Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 277 of 279
Found at i:90350583 original size:30 final size:30
Alignment explanation
Indices: 90350538--90350612 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
90350528 TTATTTTTAA
* *
90350538 ATTTTAAATATTATTTTAAATA-TTAAATAT
1 ATTTTAAATAATATTTTAAACATTTAAA-AT
*
90350568 ATTTTTAATAATA-TTTAAACATTTAAAAT
1 ATTTTAAATAATATTTTAAACATTTAAAAT
* *
90350597 -TTTTCAATAAAATTTT
1 ATTTTAAATAATATTTT
90350613 TATAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 10 0.26
29 12 0.32
30 16 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTAAATAATATTTTAAACATTTAAAAT
Found at i:90350678 original size:15 final size:14
Alignment explanation
Indices: 90350658--90350694 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
90350648 AAAAATAATT
90350658 AAAAATTATAATTTC
1 AAAAATT-TAATTTC
90350673 AAAAA-TTAATTTC
1 AAAAATTTAATTTC
90350686 AAAAATTTA
1 AAAAATTTA
90350695 GAAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAATTTAATTTC
Found at i:90350790 original size:34 final size:35
Alignment explanation
Indices: 90350717--90350803 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
90350707 ATTTTAAAAT
* *
90350717 TTTAAAATTTAGAAAAATTAATTTCAAAAATATAT
1 TTTAAAATTTAGAAAAATTAATTTCAAAAAAATAA
* *
90350752 TTTAAAATTTATAAGACA-TAATTT-AAAAAAATAA
1 TTTAAAATTTAGAA-AAATTAATTTCAAAAAAATAA
90350786 TTTAAAATTTTA-AAAAAT
1 TTTAAAA-TTTAGAAAAAT
90350804 ATATATTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 2 0.05
34 17 0.39
35 23 0.52
36 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (35 bp):
TTTAAAATTTAGAAAAATTAATTTCAAAAAAATAA
Found at i:90350876 original size:23 final size:22
Alignment explanation
Indices: 90350850--90350934 Score: 72
Period size: 23 Copynumber: 4.0 Consensus size: 22
90350840 TTTTAAAATT
*
90350850 AATAACAAAAAATAAATAAACAA
1 AATAA-AAAAAATAAATAAAAAA
*
90350873 AATAAACAAAATAAAATAAGAAAA
1 AATAAAAAAAAT-AAATAA-AAAA
90350897 AAT-AAAAAAAT---T-AAAAA
1 AATAAAAAAAATAAATAAAAAA
* *
90350914 AATAAAAAAATTAAAGAAAAA
1 AATAAAAAAAATAAATAAAAA
90350935 GACAAAAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
17 7 0.14
18 8 0.16
19 1 0.02
22 10 0.20
23 18 0.36
24 6 0.12
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (22 bp):
AATAAAAAAAATAAATAAAAAA
Found at i:90350928 original size:9 final size:8
Alignment explanation
Indices: 90350858--90350924 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 8
90350848 TTAATAACAA
90350858 AAAATAAAT
1 AAAA-AAAT
90350867 AAACAAAAT
1 AAA-AAAAT
90350876 AAACAAAAT
1 AAA-AAAAT
*
90350885 AAAATAA-
1 AAAAAAAT
*
90350892 GAAAAAAT
1 AAAAAAAT
90350900 AAAAAAATT
1 AAAAAAA-T
90350909 AAAAAAAT
1 AAAAAAAT
90350917 AAAAAAAT
1 AAAAAAAT
90350925 TAAAGAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
7 5 0.10
8 18 0.35
9 27 0.53
10 1 0.02
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:90350928 original size:17 final size:16
Alignment explanation
Indices: 90350858--90350924 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 16
90350848 TTAATAACAA
90350858 AAAATAAATAAACAAAAT
1 AAAA-AAATAAA-AAAAT
*
90350876 AAACAAAATAAAATAA-
1 AAA-AAAATAAAAAAAT
*
90350892 GAAAAAATAAAAAAATT
1 AAAAAAATAAAAAAA-T
90350909 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
90350925 TAAAGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 11 0.26
16 3 0.07
17 17 0.40
18 10 0.24
19 1 0.02
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.15
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:90350953 original size:12 final size:12
Alignment explanation
Indices: 90350909--90350967 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
90350899 TAAAAAAATT
90350909 AAAAAAA-TAAA
1 AAAAAAAGTAAA
90350920 AAAATTAAAG-AAA
1 AAAA--AAAGTAAA
*
90350933 AAGACAAAAGTTAA
1 AA-A-AAAAGTAAA
*
90350947 TAAAAAAGTAAA
1 AAAAAAAGTAAA
90350959 AAAAAAAGT
1 AAAAAAAGT
90350968 GAAAGAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
11 4 0.11
12 16 0.42
13 13 0.34
14 4 0.11
15 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (12 bp):
AAAAAAAGTAAA
Found at i:90363091 original size:18 final size:18
Alignment explanation
Indices: 90363068--90363102 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
90363058 AAGATCGTCT
90363068 GTACTAGATACTTTAACA
1 GTACTAGATACTTTAACA
90363086 GTACTAGATACTTTAAC
1 GTACTAGATACTTTAAC
90363103 TTCTGGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
GTACTAGATACTTTAACA
Found at i:90363347 original size:18 final size:18
Alignment explanation
Indices: 90363324--90363358 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
90363314 AAGATCGTCT
90363324 GTACTAGATACTTTAACA
1 GTACTAGATACTTTAACA
90363342 GTACTAGATACTTTAAC
1 GTACTAGATACTTTAAC
90363359 TTCTGGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
GTACTAGATACTTTAACA
Found at i:90363472 original size:256 final size:256
Alignment explanation
Indices: 90363017--90363528 Score: 1015
Period size: 256 Copynumber: 2.0 Consensus size: 256
90363007 AGGTCCAGCT
90363017 GCTGAACCATTTACATGCAACAAATCAATCCCCTCTGCATGAAGATCGTCTGTACTAGATACTTT
1 GCTGAACCATTTACATGCAACAAATCAATCCCCTCTGCATGAAGATCGTCTGTACTAGATACTTT
90363082 AACAGTACTAGATACTTTAACTTCTGGTTCCAATTGCAGTAGGTCATCAGTAAAGTTAGAAGGTA
66 AACAGTACTAGATACTTTAACTTCTGGTTCCAATTGCAGTAGGTCATCAGTAAAGTTAGAAGGTA
90363147 TTTGTGCAGCAGATTTAAAGATATCAGAAACTACAACACTCTTGCTGATTACAGGTGATGTCAAA
131 TTTGTGCAGCAGATTTAAAGATATCAGAAACTACAACACTCTTGCTGATTACAGGTGATGTCAAA
90363212 CTAGAACTGGAGGTAGAGATTTTTCTCTTTTTCTTCTCAGGAGACTTTCCATCTGCACTAC
196 CTAGAACTGGAGGTAGAGATTTTTCTCTTTTTCTTCTCAGGAGACTTTCCATCTGCACTAC
90363273 GCTGAACCATTTACATGCAACAAATCAATCCCCTCTGCATGAAGATCGTCTGTACTAGATACTTT
1 GCTGAACCATTTACATGCAACAAATCAATCCCCTCTGCATGAAGATCGTCTGTACTAGATACTTT
90363338 AACAGTACTAGATACTTTAACTTCTGGTTCCAATTGCAGTAGGTCATCAGTAAAGTTAGAAGGTA
66 AACAGTACTAGATACTTTAACTTCTGGTTCCAATTGCAGTAGGTCATCAGTAAAGTTAGAAGGTA
*
90363403 TTTGTGCAGCAGATTTAAAGATATCAGAAACTACAACACTCTTTCTGATTACAGGTGATGTCAAA
131 TTTGTGCAGCAGATTTAAAGATATCAGAAACTACAACACTCTTGCTGATTACAGGTGATGTCAAA
90363468 CTAGAACTGGAGGTAGAGATTTTTCTCTTTTTCTTCTCAGGAGACTTTCCATCTGCACTAC
196 CTAGAACTGGAGGTAGAGATTTTTCTCTTTTTCTTCTCAGGAGACTTTCCATCTGCACTAC
90363529 CACCAATCTC
Statistics
Matches: 255, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
256 255 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (256 bp):
GCTGAACCATTTACATGCAACAAATCAATCCCCTCTGCATGAAGATCGTCTGTACTAGATACTTT
AACAGTACTAGATACTTTAACTTCTGGTTCCAATTGCAGTAGGTCATCAGTAAAGTTAGAAGGTA
TTTGTGCAGCAGATTTAAAGATATCAGAAACTACAACACTCTTGCTGATTACAGGTGATGTCAAA
CTAGAACTGGAGGTAGAGATTTTTCTCTTTTTCTTCTCAGGAGACTTTCCATCTGCACTAC
Found at i:90367715 original size:23 final size:23
Alignment explanation
Indices: 90367642--90367716 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
90367632 CTAAAATAAT
90367642 TTTTTATTATTTATTATATGTTA
1 TTTTTATTATTTATTATATGTTA
** * * *
90367665 TTTTTAAAAGTTA-CA-AGTGATA
1 TTTTTATTATTTATTATA-TGTTA
*
90367687 CATTTTATTATTTATTATATGTTA
1 -TTTTTATTATTTATTATATGTTA
90367711 TTTTTA
1 TTTTTA
90367717 AACACATATT
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
21 1 0.03
22 5 0.14
23 24 0.67
24 5 0.14
25 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTTATTATTTATTATATGTTA
Found at i:90368095 original size:20 final size:21
Alignment explanation
Indices: 90368070--90368125 Score: 87
Period size: 20 Copynumber: 2.6 Consensus size: 21
90368060 ATTTAAATAA
90368070 AAATAATAAAAATTAGA-TTT
1 AAATAATAAAAATTAGATTTT
90368090 AAATAATAAAAATTAGATTTTT
1 AAATAATAAAAATTAGA-TTTT
90368112 AAATATATAAAAAT
1 AAATA-ATAAAAAT
90368126 AAAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.52
22 8 0.24
23 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATAATAAAAATTAGATTTT
Found at i:90368180 original size:25 final size:27
Alignment explanation
Indices: 90368138--90368197 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
90368128 AAAAAAATTA
90368138 TATATAATTACATCAAATCAAATTT-T
1 TATATAATTACATCAAATCAAATTTAT
*
90368164 TATATAATATA-AT-AAATTAAATTTAT
1 TATATAAT-TACATCAAATCAAATTTAT
90368190 TA-ATAATT
1 TATATAATT
90368198 TTGACATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 1 0.03
25 15 0.48
26 13 0.42
27 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
TATATAATTACATCAAATCAAATTTAT
Found at i:90370169 original size:26 final size:26
Alignment explanation
Indices: 90370140--90370191 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
90370130 GGCACCAAGT
90370140 CTAATTACAAAGGATCAAAGATGACG
1 CTAATTACAAAGGATCAAAGATGACG
*
90370166 CTAATTTCAAAGGATCAAAGATGACG
1 CTAATTACAAAGGATCAAAGATGACG
90370192 TACTTACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (26 bp):
CTAATTACAAAGGATCAAAGATGACG
Found at i:90386644 original size:6 final size:6
Alignment explanation
Indices: 90386635--90386662 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
90386625 AATTTAAATT
90386635 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
90386663 CATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:90386660 original size:26 final size:27
Alignment explanation
Indices: 90386617--90386669 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
90386607 CTTTTAACTA
*
90386617 ATAATTAAAATTTAAATT-TTATAATT
1 ATAATTAAAATTTAAATTATCATAATT
*
90386643 ATAATTATAA-TTATAATTATCATAATT
1 ATAATTAAAATTTA-AATTATCATAATT
90386670 TTTTTCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 13 0.57
27 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAATTAAAATTTAAATTATCATAATT
Found at i:90386833 original size:44 final size:43
