanation
Indices: 84909--84935 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
84899 GATGAAATTG
84909 AAAAGAAGA
1 AAAAGAAGA
84918 AAAAGAAGA
1 AAAAGAAGA
84927 AAAAGAAGA
1 AAAAGAAGA
84936 GGAAGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:85628 original size:9 final size:9
Alignment explanation
Indices: 85614--85647 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
85604 GATGAAATTG
85614 AAAAGAAGA
1 AAAAGAAGA
85623 AAAAGAAGA
1 AAAAGAAGA
*
85632 AGAAGAAGA
1 AAAAGAAGA
85641 ACAAAGA
1 A-AAAGA
85648 GAATGAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:88224 original size:19 final size:19
Alignment explanation
Indices: 88197--88236 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
88187 AATGTTTACA
88197 TTAGAATAT-TATTATATAT
1 TTAGAATATGT-TTATATAT
*
88216 TTAGTATATGTTTATATAT
1 TTAGAATATGTTTATATAT
88235 TT
1 TT
88237 TTTAATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTAGAATATGTTTATATAT
Found at i:98194 original size:28 final size:27
Alignment explanation
Indices: 98128--98196 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
98118 AAACGGGATT
*
98128 AAATGCAATTTTTGGATACCCGAGGGTA
1 AAATGCAA-TTTTGGATACCCGAGGGGA
* **
98156 AAATGATAATTTTGGATACTTGAGGGGA
1 AAATG-CAATTTTGGATACCCGAGGGGA
98184 AAATAGCAATTTT
1 AAAT-GCAATTTT
98197 CGAAGGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (27 bp):
AAATGCAATTTTGGATACCCGAGGGGA
Found at i:98303 original size:29 final size:29
Alignment explanation
Indices: 98266--98327 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
98256 GGATATTCGG
98266 GGGTAAAAATG-AGATTTTTGGAAAAGTTTA
1 GGGTAAAAATGTA-ATTTTTGG-AAAGTTTA
*
98296 GGGTAAAAATGTAATTTTTGGATAGTTTA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTA
98325 GGG
1 GGG
98328 ACCTTCTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.33
30 19 0.63
31 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTA
Found at i:103940 original size:3 final size:3
Alignment explanation
Indices: 103932--103958 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
103922 TTCCTTTTAT
103932 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
103959 TCTTGGTGTA
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:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109556 original size:16 final size:16
Alignment explanation
Indices: 109532--109562 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
109522 TTTATTTTCT
*
109532 TATATAAAAATAATAA
1 TATAAAAAAATAATAA
109548 TATAAAAAAATAATA
1 TATAAAAAAATAATA
109563 CAGGTGAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAAAAAATAATAA
Found at i:109559 original size:13 final size:14
Alignment explanation
Indices: 109533--109562 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
109523 TTATTTTCTT
109533 ATATAAAAATAATA
1 ATATAAAAATAATA
109547 ATATAAAAA-AATA
1 ATATAAAAATAATA
109560 ATA
1 ATA
109563 CAGGTGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATAAAAATAATA
Found at i:110075 original size:37 final size:37
Alignment explanation
Indices: 110021--110095 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
110011 CTAAAAATTC
* *
110021 AATCTATCTACTATTCACATTTCAAAGTTTAGGTCTA
1 AATCTATCTACTATTCACATTTCAAAGTTCAAGTCTA
*
110058 AATCTATCTACTTTTCACATTTCAAAGTTCAAGTCTA
1 AATCTATCTACTATTCACATTTCAAAGTTCAAGTCTA
110095 A
1 A
110096 CTATTAACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (37 bp):
AATCTATCTACTATTCACATTTCAAAGTTCAAGTCTA
Found at i:118135 original size:2 final size:2
Alignment explanation
Indices: 118128--118164 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
118118 TGAATTATTT
118128 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
118165 TTTTTCCCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:122063 original size:20 final size:21
Alignment explanation
Indices: 122035--122078 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
122025 TTTTTACTAA
122035 TATTATTAAATATT-ATA-ATT
1 TATTATTAAAT-TTAATACATT
*
122055 TATTCTTAAATTTAATACATT
1 TATTATTAAATTTAATACATT
122076 TAT
1 TAT
122079 GTAGTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTAAATTTAATACATT
Found at i:130048 original size:80 final size:80
Alignment explanation
Indices: 129915--130073 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
129905 AAGATCTATT
* *
129915 CTACTAGAGTCATGTCTATATTGTCAATTCAGTTAGTCACATCTATGTCTTTATATTTTAGGAGT
1 CTACTAGAGTCATGTCTATATTATCAATTCAGTTAGTCACATCTATATCTTTATATTTTAGGAGT
*
129980 CATCCGCTCCGGTGA
66 CATCCGCTCAGGTGA
* * * *
129995 CTACTTGAGTTATGTTTATATTATCAATTCAGTTAGTCACATCTATATCTTTATCTTTTAGGAGT
1 CTACTAGAGTCATGTCTATATTATCAATTCAGTTAGTCACATCTATATCTTTATATTTTAGGAGT
130060 CATCCGCTCAGGTG
66 CATCCGCTCAGGTG
130074 CTCAACCCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (80 bp):
CTACTAGAGTCATGTCTATATTATCAATTCAGTTAGTCACATCTATATCTTTATATTTTAGGAGT
CATCCGCTCAGGTGA
Found at i:148143 original size:25 final size:25
Alignment explanation
Indices: 148115--148185 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
148105 CGAAGTACTT
148115 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGCTGGGG
148140 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGCTGGGG
148165 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACA-AGTGC
148186 AATCCAGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 40 0.89
26 5 0.11
ACGTcount: A:0.38, C:0.23, G:0.28, T:0.11
Consensus pattern (25 bp):
AACAGTAAGCACACAAGTGCTGGGG
Found at i:148193 original size:23 final size:23
Alignment explanation
Indices: 148167--148211 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
148157 TGCTGGGGAA
148167 CAGTAAGCACACACAGTGCAATC
1 CAGTAAGCACACACAGTGCAATC
148190 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
148212 TAGTAGGCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.18, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAATC
Found at i:148262 original size:23 final size:23
Alignment explanation
Indices: 148236--148288 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
148226 AGCGCAAATT
*
148236 AGTAGGCACAC-AAGGTGCGAAAC
1 AGTAAGCACACGAA-GTGCGAAAC
*
148259 AGTAAGCACACGAAGTGTGAAAC
1 AGTAAGCACACGAAGTGCGAAAC
148282 AGTAAGC
1 AGTAAGC
148289 GCGCTAGCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.42, C:0.19, G:0.28, T:0.11
Consensus pattern (23 bp):
AGTAAGCACACGAAGTGCGAAAC
Found at i:151815 original size:97 final size:97
Alignment explanation
Indices: 151649--151842 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
151639 GACTCTTTAC
151649 AACTTTTCTAGCTCCTATTTAAATTTTCACTTCGATAACTTTGCATCTTCTATGTCCAACATTGC
1 AACTTTTCTAGCTCCTATTTAAATTTTCACTTCGATAACTTTGCATCTTCTATGTCCAACATTGC
151714 TTCGTCAATCTCCTTAAGACCTACAAGTAAGT
66 TTCGTCAATCTCCTTAAGACCTACAAGTAAGT
*
151746 AACTTTTCTAGCTCTTATTTAAATTTTCACTTCGATAACTTTGCATCTTCTATGTCCAACATTGC
1 AACTTTTCTAGCTCCTATTTAAATTTTCACTTCGATAACTTTGCATCTTCTATGTCCAACATTGC
151811 TTCGTCAATCTCCTTAAGACCTACAAGTAAGT
66 TTCGTCAATCTCCTTAAGACCTACAAGTAAGT
151843 CTTGTATACC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (97 bp):
AACTTTTCTAGCTCCTATTTAAATTTTCACTTCGATAACTTTGCATCTTCTATGTCCAACATTGC
TTCGTCAATCTCCTTAAGACCTACAAGTAAGT
Found at i:164372 original size:58 final size:58
Alignment explanation
Indices: 164211--164361 Score: 216
Period size: 58 Copynumber: 2.6 Consensus size: 58
164201 ATATTATATA
* *
164211 TTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * *
164271 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
164328 TTATTATTTTTATTAAATTATATTTAATAATAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT
164362 CTTACTAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
57 22 0.27
58 43 0.52
59 9 0.11
60 8 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:164554 original size:46 final size:44
Alignment explanation
Indices: 164461--164554 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
164451 ATTACAGCCT
*
164461 CATTCCATTCAACCAAACACAAAAATACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAAAATACTATTACAGCCCTATTC
* *
164505 CATTCCATTCAACCAAACA-ATTGAATTACTTATTACAGCCCTATTC
1 CATTCCATTCAACCAAACACA--AAAATAC-TATTACAGCCCTATTC
164551 CATT
1 CATT
164555 ACAGTCTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 19 0.43
45 5 0.11
46 19 0.43
