Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 14 of 64
Found at i:1699098 original size:16 final size:16
Alignment explanation
Indices: 1699077--1699114 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1699067 GCATAAAATC
1699077 TAAATTGTATGAAAAA-
1 TAAATTGTAT-AAAAAG
1699093 TAAATTGTATAAAAAG
1 TAAATTGTATAAAAAG
1699109 TAAATT
1 TAAATT
1699115 AAAGCATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
TAAATTGTATAAAAAG
Found at i:1699188 original size:16 final size:17
Alignment explanation
Indices: 1699164--1699199 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1699154 AATTTAACCA
1699164 ACATGAAAATTAAAAAT
1 ACATGAAAATTAAAAAT
*
1699181 ACAT-AAAATTTAAAAT
1 ACATGAAAATTAAAAAT
1699197 ACA
1 ACA
1699200 ATTAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (17 bp):
ACATGAAAATTAAAAAT
Found at i:1699597 original size:23 final size:23
Alignment explanation
Indices: 1699565--1699645 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
1699555 CCCCACAAGT
*
1699565 AGCCCTCATGCACGTCCCTTAAC
1 AGCCCCCATGCACGTCCCTTAAC
* * *
1699588 AGTCCACATGCACGTTCCTTAAC
1 AGCCCCCATGCACGTCCCTTAAC
* *
1699611 AACCCCCATGCACATCCCTTAAC
1 AGCCCCCATGCACGTCCCTTAAC
1699634 AGCCCCCATGCA
1 AGCCCCCATGCA
1699646 GAGCAAAGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (23 bp):
AGCCCCCATGCACGTCCCTTAAC
Found at i:1700890 original size:17 final size:16
Alignment explanation
Indices: 1700868--1700932 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
1700858 TTTTTTAAAA
1700868 ATATTTTAAATATTTTT
1 ATATTTT-AATATTTTT
1700885 ATATTTT-ATATTTATAT
1 ATATTTTAATATTT-T-T
*
1700902 ATATTTTATACATTTTT
1 ATATTTTA-ATATTTTT
1700919 ATATTTT-ATATTTT
1 ATATTTTAATATTTT
1700933 ATTTATCGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 12 0.29
16 1 0.02
17 23 0.55
18 1 0.02
19 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
ATATTTTAATATTTTT
Found at i:1700893 original size:7 final size:7
Alignment explanation
Indices: 1700881--1700934 Score: 54
Period size: 7 Copynumber: 6.9 Consensus size: 7
1700871 TTTTAAATAT
1700881 TTTTATA
1 TTTTATA
1700888 TTTTATA
1 TTTTATA
1700895 TTTATATATA
1 -TT-T-TATA
1700905 TTTTATACA
1 TTTTAT--A
1700914 TTTTTATA
1 -TTTTATA
1700922 TTTTATA
1 TTTTATA
1700929 TTTTAT
1 TTTTAT
1700935 TTATCGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 23 0.56
8 4 0.10
9 4 0.10
10 10 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTATA
Found at i:1700897 original size:15 final size:15
Alignment explanation
Indices: 1700877--1700932 Score: 76
Period size: 17 Copynumber: 3.5 Consensus size: 15
1700867 AATATTTTAA
1700877 ATATTTTTATATTTT
1 ATATTTTTATATTTT
1700892 ATATTTATATATATTTT
1 ATATTT-T-TATATTTT
1700909 ATACATTTTTATATTTT
1 AT--ATTTTTATATTTT
1700926 ATATTTT
1 ATATTTT
1700933 ATTTATCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.30
16 1 0.03
17 20 0.54
18 1 0.03
19 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATTTTTATATTTT
Found at i:1701331 original size:13 final size:13
Alignment explanation
Indices: 1701306--1701347 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1701296 AAGGCAAAAA
*
1701306 TTTTTT-TTCTTG
1 TTTTTTGTTTTTG
1701318 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
*
1701331 TTTTTTGTTTTGG
1 TTTTTTGTTTTTG
1701344 TTTT
1 TTTT
1701348 CGTTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:1701341 original size:12 final size:12
Alignment explanation
Indices: 1701306--1701358 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1701296 AAGGCAAAAA
1701306 TTTTTT-TTCTTG
1 TTTTTTGTT-TTG
1701318 TTTTTTGTTTTTG
1 TTTTTTG-TTTTG
1701331 TTTTTTGTTTTG
1 TTTTTTGTTTTG
* *
1701343 GTTTTCGTTTTG
1 TTTTTTGTTTTG
1701355 TTTT
1 TTTT
1701359 AATTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 24 0.67
13 10 0.28
14 2 0.06
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (12 bp):
TTTTTTGTTTTG
Found at i:1701369 original size:9 final size:9
Alignment explanation
Indices: 1701355--1701398 Score: 54
Period size: 8 Copynumber: 4.7 Consensus size: 9
1701345 TTTCGTTTTG
1701355 TTTTAATTT
1 TTTTAATTT
1701364 TTTTAATTTGT
1 TTTTAA-TT-T
1701375 TTTTGAATTT
1 TTTT-AATTT
1701385 TTTT-ATTT
1 TTTTAATTT
1701393 TTTTAA
1 TTTTAA
1701399 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.26
9 7 0.23
10 7 0.23
11 7 0.23
12 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (9 bp):
TTTTAATTT
Found at i:1701377 original size:30 final size:29
Alignment explanation
Indices: 1701343--1701421 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
1701333 TTTTGTTTTG
1701343 GTTTTCGTTTTGTTTTAATTTTTTT-AATTT
1 GTTTT-GTTTTGTTTT-ATTTTTTTAAATTT
*
1701373 GTTTTTGAATTT-TTTTATTTTTTTAAATTT
1 G-TTTTG-TTTTGTTTTATTTTTTTAAATTT
* *
1701403 ATTTTTTTTTGTTTT-TTTT
1 GTTTTGTTTTGTTTTATTTT
1701422 CCTTAAGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 7 0.17
29 16 0.39
30 11 0.27
31 7 0.17
ACGTcount: A:0.14, C:0.01, G:0.08, T:0.77
Consensus pattern (29 bp):
GTTTTGTTTTGTTTTATTTTTTTAAATTT
Found at i:1701410 original size:17 final size:18
Alignment explanation
Indices: 1701374--1701412 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1701364 TTTTAATTTG
* *
1701374 TTTTTGAATTTTTTTATT
1 TTTTTAAATTTATTTATT
1701392 TTTTTAAATTTATTT-TT
1 TTTTTAAATTTATTTATT
1701409 TTTT
1 TTTT
1701413 GTTTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTAAATTTATTTATT
Found at i:1701783 original size:33 final size:34
Alignment explanation
Indices: 1701741--1702007 Score: 146
Period size: 33 Copynumber: 7.9 Consensus size: 34
1701731 TCAAATTTTC
1701741 AAATTGGGCTT-AATTTTTCATTAAGTGCCAGAT
1 AAATTGGGCTTAAATTTTTCATTAAGTGCCAGAT
* * ***
1701774 AAATTGGGCTTAAAATTTTCATTAGGTATTAGAT
1 AAATTGGGCTTAAATTTTTCATTAAGTGCCAGAT
* * *
1701808 AAACTAGGCTTAAAATTTTTCATTGAGTGCCA-ACT
1 AAATTGGGCTT-AAATTTTTCATTAAGTGCCAGA-T
* * * * **
1701843 --ACTAGGCTTAAATTTCT-A-TAGGGTGATAGAT
1 AAATTGGGCTTAAATTTTTCATTA-AGTGCCAGAT
* ** * *
1701874 AAACTT-GG-TTCAAA-TTGTCATTGGGTGCTAAAT
1 AAA-TTGGGCTT-AAATTTTTCATTAAGTGCCAGAT
* *
1701907 AAATTGGGCTTAAATTGTTTCATTTAGTGTCAG-T
1 AAATTGGGCTTAAATT-TTTCATTAAGTGCCAGAT
*
1701941 TAATCTGGGCTTAAA-TTTTCATT-AG-GCATCAGAT
1 AAAT-TGGGCTTAAATTTTTCATTAAGTGC--CAGAT
*
1701975 AAATTGGGCTTAAAATTTTTCATTGAGTGCCAG
1 AAATTGGGCTT-AAATTTTTCATTAAGTGCCAG
1702008 GGAATCTAGC
Statistics
Matches: 179, Mismatches: 32, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
30 1 0.01
31 7 0.04
32 17 0.09
33 60 0.34
34 44 0.25
35 46 0.26
36 2 0.01
37 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (34 bp):
AAATTGGGCTTAAATTTTTCATTAAGTGCCAGAT
Found at i:1702251 original size:29 final size:29
Alignment explanation
Indices: 1702217--1702291 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
1702207 CTAATTCTAA
***
1702217 GCTTAAAACCTAGATGCCAGCTAGGTTAG