Alignment explanation
Indices: 90386760--90386845 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
90386750 TTGTCAATGG
* * *
90386760 AATTATAATTATTTTAAATGCATTCTTATCAGAACTTCTATTA
1 AATTATAATTATTTTAAATACATTATTATCACAACTTCTATTA
* *
90386803 AATTGTAATTATTTTTAAATATATTATTATCACAACTTCTATT
1 AATTATAATTA-TTTTAAATACATTATTATCACAACTTCTATT
90386846 TTACTACAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 10 0.27
44 27 0.73
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (43 bp):
AATTATAATTATTTTAAATACATTATTATCACAACTTCTATTA
Found at i:90388292 original size:23 final size:23
Alignment explanation
Indices: 90388248--90388298 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 23
90388238 ATCACTTACC
90388248 TTTGTTTCGTTCTCTTAATTTTT
1 TTTGTTTCGTTCTCTTAATTTTT
90388271 TTTGTTT-GTTCTCTTAATTTTT
1 TTTGTTTCGTTCTCTTAATTTTT
90388293 TTTGTT
1 TTTGTT
90388299 GTTGCAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.73
Consensus pattern (23 bp):
TTTGTTTCGTTCTCTTAATTTTT
Found at i:90390771 original size:50 final size:51
Alignment explanation
Indices: 90390694--90390822 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
90390684 GACCATGGCA
*
90390694 ACAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
90390745 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
90390795 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
90390823 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:90390836 original size:31 final size:31
Alignment explanation
Indices: 90390798--90391095 Score: 410
Period size: 31 Copynumber: 9.6 Consensus size: 31
90390788 ACAAATGACA
90390798 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
90390829 AGTGAAAAGTGGTAGCTTCTA-CTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-AGCTACCTGATC
*
90390860 AGTGAAAAGTGGTAG-TTACGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CAGCTACCTGATC
90390891 AGTGAAAAGTGGTAGCTTCTA-CTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-AGCTACCTGATC
*
90390922 AGTGAAAAGTGGTAG-TTACGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CAGCTACCTGATC
90390953 AGTGAAAAGTGGTAGCTTCTA-CTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-AGCTACCTGATC
*
90390984 AGTGAAAAGTGGTAG-TTACGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CAGCTACCTGATC
*
90391015 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * * *
90391046 AGTGAAAAATGGTAGCTCCGGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
90391077 AGCGAATAGTGGTAGCTTC
1 AGTGAAAAGTGGTAGCTTC
90391096 GACTACAAGT
Statistics
Matches: 241, Mismatches: 14, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
30 6 0.02
31 229 0.95
32 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:90390871 original size:62 final size:62
Alignment explanation
Indices: 90390798--90391101 Score: 495
Period size: 62 Copynumber: 4.9 Consensus size: 62
90390788 ACAAATGACA
*
90390798 AGTGAAAAGTGGTAGCTT-CAGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAG-TTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
90390860 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
90390922 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
*
90390984 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGC-TCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTA-CTACCTGATC
* * * * * * *
90391046 AGTGAAAAATGGTAGCTCCGGCTACTTGATCAGCGAATAGTGGTAGCTTCGACTAC
1 AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTAC
90391102 AAGTGACAAG
Statistics
Matches: 230, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
61 5 0.02
62 222 0.97
63 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (62 bp):
AGTGAAAAGTGGTAGTTACGGCTACCTGATCAGTGAAAAGTGGTAGCTTCTACTACCTGATC
Found at i:90391281 original size:42 final size:42
Alignment explanation
Indices: 90391177--90391332 Score: 172
Period size: 42 Copynumber: 3.6 Consensus size: 42
90391167 TGCTACTGTA
* *
90391177 TAAGACCATATCTGGGATATGGCATCAGTGAGATATGT-GAT-TCGTG
1 TAAGACCATAGCTGGGCTATGGCATCA-T----TATGTGGATAT-GTG
* *
90391223 TAAGACTATAGTTGGGCTATGGCATCATTATGTGGATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCATTATGTGGATATGTG
*
90391265 TAAGACCATAGCTGGGCTATGGCATCATTATGTGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCATTATGTGGATATGTG
* **
90391307 TAAGACCATAGTTGAACTATGGCATC
1 TAAGACCATAGCTGGGCTATGGCATC
90391333 GAGAAAACGA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
41 5 0.05
42 68 0.69
43 1 0.01
45 1 0.01
46 23 0.23
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (42 bp):
TAAGACCATAGCTGGGCTATGGCATCATTATGTGGATATGTG
Found at i:90392458 original size:17 final size:17
Alignment explanation
Indices: 90392414--90392477 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 17
90392404 CTATTTGTTT
90392414 AAAAAAAACAAAATCTA
1 AAAAAAAACAAAATCTA
90392431 ATGTTAAAAAAACAAAATCTA
1 A----AAAAAAACAAAATCTA
90392452 AAAAAAAACAAAATCTGA
1 AAAAAAAACAAAATCT-A
90392470 AAAAAAAA
1 AAAAAAAA
90392478 AGTTGTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.38
18 9 0.21
21 17 0.40
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAAAAACAAAATCTA
Found at i:90392478 original size:21 final size:19
Alignment explanation
Indices: 90392414--90392478 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 19
90392404 CTATTTGTTT
*
90392414 AAAAAAAACAAAATCTAATGT
1 AAAAAAAACAAAATCTAA--A
*
90392435 TAAAAAAACAAAATCT--A
1 AAAAAAAACAAAATCTAAA
90392452 AAAAAAAACAAAATCTGAAA
1 AAAAAAAACAAAATCT-AAA
90392472 AAAAAAA
1 AAAAAAA
90392479 GTTGTAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.39
20 8 0.21
21 15 0.39
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAAAAACAAAATCTAAA
Found at i:90392683 original size:3 final size:3
Alignment explanation
Indices: 90392655--90392739 Score: 88
Period size: 3 Copynumber: 29.3 Consensus size: 3
90392645 TTTCGACTAG
* * *
90392655 GAA GAAA GAA GTA GAA GAA -AA AAA GAA G-A GGA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
90392699 GAA GAA GAA GAA GAA -AA GAA G-A GAA GAA GAA TAA GGA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
90392740 GAGGAGGCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
2 8 0.12
3 58 0.84
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:90392699 original size:34 final size:34
Alignment explanation
Indices: 90392660--90392739 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
90392650 ACTAGGAAGA
* *
90392660 AAGAAGTAGAAGAA-AAAAAGAAGAGGAGAAGAAG
1 AAGAAGAAGAAGAAGAAAAA-AAGAAGAGAAGAAG
*
90392694 AAGAAGAAGAAGAAGAAGAAAAGAAGAGAAGAAG
1 AAGAAGAAGAAGAAGAAAAAAAGAAGAGAAGAAG
* *
90392728 AATAAGGAGAAG
1 AAGAAGAAGAAG
90392740 GAGGAGGCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 36 0.90
35 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.03
Consensus pattern (34 bp):
AAGAAGAAGAAGAAGAAAAAAAGAAGAGAAGAAG
Found at i:90392710 original size:37 final size:37
Alignment explanation
Indices: 90392655--90392739 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
90392645 TTTCGACTAG
* *
90392655 GAAGAAAGAAGTAGAAGAAAAAAAGAAGAGGAGAAGAA
1 GAAG-AAGAAGAAGAAGAAAAAAAGAAGAGAAGAAGAA
*
90392693 GAAGAAGAAGAAGAAGAAGAAAAGAAGAGAAGAAGAA
1 GAAGAAGAAGAAGAAGAAAAAAAGAAGAGAAGAAGAA
* *
90392730 TAAGGAGAAG
1 GAAGAAGAAG
90392740 GAGGAGGCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 38 0.90
38 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (37 bp):
GAAGAAGAAGAAGAAGAAAAAAAGAAGAGAAGAAGAA
Found at i:90392833 original size:11 final size:10
Alignment explanation
Indices: 90392802--90392831 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
90392792 AAGAGGGAGG
90392802 GAAGGAAAAA
1 GAAGGAAAAA
*
90392812 GAACGAAAAA
1 GAAGGAAAAA
90392822 GAAGGAAAAA
1 GAAGGAAAAA
90392832 AGGTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAGGAAAAA
Found at i:90393264 original size:12 final size:12
Alignment explanation
Indices: 90393249--90393273 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90393239 AATTTAAATA
90393249 TAAATTTGCCAT
1 TAAATTTGCCAT
90393261 TAAATTTGCCAT
1 TAAATTTGCCAT
90393273 T
1 T
90393274 CTCAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TAAATTTGCCAT
Found at i:90393623 original size:38 final size:38
Alignment explanation
Indices: 90393581--90393685 Score: 113
Period size: 38 Copynumber: 2.7 Consensus size: 38
90393571 AGTTCAAAGC
*
90393581 AAAGTTGACACCCAGTGTCTCATCAGCCTAGCCGAAGT
1 AAAGTTGACACCCAGTGTCTCATCAACCTAGCCGAAGT
** ** * *
90393619 AAAG-TGGTACCCAGTACCTCATCGAATCTATCCGAAGT
1 AAAGTTGACACCCAGTGTCTCATC-AACCTAGCCGAAGT
90393657 AACAGTATGACACCCAGTGTCTCATCAAC
1 AA-AGT-TGACACCCAGTGTCTCATCAAC
90393686 TCGAGGTCGA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
37 15 0.29
38 17 0.33
39 2 0.04
40 2 0.04
41 15 0.29
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (38 bp):
AAAGTTGACACCCAGTGTCTCATCAACCTAGCCGAAGT
Found at i:90393823 original size:28 final size:23
Alignment explanation
Indices: 90393791--90393851 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 23
90393781 TAAATCTCAA
90393791 TTCAATTCAATCGCAATTTTCTCACATT
1 TTCAATTCAAT--C-ATTTTC-CAC-TT
*
90393819 TTCAATTTAATCATTTTCCACTT
1 TTCAATTCAATCATTTTCCACTT
90393842 TTCAA-TCAAT
1 TTCAATTCAAT
90393852 TTTCAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 3 0.10
25 6 0.19
26 1 0.03
28 10 0.32
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.46
Consensus pattern (23 bp):
TTCAATTCAATCATTTTCCACTT
Found at i:90398917 original size:39 final size:39
Alignment explanation
Indices: 90398874--90398949 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