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAAAATACTATTACAGCCCTATTC
Found at i:164557 original size:16 final size:16
Alignment explanation
Indices: 164536--164605 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
164526 TGAATTACTT
164536 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
* *
164552 ATTACAGTCTTATTCC
1 ATTACAGCCCTATTCC
* *
164568 ATTACAACCCTATTTC
1 ATTACAGCCCTATTCC
* ***
164584 ACTACAGATTTATTCC
1 ATTACAGCCCTATTCC
164600 ATTACA
1 ATTACA
164606 ACGAATCAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:164579 original size:32 final size:32
Alignment explanation
Indices: 164536--164607 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
164526 TGAATTACTT
* *
164536 ATTACAGCCCTATTCCATTACAG-TCTTATTCC
1 ATTACAACCCTATTCCACTACAGAT-TTATTCC
*
164568 ATTACAACCCTATTTCACTACAGATTTATTCC
1 ATTACAACCCTATTCCACTACAGATTTATTCC
164600 ATTACAAC
1 ATTACAAC
164608 GAATCAAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (32 bp):
ATTACAACCCTATTCCACTACAGATTTATTCC
Found at i:165510 original size:26 final size:26
Alignment explanation
Indices: 165427--165510 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
165417 TTCAAAAACT
165427 AATTTAAA-AAAAAAATTCAAATCTC
1 AATTTAAATAAAAAAATTCAAATCTC
*
165452 AA--T--ATAAAAATAATTACTTAATACTC
1 AATTTAAATAAAAA-AATT-C-AAAT-CTC
* *
165478 AACTTAAATAAAAAAATTCAAATCTA
1 AATTTAAATAAAAAAATTCAAATCTC
165504 AATTTAA
1 AATTTAA
165511 GCAAAAAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
21 1 0.02
22 5 0.11
23 5 0.11
24 1 0.02
25 5 0.11
26 13 0.28
27 3 0.07
28 2 0.04
29 4 0.09
30 7 0.15
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (26 bp):
AATTTAAATAAAAAAATTCAAATCTC
Found at i:165854 original size:19 final size:19
Alignment explanation
Indices: 165830--165872 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
165820 TTTCCAAGCC
165830 TCTTTCTTTACCCCATTAT
1 TCTTTCTTTACCCCATTAT
165849 TCTTTCTTTACCCCATTAT
1 TCTTTCTTTACCCCATTAT
165868 T-TTTC
1 TCTTTC
165873 CTGCATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTTTCTTTACCCCATTAT
Found at i:178234 original size:49 final size:49
Alignment explanation
Indices: 178181--178901 Score: 223
Period size: 49 Copynumber: 14.8 Consensus size: 49
178171 AAGGTTCGTT
* *
178181 GTTGCGAATTAAACTTTTCCCTCCATTTCTTTGTGGTATTGGATTCGCC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * *
178230 GTTGCGGCTTAAA-TCTTTCCCTCCATGTT-TATGAGGTACAAGG-TTTGCC
1 GTTGCGACTTAAACT-TTTCCCTCCAT-TTCTTTGTGGTA-ATGGATTCGCC
* * * * * * *
178279 GTTACGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTAGATTCGCC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * * *
178328 GTTGTGGCTTAAATTTTTCCCTCCATGTT-TCTGAGGTGCAA-GG-TTTGCC
1 GTTGCGACTTAAACTTTTCCCTCCAT-TTCTTTGTGGT--AATGGATTCGCC
* ** * * * * * *
178377 GTTGCGACTTAAACCTTTCATTTCATATCTTCGTGTTACTGGATTCACC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * * * *
178426 GTTTCGGCTTAAATCTTTT-CCTTCA-TGCTTTTGAGGTACAAGG-TTCGTC
1 GTTGCGACTTAAA-CTTTTCCCTCCATTTC-TTTGTGGTA-ATGGATTCGCC
* * * * * * * * *
178475 ATTGTGACTTAAACCTTTCCCTCTATATCCTCGTGGTACTGGATTCGTC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * * * *
178524 GTTGCGGCTTAAA-TATTTCCCTTCATGTT-TCTGAGGTACAAGG-TTTGTC
1 GTTGCGACTTAAACT-TTTCCCTCCAT-TTCTTTGTGGTA-ATGGATTCGCC
* * * * * ** *
178573 ATTGCGACTTAAACCTTTCTCT-CATATCCTCATGGTACTGGATTCGCC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * * *
178621 GTTGCTACTTAAA-TCTTTCCCTTCATGTT-TCTGAGGTACAAGG-TTCCCC
1 GTTGCGACTTAAACT-TTTCCCTCCAT-TTCTTTGTGGTA-ATGGATTCGCC
* * ** * * * *
178670 GTTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTACTAGATTAGTC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * *
178719 GTTGCGGCTTAAA-TCTTTCCCTTCA-TGCTTCTGAGGTACAAGG-TTCGCC
1 GTTGCGACTTAAACT-TTTCCCTCCATTTCTT-TGTGGTA-ATGGATTCGCC
* * * * * **
178768 ATTGCGACTTAAACCTTTCCCT-CA-TTCCTCGTGGTACTGGATTTTCC
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
* * * * *
178815 GTTACTG-CTTAAA-TCTTTCCCTTCATGTT-TCTATGGTATAAGG-TTCGCC
1 GTTGC-GACTTAAACT-TTTCCCTCCAT-TTCTTTGTGGTA-ATGGATTCGCC
* * *
178864 GTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
1 GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTA
178902 CTAGATTCCT
Statistics
Matches: 455, Mismatches: 172, Indels: 90
0.63 0.24 0.13
Matches are distributed among these distances:
46 2 0.00
47 29 0.06
48 56 0.12
49 343 0.75
50 24 0.05
51 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
GTTGCGACTTAAACTTTTCCCTCCATTTCTTTGTGGTAATGGATTCGCC
Found at i:178274 original size:98 final size:98
Alignment explanation
Indices: 178159--178909 Score: 954
Period size: 98 Copynumber: 7.7 Consensus size: 98
178149 TCCTTTTACA
* ** * * * * * *
178159 TTTCTAAGGTACAAGGTTCGTTGTTGCGAATTAAACTTTTCCCTCCATTTCTTTGTGGTATTGGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
*
178224 TTCGCCGTTGCGGCTTAAATCTTTCCCTCCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * *
178257 TTTATGAGGTACAAGGTTTGCCGTTACGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTAGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
* * *
178322 TTCGCCGTTGTGGCTTAAATTTTTCCCTCCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * ** * * *
178355 TTTCTGAGGTGCAAGGTTTGCCGTTGCGACTTAAACCTTTCATTTCATATCTTCGTGTTACTGGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
* * *
178420 TTCACCGTTTCGGCTTAAATCTTTTCCTTCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * *
178453 CTTT-TGAGGTACAAGGTTCGTCATTGTGACTTAAACCTTTCCCTCTATATCCTCGTGGTACTGG
1 -TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGG
* *
178517 ATTCGTCGTTGCGGCTTAAATATTTCCCTTCATG
65 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * * *
178551 TTTCTGAGGTACAAGGTTTGTCATTGCGACTTAAACCTTTCTCT-CATATCCTCATGGTACTGGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
**
178615 TTCGCCGTTGCTACTTAAATCTTTCCCTTCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * *
178648 TTTCTGAGGTACAAGGTTCCCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTACTAGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
* *
178713 TTAGTCGTTGCGGCTTAAATCTTTCCCTTCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* *
178746 CTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCT-CAT-TCCTCGTGGTACTGGA
1 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
** * *
178809 TTTTCCGTTACTGCTTAAATCTTTCCCTTCATG
66 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * *
178842 TTTCT-ATGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAG
1 TTTCTGA-GGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGG
178906 ATTC
65 ATTC
178910 CTGTAAAATA
Statistics
Matches: 564, Mismatches: 83, Indels: 12
0.86 0.13 0.02
Matches are distributed among these distances:
95 1 0.00
96 80 0.14
97 95 0.17
98 385 0.68
99 3 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGGTACTGGA
TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
Found at i:180041 original size:13 final size:12
Alignment explanation
Indices: 180025--180072 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
180015 CTCTCCTTTG
180025 TCTTTTTTCTTTT
1 TCTTTTTT-TTTT
*
180038 TC-TTTTTTTTC
1 TCTTTTTTTTTT
*
180049 TC-TTTTTTTCT
1 TCTTTTTTTTTT
180060 TCTTTTTTTTTT
1 TCTTTTTTTTTT
180072 T
1 T
180073 TGAGTGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 14 0.47
12 14 0.47
13 2 0.07
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:180052 original size:11 final size:11
Alignment explanation
Indices: 180028--180069 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
180018 TCCTTTGTCT
*
180028 TTTTTCTTTTTC
1 TTTTT-TTTCTC
180040 TTTTTTTTCTC
1 TTTTTTTTCTC
180051 -TTTTTTTCTTC
1 TTTTTTTTC-TC
180062 TTTTTTTT
1 TTTTTTTT
180070 TTTTGAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 8 0.30
11 7 0.26
12 12 0.44
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:180875 original size:21 final size:21
Alignment explanation
Indices: 180850--180894 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
180840 TCATCTTGAA
*
180850 TTTCTTTTTCTTCCTTTTTCT
1 TTTCTTCTTCTTCCTTTTTCT
* *
180871 TTTCTTCTTCTTCTTTTTTTT
1 TTTCTTCTTCTTCCTTTTTCT
180892 TTT
1 TTT
180895 TAAAGATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCTTCTTCTTCCTTTTTCT
Found at i:180886 original size:14 final size:15
Alignment explanation
Indices: 180855--180887 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
180845 TTGAATTTCT
*
180855 TTTTCTTCCTTTTTC
1 TTTTCTTCCTTCTTC
180870 TTTTCTT-CTTCTTC
1 TTTTCTTCCTTCTTC
180884 TTTT
1 TTTT
180888 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTCCTTCTTC
Found at i:185271 original size:14 final size:15
Alignment explanation
Indices: 185242--185275 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
185232 AATGATACTT
185242 TGAAACATCAAAAGG
1 TGAAACATCAAAAGG
*
185257 TGAAA-ATCTAAAGG
1 TGAAACATCAAAAGG
185271 TGAAA
1 TGAAA
185276 GAAAGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (15 bp):
TGAAACATCAAAAGG
Found at i:186355 original size:24 final size:23
Alignment explanation
Indices: 186319--186373 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
186309 GTTTGGAAGT
* * *
186319 TTTTTATTCTTCTTTTTTTTAACTG
1 TTTTT-TTATTCTTTTTATT-ACTA
186344 TTTTTTTATTCTTTTTATTACTA
1 TTTTTTTATTCTTTTTATTACTA
186367 TTTTTTT
1 TTTTTTT
186374 TAAAAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 10 0.37
24 12 0.44
25 5 0.19
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTTTATTCTTTTTATTACTA
Found at i:188748 original size:21 final size:21
Alignment explanation
Indices: 188718--188770 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
188708 CAGATTATTC
*
188718 CCTTCACTCATCATTCTCTC-T
1 CCTTCTCTCAT-ATTCTCTCAT
*
188739 TCTTCTCTCA-ATTCTCTCAT
1 CCTTCTCTCATATTCTCTCAT
188759 CCTTCCTCTCAT
1 CCTT-CTCTCAT
188771 TTTCCATCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.31
20 4 0.15
21 14 0.54
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (21 bp):
CCTTCTCTCATATTCTCTCAT
Found at i:191525 original size:13 final size:14
Alignment explanation
Indices: 191505--191564 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
191495 TTAATAAAGC
191505 AAATATATAAATAAT
1 AAATATAT-AATAAT
*
191520 AAATATATGAATAAC
1 AAATATAT-AATAAT
191535 AAATA-ATAATAAAT
1 AAATATATAAT-AAT
191549 AAA-ATA-AATAACT
1 AAATATATAATAA-T
191562 AAA
1 AAA
191565 ATCATGCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 2 0.05
13 11 0.28
14 8 0.21
15 18 0.46
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATATATAATAAT
Found at i:191525 original size:15 final size:15
Alignment explanation
Indices: 191504--191550 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
191494 TTTAATAAAG
191504 CAAATATATAAATAA
1 CAAATATATAAATAA
* *
191519 TAAATATATGAATAA
1 CAAATATATAAATAA
191534 CAAATAATAATAAATAA
1 CAAAT-AT-ATAAATAA
191551 AATAAATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 17 0.65
16 2 0.08
17 7 0.27
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (15 bp):
CAAATATATAAATAA
Found at i:191556 original size:9 final size:10
Alignment explanation
Indices: 191506--191559 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
191496 TAATAAAGCA
191506 AATATATAAAT
1 AATA-ATAAAT
*
191517 AATAAATATAT
1 AAT-AATAAAT
*
191528 GAATAACAAAT
1 -AATAATAAAT
191539 AATAATAAAT
1 AATAATAAAT
191549 AA-AATAAAT
1 AATAATAAAT
191558 AA
1 AA
191560 CTAAAATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 9 0.24
10 11 0.30
11 13 0.35
12 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AATAATAAAT
Found at i:191557 original size:19 final size:22
Alignment explanation
Indices: 191506--191564 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 22
191496 TAATAAAGCA
*
191506 AATATATAAATAATAAATATATG
1 AATA-ATAAATAATAAATAAATG
*
191529 AATAACAAATAAT-AATAAAT-
1 AATAATAAATAATAAATAAATG
191549 AA-AATAAATAACTAAA
1 AATAATAAATAA-TAAA
191565 ATCATGCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.26
20 3 0.10
21 8 0.26
22 8 0.26
23 4 0.13
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAATAAATAATAAATAAATG
Found at i:191627 original size:31 final size:31
Alignment explanation
Indices: 191564--191655 Score: 96
Period size: 37 Copynumber: 2.8 Consensus size: 31
191554 AAATAACTAA
*
191564 AATCATGCAAATTAAACAAATAAAAATAAAT
1 AATCATGCAAATTAAACAAACAAAAATAAAT
* *
191595 AATCGTGCAAATTAAACACACACAAAATAATAATTAG
1 AATCATGCAAATTAAACA-A-AC-AAA-AATAA--AT
191632 AATCATGCAAATTAAACAAA-AAAA
1 AATCATGCAAATTAAACAAACAAAA
191656 TGTAAAGGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
31 17 0.33
32 2 0.04
33 4 0.08
34 3 0.06
35 6 0.12
36 1 0.02
37 18 0.35
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (31 bp):
AATCATGCAAATTAAACAAACAAAAATAAAT
Found at i:192822 original size:15 final size:17
Alignment explanation
Indices: 192802--192834 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
192792 GAAATTTTAT
192802 TTGGG-TTGT-AACAAA
1 TTGGGTTTGTAAACAAA
192817 TTGGGTTTGTAAACAAA
1 TTGGGTTTGTAAACAAA
192834 T
1 T
192835 AAATGAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 4 0.25
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TTGGGTTTGTAAACAAA
Found at i:193040 original size:15 final size:17
Alignment explanation
Indices: 193020--193052 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
193010 GAAATTTTAT
193020 TTGGG-TTGT-AACAAA
1 TTGGGTTTGTAAACAAA
193035 TTGGGTTTGTAAACAAA
1 TTGGGTTTGTAAACAAA
193052 T
1 T
193053 AAATGAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 4 0.25
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TTGGGTTTGTAAACAAA
Found at i:193449 original size:42 final size:42
Alignment explanation
Indices: 193323--193936 Score: 484
Period size: 42 Copynumber: 14.9 Consensus size: 42
193313 GGTGTTGTAA
* *
193323 CTTCAATATGCCCCTCTGGATTAGGGGTAAGAGATTGGATGATGG
1 CTTCAATCTG-CCCTCTTG-TTA-GGGTAAGAGATTGGATGATGG
* * * * *
193368 CTTTAATTTACCCTCTAGATTAGGGTAAGAGATTGGATGGTGG
1 CTTCAATCTGCCCTCTTG-TTAGGGTAAGAGATTGGATGATGG
* * *
193411 CTTCAATCTGCCCTCTTGTTTGGGTAAGAGATTAGATGGTGG
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* *
193453 CTTTAATCTGCCCTCTTGTTAGGGTAAAAGATT--A-GATGG
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * *
193492 CTTCAATCTGCCC-CATGGTTAGGGTAAGAGATTGGATGGTGT
1 CTTCAATCTGCCCTC-TTGTTAGGGTAAGAGATTGGATGATGG
193534 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGA---
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * * * * *
193573 CTTCAATCT-ACCTAATGGTTGGGGTAATAGATTGGATGATGT
1 CTTCAATCTGCCCT-CTTGTTAGGGTAAGAGATTGGATGATGG
* * * * *
193615 CTTCAATCTGTCCACTTGTTAGGGTAAAATATTGGAT-A--A
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * * * *
193654 CTTCAATCTGCCC-CATGGTTGGGGTAAAAGGTTGGATGATGT
1 CTTCAATCTGCCCTC-TTGTTAGGGTAAGAGATTGGATGATGG
* * * *
193696 CTTCAATTTGCCTTTTTGTTAGGGTAAAAGATT-G--GATGG
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * * * * *
193735 CTTCAATTTG-CCTCATGCTTGGGGGTAAGAAATTGGATGGTGT
1 CTTCAATCTGCCCTCTTG-TT-AGGGTAAGAGATTGGATGATGG
* *
193778 CTTCAATCTACCCTCTTGTTAGGGTAAAAGATTGGATGA---
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * * * *
193817 CTTCAATCTGCCC-CATGATTGGGGTAAGAAATTGGATGGTGT
1 CTTCAATCTGCCCTCTTG-TTAGGGTAAGAGATTGGATGATGG
*
193859 CTTCAATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGA---
1 CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
* * *
193898 CTTCAATCTGCCC-CATGGTCGAGGTAAGGAGATTGGATG
1 CTTCAATCTGCCCTCTTGTTAG-GGTAA-GAGATTGGATG
193937 GGATGATGTA
Statistics
Matches: 463, Mismatches: 78, Indels: 61
0.77 0.13 0.10
Matches are distributed among these distances:
38 17 0.04
39 155 0.33
40 22 0.05
41 4 0.01
42 188 0.41
43 53 0.11
44 17 0.04
45 7 0.02
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
CTTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGATGG
Found at i:193524 original size:81 final size:81
Alignment explanation
Indices: 193322--193937 Score: 739
Period size: 81 Copynumber: 7.5 Consensus size: 81
193312 TGGTGTTGTA
* * * * * * * *
193322 ACTTCAATATGCCCCTCTGGATTAGGGGTAAGAGATTGGATGATGGCTTTAATTTACCCTCTAGA
1 ACTTCAATCTGCCCC-ATGG-TT-GGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTG-
*
193387 TTAGGGTAAGAGATTGGATGGTG
62 TTAGGGTAAAAGATTGGA---TG
* * * * * *
193410 GCTTCAATCTGCCCTC-TTGTTTGGGTAAGAGATTAGATGGTGGCTTTAATCTGCCCTCTTGTTA
1 ACTTCAATCTGCCC-CATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTA
*
193474 GGGTAAAAGATTAGATG
65 GGGTAAAAGATTGGATG
* *
193491 GCTTCAATCTGCCCCATGGTTAGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