1 GCTTAAAACCTAGATGCCAGCTAAACTAG
** * * *
1702246 GCTTAAATTCTTGTTGCCAGCTAAACTGG
1 GCTTAAAACCTAGATGCCAGCTAAACTAG
1702275 GCTTAAAACCTAGATGC
1 GCTTAAAACCTAGATGC
1702292 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (29 bp):
GCTTAAAACCTAGATGCCAGCTAAACTAG
Found at i:1703316 original size:16 final size:15
Alignment explanation
Indices: 1703231--1703322 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 15
1703221 TTATCTTACT
1703231 TTTTTTCTTTC-TTC
1 TTTTTTCTTTCTTTC
*
1703245 TTTTCTT-TTTTTTTCC
1 TTTT-TTCTTTCTTT-C
*
1703261 TTTTCTTTCGTTCTTTC
1 -TTT-TTTCTTTCTTTC
*
1703278 TCTTTTTCTTCACTTTTTC
1 T-TTTTTCTT---TCTTTC
1703297 TTTTTTCTTTCTTTC
1 TTTTTTCTTTCTTTC
1703312 ATTTTTTCTTT
1 -TTTTTTCTTT
1703323 TCTCTTAGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 7 0.11
15 9 0.15
16 17 0.28
17 8 0.13
18 14 0.23
19 6 0.10
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTTTCTTTCTTTC
Found at i:1703328 original size:23 final size:24
Alignment explanation
Indices: 1703274--1703328 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1703264 TCTTTCGTTC
*
1703274 TTTCTCTTTTTCTTCACTTTTTCT
1 TTTCTCTTTCTCTTCACTTTTTCT
* *
1703298 TTTTTCTTTCT-TTCATTTTTTCT
1 TTTCTCTTTCTCTTCACTTTTTCT
1703321 TTTCTCTT
1 TTTCTCTT
1703329 AGTGGATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTCTCTTTCTCTTCACTTTTTCT
Found at i:1709608 original size:19 final size:19
Alignment explanation
Indices: 1709538--1709611 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 19
1709528 ACTTCATTTC
*
1709538 GGGTTTCACTTAGGGTTTA
1 GGGTTTCACTTAGGGTCTA
* * * * *
1709557 AGGTTTTATTTAAGGTTTTA
1 GGGTTTCACTT-AGGGTCTA
*
1709577 -GGTTTCACCTAGGGTCTA
1 GGGTTTCACTTAGGGTCTA
*
1709595 GGGTTTCATTTAGGGTC
1 GGGTTTCACTTAGGGTC
1709612 ACATTTAGGG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
18 6 0.14
19 29 0.69
20 7 0.17
ACGTcount: A:0.18, C:0.11, G:0.28, T:0.43
Consensus pattern (19 bp):
GGGTTTCACTTAGGGTCTA
Found at i:1709664 original size:27 final size:26
Alignment explanation
Indices: 1709631--1709684 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
1709621 GTTTCGAATA
1709631 TCATTTAA-GATTTAGGATTTTAGGGTT
1 TCATTTAAGGATTTA--ATTTTAGGGTT
*
1709658 TCATTTAAGGTTTTAATTTTAGGGTT
1 TCATTTAAGGATTTAATTTTAGGGTT
1709684 T
1 T
1709685 TAGATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 8 0.32
28 5 0.20
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (26 bp):
TCATTTAAGGATTTAATTTTAGGGTT
Found at i:1709692 original size:60 final size:59
Alignment explanation
Indices: 1709615--1709732 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 59
1709605 TAGGGTCACA
* *
1709615 TTTAGGGTTTCGAATATCATTTAAGATTTAGGATTTTAGGGTTTCATTTAAGGTTTTAAT
1 TTTAGGGTTTAGAATATCATTTAAGATTTAGGATTTTAGAGTTT-ATTTAAGGTTTTAAT
* *
1709675 TTTAGGGTTTTAG-ATATCATTTAAGATTTAGGATTTTTGAGTTTATTTAGGGTTTTAA
1 TTTAGGG-TTTAGAATATCATTTAAGATTTAGGATTTTAGAGTTTATTTAAGGTTTTAA
1709733 AAAATTATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 13 0.25
60 36 0.68
61 4 0.08
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.50
Consensus pattern (59 bp):
TTTAGGGTTTAGAATATCATTTAAGATTTAGGATTTTAGAGTTTATTTAAGGTTTTAAT
Found at i:1710080 original size:15 final size:15
Alignment explanation
Indices: 1710040--1710089 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
1710030 AAAAAGTATA
*
1710040 TTATTATTATTTGATTT
1 TTATTATT-TTTTA-TT
1710057 TTATATATTTTTTATT
1 TTAT-TATTTTTTATT
*
1710073 TTATTATTATTTATT
1 TTATTATTTTTTATT
1710088 TT
1 TT
1710090 TTGCATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 12 0.40
16 6 0.20
17 8 0.27
18 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTATTTTTTATT
Found at i:1710088 original size:22 final size:22
Alignment explanation
Indices: 1710036--1710091 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1710026 TTATAAAAAG
*
1710036 TATATTATTATTATTTGATTTTTA
1 TATATT-TT-TTATTTGATTATTA
*
1710060 TATATTTTTTATTTTATTATTA
1 TATATTTTTTATTTGATTATTA
*
1710082 TTTATTTTTT
1 TATATTTTTT
1710092 GCATAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 21 0.72
23 2 0.07
24 6 0.21
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TATATTTTTTATTTGATTATTA
Found at i:1710214 original size:17 final size:16
Alignment explanation
Indices: 1710145--1710217 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 16
1710135 AAATTAAAGA
1710145 TTAAAATTGCATAGAAAT
1 TTAAAA-TGCATA-AAAT
1710163 TTAACCAA--CATGAAAAT
1 TTAA--AATGCAT-AAAAT
1710180 TTAAAATGCATAAAAT
1 TTAAAATGCATAAAAT
*
1710196 TTAAAATGCAATTAAAT
1 TTAAAATGC-ATAAAAT
1710213 TTAAA
1 TTAAA
1710218 CAACATAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
15 2 0.04
16 14 0.29
17 25 0.52
18 5 0.10
20 2 0.04
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (16 bp):
TTAAAATGCATAAAAT
Found at i:1710876 original size:23 final size:23
Alignment explanation
Indices: 1710845--1710918 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
1710835 AAGCAGCCTT
1710845 CATGCACGTCCCTTAACAGGCCA
1 CATGCACGTCCCTTAACAGGCCA
* * * *
1710868 TATGCACGTTCCTTAGCA-GCCC
1 CATGCACGTCCCTTAACAGGCCA
* * * *
1710890 CATGCACATCCTTTAACAGCCCC
1 CATGCACGTCCCTTAACAGGCCA
1710913 CATGCA
1 CATGCA
1710919 GAGCAAATGA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 16 0.40
23 24 0.60
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (23 bp):
CATGCACGTCCCTTAACAGGCCA
Found at i:1712184 original size:39 final size:39
Alignment explanation
Indices: 1712126--1712211 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 39
1712116 ATTTTTTATG
*
1712126 TATATTTT-TAAAAATATTTTAAATA-ATTTTATATATTT
1 TATATTTTAAAAAAATATTTTAAATACATTTT-TATATTT
**
1712164 TGAT-TTTTAAAAAAATATTTTTTATACATTTTTATATTT
1 T-ATATTTTAAAAAAATATTTTAAATACATTTTTATATTT
1712203 TATATTTTA
1 TATATTTTA
1712212 TTTATCTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 7 0.17
39 29 0.71
40 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (39 bp):
TATATTTTAAAAAAATATTTTAAATACATTTTTATATTT
Found at i:1721728 original size:108 final size:106
Alignment explanation
Indices: 1721488--1721776 Score: 348
Period size: 108 Copynumber: 2.7 Consensus size: 106
1721478 TAGCTTCAGC
* * *
1721488 AAATGTAGTAATTGCCATACCCATAATAAATGCTCATTAAATCAAAAGCCATCAAGTCAAATAAA
1 AAATGCAGTAATTACCATACCCATAATAAATGCTCATTAAATCAAAAG-CATCAAGTCAAACAAA
1721553 TG--AAAAAAATAAATCCCAAATACTACAATTTTATTCAAAA
65 TGAAAAAAAAATAAATCCCAAATACTACAATTTTATTCAAAA
* * * *
1721593 AAATGCAATAATTACCATACCCATAATAAATTCTCATTAAATCAAAAGTCATCTAGTCAAACAGA
1 AAATGCAGTAATTACCATACCCATAATAAATGCTCATTAAATCAAAAG-CATCAAGTCAAACAAA
* * *** * *
1721658 TGAAAAAAAAATTAAATGCCAAATATTATGTTTTTGTTCAAAG
65 TGAAAAAAAAA-TAAATCCCAAATACTACAATTTTATTCAAAA
** ** * *
1721701 AAATGCAGTAATTACCATACTGATAATAAATGCTTGTTAAATTAAGAGCAATCAAGTCAAACAAA