90398864 CAAGATACTA
*
90398874 GAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTGCAG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCAG
*
90398913 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGC
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
90398950 TGGTAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCAG
Found at i:90409453 original size:19 final size:19
Alignment explanation
Indices: 90409431--90409476 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
90409421 ATTGCTTTCT
90409431 TTTGCATT-CATTCCATGCA
1 TTTGCATTGCATTCCAT-CA
*
90409450 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
*
90409469 TGTGCATT
1 TTTGCATT
90409477 AAACTTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:90414269 original size:45 final size:44
Alignment explanation
Indices: 90414220--90414363 Score: 175
Period size: 45 Copynumber: 3.2 Consensus size: 44
90414210 AGTAGCAAGA
*
90414220 GAGCAGGTTGAAAATTGCAGGTCTTATCTCCATGTATCAGCTATG
1 GAGCAGATTGAAAATTGCAGGTCTTATCTCCATGTATC-GCTATG
* * * *
90414265 GAGCAGACTGAGAATTACAGATCTTATCTCCATGTATCGTCTATG
1 GAGCAGATTGAAAATTGCAGGTCTTATCTCCATGTATCG-CTATG
*
90414310 GAGCAGATCGAAAATGGTG-A-GTCTTATCTCCATGTATCGGCTATG
1 GAGCAGATTGAAAAT--TGCAGGTCTTATCTCCATGTATC-GCTATG
90414355 GAGCAGATT
1 GAGCAGATT
90414364 TTACCCACCG
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
44 1 0.01
45 80 0.95
46 2 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
GAGCAGATTGAAAATTGCAGGTCTTATCTCCATGTATCGCTATG
Found at i:90414272 original size:178 final size:178
Alignment explanation
Indices: 90413880--90414605 Score: 930
Period size: 178 Copynumber: 4.1 Consensus size: 178
90413870 CGGTGAATTC
*
90413880 ACAAGTCTTATCTTCCTGAGGTAGC-AAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGA
1 ACAAGTCTTATCTTCCTGA-GTAGCTAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGT
* *
90413944 ATCGGCTATGGAACAGATCGAAAATGGTGAGTCTTATCTCTATGTATC-AGCTATGGAGCAGATT
65 ATCGGCTATGGAACAGATCAAAAATGGTGAGTCTTATCTCCATGTATCGA-CTATGGAGCAGATT
* * * *
90414008 TTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCA-TTTTAAAGAT
129 TTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAA-AT
* *
90414058 ACAAGTCTTATCTTCCTGAGGTAGC-AAGGAAGCAGACT-GAAATTACAGATCTTATCTCTATGT
1 ACAAGTCTTATCTTCCTGA-GTAGCTAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGT
* * * *
90414121 ATCGGCTATAGAGCAGATCAAAAATGGTGAGTCTTATCTCTATGTATCGACTATGGAACAGATTT
65 ATCGGCTATGGAACAGATCAAAAATGGTGAGTCTTATCTCCATGTATCGACTATGGAGCAGATTT
90414186 TAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAATT
130 TAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAA-T
* * * * *
90414236 GCAGGTCTTATC-TCCATGTA-TCAGCTATGG-AGCAGACTGAGAATTACAGATCTTATCTCCAT
1 ACAAGTCTTATCTTCC-TG-AGT-AGCTAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCAT
* * * *
90414298 GTATCGTCTATGGAGCAGATCGAAAATGGTGAGTCTTATCTCCATGTATCGGCTATGGAGCAGAT
63 GTATCGGCTATGGAACAGATCAAAAATGGTGAGTCTTATCTCCATGTATCGACTATGGAGCAGAT
* * * * * *
90414363 TTTACCCACCGGCCTTATCTCTCTGAGGGAGCAAGAGAGCATGTTGAAGAT
128 TTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAAT
*
90414414 ACAAGTCTTATCTTCCTGAGGTAG-TAAGGAAACAGACTAAAAATTACAGATCTTATCTCCATGT
1 ACAAGTCTTATCTTCCTGA-GTAGCTAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGT
* * * ** *
90414478 ATCAGTTATGGAACAGATAAAAAATGACGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTT
65 ATCGGCTATGGAACAGATCAAAAATGGTGAGTCTTATCTCCATGTATCGACTATGGAGCAGATTT
* * * *
90414543 TAGCCCCCAGCCTTATCTCTCTGAATTAGCAACAGAGCAGGTTAAAAATT
130 TAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAA-T
* *
90414593 GCAGGTCTTATCT
1 ACAAGTCTTATCT
90414606 CCATGTATCG
Statistics
Matches: 480, Mismatches: 55, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
177 128 0.27
178 209 0.44
179 143 0.30
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (178 bp):
ACAAGTCTTATCTTCCTGAGTAGCTAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTA
TCGGCTATGGAACAGATCAAAAATGGTGAGTCTTATCTCCATGTATCGACTATGGAGCAGATTTT
AGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAAT
Found at i:90414601 original size:89 final size:89
Alignment explanation
Indices: 90414151--90414717 Score: 374
Period size: 89 Copynumber: 6.4 Consensus size: 89
90414141 AAAATGGTGA
* * *
90414151 GTCTTATCTCTATGTATCGACTATGGAACAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
* * *
90414216 AAGAGAGCAGGTTGAAAATTGCAG
66 AACAGAGCAGGTTAAAAATTACAG
* * * * * * *
90414240 GTCTTATCTCCATGTATCAGCTATGGAGCAGA-CTGAG-AATTACAGATCTTATCTC-CATGTA-
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA--CCAG-CCTTATCTCTC-TGAAG
* * ** * ** *
90414301 TCGTCTATGGAGCAGATCGAAAATGGT-GA-
62 TAG-CAACAGAGCAGGTTAAAAAT--TACAG
* * * *
90414330 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGC
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
* * * * *
90414395 AAGAGAGCATGTTGAAGA-TACAA
66 AACAGAGCAGGTTAAAAATTACAG
* *** *** *
90414418 GTCTTATCTTCC-TG-A--GG-TAGTAAGGAAACAGACTAAAAATTA-CAGATCTTATCTC-CAT
1 GTCTTATC-TCCATGTATCGGCTA-T--GG-AGCAGA-TTTTAGCCACCAG-CCTTATCTCTC-T
* ** ** * * * *
90414476 GTA-TCAGTTATGGAACAGATAAAAAATGAC-G
58 GAAGT-AGCAACAGAGCAGGTTAAAAATTACAG
* *
90414507 AGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCCCCAGCCTTATCTCTCTGAATTAG
1 -GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAG
*
90414572 CAACAGAGCAGGTTAAAAATTGCAG
65 CAACAGAGCAGGTTAAAAATTACAG
90414597 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
* * *
90414662 AAGAGAGCAGGTTGAAAGTTACAG
66 AACAGAGCAGGTTAAAAATTACAG
* *
90414686 GTCTTATCTTCATGTACCGGCTATGGAGCAGA
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGA
90414718 CTAAGAATTA
Statistics
Matches: 357, Mismatches: 88, Indels: 66
0.70 0.17 0.13
Matches are distributed among these distances:
84 2 0.01
85 3 0.01
86 1 0.00
87 5 0.01
88 21 0.06
89 228 0.64
90 84 0.24
91 6 0.02
92 2 0.01
93 3 0.01
94 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (89 bp):
GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
AACAGAGCAGGTTAAAAATTACAG
Found at i:90414626 original size:45 final size:45
Alignment explanation
Indices: 90414446--90414763 Score: 157
Period size: 45 Copynumber: 7.1 Consensus size: 45
90414436 AGTAAGGAAA
* * * * *
90414446 CAGACTAAAAATTACAGATCTTATCTCCATGTATCAGTTATGGAA
1 CAGATTAAAAATTACAGGTCTTATCTCCATGTATCGGCTATGGAG
* *
90414491 CAGATAAAAAATGAC-GAGTCTTATCTCCATGTATCGGCTATGGAG
1 CAGATTAAAAATTACAG-GTCTTATCTCCATGTATCGGCTATGGAG
** ***** * * ** * **
90414536 CAGATTTTAGCCCCCA-GCCTTATCTCTC-TGAATTAGCAACAGAG
1 CAGATTAAAAATTACAGGTCTTATCTC-CATGTATCGGCTATGGAG
* *
90414580 CAGGTTAAAAATTGCAGGTCTTATCTCCATGTATCGGCTATGGAG
1 CAGATTAAAAATTACAGGTCTTATCTCCATGTATCGGCTATGGAG
** *** * * * *
90414625 CAGATT-TTAGCCACCA-GCCTTATCTCTC-TGAAGT-AGC-AAGAGAG
1 CAGATTAAAAATTA-CAGGTCTTATCTC-CATGTA-TCGGCTATG-GAG
* * * * *
90414669 CAGGTTGAAAGTTACAGGTCTTATCTTCATGTACCGGCTATGGAG
1 CAGATTAAAAATTACAGGTCTTATCTCCATGTATCGGCTATGGAG
* * * *
90414714 CAGACTAAGAATTACAGATCTTATCTCCATGTATCGGCTATGAAG
1 CAGATTAAAAATTACAGGTCTTATCTCCATGTATCGGCTATGGAG
90414759 CAGAT
1 CAGAT
90414764 CGAAAATGGC
Statistics
Matches: 190, Mismatches: 69, Indels: 28
0.66 0.24 0.10
Matches are distributed among these distances:
43 2 0.01
44 55 0.29
45 131 0.69
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
CAGATTAAAAATTACAGGTCTTATCTCCATGTATCGGCTATGGAG
Found at i:90414650 original size:356 final size:355
Alignment explanation
Indices: 90413910--90414628 Score: 1123
Period size: 356 Copynumber: 2.0 Consensus size: 355
90413900 GTAGCAAGGA
* * *
90413910 AGCAGACTAAAAATTACAGATCTTATCTCCATGAATCGGCTATGGAACAGATCGAAAATGGTGAG
1 AGCAGACTGAGAA-TACAGACCTTATCTCCATGAATCGGCTATGGAACAGATCGAAAATGGTGAG
* * *
90413975 TCTTATCTCTATGTATCAGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCA
65 TCTTATCTCCATGTATCAGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGCA
* * *
90414040 AGAGAGCATTTTAAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAATTACA
130 AGAGAGCATGTTAAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTAAAATTACA
* * * * ** *
90414105 GATCTTATCTCTATGTATCGGCTATAGAGCAGATCAAAAATGGTGAGTCTTATCTCTATGTATCG
195 GATCTTATCTCCATGTATCAGCTATAGAACAGATAAAAAATGACGAGTCTTATCTCCATGTATCG
* *
90414170 ACTATGGAACAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAGGTTGAAAAT
260 ACTATGGAACAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAACAGAGCAGGTTAAAAAT
90414235 TGCAGGTCTTATCTCCATGTATCAGCTATGG
325 TGCAGGTCTTATCTCCATGTATCAGCTATGG
* * * *
90414266 AGCAGACTGAGAATTACAGATCTTATCTCCATGTATCGTCTATGGAGCAGATCGAAAATGGTGAG
1 AGCAGACTGAGAA-TACAGACCTTATCTCCATGAATCGGCTATGGAACAGATCGAAAATGGTGAG
*
90414331 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGCA
65 TCTTATCTCCATGTATCAGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGCA
* *
90414396 AGAGAGCATGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGTAAGGAAACAGACTAAAAATTAC
130 AGAGAGCATGTTAAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACT-AAAATTAC
* *
90414461 AGATCTTATCTCCATGTATCAGTTATGGAACAGATAAAAAATGACGAGTCTTATCTCCATGTATC
194 AGATCTTATCTCCATGTATCAGCTATAGAACAGATAAAAAATGACGAGTCTTATCTCCATGTATC
* * * *
90414526 GGCTATGGAGCAGATTTTAGCCCCCAGCCTTATCTCTCTGAATTAGCAACAGAGCAGGTTAAAAA
259 GACTATGGAACAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAACAGAGCAGGTTAAAAA
*
90414591 TTGCAGGTCTTATCTCCATGTATCGGCTATGG
324 TTGCAGGTCTTATCTCCATGTATCAGCTATGG
90414623 AGCAGA
1 AGCAGA
90414629 TTTTAGCCAC
Statistics
Matches: 332, Mismatches: 30, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