1 ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
*
193556 GGTAAGAGATTGGATG
66 GGTAAAAGATTGGATG
* ** * * * *
193572 ACTTCAATCTACCTAATGGTTGGGGTAATAGATTGGATGATGTCTTCAATCTGTCCACTTGTTAG
1 ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
* *
193637 GGTAAAATATTGGATA
66 GGTAAAAGATTGGATG
* * * * * *
193653 ACTTCAATCTGCCCCATGGTTGGGGTAAAAGGTTGGATGATGTCTTCAATTTGCCTTTTTGTTAG
1 ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
193718 GGTAAAAGATTGGATG
66 GGTAAAAGATTGGATG
* * * * * *
193734 GCTTCAATTTGCCTCATGCTTGGGGGTAAGAAATTGGATGGTGTCTTCAATCTACCCTCTTGTTA
1 ACTTCAATCTGCCCCATGGTT-GGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTA
193799 GGGTAAAAGATTGGATG
65 GGGTAAAAGATTGGATG
* *
193816 ACTTCAATCTGCCCCATGATTGGGGTAAGAAATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
1 ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
193881 GGTAAAAGATTGGATG
66 GGTAAAAGATTGGATG
* *
193897 ACTTCAATCTGCCCCATGGTCGAGGTAAGGAGATTGGATGG
1 ACTTCAATCTGCCCCATGGTTGGGGTAA-GAGATTGGATGG
193938 GATGATGTAA
Statistics
Matches: 461, Mismatches: 63, Indels: 14
0.86 0.12 0.03
Matches are distributed among these distances:
80 1 0.00
81 313 0.68
82 80 0.17
84 16 0.03
85 34 0.07
86 2 0.00
87 2 0.00
88 12 0.03
89 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (81 bp):
ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAG
GGTAAAAGATTGGATG
Found at i:193801 original size:244 final size:243
Alignment explanation
Indices: 193341--193916 Score: 722
Period size: 244 Copynumber: 2.3 Consensus size: 243
193331 TGCCCCTCTG
* * * * * * * *
193341 GATTAGGGGTAAGAGATTGGATGATGGCTTTAATTTACCCTCTAGATTAGGGTAAGAGATTGGAT
1 GATT-GGGGTAAGAAATTGGATGATGTCTTCAATCTGCCCACTTG-TTAGGGTAAAAGATTGGA-
** * * * * * * * * * * *
193406 GGTGGCTTCAATCTGCCCTC-TTGTTTGGGTAAGAGATTAGATGGTGGCTTTAATCTGCCCTCTT
63 --TAACTTCAATCTGCCC-CATGGTTGGGGTAAAAGGTTGGATGATGTCTTCAATTTGCCTTTTT
* *
193470 GTTAGGGTAAAAGATTAGATGGCTTCAATCTGCCCCATGGTTAGGGTAAGAGATTGGATGGTGTC
125 GTTAGGGTAAAAGATTAGATGGCTTCAATCTGCCCCATGCTTAGGGTAAGAAATTGGATGGTGTC
* * *
193535 TTCAATCTGCCCTCTTGTTAGGGTAAGAGATTGGATGACTTCAATCTACCTAAT
190 TTCAATCTACCCTCTTGTTAGGGTAAAAGATTGGATGACTTCAATCTACCCAAT
* * * * *
193589 GGTTGGGGTAATAGATTGGATGATGTCTTCAATCTGTCCACTTGTTAGGGTAAAATATTGGATAA
1 GATTGGGGTAAGAAATTGGATGATGTCTTCAATCTGCCCACTTGTTAGGGTAAAAGATTGGATAA
193654 CTTCAATCTGCCCCATGGTTGGGGTAAAAGGTTGGATGATGTCTTCAATTTGCCTTTTTGTTAGG
66 CTTCAATCTGCCCCATGGTTGGGGTAAAAGGTTGGATGATGTCTTCAATTTGCCTTTTTGTTAGG
* * * *
193719 GTAAAAGATTGGATGGCTTCAATTTGCCTCATGCTTGGGGGTAAGAAATTGGATGGTGTCTTCAA
131 GTAAAAGATTAGATGGCTTCAATCTGCCCCATGCTT-AGGGTAAGAAATTGGATGGTGTCTTCAA
* *
193784 TCTACCCTCTTGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCAT
195 TCTACCCTCTTGTTAGGGTAAAAGATTGGATGACTTCAATCTACCCAAT
* * *
193833 GATTGGGGTAAGAAATTGGATGGTGTCTTCAATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGA
1 GATTGGGGTAAGAAATTGGATGATGTCTTCAATCTGCCCACTTGTTAGGGTAAAAGATTGGATAA
193898 CTTCAATCTGCCCCATGGT
66 CTTCAATCTGCCCCATGGT
193917 CGAGGTAAGG
Statistics
Matches: 283, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
242 1 0.00
243 85 0.30
244 146 0.52
246 16 0.06
247 32 0.11
248 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (243 bp):
GATTGGGGTAAGAAATTGGATGATGTCTTCAATCTGCCCACTTGTTAGGGTAAAAGATTGGATAA
CTTCAATCTGCCCCATGGTTGGGGTAAAAGGTTGGATGATGTCTTCAATTTGCCTTTTTGTTAGG
GTAAAAGATTAGATGGCTTCAATCTGCCCCATGCTTAGGGTAAGAAATTGGATGGTGTCTTCAAT
CTACCCTCTTGTTAGGGTAAAAGATTGGATGACTTCAATCTACCCAAT
Found at i:206420 original size:15 final size:15
Alignment explanation
Indices: 206400--206442 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
206390 AACATACATA
206400 CAATAAAATGTAAAG
1 CAATAAAATGTAAAG
*
206415 CAATAAAATGCAAA-
1 CAATAAAATGTAAAG
206429 -AATAAAATGTAAAG
1 CAATAAAATGTAAAG
206443 GATTACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.48
15 13 0.52
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.19
Consensus pattern (15 bp):
CAATAAAATGTAAAG
Found at i:207466 original size:31 final size:31
Alignment explanation
Indices: 207411--207520 Score: 132
Period size: 33 Copynumber: 3.4 Consensus size: 31
207401 CAAATAATAA
* *
207411 TAAATAAAATAAATAACTAAAATCATGCAAAT
1 TAAACAAAAAAAATAA-TAAAATCATGCAAAT
*
207443 TAAACAAATAAAAATAA-ATAATCATGCAAAT
1 TAAACAAA-AAAAATAATAAAATCATGCAAAT
207474 TAAACATAAAAAATAATAATTAAAATCATGCAAAT
1 TAAAC--AAAAAA-AATAA-TAAAATCATGCAAAT
207509 TAAACAAAAAAA
1 TAAACAAAAAAA
207521 TGTAAAGGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
31 18 0.26
32 11 0.16
33 21 0.31
35 18 0.26
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (31 bp):
TAAACAAAAAAAATAATAAAATCATGCAAAT
Found at i:207508 original size:35 final size:33
Alignment explanation
Indices: 207416--207521 Score: 144
Period size: 35 Copynumber: 3.2 Consensus size: 33
207406 AATAATAAAT
207416 AAAATAAATAACTAAAATCATGCAAATTAAACAAA
1 AAAAT-AATAA-TAAAATCATGCAAATTAAACAAA
* *
207451 TAAA-AATAA-ATAATCATGCAAATTAAACATAA
1 AAAATAATAATAAAATCATGCAAATTAAACA-AA
207483 AAAATAATAATTAAAATCATGCAAATTAAACAAA
1 AAAATAATAA-TAAAATCATGCAAATTAAACAAA
207517 AAAAT
1 AAAAT
207522 GTAAAGGGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
31 19 0.30
32 5 0.08
33 10 0.16
34 7 0.11
35 22 0.35
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (33 bp):
AAAATAATAATAAAATCATGCAAATTAAACAAA
Found at i:208611 original size:17 final size:16
Alignment explanation
Indices: 208584--208617 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
208574 GCAATTTTAT
208584 TTGGGTTGTAAACAAA
1 TTGGGTTGTAAACAAA
*
208600 TTGGGATTGTAAAGAAA
1 TTGGG-TTGTAAACAAA
208617 T
1 T
208618 AAATGAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (16 bp):
TTGGGTTGTAAACAAA
Found at i:209747 original size:21 final size:20
Alignment explanation
Indices: 209709--209755 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
209699 TTTGAAAGAG
*
209709 TTAAAAAATTAAAATTTTGT
1 TTAAAAAATTAAAATTTTCT
* *
209729 TTAAAAATTTAAACTTTTTCT
1 TTAAAAAATTAAA-ATTTTCT
209750 TTAAAA
1 TTAAAA
209756 TCACTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAAAAATTAAAATTTTCT
Found at i:209994 original size:148 final size:148
Alignment explanation
Indices: 209689--210321 Score: 859
Period size: 147 Copynumber: 4.3 Consensus size: 148
209679 TTTAAAATGA
* * * *
209689 AAACTTTTATTTTGAAAGAGTT-AAAAAATTAAAATTTTGTTTAAAAATTTAAACTTTTTCTTTA
1 AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
* * *
209753 AAATCACTAAAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCTTTCTTTTTTAATGAAAAT
66 AAATGACT--AAAAACATATTTTTATTTTTAAAAATCTAAACTTTC--TCTTTTTTAAAGAAAAT
*
209818 CACTACTTTACTTAAAAATT-C
127 CACTATTTTACTTAAAAATTCC
* *
209839 AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAATTTTAAAC-TTTTATTTA
1 AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
* *
209903 AAATAACT-AAAACATATTTTTATTTTTAAAAATCTAAACTTTTCTTTTTTTTTTAAAGAAAATC
66 AAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAAC-TTTC--TCTTTTTTAAAGAAAATC
209967 ACTATTTTACTT-AAAATTCC
128 ACTATTTTACTTAAAAATTCC
* * * *
209987 AAACTTTTTTTTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAATTTTAAACTTTTTCTTT
1 AAAC-TTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTT
*
210052 AAAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAACTTTCTATTTTTTAAAGAAAATCAC
65 AAAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCAC
210117 TATTTTACTTAAAAATAT--
130 TATTTTACTTAAAAAT-TCC
* * * **
210135 AAATTTTTATTTTGAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAATTTTTTTCTTTA
1 AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
* * *
210200 AAATGACTAAAAGCATATTTTTATTTTTAAAAATCTAAATTTTCTCTTTTTTAAAGAAAATAACT
66 AAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACT
* * *
210265 ATTTT-TTTAAAAACTCA
131 ATTTTACTTAAAAATTCC
*
210282 AAACTTTTATTTCGAAATTGTTAAAAAAATCAAAAATTTT
1 AAACTTTTATTTCGAAATAGTTAAAAAAATC-AAAATTTT
210322 CCCAATATTA
Statistics
Matches: 438, Mismatches: 34, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
145 1 0.00
146 7 0.02
147 185 0.42
148 77 0.18
149 53 0.12
150 55 0.13
151 60 0.14
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (148 bp):
AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
AAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACT
ATTTTACTTAAAAATTCC
Found at i:210241 original size:51 final size:48
Alignment explanation
Indices: 209864--210242 Score: 132
Period size: 48 Copynumber: 7.7 Consensus size: 48
209854 AATAGTTAAA
* * * * * * *
209864 AAAATCAAAATTTTATTTAAAATTTTAAA-CTTTTATTTAAAATAACT
1 AAAATCATATTTTTATTTAAAAATCTAAATTTTTTTTTTAAAATGACT
*** * **
209911 AAAA-CATATTTTTATTTTTAAAAATCTAAACTTTTCTTTTTT-TTTTAAAG
1 AAAATCATATTTTTA--TTTAAAAATCTAAA-TTTT-TTTTTTAAAATGACT
* * * * * **
209961 AAAATCACTA-TTTTACTTAAAATTCCAAACTTTTTTTTTCGAAATAGTTAAA
1 AAAATCA-TATTTTTATTTAAAAATCTAAA-TTTTTTTTT-TAAA-A-TGACT
* ** * * * * *
210013 AAAATCAAAACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATGACT
1 AAAATCATATTTTTATTTAAAAATCTAAATTTTTTTTTTAAAATGACT
*
210061 AAAAACATATTTTTATTTTTAAAAATCTAAACTTTCTATTTTTT-AAA-G---
1 AAAATCATATTTTTA--TTTAAAAATCTAAA-TTT-T-TTTTTTAAAATGACT
* * * * **
210109 AAAATCACTA-TTTTACTTAAAAATATAAATTTTTATTTTGAAATAGTTAAA
1 AAAATCA-TATTTTTATTTAAAAATCTAAATTTTT-TTTTTAAA-A-TGACT
* ** *
210160 AAAATCAAAACTTTATTTAAAAAT-TTAATTTTTTTCTTTAAAATGACT
1 AAAATCATATTTTTATTTAAAAATCTAAATTTTTTT-TTTAAAATGACT
*
210208 AAAAGCATATTTTTATTTTTAAAAATCTAAATTTT
1 AAAATCATATTTTTA--TTTAAAAATCTAAATTTT
210243 CTCTTTTTTA
Statistics
Matches: 242, Mismatches: 59, Indels: 58
0.67 0.16 0.16
Matches are distributed among these distances:
43 1 0.00
44 5 0.02
45 5 0.02
46 21 0.09
47 4 0.02
48 53 0.22
49 22 0.09
50 47 0.19
51 49 0.20
52 30 0.12
53 5 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (48 bp):
AAAATCATATTTTTATTTAAAAATCTAAATTTTTTTTTTAAAATGACT
Found at i:210753 original size:3 final size:3
Alignment explanation
Indices: 210745--210810 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
210735 AAACCCTAAA
210745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
210793 AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT
210811 TTGGGCCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:211301 original size:42 final size:42
Alignment explanation
Indices: 211243--211838 Score: 697
Period size: 42 Copynumber: 14.2 Consensus size: 42
211233 CCTTCATATA
* ** * ** *
211243 CAATGAAGAAATAAATGGACCTTTACGCCTAAGCCTCTAAAGG
1 CAATGAA-AAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
211286 CAATAAAAAGTAAATGGACCTCTACACCTAGGTCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
211328 CGATGAAAAGTAAATGGACCTCCACACTTGGGTCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
211370 CGATGAAAAATAAATGGGCCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
211412 TAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* *
211454 CAATGAAGAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
211496 CAATGAAAAGTAAATGGACCTTCATACCTAGGCCTTTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
211538 CAATGAAAAGAAAATAGACCTCCACACCTAGGCATCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
211580 CAATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * * **
211622 CAATGATATGTAAATTGATCTCCACACCTTAGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * **
211664 CAATGAAAACTAAATGGACATCAACATATGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * * *
211706 CAATGAAAAGTAAATGAACCTCCATACCTAGGTCTCTAAACG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
211748 CAATGAAAAGTAAATGGACCTCCACTCTTGGGCCTCTAAATT
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * **
211790 CAATGAAATGTAAATGGCCCTCCACATTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
211832 TAATGAA
1 CAATGAA
211839 CGTTTTCCTT
Statistics
Matches: 474, Mismatches: 79, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
42 468 0.99
43 6 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
Found at i:212266 original size:20 final size:23
Alignment explanation
Indices: 212241--212287 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
212231 GCTCTCTTTA
212241 TTTTTTCT-TCTTTT-TTGTTGT
1 TTTTTTCTCTCTTTTATTGTTGT
*
212262 TTTTTTCTCTCTTTTATTTTTGT
1 TTTTTTCTCTCTTTTATTGTTGT
212285 TTT
1 TTT
212288 GTTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 9 0.39
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (23 bp):
TTTTTTCTCTCTTTTATTGTTGT
Found at i:212848 original size:11 final size:11
Alignment explanation
Indices: 212834--212886 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
212824 TTCTATTTCC
212834 TTTCTTTTTTG
1 TTTCTTTTTTG
*
212845 TTTCTTATTTG
1 TTTCTTTTTTG
*
212856 TTTTTTTTTTG
1 TTTCTTTTTTG
*
212867 TTTCTTCTTT-
1 TTTCTTTTTTG
212877 TTTCTTTTTT
1 TTTCTTTTTT
212887 TTTGGAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.02, C:0.09, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTG
Found at i:215670 original size:21 final size:21
Alignment explanation
Indices: 215636--215675 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
215626 TAGTACAGAC
*
215636 TTCTACCGATACAAGTGACAT
1 TTCTACCGACACAAGTGACAT
*
215657 TTCTATCGACACAAGTGAC
1 TTCTACCGACACAAGTGAC
215676 TATGTTACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGACACAAGTGACAT
Found at i:228065 original size:30 final size:30
Alignment explanation
Indices: 228005--228093 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
227995 TGTTAAAAAT
*
228005 ATTTAAA-ATTA-ATAACTCATTTAT-ATATA
1 ATTTAAACATTAGATAATTC-TTT-TCATATA
228034 ATTTAAACATTAGATAATTCTTTTCATATA
1 ATTTAAACATTAGATAATTCTTTTCATATA
228064 ATTTAAACATTAGATAATTCTTTTCATATA
1 ATTTAAACATTAGATAATTCTTTTCATATA
228094 TTTTCCTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
29 8 0.14
30 42 0.75
31 6 0.11
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (30 bp):
ATTTAAACATTAGATAATTCTTTTCATATA
Found at i:228179 original size:18 final size:18
Alignment explanation
Indices: 228158--228194 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
228148 AATATTATAA
228158 AATAAAATAATTATTTTT
1 AATAAAATAATTATTTTT
* *
228176 AATATAATTATTATTTTT
1 AATAAAATAATTATTTTT
228194 A
1 A
228195 TACGAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAAAATAATTATTTTT
Found at i:228288 original size:39 final size:43
Alignment explanation
Indices: 228244--228323 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
228234 GTTAATATGA
228244 TATTTTAAATA-T-TT-T-TATATGTGAAATATTTTAATTAAT
1 TATTTTAAATATTATTATGTATATGTGAAATATTTTAATTAAT
*
228283 TATTTTAAATATTATTATGTTTATGTGAAATATTTTAATTA
1 TATTTTAAATATTATTATGTATATGTGAAATATTTTAATTA
228324 CACATACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 11 0.31
40 1 0.03
41 2 0.06
42 1 0.03
43 21 0.58
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (43 bp):
TATTTTAAATATTATTATGTATATGTGAAATATTTTAATTAAT
Found at i:234276 original size:342 final size:342
Alignment explanation
Indices: 233645--234329 Score: 980
Period size: 342 Copynumber: 2.0 Consensus size: 342
233635 CAGCACTTTC
* * *
233645 ATCACTATTTCTTGAGTTTAATGCGTGTTCTGTTAGCCTTTTAGGCAGCATGTTTTTTGCATGAG
1 ATCACTATTTCTTGAGTTAAATACATGTTCTGTTAGCCTTTTAGGCAGCATGTTTTTTGCATGAG
* * ** * * *
233710 ACGGTTCACTTATGTGATTGAATTTTGAGACAAACATAGGAGCTGTTTTAGTTGCATCATGATTT
66 AAGGTTCACTTATGTGATTGAATTTTGAGACAAACACACCAGCTATTTCAGTTGCATCATGACTT
* * * *
233775 TCTGGACCATCACATACAGTCCTGTTCTTTTCTCCACTAGCATTATATCTTTTCACAACTATATT
131 TCTGGACCATCACATACAGTCCTATTCTTTCCTCCACTAGCATCATATCCTTTCACAACTATATT
* *
233840 TTCATTTTGTTGACTCACTTGGCATCGTACATCATTAAATATTCTACAATGATGTCCAACTGTCT
196 TTCATTTTGTTGACTCACTTGGCATCGTACATCATTAAATATGCTACAATGATGTCCAACTGCCT
*
233905 GATCTGCATTGTGTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCATCAAAGCATGCATCT
261 GATCTGCATTGTCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCATCAAAGCATGCATCT
*
233970 CTATTTGAATCACCAAA
326 CTAGTTGAATCACCAAA
* * *
233987 ATCACTATTTCTTGAGTTAAATACATGTTTTGTTTGCCTTTTAGGCAGGATGTTTTTTGCACT-A
1 ATCACTATTTCTTGAGTTAAATACATGTTCTGTTAGCCTTTTAGGCAGCATGTTTTTTGCA-TGA
* * * *
234051 GAAGGTTCACTTCTTTGGTTGAATTTTGAGACAATCACACCAGCTATTTCAGTTGCATCATGACT
65 GAAGGTTCACTTATGTGATTGAATTTTGAGACAAACACACCAGCTATTTCAGTTGCATCATGACT
* * * *
234116 TTCTGGCCCATCACATGA-GGTCCTATTGTTTCCTCCACTAGCATCATCTCCTTTCACAACTATA
130 TTCTGGACCATCACAT-ACAGTCCTATTCTTTCCTCCACTAGCATCATATCCTTTCACAACTATA
* * *
234180 TTTTCATTTTGTTGACTCACTTGGCATCGTATATTATTAAATCTGCTGA-AATGATGTCCAACTG