1 AAATGCAGTAATTACCATACCCATAATAAATGCTCATTAAATCAAAAGC-ATCAAGTCAAACAAA
1721766 TGAAAAAAAAA
65 TGAAAAAAAAA
1721777 AAAACAAATT
Statistics
Matches: 155, Mismatches: 25, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
105 59 0.38
107 8 0.05
108 88 0.57
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.27
Consensus pattern (106 bp):
AAATGCAGTAATTACCATACCCATAATAAATGCTCATTAAATCAAAAGCATCAAGTCAAACAAAT
GAAAAAAAAATAAATCCCAAATACTACAATTTTATTCAAAA
Found at i:1756909 original size:20 final size:20
Alignment explanation
Indices: 1756886--1756932 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1756876 CAAGATTGAT
* *
1756886 CAAGAATAATTAAGATTTTC
1 CAAGAACAACTAAGATTTTC
*
1756906 CAAGAACCACTAAGATTTTC
1 CAAGAACAACTAAGATTTTC
1756926 CAAGAAC
1 CAAGAAC
1756933 CAATCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (20 bp):
CAAGAACAACTAAGATTTTC
Found at i:1756933 original size:20 final size:20
Alignment explanation
Indices: 1756896--1756934 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1756886 CAAGAATAAT
1756896 TAAGATTTTCCAAGAACCAC
1 TAAGATTTTCCAAGAACCAC
1756916 TAAGATTTTCCAAGAACCA
1 TAAGATTTTCCAAGAACCA
1756935 ATCTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (20 bp):
TAAGATTTTCCAAGAACCAC
Found at i:1757146 original size:63 final size:63
Alignment explanation
Indices: 1757066--1757192 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
1757056 AGTGTTATCA
* * ** * *
1757066 ATATGATAGAAAGATGTAAAATGAGTTGTAGGGTTTTATTGGGTAGATGTCCCATAGGACTAG
1 ATATGAGAGAAAAATGTAAAATGAGTTACAGGGATTTATTAGGTAGATGTCCCATAGGACTAG
*
1757129 ATATGAGAGAAAAATGTAAAGTGAGTTACAGGGATTTATTAGGTAGATGTCCCATAGGACTAG
1 ATATGAGAGAAAAATGTAAAATGAGTTACAGGGATTTATTAGGTAGATGTCCCATAGGACTAG
1757192 A
1 A
1757193 GGAGATTGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (63 bp):
ATATGAGAGAAAAATGTAAAATGAGTTACAGGGATTTATTAGGTAGATGTCCCATAGGACTAG
Found at i:1757382 original size:21 final size:21
Alignment explanation
Indices: 1757357--1757396 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1757347 GTGTGAATGT
*
1757357 TTAGATTAAGATCATTAGATA
1 TTAGATTAAAATCATTAGATA
1757378 TTAGATTAAAATCATTAGA
1 TTAGATTAAAATCATTAGA
1757397 GAGAATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (21 bp):
TTAGATTAAAATCATTAGATA
Found at i:1757430 original size:21 final size:21
Alignment explanation
Indices: 1757406--1757473 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
1757396 AGAGAATATG
* *
1757406 GGGATCGTTAGAGATTAGTTT
1 GGGATCATTAAAGATTAGTTT
*
1757427 GGGATCATTAAAGATTAGATT
1 GGGATCATTAAAGATTAGTTT
* * *
1757448 AGGATCATCAAATATTAGTTT
1 GGGATCATTAAAGATTAGTTT
1757469 GGGAT
1 GGGAT
1757474 TGAAATTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (21 bp):
GGGATCATTAAAGATTAGTTT
Found at i:1762273 original size:17 final size:18
Alignment explanation
Indices: 1762253--1762298 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1762243 CCAACAACCT
1762253 AACTAAAAGAAA-TAAAA
1 AACTAAAAGAAACTAAAA
* *
1762270 AACTAAAA-AAACTTAGA
1 AACTAAAAGAAACTAAAA
1762287 AACTAAAAGAAA
1 AACTAAAAGAAA
1762299 AAAGAGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.13
Consensus pattern (18 bp):
AACTAAAAGAAACTAAAA
Found at i:1776605 original size:29 final size:28
Alignment explanation
Indices: 1776555--1776615 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1776545 CTACAAATAT
* * *
1776555 AAAATCAAAACATGATATCAAAAACAAGG
1 AAAACCAAAACATAATATC-AAAACAAGA
1776584 AAAACCAAAA-ATAATATGCAAAACAAGA
1 AAAACCAAAACATAATAT-CAAAACAAGA
1776612 AAAA
1 AAAA
1776616 TAAAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.11
Consensus pattern (28 bp):
AAAACCAAAACATAATATCAAAACAAGA
Found at i:1795908 original size:28 final size:28
Alignment explanation
Indices: 1795876--1795943 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 28
1795866 ATAACATCAA
1795876 GAAAAACAAAGAAAATAAAAAATAATGT
1 GAAAAACAAAGAAAATAAAAAATAATGT
*
1795904 GAAAAAC-AAG--GA-AAAAAATAATGT
1 GAAAAACAAAGAAAATAAAAAATAATGT
* *
1795928 GCAAAACAAGGAAAAT
1 GAAAAACAAAGAAAAT
1795944 CGAAAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 18 0.56
25 3 0.09
27 4 0.12
28 7 0.22
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (28 bp):
GAAAAACAAAGAAAATAAAAAATAATGT
Found at i:1795921 original size:24 final size:24
Alignment explanation
Indices: 1795892--1795942 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1795882 CAAAGAAAAT
1795892 AAAAAATAATGTGAAAAACAAGGA
1 AAAAAATAATGTGAAAAACAAGGA
*
1795916 AAAAAATAATGTGCAAAACAAGGA
1 AAAAAATAATGTGAAAAACAAGGA
1795940 AAA
1 AAA
1795943 TCGAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.67, C:0.06, G:0.16, T:0.12
Consensus pattern (24 bp):
AAAAAATAATGTGAAAAACAAGGA
Found at i:1804729 original size:223 final size:224
Alignment explanation
Indices: 1804329--1804767 Score: 648
Period size: 223 Copynumber: 2.0 Consensus size: 224
1804319 TTCCATCAAC
*
1804329 TACTCAATATCACCCACTACCTATACAAGAAATGAAACCTTCCCATGAGAAAATCTTTCACTGAA
1 TACTCAATATCACCCACTACCTATACAAGAAATGAAACCTTCCCATGAG-AAATCTTTCACCGAA
* **** ** * * *
1804394 TTCATTTGGAACCAAACTAACCTCCTTTAAACCCAAGTAGTTACTTTGAAAAGCCTTAATAGACT
65 TACATCCAAAACCAAACTAACCTCCTCCAAACCCAAATAGCTACTTTGAAAAGCCTTAATAGACC
* * * *
1804459 AGTAGATCCTAGTTAGTTGGATGGAATAGAAGGCATATTTAAGGATGATTAAAGGAAATGAGGTA
130 AATAAATCCCAGTTAGTTGGATGGAATAGAAGGCATATTTAAGGATGATTAAAGGAAAAGAGGTA
1804524 TAGTGTATGTTGATGATGATGGCGATCACT
195 TAGTGTATGTTGATGATGATGGCGATCACT
* *
1804554 TACTCAATATCACCCACTACCTCTACAAGAAATGAAACCTTCCTATGTAG-AATCTTTCACCGAA
1 TACTCAATATCACCCACTACCTATACAAGAAATGAAACCTTCCCATG-AGAAATCTTTCACCGAA
1804618 TACATCCAAAACCAAACTAACCTCCTCCAAACCCAAATAGCTACTTTG-AAAGCCTTAATAGACC
65 TACATCCAAAACCAAACTAACCTCCTCCAAACCCAAATAGCTACTTTGAAAAGCCTTAATAGACC
* * * *
1804682 AATAAATCCCAGTTGGTTGGATGGAGTGGAAGGCATATTTAAGGATGATTGAAGGAAAAGAGGTA
130 AATAAATCCCAGTTAGTTGGATGGAATAGAAGGCATATTTAAGGATGATTAAAGGAAAAGAGGTA
*
1804747 TAGTGTATGTTGATGTTGATG
195 TAGTGTATGTTGATGATGATG
1804768 ATGATGATAA
Statistics
Matches: 191, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
223 92 0.48
224 52 0.27
225 45 0.24
226 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (224 bp):
TACTCAATATCACCCACTACCTATACAAGAAATGAAACCTTCCCATGAGAAATCTTTCACCGAAT
ACATCCAAAACCAAACTAACCTCCTCCAAACCCAAATAGCTACTTTGAAAAGCCTTAATAGACCA
ATAAATCCCAGTTAGTTGGATGGAATAGAAGGCATATTTAAGGATGATTAAAGGAAAAGAGGTAT
AGTGTATGTTGATGATGATGGCGATCACT
Found at i:1823161 original size:8 final size:7
Alignment explanation
Indices: 1823117--1823279 Score: 105
Period size: 7 Copynumber: 24.3 Consensus size: 7
1823107 AAGGTTAGTA
1823117 TTAGGGT
1 TTAGGGT
*
1823124 CTA-GG-
1 TTAGGGT
1823129 TTAGGGT
1 TTAGGGT
**
1823136 TTAAGATT
1 TT-AGGGT
*
1823144 TTAAGGT
1 TTAGGGT
1823151 TTAGGGTT
1 TTAGGG-T
1823159 TTAGGG-
1 TTAGGGT
*
1823165 TTAGGAAT
1 TTAGG-GT
1823173 TTAGGGAT