356 173 0.52
357 159 0.48
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (355 bp):
AGCAGACTGAGAATACAGACCTTATCTCCATGAATCGGCTATGGAACAGATCGAAAATGGTGAGT
CTTATCTCCATGTATCAGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGCAA
GAGAGCATGTTAAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTAAAATTACAG
ATCTTATCTCCATGTATCAGCTATAGAACAGATAAAAAATGACGAGTCTTATCTCCATGTATCGA
CTATGGAACAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAACAGAGCAGGTTAAAAATT
GCAGGTCTTATCTCCATGTATCAGCTATGG
Found at i:90414828 original size:268 final size:266
Alignment explanation
Indices: 90414330--90414871 Score: 725
Period size: 268 Copynumber: 2.0 Consensus size: 266
90414320 AAAATGGTGA
* *
90414330 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCGGCCTTATCTCTCTGAGGGAGC
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCAGCCTTATCTCTCTGAAGGAGC
* *
90414395 AAGAGAGCATGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGTAAGGAAACAGACTAAAAATTA
66 AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCATGAGGTAGT-AGGAAACAGACTAAAAATTA
* *
90414460 CAGATCTTATCTCCATGTATCAGTTATGGAACAGATAAAAAATGACGAGTCTTATCTCCATGTAT
130 CAGATCTTATCTCCATGTATCAGCTATGGAACAGATAAAAAATGACGAGTCCTATCTCCATGTAT
* * * * * * *
90414525 CGGCTATGGAGCAGATTTTAGCCCCCAGCCTTATCTCTCTGAA-TTAGCAACAGAGCAGGTTAAA
195 CAGCTATAGAACAAATTTTAGCCACCAACCTTATCTCTCT-AAGGTAGCAACAGAGCAGGTTAAA
*
90414589 AATTGCAG
259 AATTACAG
* *
90414597 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
1 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCAGCCTTATCTCTCTGAAGGAGC
* * * *
90414662 AAGAGAGCAGGTTGAAAGTTACAGGTCTTATCTTCATGTACCGGCTA-T-GG-AGCAGACTAAGA
66 AAGAGAGCAGGTTG-AAGATACAAGTCTTATCTTCATG-A--GG-TAGTAGGAAACAGACTAAAA
* ** * *
90414724 ATTACAGATCTTATCTCCATGTATCGGCTAT-GAAGCAGATCGAAAATGGCGAGTCCTATCTCTA
126 ATTACAGATCTTATCTCCATGTATCAGCTATGGAA-CAGATAAAAAATGACGAGTCCTATCTCCA
* *
90414788 TGTATCAGTTATAGAACAAATTTTAGCCACCAACCTTATCTCTCTAAGGTAGCAAGAGAGCAGGT
190 TGTATCAGCTATAGAACAAATTTTAGCCACCAACCTTATCTCTCTAAGGTAGCAACAGAGCAGGT
*
90414853 TGAAAATTACAG
255 TAAAAATTACAG
90414865 GTCTTAT
1 GTCTTAT
90414872 TTCGGCTATG
Statistics
Matches: 240, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
267 79 0.33
268 153 0.64
269 3 0.01
271 3 0.01
272 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (266 bp):
GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTACCCACCAGCCTTATCTCTCTGAAGGAGC
AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCATGAGGTAGTAGGAAACAGACTAAAAATTAC
AGATCTTATCTCCATGTATCAGCTATGGAACAGATAAAAAATGACGAGTCCTATCTCCATGTATC
AGCTATAGAACAAATTTTAGCCACCAACCTTATCTCTCTAAGGTAGCAACAGAGCAGGTTAAAAA
TTACAG
Found at i:90415039 original size:44 final size:44
Alignment explanation
Indices: 90414990--90415130 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
90414980 ATACAAATCT
90414990 CCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGAC
1 CCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGAC
* * * ** **
90415034 CCCCTAAACAGTA--GG-GTA-A-C--AGGCTGGAAAATACAGATC
1 CCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCT-TTGA-C
*
90415073 TCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGAC
1 CCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGAC
90415117 CCCCTAAACAGTAG
1 CCCCTAAACAGTAG
90415131 GGTAACAGGC
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
37 7 0.10
38 2 0.03
39 14 0.19
40 1 0.01
41 5 0.07
42 5 0.07
43 1 0.01
44 28 0.39
45 2 0.03
46 7 0.10
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (44 bp):
CCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGAC
Found at i:90415078 original size:39 final size:39
Alignment explanation
Indices: 90415035--90415169 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
90415025 AGCTTTGACC
90415035 CCCTAAACAGTAGGGTAACAGGCTGGAAAATACAGATCT
1 CCCTAAACAGTAGGGTAACAGGCTGGAAAATACAGATCT
** * * * * * *
90415074 CCCTAAACAGTAGTGG-AGTA-GATCGAAGACAGCAAGCTTTGACC
1 CCCTAAACAGTAG-GGTAACAGGCTGGAAAATA-C-AG--AT--CT
90415118 CCCTAAACAGTAGGGTAACAGGCTGGAAAATACAGATCT
1 CCCTAAACAGTAGGGTAACAGGCTGGAAAATACAGATCT
90415157 CCCTAAACAGTAG
1 CCCTAAACAGTAG
90415170 TGGAGTAGAT
Statistics
Matches: 71, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
38 7 0.10
39 30 0.42
40 4 0.06
41 1 0.01
42 1 0.01
43 4 0.06
44 17 0.24
45 7 0.10
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (39 bp):
CCCTAAACAGTAGGGTAACAGGCTGGAAAATACAGATCT
Found at i:90415446 original size:87 final size:87
Alignment explanation
Indices: 90414909--90416216 Score: 1949
Period size: 87 Copynumber: 15.2 Consensus size: 87
90414899 CAGATCTCCT
* * * * * * *
90414909 CTAAACAATAATGGAGCAGATCGAAGGCAACAAGCCTTAACCCCCTAAGCAGTAGGGTAATAAGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
* * *
90414974 T-GAAAAATACAAATC-T-CCC
66 TGGAAAATTACAGATCTTATCC
* * * **
90414993 CTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGACCCCCTAAACAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415058 TGGAAAA-TACAGATC---TCC
66 TGGAAAATTACAGATCTTATCC
* * * **
90415076 CTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCTTTGACCCCCTAAACAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415141 TGGAAAA-TACAGATC---TCC
66 TGGAAAATTACAGATCTTATCC
* * * * *
90415159 CTAAACAGTAGTGGAGTAGATCGAAGACAGCAAGCCTTAACCCCTTAAGCAATAAGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
*
90415224 T-GAAAAATACAGA-C--ATCCC
66 TGGAAAATTACAGATCTTAT-CC
* * * * * *
90415243 CTAAATAGTAGTGGAGCAGATCGAAGATAGCAAGCCTTAACCCCCTAAGCAGTAGAGTAATAGTC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
* *
90415308 TGGAAAA-TAAAGATC-T-CCC
66 TGGAAAATTACAGATCTTATCC
90415327 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415392 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415414 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415479 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415501 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415566 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415588 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415653 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415675 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415740 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415762 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415827 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415849 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90415914 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
90415936 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90416001 TGGAAAATTACAGATCTTATCC
66 TGGAAAATTACAGATCTTATCC
* * * *
90416023 CTAAACAGTAGTGGAGCAGATCGAAGACAGCGAGCCTTAACTCCCTAAGCAGTAGGATAACAGGC
1 CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
90416088 T-GAAAATTACAGATCTTATCTCC
66 TGGAAAATTACAGATCTTA--TCC
* * * * ** * * * * *
90416111 CTAAGCAGTAGCT-GAGCAGATTGAAAACGGTGAGCCTGATCTCCTTAAGTAGTAGTGG-AGCAG
1 CTAAACAGTAG-TGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAG-GGTAACAG
90416174 GCT-GAAAATTACAGATCTTATCTCC
64 GCTGGAAAATTACAGATCTTA--TCC
*
90416199 CTAAGCAGTAGTGGAGCA
1 CTAAACAGTAGTGGAGCA
90416217 ACCTGAAGAT
Statistics
Matches: 1157, Mismatches: 52, Indels: 26
0.94 0.04 0.02
Matches are distributed among these distances:
82 6 0.01
83 152 0.13
84 195 0.17
85 18 0.02
86 18 0.02
87 674 0.58
88 92 0.08
89 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (87 bp):
CTAAACAGTAGTGGAGCAGATCGAAGACAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
TGGAAAATTACAGATCTTATCC
Found at i:90416111 original size:44 final size:43
Alignment explanation
Indices: 90416058--90416244 Score: 137
Period size: 44 Copynumber: 4.3 Consensus size: 43
90416048 GACAGCGAGC
* *
90416058 CTTAACTCCCTAAGCAGTAGGATAACAGGCTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAGG-TAGCAGGCTGAAAATTACAGAT
* ** * * *
90416102 CTTATCTCCCTAAGCAGTAGCTGAGCAGATTGAAAACGGT-GAG-C
1 CTTATCTCCCTAAGCAGTAGGT-AGCAGGCTGAAAA--TTACAGAT
* * * *
90416146 CTGATCTCCTTAAGTAGTAGTGGAGCAGGCTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAG-GTAGCAGGCTGAAAATTACAGAT
* ** *
90416190 CTTATCTCCCTAAGCAGTAGTGGAGCAACCTGAAGATTACCAGAT
1 CTTATCTCCCTAAGCAGTAG-GTAGCAGGCTGAAAATTA-CAGAT
*
90416235 TTTATC-CCCT
1 CTTATCTCCCT
90416245 TTAAGTTTCA
Statistics
Matches: 111, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 94 0.85
45 12 0.11
46 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGTAGGTAGCAGGCTGAAAATTACAGAT
Found at i:90416427 original size:35 final size:35
Alignment explanation
Indices: 90416381--90416450 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
90416371 CAGCAGGTCC
90416381 AGGCAAAATTGGCCCTTTTATAGTCTTTGCACCAT
1 AGGCAAAATTGGCCCTTTTATAGTCTTTGCACCAT
90416416 AGGCAAAATTGGCCCTTTTATAGTCTTTGCACCAT
1 AGGCAAAATTGGCCCTTTTATAGTCTTTGCACCAT
90416451 TCTCGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (35 bp):
AGGCAAAATTGGCCCTTTTATAGTCTTTGCACCAT
Found at i:90419404 original size:5 final size:6
Alignment explanation
Indices: 90419389--90419429 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
90419379 AAATTATATG
90419389 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTTGA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTT-A TTTTTA TTT
90419430 ATTAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 22 0.67
7 10 0.30
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:90421924 original size:20 final size:20
Alignment explanation
Indices: 90421885--90421935 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
90421875 CGTGTTTGCT
* *