194 TTTTCATTTTGTTGACTCACTTGGCATCGTACATCATTAAATATGCT-ACAATGATGTCCAACTG
** * * * *
234244 CCTGATCTGCATTGTCTGAGTGGTAGTGTGTGCTTCTCCAGCCACCTTTTTCTTCACAGCATGCA
258 CCTGATCTGCATTGTCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCATCAAAGCATGCA
234309 TCTCTAGTTGAATCACCAAA
323 TCTCTAGTTGAATCACCAAA
234329 A
1 A
234330 CCATTAGCTT
Statistics
Matches: 302, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
342 299 0.99
343 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (342 bp):
ATCACTATTTCTTGAGTTAAATACATGTTCTGTTAGCCTTTTAGGCAGCATGTTTTTTGCATGAG
AAGGTTCACTTATGTGATTGAATTTTGAGACAAACACACCAGCTATTTCAGTTGCATCATGACTT
TCTGGACCATCACATACAGTCCTATTCTTTCCTCCACTAGCATCATATCCTTTCACAACTATATT
TTCATTTTGTTGACTCACTTGGCATCGTACATCATTAAATATGCTACAATGATGTCCAACTGCCT
GATCTGCATTGTCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCATCAAAGCATGCATCT
CTAGTTGAATCACCAAA
Found at i:237247 original size:23 final size:24
Alignment explanation
Indices: 237195--237250 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
237185 TAACATTGTT
*
237195 CATGAACATGTTCAATTATATGTT
1 CATGAACATGTTCAATTATATGTC
**
237219 CATGAACATGTTCGGTTA-ATGTC
1 CATGAACATGTTCAATTATATGTC
*
237242 CGTGAACAT
1 CATGAACAT
237251 ATTAACATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (24 bp):
CATGAACATGTTCAATTATATGTC
Found at i:238892 original size:56 final size:56
Alignment explanation
Indices: 238780--239049 Score: 169
Period size: 56 Copynumber: 4.7 Consensus size: 56
238770 TATATTGTTT
* * * *
238780 TTTTTATTGTTTTTGGTGTGTGTTTTTGCTG---TTTTGGTTGTTG-TTTTA-TA-TT
1 TTTTTA-TGGTTTTGGTGT-TGCTTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTA
* *
238832 TTTTTACGGTTTTGGTGCTGCTTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTA
1 TTTTTATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTA
* * * * ** *
238888 TTTTTATTGTTTTTGTTTTTG-TTTTGCTATTATTTTTGCTATTGTTTTGGTTGTTATTTTGTAT
1 TTTTTA-TGGTTTTGGTGTTGCTTTTGCTGTTA---TT--T-TTG--TT-GTTGTT-TTTACTAC
*
238952 TGT
55 T-A
*
238955 TTTTTAATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTGTTGTTGTTTTTGCTACTA
1 TTTTT-ATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTA
* * * *
239012 TTTTTGTTGTTTTTGTTTTTG-TTTTGCTGTTATTTTTG
1 TTTTT-ATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTG
239050 CTATTATTTT
Statistics
Matches: 169, Mismatches: 29, Indels: 36
0.72 0.12 0.15
Matches are distributed among these distances:
50 10 0.06
51 9 0.05
52 6 0.04
53 11 0.07
54 5 0.03
55 2 0.01
56 34 0.20
57 25 0.15
58 6 0.04
59 8 0.05
60 2 0.01
61 1 0.01
62 6 0.04
63 1 0.01
64 2 0.01
65 8 0.05
66 6 0.04
67 16 0.09
68 11 0.07
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (56 bp):
TTTTTATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTA
Found at i:238925 original size:68 final size:67
Alignment explanation
Indices: 238853--239072 Score: 219
Period size: 68 Copynumber: 3.4 Consensus size: 67
238843 TTGGTGCTGC
*
238853 TTTTGCTGTTATTTTTGTTGTTGTTTTTACTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTAT
1 TTTTGCTGTTATTTTTGTTGTTGTTTTT-CTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTGT
238918 TAT
65 TAT
* * * ** * *
238921 TTTTGC---TA---TTGTT-TTGGTTGT-TA-T-TTTGTATTGTTTTT-TAATGGTTTTGGTGTT
1 TTTTGCTGTTATTTTTGTTGTTGTTTTTCTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTGTT
**
238975 GC
66 AT
*
238977 TTTTGCTGTTATTTTTGTTGTTGTTTTTGCTACTATTTTTGTTGTTTTTGTTTTTGTTTTGCTGT
1 TTTTGCTGTTATTTTTGTTGTTGTTTTT-CTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTGT
239042 TAT
65 TAT
* * *
239045 TTTTGCTATTATTTTGGTTGTTTTTTTT
1 TTTTGCTGTTATTTTTGTTGTTGTTTTT
239073 TTTGCGTTTT
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
56 17 0.15
57 13 0.11
58 1 0.01
59 4 0.03
61 6 0.05
62 10 0.09
63 6 0.05
65 4 0.03
66 1 0.01
67 12 0.10
68 43 0.37
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (67 bp):
TTTTGCTGTTATTTTTGTTGTTGTTTTTCTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTGTT
AT
Found at i:238970 original size:124 final size:121
Alignment explanation
Indices: 238809--239071 Score: 418
Period size: 124 Copynumber: 2.1 Consensus size: 121
238799 GTGTTTTTGC
*
238809 TGTTTTGGTTGTTGTTTTATATTTTTTTACGGTTTTGGTGCTGCTTTTGCTGTTATTTTTGTTGT
1 TGTTTTGGTTGTTATTTTATATTTTTTTACGGTTTTGGTGCTGCTTTTGCTGTTATTTTTGTTGT
238874 TGTTTTTACTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTATTATTTTTGCTAT
66 TGTTTTTACTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTATTATTTTTGCTAT
* * *
238930 TGTTTTGGTTGTTATTTTGTATTGTTTTTTAATGGTTTTGGTGTTGCTTTTGCTGTTATTTTTGT
1 TGTTTTGGTTGTTATTTTATA-T-TTTTTT-ACGGTTTTGGTGCTGCTTTTGCTGTTATTTTTGT
* * *
238995 TGTTGTTTTTGCTACTATTTTTGTTGTTTTTGTTTTTGTTTTGCTGTTATTTTTGCTAT
63 TGTTGTTTTTACTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTATTATTTTTGCTAT
* *
239054 TATTTTGGTTGTTTTTTT
1 TGTTTTGGTTGTTATTTT
239072 TTTTGCGTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 19 0.15
122 1 0.01
123 6 0.05
124 104 0.80
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (121 bp):
TGTTTTGGTTGTTATTTTATATTTTTTTACGGTTTTGGTGCTGCTTTTGCTGTTATTTTTGTTGT
TGTTTTTACTACTATTTTTATTGTTTTTGTTTTTGTTTTGCTATTATTTTTGCTAT
Found at i:238986 original size:12 final size:12
Alignment explanation
Indices: 238965--239051 Score: 56
Period size: 12 Copynumber: 7.6 Consensus size: 12
238955 TTTTTAATGG
* *
238965 TTTTGGTGTTGC
1 TTTTGCTGTTGT
*
238977 TTTTGCTGTTAT
1 TTTTGCTGTTGT
*
238989 TTTTGTTGTTGT
1 TTTTGCTGTTGT
** *
239001 TTTTGCTACT-A
1 TTTTGCTGTTGT
239012 TTTT--TGTTGT
1 TTTTGCTGTTGT
* *
239022 TTTTGTTTTTG-
1 TTTTGCTGTTGT
*
239033 TTTTGCTGTTAT
1 TTTTGCTGTTGT
239045 TTTTGCT
1 TTTTGCT
239052 ATTATTTTGG
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
11 12 0.22
12 37 0.67
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.69
Consensus pattern (12 bp):
TTTTGCTGTTGT
Found at i:238998 original size:24 final size:24
Alignment explanation
Indices: 238965--239022 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
238955 TTTTTAATGG
* **
238965 TTTTGGTGTTGCTTTTGCTGTTAT
1 TTTTGTTGTTGCTTTTGCTACTAT
*
238989 TTTTGTTGTTGTTTTTGCTACTAT
1 TTTTGTTGTTGCTTTTGCTACTAT
239013 TTTTGTTGTT
1 TTTTGTTGTT
239023 TTTGTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (24 bp):
TTTTGTTGTTGCTTTTGCTACTAT
Found at i:239046 original size:32 final size:33
Alignment explanation
Indices: 238983--239069 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 33
238973 TTGCTTTTGC
238983 TGTTATTTTTGTTGTTGTTTTTGCTACTATTTT
1 TGTTATTTTTGTTGTTGTTTTTGCTACTATTTT
* * **
239016 TGTTGTTTTTGTTTTTG-TTTTGCTGTTATTTT
1 TGTTATTTTTGTTGTTGTTTTTGCTACTATTTT
* *
239048 TGCTATTATTT-TGGTTGTTTTT
1 TGTTATT-TTTGTTGTTGTTTTT
239070 TTTTTTGCGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 22 0.50
33 22 0.50
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (33 bp):
TGTTATTTTTGTTGTTGTTTTTGCTACTATTTT
Found at i:239056 original size:12 final size:12
Alignment explanation
Indices: 238977--239059 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
238967 TTGGTGTTGC
238977 TTTTGCTGTTAT
1 TTTTGCTGTTAT
* *
238989 TTTTGTTGTTGT
1 TTTTGCTGTTAT
**
239001 TTTTGCTACTAT
1 TTTTGCTGTTAT
*
239013 TTTTGTTGTT-T
1 TTTTGCTGTTAT
*
239024 TTGTT--T-TT-G
1 TT-TTGCTGTTAT
239033 TTTTGCTGTTAT
1 TTTTGCTGTTAT
*
239045 TTTTGCTATTAT
1 TTTTGCTGTTAT
239057 TTT
1 TTT
239060 GGTTGTTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
8 2 0.04
9 4 0.07
10 2 0.04
11 5 0.09
12 41 0.76
ACGTcount: A:0.07, C:0.06, G:0.16, T:0.71
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:239072 original size:24 final size:24
Alignment explanation
Indices: 238977--239072 Score: 92
Period size: 24 Copynumber: 4.2 Consensus size: 24
238967 TTGGTGTTGC
* *
238977 TTTTGCTGTTATTTTTGTTGTTGT
1 TTTTGCTATTATTTTTGTTGTTTT
*
239001 TTTTGCTACTATTTTTGTTGTTTT
1 TTTTGCTATTATTTTTGTTGTTTT
* * * *
239025 TGTT--T-TT-GTTTTGCTGTTAT
1 TTTTGCTATTATTTTTGTTGTTTT
*
239045 TTTTGCTATTATTTTGGTTGTTTT
1 TTTTGCTATTATTTTTGTTGTTTT
239069 TTTT
1 TTTT
239073 TTTGCGTTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
20 13 0.24
21 1 0.02
22 2 0.04
23 2 0.04
24 37 0.67
ACGTcount: A:0.06, C:0.05, G:0.17, T:0.72
Consensus pattern (24 bp):
TTTTGCTATTATTTTTGTTGTTTT
Found at i:241865 original size:27 final size:27