1 TTAGGG-T
1823181 TTAGGG-
1 TTAGGGT
*
1823187 TTAGGCT
1 TTAGGGT
1823194 TTAGGGT
1 TTAGGGT
1823201 TTAGGG-
1 TTAGGGT
1823207 TTAGGG-
1 TTAGGGT
1823213 TTAGGG-
1 TTAGGGT
1823219 TTAGGGT
1 TTAGGGT
* *
1823226 TTA-AGA
1 TTAGGGT
1823232 TTAGGGT
1 TTAGGGT
*
1823239 TTAGGTT
1 TTAGGGT
**
1823246 TTAAAGT
1 TTAGGGT
1823253 TT--GGT
1 TTAGGGT
1823258 TTAGGGT
1 TTAGGGT
*
1823265 TT-GGTT
1 TTAGGGT
1823271 TTAGGGT
1 TTAGGGT
1823278 TT
1 TT
1823280 CAATTTAGGT
Statistics
Matches: 120, Mismatches: 23, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
5 6 0.05
6 41 0.34
7 49 0.41
8 24 0.20
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.43
Consensus pattern (7 bp):
TTAGGGT
Found at i:1823163 original size:30 final size:30
Alignment explanation
Indices: 1823129--1823188 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1823119 AGGGTCTAGG
*
1823129 TTAGGGTTTAAGATTTTAAGG-TTTAGGGTT
1 TTAGGG-TTAAGAATTTAAGGATTTAGGGTT
* *
1823159 TTAGGGTTAGGAATTTAGGGATTTAGGGTT
1 TTAGGGTTAAGAATTTAAGGATTTAGGGTT
1823189 AGGCTTTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (30 bp):
TTAGGGTTAAGAATTTAAGGATTTAGGGTT
Found at i:1823175 original size:22 final size:20
Alignment explanation
Indices: 1823150--1823243 Score: 104
Period size: 22 Copynumber: 4.7 Consensus size: 20
1823140 GATTTTAAGG
1823150 TTTAGGGTTTTAGGGTTAGGAA
1 TTTAGGG-TTTAGGGTTAGG-A
*
1823172 TTTAGGGATTTAGGGTTAGGC
1 TTTAGGG-TTTAGGGTTAGGA
1823193 TTTAGGGTTTAGGGTTAGG-
1 TTTAGGGTTTAGGGTTAGGA
* *
1823212 GTTAGGG-TTAGGGTTTAAGA
1 TTTAGGGTTTAGGG-TTAGGA
1823232 -TTAGGGTTTAGG
1 TTTAGGGTTTAGG
1823244 TTTTAAAGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
18 6 0.09
19 16 0.25
20 17 0.26
21 7 0.11
22 19 0.29
ACGTcount: A:0.20, C:0.01, G:0.39, T:0.39
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTAGGA
Found at i:1823210 original size:6 final size:6
Alignment explanation
Indices: 1823181--1823226 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
1823171 ATTTAGGGAT
*
1823181 TTAGGG TTAGGCT TTAGGG TTTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGG-G TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG TT
1823227 TAAGATTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.15, C:0.02, G:0.43, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:1823237 original size:13 final size:13
Alignment explanation
Indices: 1823151--1823243 Score: 91
Period size: 13 Copynumber: 6.9 Consensus size: 13
1823141 ATTTTAAGGT
1823151 TTAGGGTTTTAGGG
1 TTAGGG-TTTAGGG
*
1823165 TTAGGAATTTAGGG
1 TTAGG-GTTTAGGG
*
1823179 ATTTAGGG-TTAGGCT
1 --TTAGGGTTTAGG-G
1823194 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
1823207 TTAGGG-TTAGGG
1 TTAGGGTTTAGGG
* *
1823219 TTAGGGTTTAAGA
1 TTAGGGTTTAGGG
1823232 TTAGGGTTTAGG
1 TTAGGGTTTAGG
1823244 TTTTAAAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
12 12 0.18
13 27 0.41
14 22 0.33
16 5 0.08
ACGTcount: A:0.20, C:0.01, G:0.40, T:0.39
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:1823245 original size:19 final size:19
Alignment explanation
Indices: 1823194--1823246 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1823184 GGGTTAGGCT
* * *
1823194 TTAGGGTTTAGGGTTAGGG
1 TTAGGGTTTAGGTTTAAGA
1823213 TTAGGG-TTAGGGTTTAAGA
1 TTAGGGTTTA-GGTTTAAGA
1823232 TTAGGGTTTAGGTTT
1 TTAGGGTTTAGGTTT
1823247 TAAAGTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.42
Consensus pattern (19 bp):
TTAGGGTTTAGGTTTAAGA
Found at i:1823297 original size:12 final size:13
Alignment explanation
Indices: 1823177--1823298 Score: 74
Period size: 13 Copynumber: 9.5 Consensus size: 13
1823167 AGGAATTTAG
*
1823177 GGATTTAGGGTTA
1 GGATTTAGGGTTT
*
1823190 GGCTTTAGGGTTT
1 GGATTTAGGGTTT
* *
1823203 AGG-GTTAGGGTTA
1 -GGATTTAGGGTTT
*
1823216 GG-GTTAGGGTTT
1 GGATTTAGGGTTT
*
1823228 AAGA-TTAGGGTTT
1 -GGATTTAGGGTTT
* **
1823241 AGGTTTTAAAGTTT
1 -GGATTTAGGGTTT
1823255 GG-TTTAGGGTTT
1 GGATTTAGGGTTT
*
1823267 GGTTTTAGGGTTT
1 GGATTTAGGGTTT
**
1823280 CAATTTA-GGTTT
1 GGATTTAGGGTTT
1823292 GGATTTA
1 GGATTTA
1823299 TGATTTAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
12 31 0.36
13 47 0.54
14 9 0.10
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (13 bp):
GGATTTAGGGTTT
Found at i:1823358 original size:13 final size:13
Alignment explanation
Indices: 1823342--1823377 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1823332 AAGATTTAAT
*
1823342 TTTAGTGTTTCGA
1 TTTAGGGTTTCGA
*
1823355 TTTAGGGTTTGGA
1 TTTAGGGTTTCGA
1823368 TTTAGGGTTT
1 TTTAGGGTTT
1823378 AAGGTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.03, G:0.31, T:0.53
Consensus pattern (13 bp):
TTTAGGGTTTCGA
Found at i:1827553 original size:15 final size:16
Alignment explanation
Indices: 1827499--1827545 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1827489 TATTTAAATT
* **
1827499 TTCTATTTTTAGAAAT
1 TTCTATTTTTAGTACG
1827515 TTCATATTTTTAGTACG
1 TTC-TATTTTTAGTACG
1827532 TTCTATTTTTAGTA
1 TTCTATTTTTAGTA
1827546 GATTTATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (16 bp):
TTCTATTTTTAGTACG
Found at i:1830524 original size:13 final size:12
Alignment explanation
Indices: 1830508--1830552 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 12
1830498 CAAAAAAACC
1830508 AAAAAATCTAAAA
1 AAAAAATC-AAAA
1830521 AAAAAATTCAAAAA
1 AAAAAA-TC-AAAA
1830535 AAATAAATCAAAA
1 AAA-AAATCAAAA
1830548 AAAAA
1 AAAAA
1830553 GGAAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.07
13 13 0.45
14 11 0.38
15 3 0.10
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAATCAAAA
Found at i:1830534 original size:14 final size:13
Alignment explanation
Indices: 1830508--1830552 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
1830498 CAAAAAAACC
1830508 AAAAAATCTAAAAA
1 AAAAAATC-AAAAA
*
1830522 AAAAATTCAAAAA
1 AAAAAATCAAAAA
1830535 AAATAAATCAAAAA
1 AAA-AAATCAAAAA
1830549 AAAA
1 AAAA
1830553 GGAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATCAAAAA
Found at i:1830541 original size:22 final size:22
Alignment explanation
Indices: 1830498--1830550 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1830488 TAAAATTTTG
**
1830498 CAAAAAAACCAAAAAATCTAAA
1 CAAAAAAACCAAAAAAAATAAA
*
1830520 -AAAAAAATTCAAAAAAAATAAA
1 CAAAAAAA-CCAAAAAAAATAAA
1830542 TCAAAAAAA
1 -CAAAAAAA
1830551 AAGGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 7 0.28
22 11 0.44
24 7 0.28
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (22 bp):
CAAAAAAACCAAAAAAAATAAA
Found at i:1831328 original size:7 final size:7
Alignment explanation
Indices: 1831316--1831345 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1831306 GACCATGAAC
1831316 CCCTAAG
1 CCCTAAG
1831323 CCCTAAG
1 CCCTAAG
1831330 CCCTAAG
1 CCCTAAG
1831337 CCCTAAG
1 CCCTAAG
1831344 CC
1 CC
1831346 ACCAATAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (7 bp):