90421885 TTCCGTTTAGCTCTTATGAGC
1 TTCCG-TTAACTCATATGAGC
*
90421906 TTCCGTTAACTCATATGAGT
1 TTCCGTTAACTCATATGAGC
*
90421926 TTCAGTTAAC
1 TTCCGTTAAC
90421936 CCTTTTGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (20 bp):
TTCCGTTAACTCATATGAGC
Found at i:90422139 original size:39 final size:39
Alignment explanation
Indices: 90421966--90422144 Score: 268
Period size: 39 Copynumber: 4.6 Consensus size: 39
90421956 GCTCTGATGA
*
90421966 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
90422005 GCTTCAGTTAGCCTTCGGGCTCCCGTTTAGCACTTACAT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
90422044 GCTTCAATTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
90422083 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* * **
90422122 ACTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
90422145 AGATCACGAT
Statistics
Matches: 125, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 125 1.00
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:90425010 original size:44 final size:45
Alignment explanation
Indices: 90424904--90425015 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 45
90424894 ACAGGACAGA
* * **
90424904 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGTTTTGGAG
1 ACAGGAATGAACCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
90424950 ACAGGATTGAACCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAACCATGTAAGTCCATATTAAAATATGGCATTGGAG
*
90424994 ACAGGAAT-AATTCATGTAAGTC
1 ACAGGAATGAA-CCATGTAAGTC
90425016 AATGTCAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
43 2 0.04
44 30 0.53
46 25 0.44
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (45 bp):
ACAGGAATGAACCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:90426428 original size:7 final size:7
Alignment explanation
Indices: 90426416--90426451 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
90426406 TTATATATGT
90426416 AATACTA
1 AATACTA
90426423 AATACTA
1 AATACTA
90426430 AATACTA
1 AATACTA
*
90426437 AATACGA
1 AATACTA
90426444 AATGACTA
1 AAT-ACTA
90426452 TTTTATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 23 0.88
8 3 0.12
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:90429968 original size:78 final size:78
Alignment explanation
Indices: 90429833--90429986 Score: 272
Period size: 78 Copynumber: 2.0 Consensus size: 78
90429823 TCCCCCTTCT
*
90429833 AATTGTAGACTGTTTTTGTTAGCTTTGTTTAATGTCTATTTTCCATAGAGAAAAAATTGGATTCT
1 AATTGTAGACTGTTTTTGTTAGCTGTGTTTAATGTCTATTTTCCATAGAGAAAAAATTGGATTCT
90429898 CTTTTATTGCAAA
66 CTTTTATTGCAAA
* *
90429911 AATTTTAGACTGTTTTTGTTAGCTGTGTTTAATGTCTATTTTCCATAGAGAAGAAATTGGATTCT
1 AATTGTAGACTGTTTTTGTTAGCTGTGTTTAATGTCTATTTTCCATAGAGAAAAAATTGGATTCT
*
90429976 CTTTTCTTGCA
66 CTTTTATTGCA
90429987 TCATCTGACA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (78 bp):
AATTGTAGACTGTTTTTGTTAGCTGTGTTTAATGTCTATTTTCCATAGAGAAAAAATTGGATTCT
CTTTTATTGCAAA
Found at i:90437588 original size:25 final size:25
Alignment explanation
Indices: 90437547--90437598 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
90437537 CTTCTTGATC
*
90437547 ATAAATTTTTATAAATAAATATATT
1 ATAAATTTTTATAAATAAATAAATT
*
90437572 ATAACATTTTTAT-AATAGATAAATT
1 ATAA-ATTTTTATAAATAAATAAATT
90437597 AT
1 AT
90437599 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
ATAAATTTTTATAAATAAATAAATT
Found at i:90455116 original size:10 final size:10
Alignment explanation
Indices: 90455101--90455125 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
90455091 AATGTTCTAT
90455101 CTTCTTAGGA
1 CTTCTTAGGA
90455111 CTTCTTAGGA
1 CTTCTTAGGA
90455121 CTTCT
1 CTTCT
90455126 ACATGCCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (10 bp):
CTTCTTAGGA
Found at i:90456599 original size:15 final size:16
Alignment explanation
Indices: 90456579--90456608 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
90456569 GAAAATTGCC
90456579 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
90456594 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
90456609 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:90464866 original size:26 final size:26
Alignment explanation
Indices: 90464858--90464912 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
90464848 CTTAATATTT
90464858 AAGTAAATATATATAATATAATAATA
1 AAGTAAATATATATAATATAATAATA
*
90464884 AAGTAAATATA-ATAAAATAAATAAGTA
1 AAGTAAATATATATAATAT-AATAA-TA
90464911 AA
1 AA
90464913 TGAAATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 16 0.62
27 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (26 bp):
AAGTAAATATATATAATATAATAATA
Found at i:90464896 original size:22 final size:22
Alignment explanation
Indices: 90464857--90464921 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
90464847 ACTTAATATT
*
90464857 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAAAAT-A-AA
90464882 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
90464905 TAAGTAAATGA-AATAAA
1 TAAGTAAAT-ATAATAAA
90464922 GAAAGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 14 0.38
23 4 0.11
24 1 0.03
25 7 0.19
26 11 0.30
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:90465955 original size:37 final size:37
Alignment explanation
Indices: 90465910--90466029 Score: 132
Period size: 37 Copynumber: 3.2 Consensus size: 37
90465900 GATTAATTCA
* *
90465910 ATGAGGCACTGGGTGCCAATTTACTTCGGTTTAGCCG
1 ATGAGGCACTGAGTGCCAATTTACTTCGATTTAGCCG
* *
90465947 ATGAGGCACCGAGTGTCAATTTACTTCGATTTAGCCG
1 ATGAGGCACTGAGTGCCAATTTACTTCGATTTAGCCG
* * * * *
90465984 ATGAGACACTAAGTGTCAAATTATTACTTCGAATTATCCG
1 ATGAGGCACTGAGTG-CCAA-T-TTACTTCGATTTAGCCG
90466024 ATGAGG
1 ATGAGG
90466030 TGCTGGGTAC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 45 0.66
38 2 0.03
39 1 0.01
40 20 0.29
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (37 bp):
ATGAGGCACTGAGTGCCAATTTACTTCGATTTAGCCG
Found at i:90466207 original size:21 final size:20
Alignment explanation
Indices: 90466159--90466207 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
90466149 GAAAAACTAT
* *
90466159 TTGAATAGCAAGTATGAGAT
1 TTGAATAGCAAGGATGAGAA
*
90466179 TTGAAATAGTAAGAGATGAGAA
1 TTG-AATAGCAAG-GATGAGAA
90466201 TTGAATA
1 TTGAATA
90466208 TGTTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 9 0.38
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (20 bp):
TTGAATAGCAAGGATGAGAA
Found at i:90481807 original size:29 final size:32
Alignment explanation
Indices: 90481755--90481821 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
90481745 TAATATGTAA
90481755 TTATATACATAAATTTTAATTTTG-TATAATT
1 TTATATACATAAATTTTAATTTTGATATAATT
* *
90481786 TTATATATA-AAATTTTAA-TTTGATCTAATT
1 TTATATACATAAATTTTAATTTTGATATAATT
90481816 TT-TATA
1 TTATATA
90481822 AACTATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.24
30 17 0.52
31 8 0.24
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (32 bp):
TTATATACATAAATTTTAATTTTGATATAATT
Found at i:90484114 original size:6 final size:6
Alignment explanation
Indices: 90484103--90484128 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
90484093 ATGCATTTAC
90484103 ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT AT
90484129 TAAATTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATACAT
Found at i:90487994 original size:6 final size:6
Alignment explanation
Indices: 90487983--90488007 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90487973 GGAGGAGGGA
90487983 AAAGAC AAAGAC AAAGAC AAAGAC A
1 AAAGAC AAAGAC AAAGAC AAAGAC A
90488008 GAGTGGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAC
Found at i:90496534 original size:25 final size:25
Alignment explanation
Indices: 90496487--90496536 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
90496477 ATTTTCTAAG
90496487 TAAAAAATTTTTATATAGTAATTTT
1 TAAAAAATTTTTATATAGTAATTTT
90496512 TAAAAAATCTTTTATATAG-AATTTT
1 TAAAAAAT-TTTTATATAGTAATTTT
90496537 AAAGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
TAAAAAATTTTTATATAGTAATTTT
Found at i:90511824 original size:21 final size:21
Alignment explanation
Indices: 90511759--90511848 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
90511749 TAGTTCTCAC
* *
90511759 GAGCTTATGTTTAACTCATAT
1 GAGCTTTTGTTTAACTCTTAT
* * *
90511780 GAG-TTTTCGTTCAGCTCTTTT
1 GAGCTTTT-GTTTAACTCTTAT
*
90511801 GAGCTTTTGTTTAACCCTTAT
1 GAGCTTTTGTTTAACTCTTAT
* * *
90511822 GAG-TTTCCGTTCAGCTCTTAT
1 GAGCTTT-TGTTTAACTCTTAT
90511843 GAGCTT
1 GAGCTT
90511849 CCGTTCAACC
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
20 6 0.12
21 40 0.77
22 6 0.12
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.46
Consensus pattern (21 bp):
GAGCTTTTGTTTAACTCTTAT
Found at i:90511850 original size:21 final size:21
Alignment explanation
Indices: 90511777--90511855 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
90511767 GTTTAACTCA
* *
90511777 TATGAGTTTTCGTTCAGCTCT
1 TATGAGCTTCCGTTCAGCTCT
* ** * * *
90511798 TTTGAGCTTTTGTTTAACCCT
1 TATGAGCTTCCGTTCAGCTCT
*
90511819 TATGAGTTTCCGTTCAGCTCT
1 TATGAGCTTCCGTTCAGCTCT
90511840 TATGAGCTTCCGTTCA
1 TATGAGCTTCCGTTCA
90511856 ACCCTTATAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (21 bp):
TATGAGCTTCCGTTCAGCTCT
Found at i:90511870 original size:42 final size:42
Alignment explanation
Indices: 90511741--90511897 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
90511731 TTGTGTTTAC
* * * * * * * *
90511741 TTTCCGTTTAGTTCTCACGAGCTTATGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGAG
* * * *
90511783 TTTTCGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGAG
*