Alignment explanation
Indices: 241832--241909 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
241822 ATGGTATACT
*
241832 CCATGTTTATTGTCCTGGTGGACTATC
1 CCATGTTTATTGTCCTGATGGACTATC
* * *
241859 CCGTGTTTACTGTCCTAATGGACTATC
1 CCATGTTTATTGTCCTGATGGACTATC
*
241886 CCATGTTTATTGTCTTGATGGACT
1 CCATGTTTATTGTCCTGATGGACT
241910 TCATTGGTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.41
Consensus pattern (27 bp):
CCATGTTTATTGTCCTGATGGACTATC
Found at i:246265 original size:59 final size:58
Alignment explanation
Indices: 246174--246636 Score: 624
Period size: 59 Copynumber: 7.9 Consensus size: 58
246164 GCACGGGGGC
* ** * *
246174 AAAATGGTAGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
246232 AAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGAACTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTT-AAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
246291 AAAATGGTAATTTTTGAAAGGTTCGGGGTTAAAAATGGGGTTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTT-AAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
246350 AAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
246409 AAAATGGTAATTTTTATAAAGTTTCGGGGTC-AAAATGGGATTTTTGGGAGTTTGGGGGT
1 AAAATGGTAA-TTTT-TAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
246468 AAAATGGTAATTTTTAGAACGTTCGGGGTCAAAAGTGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
246527 AAAATGGTAATTTTTAGAGGGTTCGGGGTCAAAAATGGTATTTTTGGGAGTTCG-GGGTT
1 AAAATGGTAATTTTTA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-T
* * *
246586 AAAATGGTAATTTTAAAAGGTTTGGGGTCAAAAGTGGGATTTTTGGAAGTT
1 AAAATGGTAATTTTTAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
246637 TAGGGACCTC
Statistics
Matches: 358, Mismatches: 40, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
57 2 0.01
58 62 0.17
59 277 0.77
60 15 0.04
61 2 0.01
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:247857 original size:7 final size:7
Alignment explanation
Indices: 247845--247883 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
247835 CCCCCCTTTT
247845 TTATTAA
1 TTATTAA
247852 TTATTAA
1 TTATTAA
*
247859 TTAATAA
1 TTATTAA
247866 TTATTAA
1 TTATTAA
247873 -TATT-A
1 TTATTAA
247878 TTATTA
1 TTATTA
247884 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:247885 original size:15 final size:15
Alignment explanation
Indices: 247845--247890 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
247835 CCCCCCTTTT
247845 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
247860 TAATAATTATTAATA
1 TTATTATTATTAATA
247875 TTATTATTATTAATA
1 TTATTATTATTAATA
247890 T
1 T
247891 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:248640 original size:18 final size:17
Alignment explanation
Indices: 248614--248677 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
248604 TTATTTATTT
248614 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* * *
248633 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
248650 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
248668 TAAATTTAAA
1 TAAATTTAAA
248678 GGGAATATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 12 0.32
18 23 0.61
19 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:251754 original size:9 final size:9
Alignment explanation
Indices: 251742--251776 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
251732 CATATTCAAA
251742 TTATTCGAG
1 TTATTCGAG
*
251751 TTATTCGAA
1 TTATTCGAG
251760 TTATTCGAG
1 TTATTCGAG
251769 TTATTCGA
1 TTATTCGA
251777 ATTGTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (9 bp):
TTATTCGAG
Found at i:251761 original size:18 final size:18
Alignment explanation
Indices: 251734--251779 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
251724 ACCAATCTCA
*
251734 TATTCAAATTATTCGAGT
1 TATTCGAATTATTCGAGT
251752 TATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAGT
251770 TATTCGAATT
1 TATTCGAATT
251780 GTGAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (18 bp):
TATTCGAATTATTCGAGT
Found at i:252460 original size:12 final size:12
Alignment explanation
Indices: 252335--252463 Score: 53
Period size: 12 Copynumber: 11.0 Consensus size: 12
252325 TAAATATTAG
*
252335 ATTAAATTTAAT
1 ATTAAATTAAAT
252347 ATTAAATCTATTAA-
1 ATTAAAT-TA--AAT
*
252361 ATT-AATAAAAT
1 ATTAAATTAAAT
252372 ATTAAATTAAAT
1 ATTAAATTAAAT
252384 -TTAATATTAAGAT
1 ATTAA-ATTAA-AT
* * * *
252397 AATCAGTTTAAT
1 ATTAAATTAAAT
252409 ATTAAATT-AAT
1 ATTAAATTAAAT
*
252420 A--AAA-T-ACT
1 ATTAAATTAAAT
*
252428 ATCAAGA-TAAAT
1 ATTAA-ATTAAAT
252440 ATTAAATTAAAT
1 ATTAAATTAAAT
252452 -TTAATATTAAAT
1 ATTAA-ATTAAAT
252464 CAATTAAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
8 4 0.04
9 3 0.03
10 4 0.04
11 18 0.20
12 45 0.50
13 9 0.10
14 5 0.06
15 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (12 bp):
ATTAAATTAAAT
Found at i:252474 original size:17 final size:17
Alignment explanation
Indices: 252335--252463 Score: 72
Period size: 17 Copynumber: 7.4 Consensus size: 17
252325 TAAATATTAG
252335 ATTAAATTTAATATTAAATCT
1 ATTAAA-TTAA-ATTAAA--T
*
252356 ATTAAATT-AATAAAAT
1 ATTAAATTAAATTAAAT
*
252372 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTAAAT
*
252389 ATTAAGA-TAATCAGTTTAAT
1 ATTAA-ATTAA--A-TTAAAT
*
252409 ATTAAATT-AATAAAAT
1 ATTAAATTAAATTAAAT
* *
252425 ACT--ATCAAGA-TAAAT
1 ATTAAATTAA-ATTAAAT
*
252440 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTAAAT
252457 ATTAAAT
1 ATTAAAT
252464 CAATTAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.02
15 7 0.08
16 17 0.20
17 30 0.35
18 6 0.07
19 4 0.05
20 14 0.16
21 6 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTAAATTAAATTAAAT
Found at i:254320 original size:29 final size:29
Alignment explanation
Indices: 254278--254335 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
254268 ATATGAGATG
254278 GAGTGATTGAATTGTTCACTTCCCAATTA
1 GAGTGATTGAATTGTTCACTTCCCAATTA
254307 GAGTGATTGAATTGTTCACTTCCCAATTA
1 GAGTGATTGAATTGTTCACTTCCCAATTA
254336 TTGTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (29 bp):
GAGTGATTGAATTGTTCACTTCCCAATTA
Found at i:271501 original size:26 final size:26
Alignment explanation
Indices: 271472--271524 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
271462 AGTATAGATA
271472 GAAAGGTATTATTGATACCAAGTGAT
1 GAAAGGTATTATTGATACCAAGTGAT
271498 GAAAGGTATTATTGATACCAAGTGAT
1 GAAAGGTATTATTGATACCAAGTGAT
271524 G
1 G
271525 TGCATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (26 bp):
GAAAGGTATTATTGATACCAAGTGAT
Found at i:277129 original size:23 final size:24
Alignment explanation
Indices: 277102--277156 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
277092 TTAAAATATA
277102 ATTAAATAAAAAT-TTATATTAAT
1 ATTAAATAAAAATATTATATTAAT
*
277125 ATTAAATAAAAATAATTATATTTAT
1 ATTAAATAAAAAT-ATTATATTAAT
277150 ATTAAAT
1 ATTAAAT
277157 TAAATGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 13 0.45
25 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAAATAAAAATATTATATTAAT
Found at i:278575 original size:47 final size:47
Alignment explanation
Indices: 278506--278601 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
278496 TACCGCCTTC
*
278506 AGAGGATGTGGGAATGAATGTTGATAATGCAAAGTTGTCGAGGATTT
1 AGAGGATGCGGGAATGAATGTTGATAATGCAAAGTTGTCGAGGATTT
* * * *
278553 AGAGGATGCGGGAGTGGATGTTGGTAATGTAAAGTTGTCGAGGATTT
1 AGAGGATGCGGGAATGAATGTTGATAATGCAAAGTTGTCGAGGATTT
278600 AG
1 AG
278602 TAAGGGTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (47 bp):
AGAGGATGCGGGAATGAATGTTGATAATGCAAAGTTGTCGAGGATTT
Found at i:281097 original size:3 final size:3
Alignment explanation
Indices: 281089--281114 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
281079 TTTTTGTCTA
281089 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
281115 GAGTTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:290837 original size:2 final size:2
Alignment explanation
Indices: 290818--290853 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
290808 CTTAATTTAT
*
290818 TA TA TG TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
290854 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:296906 original size:21 final size:21
Alignment explanation
Indices: 296877--296926 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