CCCTAAG
Found at i:1833477 original size:19 final size:19
Alignment explanation
Indices: 1833441--1833478 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1833431 CACTTGTACG
**
1833441 TTTAATTTTCTGTTTTTAA
1 TTTAATTTTCTGCATTTAA
1833460 TTTAATTTTCTGCATTTAA
1 TTTAATTTTCTGCATTTAA
1833479 ATTATTATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTAATTTTCTGCATTTAA
Found at i:1834352 original size:39 final size:39
Alignment explanation
Indices: 1834308--1834422 Score: 93
Period size: 36 Copynumber: 3.0 Consensus size: 39
1834298 AATTTGGTTG
1834308 TGAATTTTAAGGGTGTCAAAGTGTTCATGTCACCCCACA
1 TGAATTTTAAGGGTGTCAAAGTGTTCATGTCACCCCACA
* *
1834347 TGAA-TTTAGTAGGGTGTCATGAA-T-TT-AT-T-A--TCTCA
1 TGAATTTTA--AGGGTGTCA--AAGTGTTCATGTCACCCCACA
*
1834382 TGAATTTATTTAGGGTGTCAAAGTGTTCATGTCACCCCACA
1 TGAA-TT-TTAAGGGTGTCAAAGTGTTCATGTCACCCCACA
1834423 ACAAGGAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 26
0.65 0.06 0.30
Matches are distributed among these distances:
34 2 0.04
35 8 0.14
36 11 0.19
37 4 0.07
38 8 0.14
39 7 0.12
40 11 0.19
41 4 0.07
42 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (39 bp):
TGAATTTTAAGGGTGTCAAAGTGTTCATGTCACCCCACA
Found at i:1839868 original size:145 final size:139
Alignment explanation
Indices: 1839547--1839945 Score: 441
Period size: 145 Copynumber: 2.8 Consensus size: 139
1839537 TTAAAACAAC
* *
1839547 AAAAATCATG-AATATTATAAAATTGAGATCT-GAAAAGTTTCATGAAAATGCG-GCTCAGAAGG
1 AAAAATCATGAAATATTATGAAATTGAGATCTAG-AAAGTTTCATGAAAATCCGAGCTCAGAAGG
* * * **
1839609 TCAAATTACGAAAATATCATTTATAAGGATATTTTGATAATTTCATGCTTTTCAAGGTATCACTG
65 T-AAATTACGAAAATATCCTTTATAAGGGTATTTTGGTAATTTCACACTTTTCAAGGTATCACTG
* *
1839674 TGAAATGCACT
129 TCAAATACACT
* * * * * *
1839685 AAAAATTATGAAATATTATGAAATTAATATTTAGAAAGTTTCTTGAAAATCCGAGCTTATGAAGG
1 AAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAATCCGAGCTCA-GAAGG
*
1839750 ATAAATTACGAAAATA-CCTTTATAAGGGTATTTTGGTAATTTCACACTTTTTAAGGTACTGCTA
65 -TAAATTACGAAAATATCCTTTATAAGGGTATTTTGGTAATTTCACACTTTTCAAGGTA-T-C-A
1839814 -TGATTTCAAATACACT
126 CTG---TCAAATACACT
* **
1839830 AAAAATCATGAAATGTTATGAAATTGAGATCTAGAAAGTTTCATGAAAATTTGAGCTCGAGAAGG
1 AAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAATCCGAGCTC-AGAAGG
* * *
1839895 CCAAATTATGAAAATATCCCTTA-AATGGGTATTTTGGTAATTTCACACTTT
65 -TAAATTACGAAAATATCCTTTATAA-GGGTATTTTGGTAATTTCACACTTT
1839946 CCCAGTACAA
Statistics
Matches: 218, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
138 9 0.04
139 34 0.16
140 41 0.19
141 20 0.09
142 4 0.02
143 1 0.00
145 78 0.36
146 31 0.14
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (139 bp):
AAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAATCCGAGCTCAGAAGGT
AAATTACGAAAATATCCTTTATAAGGGTATTTTGGTAATTTCACACTTTTCAAGGTATCACTGTC
AAATACACT
Found at i:1842131 original size:25 final size:25
Alignment explanation
Indices: 1842077--1842131 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1842067 ATAAAGATCA
*
1842077 ACAATATATAATAAATGACATAATT
1 ACAATATACAATAAATGACATAATT
* * *
1842102 GCAATATACATTAAATGACATATTT
1 ACAATATACAATAAATGACATAATT
1842127 ACAAT
1 ACAAT
1842132 TTGCATGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (25 bp):
ACAATATACAATAAATGACATAATT
Found at i:1842222 original size:97 final size:97
Alignment explanation
Indices: 1842112--1842309 Score: 342
Period size: 97 Copynumber: 2.0 Consensus size: 97
1842102 GCAATATACA
* *
1842112 TTAAATGACATATTTACAATTTGCATGAGAATAATTAAAAGATACATGAAATGACATTATTATAA
1 TTAAATGACATATTTACAATTTGCATGAAAATAATTAAAAGATACATGAAATGACATTATTACAA
*
1842177 TATATATGAAATGTAAAACACACACTTTTTTT
66 TATATATGAAATGTAAAACACAAACTTTTTTT
* *
1842209 TTAAATGACATATTTCCAATTTGCATGAAAATAATTACAAGATACATGAAATGACATTATTACAA
1 TTAAATGACATATTTACAATTTGCATGAAAATAATTAAAAGATACATGAAATGACATTATTACAA
*
1842274 TATATGTGAAATGTAAAACACAAACTTTTTTT
66 TATATATGAAATGTAAAACACAAACTTTTTTT
1842306 TTAA
1 TTAA
1842310 TTTGAATTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (97 bp):
TTAAATGACATATTTACAATTTGCATGAAAATAATTAAAAGATACATGAAATGACATTATTACAA
TATATATGAAATGTAAAACACAAACTTTTTTT
Found at i:1843398 original size:17 final size:19
Alignment explanation
Indices: 1843358--1843400 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
1843348 GCATGATTGA
*
1843358 TTTAGGGTCTGAGAGTTAGT
1 TTTA-GGTCTGAGAGTTAGG
1843378 TTTAGGTCT-AG-GTTAGG
1 TTTAGGTCTGAGAGTTAGG
1843395 TTTAGG
1 TTTAGG
1843401 ATTTTAGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 2 0.09
19 5 0.23
20 4 0.18
ACGTcount: A:0.19, C:0.05, G:0.35, T:0.42
Consensus pattern (19 bp):
TTTAGGTCTGAGAGTTAGG
Found at i:1843455 original size:7 final size:7
Alignment explanation
Indices: 1843429--1843659 Score: 123
Period size: 7 Copynumber: 34.4 Consensus size: 7
1843419 AGGATGTAGT
1843429 TTTAGGG
1 TTTAGGG
* *
1843436 TTAAGGA
1 TTTAGGG
1843443 TTTAGGG
1 TTTAGGG
1843450 TTTAGGG
1 TTTAGGG
1843457 TTTTAGGG
1 -TTTAGGG
* *
1843465 -TTACAGA
1 TTTA-GGG
1843472 TTTAGGG
1 TTTAGGG
*
1843479 ATTTATGG
1 -TTTAGGG
1843487 -TTAGGG
1 TTTAGGG
1843493 TTTA-GG
1 TTTAGGG
1843499 TTTAGGG
1 TTTAGGG
**
1843506 -TTAGCA
1 TTTAGGG
1843512 TTTA-GG
1 TTTAGGG
1843518 TTTAGGG
1 TTTAGGG
* *
1843525 CTTAGGT
1 TTTAGGG
*
1843532 TTTGGGG
1 TTTAGGG
1843539 TTT--GG
1 TTTAGGG
1843544 TTTAGGG
1 TTTAGGG
*
1843551 TTT-GGA
1 TTTAGGG
*
1843557 TTTAGGA
1 TTTAGGG
1843564 TTT--GG
1 TTTAGGG
1843569 TTTAGGG
1 TTTAGGG
* *
1843576 TTT-TGA
1 TTTAGGG
1843582 TTTAGGG
1 TTTAGGG
*
1843589 TTT-GGA
1 TTTAGGG
1843595 TTTAGGG
1 TTTAGGG
*
1843602 TTTAAGG
1 TTTAGGG
*
1843609 TTT-CGG
1 TTTAGGG
*
1843615 -TTAGGA
1 TTTAGGG
*
1843621 TTT-GGA
1 TTTAGGG
*
1843627 TTTAAGG
1 TTTAGGG
*
1843634 TTTAAGGAA
1 TTT-AGG-G
1843643 TTTAGGG
1 TTTAGGG
1843650 TTTAGGG
1 TTTAGGG
1843657 TTT
1 TTT
1843660 GTTGGGAAAT
Statistics
Matches: 168, Mismatches: 36, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
5 11 0.07
6 45 0.27
7 88 0.52
8 21 0.12
9 3 0.02
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:1843464 original size:29 final size:29
Alignment explanation
Indices: 1843427--1843507 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
1843417 TTAGGATGTA
1843427 GTTTTAGGGTTAAGGATTTAGGGTTTAGG
1 GTTTTAGGGTTAAGGATTTAGGGTTTAGG
*
1843456 GTTTTAGGGTTACA-GATTTAGGGATTTATG
1 GTTTTAGGGTTA-AGGATTTAGGG-TTTAGG
*
1843486 G--TTAGGGTTTAGG-TTTAGGGTT
1 GTTTTAGGGTTAAGGATTTAGGGTT
1843508 AGCATTTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.04
27 8 0.17
28 9 0.19
29 21 0.45
30 7 0.15
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.43
Consensus pattern (29 bp):
GTTTTAGGGTTAAGGATTTAGGGTTTAGG
Found at i:1843503 original size:13 final size:13
Alignment explanation
Indices: 1843373--1843659 Score: 121
Period size: 13 Copynumber: 21.2 Consensus size: 13