90511825 TTTCCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTTAT-ATG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGA-G
* * *
90511867 TTTCTGTTTAGCACTTAT-ATGCTTCTGTTCA
1 TTTCCGTTCAGCTCTTATGA-GCTTCTGTTCA
90511898 GCCTTTGGGC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 93 0.98
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGAG
Found at i:90524073 original size:18 final size:18
Alignment explanation
Indices: 90524050--90524086 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
90524040 AAGGAAAGGT
90524050 AATCAGAGACTCAAGAAA
1 AATCAGAGACTCAAGAAA
90524068 AATCAGAGACTCAAGAAA
1 AATCAGAGACTCAAGAAA
90524086 A
1 A
90524087 GGATAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (18 bp):
AATCAGAGACTCAAGAAA
Found at i:90526429 original size:45 final size:45
Alignment explanation
Indices: 90526365--90526570 Score: 299
Period size: 45 Copynumber: 4.6 Consensus size: 45
90526355 CTCTGGAGCA
90526365 GCTCTATAATTGGGATCAATCGG-AGCACCTCTAGCA-CTCGGATCC
1 GCTCTATAATTGGGATCAAT-GGAAGCACCTCTAG-AGCTCGGATCC
* * *
90526410 GCTCTATAATTGGGCTCAATGGAAGCACCTCTAGCGCTTGGATCC
1 GCTCTATAATTGGGATCAATGGAAGCACCTCTAGAGCTCGGATCC
*
90526455 GCTCTATAATTGGGATCAATGGAAGCAACTCTAGAGCTCGGATCC
1 GCTCTATAATTGGGATCAATGGAAGCACCTCTAGAGCTCGGATCC
* * * *
90526500 ACTCTATAATTGGGATCAATGGGAGCAGCTCTAGAGCCCGGATCC
1 GCTCTATAATTGGGATCAATGGAAGCACCTCTAGAGCTCGGATCC
*
90526545 GCTCTATAGTTGGGATCAATGGAAGC
1 GCTCTATAATTGGGATCAATGGAAGC
90526571 GGGTCTGGGA
Statistics
Matches: 145, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
44 2 0.01
45 143 0.99
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (45 bp):
GCTCTATAATTGGGATCAATGGAAGCACCTCTAGAGCTCGGATCC
Found at i:90526587 original size:66 final size:66
Alignment explanation
Indices: 90526510--90526642 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
90526500 ACTCTATAAT
* * * * *
90526510 TGGGATCAATGGGAGCAGCTCTAGAGCCCGGATCCGCTCTATAGTTGGGATCAATGGAAGCGGGT
1 TGGGATCAATGGAAGCAGATCTAGAGCCCGGATCCGCTCTATAATTAGGATCAATGGAAGCAGGT
90526575 C
66 C
* ** *
90526576 TGGGATCAATGGAAGCAGATCTGGAGCTTGGATCCGCTCTATAATTAGGATCGATGGAAGCAGGT
1 TGGGATCAATGGAAGCAGATCTAGAGCCCGGATCCGCTCTATAATTAGGATCAATGGAAGCAGGT
90526641 C
66 C
90526642 T
1 T
90526643 AGAGCTTGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (66 bp):
TGGGATCAATGGAAGCAGATCTAGAGCCCGGATCCGCTCTATAATTAGGATCAATGGAAGCAGGT
C
Found at i:90526598 original size:21 final size:21
Alignment explanation
Indices: 90526555--90526599 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
90526545 GCTCTATAGT
* *
90526555 TGGGATCAATGGAAGCGGGTC
1 TGGGATCAATGGAAGCAGATC
90526576 TGGGATCAATGGAAGCAGATC
1 TGGGATCAATGGAAGCAGATC
90526597 TGG
1 TGG
90526600 AGCTTGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (21 bp):
TGGGATCAATGGAAGCAGATC
Found at i:90534459 original size:24 final size:24
Alignment explanation
Indices: 90534418--90534464 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
90534408 AAAATGGAAC
*
90534418 TTTGATTTTAAATGCTGACAGCAA
1 TTTGATTATAAATGCTGACAGCAA
90534442 TTTGATTCATAAAT-CTGACAGCA
1 TTTGATT-ATAAATGCTGACAGCA
90534465 TAGCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (24 bp):
TTTGATTATAAATGCTGACAGCAA
Found at i:90535894 original size:26 final size:25
Alignment explanation
Indices: 90535858--90535908 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
90535848 TTGGCGTCAC
* *
90535858 AACTTCAGCAGTAGAGTGTCGCGAT
1 AACTTCAGCAGGAGAATGTCGCGAT
90535883 NAACTTCAGCAGGAGAATGTCGCGAT
1 -AACTTCAGCAGGAGAATGTCGCGAT
90535909 GTTAAGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.22
Consensus pattern (25 bp):
AACTTCAGCAGGAGAATGTCGCGAT
Found at i:90540062 original size:24 final size:24
Alignment explanation
Indices: 90540035--90540083 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
90540025 GAAATGACCT
90540035 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
90540059 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
90540083 T
1 T
90540084 CGTCGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:90542028 original size:46 final size:46
Alignment explanation
Indices: 90541966--90542180 Score: 324
Period size: 46 Copynumber: 4.7 Consensus size: 46
90541956 GATGCCATAA
* * * *
90541966 TATCTTTCAACTATGGTTTTACTCACTTTC-TGTCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGG
** * *
90542012 TATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
* *
90542058 TATCTTTCAACCATGGTCTTACACATTTTATATCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
90542104 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
90542150 TATCTTTCAACCATGGTCTTACACATTTCAT
1 TATCTTTCAACCATGGTCTTACACATTTCAT
90542181 TTCAAAGAGC
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
45 4 0.03
46 153 0.97
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
Found at i:90545990 original size:18 final size:19
Alignment explanation
Indices: 90545963--90545998 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
90545953 AAATGTACTA
90545963 TTCACATACA-CATATATT
1 TTCACATACATCATATATT
*
90545981 TTCACTTACATCATATAT
1 TTCACATACATCATATAT
90545999 AAATTGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCACATACATCATATATT
Found at i:90547649 original size:21 final size:21
Alignment explanation
Indices: 90547624--90547688 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
90547614 TAGCCTTTGG
90547624 GCTTCCATTTAGCACTTGTGT
1 GCTTCCATTTAGCACTTGTGT
*
90547645 GCTT-CAGTTAGC-CTTCG-G-
1 GCTTCCATTTAGCACTT-GTGT
* * *
90547663 GCTTCCGTTTAGCACTTATAT
1 GCTTCCATTTAGCACTTGTGT
90547684 GCTTC
1 GCTTC
90547689 AGCTAGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 11 0.32
21 9 0.26
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (21 bp):
GCTTCCATTTAGCACTTGTGT
Found at i:90547650 original size:39 final size:39
Alignment explanation
Indices: 90547606--90547706 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
90547596 ACTCTGATGA
* * *
90547606 GCTTCAGTTAGCCTTTGGGCTTCCATTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATAT
*
90547645 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATAT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATAT
* *
90547684 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
90547707 AAATCATGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATAT
Found at i:90549007 original size:56 final size:56
Alignment explanation
Indices: 90548875--90549010 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
90548865 TCCCAGACAG
* * *
90548875 GGTCTTACTCGCACACATAAATCAGAATCACATATCGGTGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
*
90548931 GCTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
*
90548987 GGTCTTACTCGCACATATATATCG
1 GGTCTTACTCGCACACATATATCG
90549011 ATGCCATGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:90550714 original size:20 final size:20
Alignment explanation
Indices: 90550657--90550708 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
90550647 TGTGGATTCC
90550657 ACACGCCCGTGTGGCTTGAG
1 ACACGCCCGTGTGGCTTGAG
* * *
90550677 ACACGCTCATGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGAG
90550697 ACACGCCCGTGT
1 ACACGCCCGTGT
90550709 CCCTTGTCCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGAG
Found at i:90553636 original size:13 final size:14
Alignment explanation
Indices: 90553618--90553647 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
90553608 TTATACTAAG
90553618 ATTAATCAA-CTTA
1 ATTAATCAAGCTTA
90553631 ATTAATCAAGCTTA
1 ATTAATCAAGCTTA
90553645 ATT
1 ATT
90553648 TACTAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (14 bp):
ATTAATCAAGCTTA
Found at i:90560057 original size:12 final size:12
Alignment explanation
Indices: 90560024--90560057 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
90560014 TCAAATACAT
*
90560024 TTAAAACAAATA
1 TTAAAACAATTA
*
90560036 TTAAAACAATTC
1 TTAAAACAATTA
90560048 TTAAAACAAT
1 TTAAAACAAT
90560058 ACACAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAAAACAATTA
Found at i:90560123 original size:17 final size:17
Alignment explanation
Indices: 90560103--90560137 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
90560093 TTAAAATTAA
90560103 AATT-AAAATATAAATAT
1 AATTAAAAATA-AAATAT
90560120 AATTAAAAATAAAATAT
1 AATTAAAAATAAAATAT
90560137 A
1 A
90560138 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAATAAAATAT
Found at i:90586541 original size:13 final size:14
Alignment explanation
Indices: 90586517--90586576 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 14
90586507 TGTAATGTCT
90586517 AAATAGATTAATA-A
1 AAATA-ATTAATATA
90586531 AAATAATTAATATA
1 AAATAATTAATATA
* *
90586545 TAATAATT-TTATA
1 AAATAATTAATATA
* *
90586558 ATATAATTTATAATA
1 AAATAATTAAT-ATA
90586573 AAAT
1 AAAT
90586577 TAAATGTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
13 17 0.46
14 14 0.38
15 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATAATTAATATA
Found at i:90586727 original size:21 final size:20
Alignment explanation
Indices: 90586686--90586724 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
90586676 AGTCGAAATC
90586686 AAAATAAAAATAATTTTTTA
1 AAAATAAAAATAATTTTTTA
**
90586706 AAAATAAATTTAATTTTTT
1 AAAATAAAAATAATTTTTT
90586725 TAATTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAAAATAATTTTTTA
Found at i:90592509 original size:30 final size:29
Alignment explanation
Indices: 90592473--90592531 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
90592463 TAGATTTTAG
*
90592473 GTTTTTTTACTCCATTAATACCAAAAAAAA
1 GTTTTTTTACTCCATTAATA-AAAAAAAAA
*