296867 ATTTAACTTT
*
296877 TTAAAAAATAT-ATTTTTAATA
1 TTAATAAATATGATTTTT-ATA
*
296898 TTAGTAAATATGATTTTTATA
1 TTAATAAATATGATTTTTATA
296919 TTAATAAA
1 TTAATAAA
296927 ATTTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAATAAATATGATTTTTATA
Found at i:297141 original size:2 final size:2
Alignment explanation
Indices: 297134--297159 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
297124 AGAGAAAAAC
297134 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
297160 TTTAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301910 original size:30 final size:28
Alignment explanation
Indices: 301846--301915 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
301836 TTATATTGTT
*
301846 TTATTTTAATATTTAATAATTTTATAAA
1 TTATTTTAATATTGAATAATTTTATAAA
*
301874 TT-TTTTATTTATTGAA-AATTTTCATATAA
1 TTATTTTA-ATATTGAATAATTTT-ATA-AA
301903 TTATTTTAATATT
1 TTATTTTAATATT
301916 TTTTTTAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 11 0.31
28 11 0.31
29 8 0.23
30 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
TTATTTTAATATTGAATAATTTTATAAA
Found at i:303216 original size:38 final size:40
Alignment explanation
Indices: 303138--303218 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 40
303128 TTATAAAAAT
* **
303138 AAAAATCAATAAAAGTTATAAAATTTATAAATTTTAATAA
1 AAAAATAAATAAAAGTTATAAAATTTATAAAAATTAATAA
*
303178 AAAAATAAATAATA-TT-TAAAATTTATTAAAAATT-ATAA
1 AAAAATAAATAAAAGTTATAAAATTTA-TAAAAATTAATAA
303216 AAA
1 AAA
303219 TCGTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 16 0.44
39 8 0.22
40 12 0.33
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAAATAAATAAAAGTTATAAAATTTATAAAAATTAATAA
Found at i:303218 original size:9 final size:9
Alignment explanation
Indices: 303124--303272 Score: 65
Period size: 9 Copynumber: 16.3 Consensus size: 9
303114 ATGTGGCAAT
303124 AAAATTAT-
1 AAAATTATA
303132 AAAA--ATA
1 AAAATTATA
*
303139 AAAATCAATA
1 AAAAT-TATA
*
303149 AAAGTTATA
1 AAAATTATA
*
303158 AAATTTATA
1 AAAATTATA
**
303167 AATTTTAATA
1 AAAATT-ATA
*
303177 AAAA-AATA
1 AAAATTATA
*
303185 AATAATATTTA
1 AA-AAT-TATA
*
303196 AAATTTATTA
1 AAAATTA-TA
303206 AAAATTATA
1 AAAATTATA
**
303215 AAAATCGTA
1 AAAATTATA
*
303224 AAAAATATAA
1 AAAATTAT-A
*
303234 AAAATTGTA
1 AAAATTATA
**
303243 AAGGTTTATA
1 AA-AATTATA
*
303253 AAAATCATA
1 AAAATTATA
303262 AAAA-TATA
1 AAAATTATA
303270 AAA
1 AAA
303273 TGCATAAAAA
Statistics
Matches: 104, Mismatches: 26, Indels: 22
0.68 0.17 0.14
Matches are distributed among these distances:
6 2 0.02
7 4 0.04
8 15 0.14
9 44 0.42
10 35 0.34
11 4 0.04
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:303227 original size:19 final size:19
Alignment explanation
Indices: 303205--303265 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
303195 AAAATTTATT
303205 AAAAATTATAAAAATCGTA
1 AAAAATTATAAAAATCGTA
*
303224 AAAAA-TATAAAAAATTGTA
1 AAAAATTAT-AAAAATCGTA
*** *
303243 AAGGTTTATAAAAATCATA
1 AAAAATTATAAAAATCGTA
303262 AAAA
1 AAAA
303266 TATAAAATGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 3 0.09
19 26 0.81
20 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAATTATAAAAATCGTA
Found at i:303256 original size:47 final size:47
Alignment explanation
Indices: 303175--303266 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
303165 TAAATTTTAA
*
303175 TAAAAAAATAAATAATATTTAAAATTTATTAAAAATTATAAAAATCG
1 TAAAAAAATAAATAATATTTAAAATTTATTAAAAATCATAAAAATCG
*
303222 TAAAAAATATAAA-AA-ATTGTAAAGGTTTA-TAAAAATCATAAAAAT
1 TAAAAAA-ATAAATAATATT-TAAA-ATTTATTAAAAATCATAAAAAT
303267 ATAAAATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
46 3 0.08
47 28 0.70
48 9 0.22
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (47 bp):
TAAAAAAATAAATAATATTTAAAATTTATTAAAAATCATAAAAATCG
Found at i:303493 original size:19 final size:19
Alignment explanation
Indices: 303444--303515 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
303434 TGATACGATA
303444 ATTTTTATAATTTTTTACG
1 ATTTTTATAATTTTTTACG
* *
303463 AATTTTA-CATTTATTTAC-
1 ATTTTTATAATTT-TTTACG
303481 ATTTTTATAATTTTCTTACG
1 ATTTTTATAATTTT-TTACG
* *
303501 ACTTTATAAAATTTT
1 A-TTTTTATAATTTT
303516 ATAAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.26
19 19 0.45
20 1 0.02
21 11 0.26
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACG
Found at i:303562 original size:29 final size:29
Alignment explanation
Indices: 303489--303563 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
303479 ACATTTTTAT
* *
303489 AATTTTCTTACGACTTTATAAAATTTTATA
1 AATTTT-TTACGATTTTATAAAATTTGATA
* *
303519 AATTTTTCTA-TATTTCTAT-ATATTTGATA
1 AATTTTT-TACGATTT-TATAAAATTTGATA
303548 AATTTTTTACGATTTT
1 AATTTTTTACGATTTT
303564 TTTACGACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.08
29 23 0.62
30 11 0.30
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (29 bp):
AATTTTTTACGATTTTATAAAATTTGATA
Found at i:303628 original size:21 final size:20
Alignment explanation
Indices: 303604--303662 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 20
303594 TTAATAAAAT
303604 TTAAATATTT-TTATATTTTTA
1 TTAAA-ATTTATTAT-TTTTTA
303625 TTAAAATTTATTATTTTTTA
1 TTAAAATTTATTATTTTTTA
303645 -T--AA-TTATTATTTTTTA
1 TTAAAATTTATTATTTTTTA
303661 TT
1 TT
303663 TTTTTATCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.36
17 3 0.08
19 1 0.03
20 10 0.28
21 9 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTAAAATTTATTATTTTTTA
Found at i:303641 original size:19 final size:18
Alignment explanation
Indices: 303603--303659 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
303593 TTTAATAAAA
*
303603 TTTAAATATTTTTATATTTT
1 TTTAAA-ATTTAT-TATTTT
303623 TATTAAAATTTATTA-TTT
1 T-TTAAAATTTATTATTTT
*
303641 TTTATAA-TTATTATTTT
1 TTTAAAATTTATTATTTT
303658 TT
1 TT
303660 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 6 0.18
17 10 0.30
18 4 0.12
19 2 0.06
20 6 0.18
21 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAAAATTTATTATTTT
Found at i:303655 original size:29 final size:29
Alignment explanation
Indices: 303577--303655 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
303567 ACGACATTTC
* *
303577 TATT-TTTTTTCTAATTTTTAATAAAATT
1 TATTATTTTTTATAATTTTTATTAAAATT
*
303605 TA-AATATTTTTAT-ATTTTTATTAAAATT
1 TATTAT-TTTTTATAATTTTTATTAAAATT
*
303633 TATTATTTTTTATAATTATTATT
1 TATTATTTTTTATAATTTTTATT
303656 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 26 0.62
29 16 0.38
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTATTTTTTATAATTTTTATTAAAATT
Found at i:303869 original size:23 final size:22
Alignment explanation
Indices: 303817--303868 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
303807 GAGCTTAATT
303817 GTTTTTTTGAAAAAGTTTGAGG
1 GTTTTTTTGAAAAAGTTTGAGG
*
303839 GTTTTTTTGAAAAAGTTTGAAG
1 GTTTTTTTGAAAAAGTTTGAGG
303861 GTTTTTTT
1 GTTTTTTT
303869 TTACATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (22 bp):
GTTTTTTTGAAAAAGTTTGAGG
Found at i:304267 original size:12 final size:12
Alignment explanation
Indices: 304252--304279 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
304242 TCATTTATGT
304252 TAATTATAAATA
1 TAATTATAAATA
304264 TAATTATAAATA
1 TAATTATAAATA
304276 TAAT
1 TAAT
304280 AATTTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATTATAAATA
Found at i:304640 original size:9 final size:9
Alignment explanation
Indices: 304626--304675 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
304616 TATTAGATTT
304626 TTTTTATAA
1 TTTTTATAA
304635 TTTTTATAA
1 TTTTTATAA
*
304644 TTTTTAAAA
1 TTTTTATAA
304653 TTTTTATAAA
1 TTTTTAT-AA
*
304663 TATTTTAAAA
1 T-TTTTATAA
304673 TTT
1 TTT
304676 AAAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 25 0.69
10 6 0.17
11 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:304647 original size:18 final size:19
Alignment explanation
Indices: 304626--304675 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
304616 TATTAGATTT
*
304626 TTTTTATAATTTTTAT-AA
1 TTTTTAAAATTTTTATAAA
304644 TTTTTAAAATTTTTATAAA
1 TTTTTAAAATTTTTATAAA
304663 TATTTTAAAATTT
1 T-TTTTAAAATTT
304676 AAAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 15 0.52
19 3 0.10
20 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAAATTTTTATAAA
Done.