1843363 GGTCTGAGAG
*
1843373 TTAGTTTTA-GGT
1 TTAGGTTTAGGGT
*
1843385 CTAGG-TTA-GGT
1 TTAGGTTTAGGGT
*
1843396 TTAGGATTTTAGGTT
1 TTAGG--TTTAGGGT
*
1843411 TTAAGG-TTAGGAT
1 TT-AGGTTTAGGGT
* *
1843424 GTAGTTTTAGGGT
1 TTAGGTTTAGGGT
*
1843437 TAAGGATTTAGGGT
1 TTAGG-TTTAGGGT
1843451 TTAGGGTTTTAGGGT
1 TTA-GG-TTTAGGGT
* *
1843466 TACAGATTTAGGGAT
1 T-TAGGTTTAGGG-T
1843481 TTATGG-TTAGGGT
1 TTA-GGTTTAGGGT
1843494 TTAGGTTTAGGGTTAGCAT
1 TTAGGTTTA-GG---G--T
*
1843513 TTAGGTTTAGGGC
1 TTAGGTTTAGGGT
*
1843526 TTAGGTTTTGGGGT
1 TTAGG-TTTAGGGT
1843540 TT-GGTTTAGGGT
1 TTAGGTTTAGGGT
*
1843552 TT-GGATTTAGGAT
1 TTAGG-TTTAGGGT
1843565 TT-GGTTTAGGGT
1 TTAGGTTTAGGGT
* *
1843577 TTTGATTTAGGGT
1 TTAGGTTTAGGGT
1843590 TT-GGATTTAGGGT
1 TTAGG-TTTAGGGT
*
1843603 TTAAGGTTT-CGG-
1 TT-AGGTTTAGGGT
*
1843615 TTAGGATTT-GGAT
1 TTAGG-TTTAGGGT
*
1843628 TTAAGGTTTAAGGAAT
1 TT-AGGTTT-AGG-GT
1843644 TTAGGGTTTAGGGT
1 TTA-GGTTTAGGGT
1843658 TT
1 TT
1843660 GTTGGGAAAT
Statistics
Matches: 215, Mismatches: 29, Indels: 60
0.71 0.10 0.20
Matches are distributed among these distances:
11 13 0.06
12 34 0.16
13 68 0.32
14 46 0.21
15 28 0.13
16 13 0.06
17 1 0.00
18 2 0.01
19 10 0.05
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (13 bp):
TTAGGTTTAGGGT
Found at i:1843562 original size:32 final size:32
Alignment explanation
Indices: 1843526--1843636 Score: 89
Period size: 38 Copynumber: 3.2 Consensus size: 32
1843516 GGTTTAGGGC
1843526 TTAGGTTTTGGGGTTTGGTTTAGGGTTTGGAT
1 TTAGGTTTTGGGGTTTGGTTTAGGGTTTGGAT
* *
1843558 TTAGGATTTGGTTTAGGGTTTTGATTTAGGGTTTGGAT
1 TTAGG---T--TTT-GGGGTTTGGTTTAGGGTTTGGAT
* ** *
1843596 TTAGGGTTTAAGGTTTCGG-TTAGGATTTGGAT
1 TTAGGTTTTGGGGTTT-GGTTTAGGGTTTGGAT
1843628 TTAAGGTTT
1 TT-AGGTTT
1843637 AAGGAATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
32 23 0.37
33 9 0.15
35 1 0.02
37 3 0.05
38 26 0.42
ACGTcount: A:0.15, C:0.01, G:0.35, T:0.49
Consensus pattern (32 bp):
TTAGGTTTTGGGGTTTGGTTTAGGGTTTGGAT
Found at i:1843572 original size:25 final size:25
Alignment explanation
Indices: 1843506--1843604 Score: 108
Period size: 25 Copynumber: 3.8 Consensus size: 25
1843496 AGGTTTAGGG
* * *
1843506 TTAGCATTTAGGTTTAGGGCTTAGGTT
1 TTAGGATTT-GGTTTAGGG-TTTGGAT
* *
1843533 TTGGGGTTTGGTTTAGGGTTTGGAT
1 TTAGGATTTGGTTTAGGGTTTGGAT
*
1843558 TTAGGATTTGGTTTAGGGTTTTGAT
1 TTAGGATTTGGTTTAGGGTTTGGAT
*
1843583 TTAGGGTTTGGATTTAGGGTTT
1 TTAGGATTTGG-TTTAGGGTTT
1843605 AAGGTTTCGG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
25 37 0.60
26 19 0.31
27 6 0.10
ACGTcount: A:0.14, C:0.02, G:0.35, T:0.48
Consensus pattern (25 bp):
TTAGGATTTGGTTTAGGGTTTGGAT
Found at i:1843636 original size:25 final size:26
Alignment explanation
Indices: 1843587--1843636 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1843577 TTTGATTTAG
* *
1843587 GGTTTGGATTTAGGGTTTAAGGTTTC
1 GGTTAGGATTTAGGATTTAAGGTTTC
1843613 GGTTAGGATTT-GGATTTAAGGTTT
1 GGTTAGGATTTAGGATTTAAGGTTT
1843637 AAGGAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.46
Consensus pattern (26 bp):
GGTTAGGATTTAGGATTTAAGGTTTC
Found at i:1843637 original size:32 final size:31
Alignment explanation
Indices: 1843549--1843640 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
1843539 TTTGGTTTAG
* * *
1843549 GGTTTGGATTTAGGATTT-GGTTTAGGGTTTT
1 GGTTAGGATTT-GGATTTAGGTTTAAGGTTTC
* *
1843580 GATTTAGGGTTTGGATTTAGGGTTTAAGGTTTC
1 G-GTTAGGATTTGGATTTA-GGTTTAAGGTTTC
1843613 GGTTAGGATTTGGATTTAAGGTTTAAGG
1 GGTTAGGATTTGGATTT-AGGTTTAAGG
1843641 AATTTAGGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
31 7 0.14
32 30 0.60
33 13 0.26
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.46
Consensus pattern (31 bp):
GGTTAGGATTTGGATTTAGGTTTAAGGTTTC
Found at i:1844057 original size:7 final size:7
Alignment explanation
Indices: 1844045--1844074 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1844035 TGAAATAAAG
1844045 AACCATC
1 AACCATC
1844052 AACCATC
1 AACCATC
1844059 AACCATC
1 AACCATC
1844066 AACCATC
1 AACCATC
1844073 AA
1 AA
1844075 GGAATGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCATC
Found at i:1846125 original size:164 final size:164
Alignment explanation
Indices: 1845887--1846216 Score: 581
Period size: 164 Copynumber: 2.0 Consensus size: 164
1845877 TTCTTTCTCT
*
1845887 AAAATTTCAATTTCGGTCTATCTTTAAAACTCAAATTCTTCCTATAGTACTACTACTTGTTTGCA
1 AAAATTTCAATTTCGGTCCATCTTTAAAACTCAAATTCTTCCTATAGTACTACTACTTGTTTGCA
* * *
1845952 TCTTTGCATCCCTAAATTTCATTATTTTTTCTTGTCAAACCTTTTATTACATCTATCCAATTAAA
66 TCTTTGCATCCCAAAATTTCATTATTTCTTCTTGTCAAACCTTTCATTACATCTATCCAATTAAA
*
1846017 TTTCTTTATAGTTGTCTAAAAATTCATAGATCTA
131 TTTCTTTATAGTTGTCTAAAAACTCATAGATCTA
*
1846051 AAAATTT-AAGTTTCGGTCCATCTTTAAAACTCAAATTCTTGCTATAGTACTACTACTTGTTTGC
1 AAAATTTCAA-TTTCGGTCCATCTTTAAAACTCAAATTCTTCCTATAGTACTACTACTTGTTTGC
*
1846115 ATCTTTGCATCCCAAAATTTCATTATTTCTTCTTGTCAAACCTTTCATTGCATCTATCCAATTAA
65 ATCTTTGCATCCCAAAATTTCATTATTTCTTCTTGTCAAACCTTTCATTACATCTATCCAATTAA
1846180 ATTTCTTTATAGTTGTCTAAAAACTCATAGATCTA
130 ATTTCTTTATAGTTGTCTAAAAACTCATAGATCTA
1846215 AA
1 AA
1846217 TCACCTCTGT
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
163 2 0.01
164 156 0.99
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (164 bp):
AAAATTTCAATTTCGGTCCATCTTTAAAACTCAAATTCTTCCTATAGTACTACTACTTGTTTGCA
TCTTTGCATCCCAAAATTTCATTATTTCTTCTTGTCAAACCTTTCATTACATCTATCCAATTAAA
TTTCTTTATAGTTGTCTAAAAACTCATAGATCTA
Found at i:1847741 original size:20 final size:20
Alignment explanation
Indices: 1847692--1847741 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1847682 AGTTTTGCCC
*
1847692 AATTTTAACCTTGTTTGACT
1 AATTTTAACTTTGTTTGACT
1847712 AATTTTAACTTTG-TTGACT
1 AATTTTAACTTTGTTTGACT
1847731 AAGTTTTAACT
1 AA-TTTTAACT
1847742 AGATTTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (20 bp):
AATTTTAACTTTGTTTGACT
Found at i:1851498 original size:147 final size:146
Alignment explanation
Indices: 1851309--1851597 Score: 443
Period size: 147 Copynumber: 2.0 Consensus size: 146
1851299 TCCACTTTTC
*
1851309 CATTGCTTGATGAAGATAGAACTCTGATGAAGGAACCAATTGCAATTTTGGATAGAAGGATGAAT
1 CATTGCTTGATGAAGATAGAACTCTGATGAAGGAACCAATTGCAATTTTAGATAGAAGGATGAAT
**
1851374 GACAAACACAAGAAACTAGTAATTGAAGTGCTCATAAAATAGAGCAATTACTTTTCTAATGATGC
66 GACAAACA-AAGAAACTAGTAATTGAAGTGCTCATAAAATAGAGCAATTACTTTTCTAACAATGC
*
1851439 AACTTAGGAAGTCATAA
130 AACTTAAGAAGTCATAA
*
1851456 CATTGCTTGATGAAGATAGAACTCTGGTGAAGGAACCAATTGCAATTTTAGATAGAAGGATGAAT
1 CATTGCTTGATGAAGATAGAACTCTGATGAAGGAACCAATTGCAATTTTAGATAGAAGGATGAAT
* * * * * * * * *
1851521 GAGAAACATAGGAGCTGGTAATTTAAGTGCTCATAAAGTAGAGCAATTACTTTTTTGACAATGCA
66 GACAAACAAAGAAACTAGTAATTGAAGTGCTCATAAAATAGAGCAATTACTTTTCTAACAATGCA
1851586 ACTTAAGAAGTC
131 ACTTAAGAAGTC
1851598 TTATACAAAC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
146 58 0.45
147 70 0.55