90592503 GTTTTTTTATTCCATTAATAAAAAAAAAA
1 GTTTTTTTACTCCATTAATAAAAAAAAAA
90592532 TTATCACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (29 bp):
GTTTTTTTACTCCATTAATAAAAAAAAAA
Found at i:90596051 original size:12 final size:12
Alignment explanation
Indices: 90596036--90596061 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
90596026 ATTTTCTACT
90596036 TCTTTTTCTTTC
1 TCTTTTTCTTTC
90596048 TCTTTTTCTTTC
1 TCTTTTTCTTTC
90596060 TC
1 TC
90596062 CCTTTTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTTTCTTTC
Found at i:90598903 original size:61 final size:62
Alignment explanation
Indices: 90598829--90598946 Score: 177
Period size: 61 Copynumber: 1.9 Consensus size: 62
90598819 TTTGTATTAT
*
90598829 ATATTATAATTATTTAAGTTTATTTTTATCTAA-TTAATATTTAAATACTA-TTTATACTTAA
1 ATATTATAATTATTAAAGTTTATTTTTATC-AACTTAATATTTAAATACTACTTTATACTTAA
* * *
90598890 ATATTGTAATTATTAAATTTTATTTTTTTCAACTTAATATTTAAATACTACTTTATA
1 ATATTATAATTATTAAAGTTTATTTTTATCAACTTAATATTTAAATACTACTTTATA
90598947 TTACTTCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 2 0.04
61 43 0.84
62 6 0.12
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (62 bp):
ATATTATAATTATTAAAGTTTATTTTTATCAACTTAATATTTAAATACTACTTTATACTTAA
Found at i:90599383 original size:14 final size:14
Alignment explanation
Indices: 90599361--90599403 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
90599351 TCTTCGTAAA
90599361 ATTAGAATTTAATT
1 ATTAGAATTTAATT
* *
90599375 ATTATAATTTTATT
1 ATTAGAATTTAATT
*
90599389 TTTAGGAATTTAATT
1 ATTA-GAATTTAATT
90599404 TTTTATCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTAGAATTTAATT
Found at i:90604657 original size:6 final size:6
Alignment explanation
Indices: 90604646--90604670 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90604636 TCCCCGACTC
90604646 TGATTA TGATTA TGATTA TGATTA T
1 TGATTA TGATTA TGATTA TGATTA T
90604671 AATACAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTA
Found at i:90604915 original size:34 final size:34
Alignment explanation
Indices: 90604872--90604939 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
90604862 TTTGAAGGGA
90604872 AAAGAAAGGTATCTATCTTGCCACTCTTTCACAC
1 AAAGAAAGGTATCTATCTTGCCACTCTTTCACAC
90604906 AAAGAAAGGTATCTATCTTGCCACTCTTTCACAC
1 AAAGAAAGGTATCTATCTTGCCACTCTTTCACAC
90604940 TATCTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (34 bp):
AAAGAAAGGTATCTATCTTGCCACTCTTTCACAC
Found at i:90606067 original size:15 final size:15
Alignment explanation
Indices: 90606047--90606107 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
90606037 TTACTTAAAC
*
90606047 TCAATAGTTAAATTT
1 TCAATACTTAAATTT
*
90606062 TCAATACTTAATTTT
1 TCAATACTTAAATTT
* * *
90606077 TCAACA-TTTATTTT
1 TCAATACTTAAATTT
*
90606091 TCAACACTTACAATTT
1 TCAATACTTA-AATTT
90606107 T
1 T
90606108 TTTCAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.34
15 20 0.53
16 5 0.13
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (15 bp):
TCAATACTTAAATTT
Found at i:90606076 original size:14 final size:14
Alignment explanation
Indices: 90606057--90606100 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
90606047 TCAATAGTTA
*
90606057 AATTTTCAATACTT
1 AATTTTCAACACTT
*
90606071 AATTTTTCAACATTT
1 AA-TTTTCAACACTT
*
90606086 ATTTTTCAACACTT
1 AATTTTCAACACTT
90606100 A
1 A
90606101 CAATTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTCAACACTT
Found at i:90606645 original size:17 final size:17
Alignment explanation
Indices: 90606625--90606659 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
90606615 TAAGTAACGT
90606625 AAAAA-AATATGATATAA
1 AAAAATAATAT-ATATAA
90606642 AAAAATAATATATATAA
1 AAAAATAATATATATAA
90606659 A
1 A
90606660 GTTTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATAATATATATAA
Found at i:90611240 original size:6 final size:7
Alignment explanation
Indices: 90611218--90611247 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
90611208 TTCTCAAATC
90611218 TTTATTTT
1 TTTA-TTT
90611226 TTTATTT
1 TTTATTT
90611233 TTTATTT
1 TTTATTT
90611240 TTTATTT
1 TTTATTT
90611247 T
1 T
90611248 ACTTCGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:90614609 original size:14 final size:14
Alignment explanation
Indices: 90614590--90614619 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
90614580 TTATATCGAG
90614590 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
90614604 ACCAATCCAATTCA
1 ACCAATCCAAATCA
90614618 AC
1 AC
90614620 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:90619087 original size:44 final size:44
Alignment explanation
Indices: 90619020--90619147 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 44
90619010 CATAGGGTTC
* *
90619020 CGATATGTGATTT-TGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
90619063 CGATTTGTGATTTACGTGTAAGACC-CTGCCTGGGACAG-TGACAT
1 CGATATGTGATTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
90619107 CGATATGTGA-TTACATGTAAGACCACGTCTGGGACGTTGGC
1 CGATATGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGC
90619148 GTTGTACGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
42 1 0.01
43 37 0.52
44 32 0.45
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (44 bp):
CGATATGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:90619140 original size:43 final size:43
Alignment explanation
Indices: 90619020--90619145 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 43
90619010 CATAGGGTTC
** * *
90619020 CGATATGTGATTTTGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGACAT
* *
90619063 CGATTTGTGATTTACGTGTAAGACC-CTGCCTGGGACAG-TGACAT
1 CGATATGTGA-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGACAT
*
90619107 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTG
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTG
90619146 GCGTTGTACG
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
42 1 0.01
43 33 0.48
44 34 0.49
45 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGACAT
Found at i:90622204 original size:2 final size:2
Alignment explanation
Indices: 90622197--90622222 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90622187 TACCATATTC
90622197 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
90622223 TTCTGAAAGC
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:90631318 original size:16 final size:14
Alignment explanation
Indices: 90631297--90631348 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
90631287 ATTCATAGTG
90631297 TTTATTTTTACATATA
1 TTTATTTTTA-ATA-A
90631313 TTTATTTTTAATAA
1 TTTATTTTTAATAA
90631327 TATTA-TTTT-ATAA
1 T-TTATTTTTAATAA
90631340 TTGTATTTT
1 TT-TATTTT
90631349 AAATTTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.21
14 9 0.27
15 6 0.18
16 10 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTATTTTTAATAA
Found at i:90632169 original size:29 final size:28
Alignment explanation
Indices: 90632119--90632193 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
90632109 ACATTAATAA
* * *
90632119 ATTTAATATTTTAACAATTAAACTTAAAT
1 ATTTAA-ATTTAAAAAATTAAAATTAAAT
*
90632148 TTTTAAATTTAAAAAATGTAAAATTAAAT
1 ATTTAAATTTAAAAAAT-TAAAATTAAAT
90632177 ATTTAAATTTATAAAAA
1 ATTTAAATTTA-AAAAA
90632194 ATATAAAGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.23
29 25 0.64
30 5 0.13
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (28 bp):
ATTTAAATTTAAAAAATTAAAATTAAAT
Found at i:90636230 original size:32 final size:32
Alignment explanation
Indices: 90636181--90636241 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
90636171 TTATAAATTT
*
90636181 ATAAATTGATTACTTTAATTTAATAACTCGTG
1 ATAAATTAATTACTTTAATTTAATAACTCGTG
* *
90636213 ATAAATTAATTATTTTAATTTGATAACTC
1 ATAAATTAATTACTTTAATTTAATAACTC
90636242 ATAATGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (32 bp):
ATAAATTAATTACTTTAATTTAATAACTCGTG
Found at i:90636842 original size:29 final size:29
Alignment explanation
Indices: 90636810--90636865 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
90636800 TTATTTGATT
*
90636810 ATTTT-AAAATATTTAACATTTATATAATC
1 ATTTTGAAAA-ATTTAACACTTATATAATC
* *
90636839 ATTTTGAAAAGTTTAACCCTTATATAA
1 ATTTTGAAAAATTTAACACTTATATAA
90636866 ACAACCTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (29 bp):
ATTTTGAAAAATTTAACACTTATATAATC
Found at i:90637126 original size:41 final size:41
Alignment explanation
Indices: 90637069--90637152 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
90637059 GATCAATCGG
90637069 ATAAAAAATTGATTAGGAATCAATGTAGAGAGAGAGATTGA
1 ATAAAAAATTGATTAGGAATCAATGTAGAGAGAGAGATTGA
90637110 ATAAAAAATTGATTAGGAATCAATGTAGAGAGAGAGATTGA
1 ATAAAAAATTGATTAGGAATCAATGTAGAGAGAGAGATTGA
90637151 AT
1 AT
90637153 CGGTTGACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.25
Consensus pattern (41 bp):
ATAAAAAATTGATTAGGAATCAATGTAGAGAGAGAGATTGA
Found at i:90637231 original size:17 final size:19
Alignment explanation
Indices: 90637211--90637257 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
90637201 GTTGAATCAG
90637211 TTTAATTAATTT-T-AATT
1 TTTAATTAATTTATGAATT
90637228 TTTAATT--TTTATGAATT
1 TTTAATTAATTTATGAATT
90637245 TTTAA-TAATTTAT
1 TTTAATTAATTTAT
90637258 TTGATAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 16 0.62
18 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTAATTAATTTATGAATT
Found at i:90644895 original size:11 final size:11
Alignment explanation
Indices: 90644879--90644911 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
90644869 TGGTTAAATT
90644879 AAAATTTCAAA
1 AAAATTTCAAA
90644890 AAAATTT-AAA
1 AAAATTTCAAA
90644900 AAAA-TTCAAA
1 AAAATTTCAAA
90644910 AA
1 AA
90644912 TCTTGGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.10
10 12 0.57
11 7 0.33
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATTTCAAA
Found at i:90646247 original size:3 final size:3
Alignment explanation
Indices: 90646236--90646270 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
90646226 ATCCATTTTT
*
90646236 TTC TGC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
90646271 TACTACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:90648585 original size:30 final size:31
Alignment explanation
Indices: 90648549--90648611 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
90648539 TACTGATATA
*
90648549 ATTCTGAATTACT-TAACTTTTTCACTTTTG
1 ATTCTGAATGACTATAACTTTTTCACTTTTG
90648579 ATTCTGAATGACTATAACTTTTTCACTTTTG
1 ATTCTGAATGACTATAACTTTTTCACTTTTG
90648610 AT
1 AT
90648612 GTCACTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (31 bp):
ATTCTGAATGACTATAACTTTTTCACTTTTG
Found at i:90649700 original size:29 final size:30
Alignment explanation
Indices: 90649654--90649751 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
90649644 ATAAGGGCTC
*
90649654 AACCTTTGCAAAAGTGCTCAAATGAA-AGCCA
1 AACCTTTGC-GAAGTGCTCAAAT-AAGAGCCA
*
90649685 AACCTTT-CGAAGTGCTCAAGTAATG-GCCAA
1 AACCTTTGCGAAGTGCTCAAATAA-GAGCC-A
* *
90649715 AACATTTGGGAAGTGCTCAAATAAGAGCCA
1 AACCTTTGCGAAGTGCTCAAATAAGAGCCA
*
90649745 GACCTTT
1 AACCTTT
90649752 TTGAACTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.04
29 14 0.25
30 15 0.27
31 24 0.44
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (30 bp):
AACCTTTGCGAAGTGCTCAAATAAGAGCCA
Found at i:90657166 original size:6 final size:6
Alignment explanation
Indices: 90657157--90657276 Score: 84
Period size: 6 Copynumber: 19.7 Consensus size: 6
90657147 TTCGATTTCA
* * * **
90657157 ATTTTG ATTTTG ATTTTG ATTGTT- ATTTTG ATTTAGG GTTATTT AGGGTT-
1 ATTTTG ATTTTG ATTTTG ATT-TTG ATTTTG ATTT-TG ATT-TTG A-TTTTG
* ** * *
90657207 ATTTCG ATTTCA ATTTTG ATTTTG ATTTCG ATTCTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
90657255 ATTTCT- ATTTTG ATTTTG ATTT
1 ATTT-TG ATTTTG ATTTTG ATTT
90657277 CAATTTTGAA
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
5 4 0.04
6 76 0.85
7 8 0.09
8 1 0.01
ACGTcount: A:0.18, C:0.04, G:0.17, T:0.61
Consensus pattern (6 bp):
ATTTTG
Found at i:90657171 original size:18 final size:18
Alignment explanation
Indices: 90657109--90657190 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
90657099 GTTTTAAATT
90657109 TTTTGGATTTCAATGTTGTTA
1 TTTT-GATTTCAA--TTGTTA
**
90657130 TTTTGATTT--AGGGTTA
1 TTTTGATTTCAATTGTTA
*
90657146 TTTCGATTTCAATT-TTGA
1 TTTTGATTTCAATTGTT-A
**
90657164 TTTTGATTTTGATTGTTA
1 TTTTGATTTCAATTGTTA
90657182 TTTTGATTT
1 TTTTGATTT
90657191 AGGGTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 24 0.49
19 2 0.04
20 5 0.10
21 4 0.08
ACGTcount: A:0.18, C:0.04, G:0.17, T:0.61
Consensus pattern (18 bp):
TTTTGATTTCAATTGTTA
Found at i:90657206 original size:62 final size:62
Alignment explanation
Indices: 90657135--90657252 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
90657125 TGTTATTTTG
* * *
90657135 ATTTAGGGTTATTTCGATTTCAATTTTGATTTTGATTTTGATTGTTATTTTGATTTAGGGTT
1 ATTTAGGGTTATTTCGATTTCAATTTTGATTTTGATTTCGATTCTGATTTTGATTTAGGGTT
90657197 ATTTAGGGTTATTTCGATTTCAATTTTGATTTTGATTTCGATTCTGATTTTGATTT
1 ATTTAGGGTTATTTCGATTTCAATTTTGATTTTGATTTCGATTCTGATTTTGATTT
90657253 TGATTTCTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.19, C:0.05, G:0.18, T:0.58
Consensus pattern (62 bp):
ATTTAGGGTTATTTCGATTTCAATTTTGATTTTGATTTCGATTCTGATTTTGATTTAGGGTT
Found at i:90657233 original size:18 final size:18
Alignment explanation
Indices: 90657207--90657285 Score: 86
Period size: 18 Copynumber: 4.1 Consensus size: 18
90657197 ATTTAGGGTT
*
90657207 ATTTCGATTTCAATTTTG
1 ATTTTGATTTCAATTTTG
90657225 ATTTTGATTTCGATTCTGATTTTG
1 ATTTTGATTTC-A-----ATTTTG
*
90657249 ATTTTGATTTCTATTTTG
1 ATTTTGATTTCAATTTTG
90657267 ATTTTGATTTCAATTTTG
1 ATTTTGATTTCAATTTTG
90657285 A
1 A
90657286 AACACTAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 34 0.65
19 1 0.02
24 17 0.33
ACGTcount: A:0.20, C:0.08, G:0.13, T:0.59
Consensus pattern (18 bp):
ATTTTGATTTCAATTTTG
Found at i:90657307 original size:6 final size:6
Alignment explanation
Indices: 90657296--90657355 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
90657286 AACACTAAAC
* * * * * * *
90657296 TGATTT TGATTT TGATTT TAATTT CGATCT CGATTT AGCTTT AGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
90657344 TGATTT TGATTT
1 TGATTT TGATTT
90657356 CAATTTGGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.58
Consensus pattern (6 bp):
TGATTT
Found at i:90657547 original size:48 final size:48
Alignment explanation
Indices: 90657427--90657549 Score: 201
Period size: 48 Copynumber: 2.6 Consensus size: 48
90657417 CATGTGCATG
* * *
90657427 ATGTTTACTGTTTGTATCTGCCATCGTATGGATGCCATTATCAAACTG
1 ATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTA
90657475 ATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTA
1 ATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTA
* *
90657523 ATGTTTATTGTGTATATCTGCCATTGT
1 ATGTTTATTGTTTGTATCTGCCATTGT
90657550 TTGTATCCAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (48 bp):
ATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTA
Found at i:90657610 original size:89 final size:89
Alignment explanation
Indices: 90657506--90657672 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
90657496 CATTGTATGG
90657506 ATGCCATTATCAAACTAATGTTTATTGTGTATATCTGCCATTGTTTGTATCCAAGCTACTATATT
1 ATGCCATTATCAAACTAATGTTTATTGTGTATATCTGCCATTGTTTGTATCCAAGCTACTATATT
* *
90657571 GTATGTGGCAAAATCAAAATTTGA
66 GTATATGACAAAATCAAAATTTGA
*
90657595 ATGCCATTATCAAACTAATGTTTATTGTGTATATCTGCCATTGTTTGTATCCAAGCTGCTATATT
1 ATGCCATTATCAAACTAATGTTTATTGTGTATATCTGCCATTGTTTGTATCCAAGCTACTATATT
90657660 GTATATGACAAAA
66 GTATATGACAAAA
90657673 ATGGTTGTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (89 bp):
ATGCCATTATCAAACTAATGTTTATTGTGTATATCTGCCATTGTTTGTATCCAAGCTACTATATT
GTATATGACAAAATCAAAATTTGA
Found at i:90657907 original size:15 final size:15
Alignment explanation
Indices: 90657887--90657936 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
90657877 AAAGAAGACA
90657887 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
90657902 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
** **
90657917 CATCTGAAAGTGATG
1 TGTCTGGTAGTGATG
90657932 TGTCT
1 TGTCT
90657937 AATAGGATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.18, C:0.10, G:0.34, T:0.38
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:90659979 original size:20 final size:20
Alignment explanation
Indices: 90659954--90659995 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
90659944 GCTTAGTAAG
90659954 CTCATGTAACAAGAATTATA
1 CTCATGTAACAAGAATTATA
90659974 CTCATGTAACAAGAATTATA
1 CTCATGTAACAAGAATTATA
90659994 CT
1 CT
90659996 TACCTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (20 bp):
CTCATGTAACAAGAATTATA
Found at i:90662260 original size:8 final size:9
Alignment explanation
Indices: 90662230--90662265 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
90662220 ATAGAGCAGG
90662230 AAAAAAGAA
1 AAAAAAGAA
90662239 AGAAAGAAGAA
1 A-AAA-AAGAA
90662250 AAAAAAGAA
1 AAAAAAGAA
90662259 AAAAAAG
1 AAAAAAG
90662266 GGGAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.52
10 6 0.24
11 6 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:90662744 original size:39 final size:39
Alignment explanation
Indices: 90662688--90662794 Score: 144
Period size: 39 Copynumber: 2.7 Consensus size: 39
90662678 CGAGTCGATG
*
90662688 ACTACTGTACTGAATAATTGATAGATACTGAATAACTAA
1 ACTACTGTACTGAATAATTGATAGTTACTGAATAACTAA
* * *
90662727 ATTACTGTA-TAGAATAATTAATAGTTATTGAATAACTAA
1 ACTACTGTACT-GAATAATTGATAGTTACTGAATAACTAA
* *
90662766 ACTACTGCACTGAATATTTGATAGTTACT
1 ACTACTGTACTGAATAATTGATAGTTACT
90662795 AAATGACTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.02
39 55 0.96
40 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (39 bp):
ACTACTGTACTGAATAATTGATAGTTACTGAATAACTAA
Found at i:90663741 original size:28 final size:27
Alignment explanation
Indices: 90663705--90663763 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
90663695 GTGTTGACTA
* *
90663705 TTTTTTAATATGCATGTAGTGAGTATT
1 TTTTTTAATATGCATATAGTGACTATT
*
90663732 TTTTTATAATATGCATATAGTGACTGTT
1 TTTTT-TAATATGCATATAGTGACTATT
90663760 TTTT
1 TTTT
90663764 AGGGTGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.54
Consensus pattern (27 bp):
TTTTTTAATATGCATATAGTGACTATT
Found at i:90663761 original size:26 final size:25
Alignment explanation
Indices: 90663699--90663764 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 25
90663689 GTTGGTGTGT
*
90663699 TGACTATTTTTTAATATGCATGTAG
1 TGACTATTTTTTAATATGCATATAG
*
90663724 TGAGTATTTTTTTATAATATGCATATAG
1 TGACTA--TTTTT-TAATATGCATATAG
*
90663752 TGACTGTTTTTTA
1 TGACTATTTTTTA
90663765 GGGTGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 7 0.21
26 5 0.15
27 5 0.15
28 17 0.50
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (25 bp):
TGACTATTTTTTAATATGCATATAG
Found at i:90663772 original size:2 final size:2
Alignment explanation
Indices: 90663767--90663793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90663757 GTTTTTTAGG
90663767 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
90663794 ACTTATCAAC
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:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Done.