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (146 bp):
CATTGCTTGATGAAGATAGAACTCTGATGAAGGAACCAATTGCAATTTTAGATAGAAGGATGAAT
GACAAACAAAGAAACTAGTAATTGAAGTGCTCATAAAATAGAGCAATTACTTTTCTAACAATGCA
ACTTAAGAAGTCATAA
Found at i:1851876 original size:2 final size:2
Alignment explanation
Indices: 1851869--1851915 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1851859 TTAACAAATT
1851869 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1851911 TC TC T
1 TC TC T
1851916 TTTCTTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1854897 original size:33 final size:34
Alignment explanation
Indices: 1854855--1854918 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1854845 TAGTATCATT
* *
1854855 AAAAAAAACTTTGAAAATC-AAAACAAAAAGTAG
1 AAAAAAAACTGTGAAAACCAAAAACAAAAAGTAG
*
1854888 AAAAAAAACTGTGAAACCCAAAAACAAAAAG
1 AAAAAAAACTGTGAAAACCAAAAACAAAAAG
1854919 AATCCAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.11
Consensus pattern (34 bp):
AAAAAAAACTGTGAAAACCAAAAACAAAAAGTAG
Found at i:1856991 original size:17 final size:17
Alignment explanation
Indices: 1856969--1857027 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1856959 CAAATTGCAT
*
1856969 AAATTTAAATATCATAG
1 AAATTTAAATATCATAC
1856986 AAATTTAAAT-TGC-TAC
1 AAATTTAAATAT-CATAC
* *
1857002 AAATTTAAATAACATAT
1 AAATTTAAATATCATAC
*
1857019 AAAATTAAA
1 AAATTTAAA
1857028 GTGCTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 14 0.40
17 21 0.60
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTTAAATATCATAC
Found at i:1857007 original size:16 final size:16
Alignment explanation
Indices: 1856960--1857011 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1856950 CAAAAAAAGC
*
1856960 AAATTGC-ATAAATTT
1 AAATTGCTACAAATTT
*
1856975 AAATAT-CATAGAAATTT
1 AAAT-TGC-TACAAATTT
1856992 AAATTGCTACAAATTT
1 AAATTGCTACAAATTT
1857008 AAAT
1 AAAT
1857012 AACATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 14 0.45
17 12 0.39
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (16 bp):
AAATTGCTACAAATTT
Found at i:1857008 original size:33 final size:33
Alignment explanation
Indices: 1856960--1857032 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1856950 CAAAAAAAGC
* * *
1856960 AAATTGC-ATAAATTTAAATATCATAGAAATTT
1 AAATTGCTACAAATTTAAATAACATAGAAAATT
*
1856992 AAATTGCTACAAATTTAAATAACATATAAAATT
1 AAATTGCTACAAATTTAAATAACATAGAAAATT
*
1857025 AAAGTGCT
1 AAATTGCT
1857033 TGAAACATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (33 bp):
AAATTGCTACAAATTTAAATAACATAGAAAATT
Found at i:1865853 original size:40 final size:40
Alignment explanation
Indices: 1865783--1865859 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
1865773 TTTTCAAATC
* *
1865783 AATAAAATCCTTTAATAGTTTAGAAAGATTTCATTTCTCA
1 AATAAAATCCTCTAATAGTTTAGAAAGATTTAATTTCTCA
* *
1865823 AATAAAATCCTCTCATAGTTT-GATAGGATTTAATTTC
1 AATAAAATCCTCTAATAGTTTAGA-AAGATTTAATTTC
1865860 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (40 bp):
AATAAAATCCTCTAATAGTTTAGAAAGATTTAATTTCTCA
Found at i:1880132 original size:12 final size:13
Alignment explanation
Indices: 1880106--1880130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1880096 TTATTTATCA
1880106 AATAAATTTTTTT
1 AATAAATTTTTTT
1880119 AATAAATTTTTT
1 AATAAATTTTTT
1880131 AAATTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATAAATTTTTTT
Found at i:1881890 original size:21 final size:21
Alignment explanation
Indices: 1881864--1881905 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1881854 TTATAATTAA
1881864 TTTTAATTTTATCATTATAAT
1 TTTTAATTTTATCATTATAAT
1881885 TTTTAATTTTATCATTATAAT
1 TTTTAATTTTATCATTATAAT
1881906 AATTGATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATTTTATCATTATAAT
Found at i:1883012 original size:20 final size:21
Alignment explanation
Indices: 1882987--1883027 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1882977 AAATGGATTG
*
1882987 TTTGTTTT-TTTTTTTTAGTT
1 TTTGTTTTCTTTTTGTTAGTT
1883007 TTTGTTTTCTTTTTGTTAGTT
1 TTTGTTTTCTTTTTGTTAGTT
1883028 GTTAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.05, C:0.02, G:0.12, T:0.80
Consensus pattern (21 bp):
TTTGTTTTCTTTTTGTTAGTT
Found at i:1884729 original size:39 final size:39
Alignment explanation
Indices: 1884632--1884731 Score: 94
Period size: 39 Copynumber: 2.6 Consensus size: 39
1884622 AATCTGATGG
* *** *
1884632 ATCAGCAGTTGCAGCCTCAATTGAATTTCGTTGGGGATA
1 ATCAGCGGTTGCAGCCTCAATTGAACACCATTGGGGATA
* ** * *
1884671 ATCAACAGG-CACAGTCTCAATTGAACACCATTGGTGATA
1 ATCAGC-GGTTGCAGCCTCAATTGAACACCATTGGGGATA
1884710 ATCAGCGGTTGCAGCCTCAATT
1 ATCAGCGGTTGCAGCCTCAATT
1884732 TAATGCCTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
38 2 0.04
39 42 0.93
40 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (39 bp):
ATCAGCGGTTGCAGCCTCAATTGAACACCATTGGGGATA
Found at i:1886190 original size:12 final size:12
Alignment explanation
Indices: 1886173--1886202 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1886163 ATTGGTATCT
1886173 TGAGTTTCCTGA
1 TGAGTTTCCTGA
1886185 TGAGTTTCCTGA
1 TGAGTTTCCTGA
*
1886197 TAAGTT
1 TGAGTT
1886203 CCTAGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.43
Consensus pattern (12 bp):
TGAGTTTCCTGA
Found at i:1887086 original size:13 final size:13
Alignment explanation
Indices: 1887068--1887093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1887058 TATTCTCATA
1887068 AAATATATTTTAT
1 AAATATATTTTAT
1887081 AAATATATTTTAT
1 AAATATATTTTAT
1887094 TTTATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATATATTTTAT
Found at i:1887160 original size:2 final size:2
Alignment explanation
Indices: 1887155--1887186 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1887145 ATTGATGAAC
1887155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1887187 CATGTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1888408 original size:2 final size:2
Alignment explanation
Indices: 1888403--1888427 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1888393 CAAATCCATG
1888403 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1888428 TTGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1888723 original size:7 final size:7
Alignment explanation
Indices: 1888711--1888742 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1888701 TTAAAAGGTT
1888711 AAAATAA
1 AAAATAA
1888718 AAAATAA
1 AAAATAA
1888725 AAAATAA
1 AAAATAA
1888732 AAAATAA
1 AAAATAA
1888739 AAAA
1 AAAA
1888743 ATTCATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:1888846 original size:16 final size:16
Alignment explanation
Indices: 1888802--1888880 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
1888792 TTTTTAAAAG
1888802 TAATATATTAA-ATAA
1 TAATATATTAATATAA
*
1888817 TAATTTTATTAATATAA
1 TAA-TATATTAATATAA
*
1888834 TAATATATAAATATAA
1 TAATATATTAATATAA
*
1888850 -AATTAAATTAATAATAA
1 TAA-TATATTAAT-ATAA
*
1888867 -AATATATTTATATA
1 TAATATATTAATATA
1888881 TATACATTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
15 8 0.15
16 32 0.60
17 13 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATATATTAATATAA
Found at i:1888860 original size:32 final size:32
Alignment explanation
Indices: 1888802--1888873 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1888792 TTTTTAAAAG
* **
1888802 TAATATATTAAATAATAATTTTATTAAT-ATAA
1 TAATATA-TAAATAAAAATTAAATTAATAATAA
1888834 TAATATATAAATATAAAATTAAATTAATAATAA
1 TAATATATAAATA-AAAATTAAATTAATAATAA
1888867 -AATATAT
1 TAATATAT
1888874 TTATATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.17
32 25 0.71
33 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TAATATATAAATAAAAATTAAATTAATAATAA
Found at i:1889664 original size:17 final size:18
Alignment explanation
Indices: 1889642--1889676 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1889632 CATTAGTATC
*
1889642 AAATAAATTC-TAAAAAA
1 AAATAAAATCTTAAAAAA
1889659 AAATAAAATCTTAAAAAA
1 AAATAAAATCTTAAAAAA
1889677 TATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAATCTTAAAAAA
Found at i:1889796 original size:11 final size:11
Alignment explanation
Indices: 1889782--1889806 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1889772 ATAATTTAAA
1889782 AAATATTTTTT
1 AAATATTTTTT
1889793 AAATATTTTTT
1 AAATATTTTTT
1889804 AAA
1 AAA
1889807 AAAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:1889800 original size:22 final size:22
Alignment explanation
Indices: 1889754--1889800 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1889744 AATAAAATCT
*
1889754 TTTAAAAAATATATTTTTATAA
1 TTTAAAAAATATATTTTTAAAA
1889776 TTTAAAAAATAT-TTTTTAAATA
1 TTTAAAAAATATATTTTTAAA-A
1889798 TTT
1 TTT
1889801 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAAAAATATATTTTTAAAA
Found at i:1891705 original size:53 final size:50
Alignment explanation
Indices: 1891648--1891772 Score: 155
Period size: 50 Copynumber: 2.4 Consensus size: 50
1891638 TATTTGTAAA
1891648 ATTAATAAATTATTAAAAATTATTAAAATTATATTATATCAAATAATATTTTT
1 ATTAATAAA-TATTAAAAATTATT-AAATTATATTATATCAAATAATA-TTTT
* * *
1891701 ATTAATAAA-ATAAAAAAATT-TTAAATTATTTTATATCAAGTAATATTTT
1 ATTAATAAATAT-TAAAAATTATTAAATTATATTATATCAAATAATATTTT
*
1891750 ATTATTAAATATTTAAAAATTAT
1 ATTAATAAATA-TTAAAAATTAT
1891773 ATTTTATGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
49 12 0.19
50 29 0.46
51 6 0.10
52 7 0.11
53 9 0.14
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (50 bp):
ATTAATAAATATTAAAAATTATTAAATTATATTATATCAAATAATATTTT
Found at i:1892565 original size:49 final size:52
Alignment explanation
Indices: 1892447--1892565 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 52
1892437 TATATAAAAA
* *
1892447 AATAATTTTTAAATATATAATAATAAATTATTATTTGTTATAAAAATAATTTT
1 AATAATTTTTAATTAT-TAATAATAAATTATTATTTGATATAAAAATAATTTT
* * *
1892500 AAT-GTTTTTAGTTTATTAATAA-GAA-TATTATTTGATAT-AAAATAATTTT
1 AATAATTTTTA-ATTATTAATAATAAATTATTATTTGATATAAAAATAATTTT
*
1892549 AATAAATTTTAATTATT
1 AATAATTTTTAATTATT
1892566 TATTAATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
49 19 0.34
50 17 0.30
51 2 0.04
52 12 0.21
53 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.50
Consensus pattern (52 bp):
AATAATTTTTAATTATTAATAATAAATTATTATTTGATATAAAAATAATTTT
Found at i:1894462 original size:14 final size:15
Alignment explanation
Indices: 1894443--1894471 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1894433 TTTTAATTAA
1894443 ATTTTCAAAA-AAAT
1 ATTTTCAAAATAAAT
1894457 ATTTTCAAAATAAAT
1 ATTTTCAAAATAAAT
1894472 TCATGAGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTTCAAAATAAAT
Found at i:1895989 original size:21 final size:21
Alignment explanation
Indices: 1895963--1896013 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1895953 TTGTCTATTT
*
1895963 TCATTCATTTATGCATC-TCAC
1 TCATTCATTGAT-CATCATCAC
* *
1895984 TCATTCATAGATCATCATCAT
1 TCATTCATTGATCATCATCAC
1896005 TCATTCATT
1 TCATTCATT
1896014 ACATCGTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.43
Consensus pattern (21 bp):
TCATTCATTGATCATCATCAC
Found at i:1899459 original size:11 final size:11
Alignment explanation
Indices: 1899443--1899494 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
1899433 TTTAATCATG
1899443 AAAAAAATACT
1 AAAAAAATACT
1899454 AAAAAAATACAT
1 AAAAAAATAC-T
* *
1899466 AAATAAAAAAAT
1 AAA-AAAATACT
*
1899478 -AAAAAATACC
1 AAAAAAATACT
1899488 AAAAAAA
1 AAAAAAA
1899495 AAAAACAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 5 0.15
11 18 0.55
12 5 0.15
13 5 0.15
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATACT
Found at i:1899485 original size:23 final size:23
Alignment explanation
Indices: 1899455--1899499 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1899445 AAAAATACTA
*
1899455 AAAAAATA-CATAAATAAAAAAAT
1 AAAAAATACCA-AAAAAAAAAAAT
1899478 AAAAAATACCAAAAAAAAAAAA
1 AAAAAATACCAAAAAAAAAAAA
1899500 CAAATGACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (23 bp):
AAAAAATACCAAAAAAAAAAAAT
Found at i:1900694 original size:40 final size:40
Alignment explanation
Indices: 1900532--1900759 Score: 197
Period size: 40 Copynumber: 5.5 Consensus size: 40
1900522 AGAAGCTCAC
* * * *
1900532 AACTTTGAAAAAATAAATACGACTCCTCTAAATAAAAGCTCAAT
1 AACTTTG-AAAAATAAAT--G-CTCCTCTAAACAGAGGCACAAT
* * * * **
1900576 GACTTTTGAAAAATAAAAAGCTCATCTAATCAGAGGCTTAAT
1 AAC-TTTGAAAAAT-AAATGCTCCTCTAAACAGAGGCACAAT
* * * *
1900618 GACTTTAAAAAATAAAAGGCTCCTATAAACAGAGGCACAAT
1 AACTTTGAAAAAT-AAATGCTCCTCTAAACAGAGGCACAAT
* * * *
1900659 AACTTTGAAAAATAAATGCTCCTTTAAACAAAGGCACCAC
1 AACTTTGAAAAATAAATGCTCCTCTAAACAGAGGCACAAT
**
1900699 AACTTCAAAAAATAAATGCTCCTCTAAACAGAGGCACTAA-
1 AACTTTGAAAAATAAATGCTCCTCTAAACAGAGGCAC-AAT
1900739 AACTTTGAAAAATAAATGCTC
1 AACTTTGAAAAATAAATGCTC
1900760 TTTGACAATC
Statistics
Matches: 152, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
40 74 0.49
41 43 0.28
42 19 0.12
43 1 0.01
44 8 0.05
45 7 0.05
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (40 bp):
AACTTTGAAAAATAAATGCTCCTCTAAACAGAGGCACAAT
Found at i:1905118 original size:20 final size:21
Alignment explanation
Indices: 1905093--1905140 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
1905083 CTGATGAGGG
1905093 TTAATCAGTTTACTTTCTTA-
1 TTAATCAGTTTACTTTCTTAC
1905113 TTAATCAGTTTACTTTCTTAC
1 TTAATCAGTTTACTTTCTTAC
1905134 TTAATCA
1 TTAATCA
1905141 ATTTTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (21 bp):
TTAATCAGTTTACTTTCTTAC
Found at i:1907099 original size:75 final size:79
Alignment explanation
Indices: 1907004--1907162 Score: 272
Period size: 79 Copynumber: 2.0 Consensus size: 79
1906994 GTTTTGATGG
1907004 TTGGTCGGTCATAGACACTTCAACATTCTTTGAA-TTT-TTTTTTCATAGAGTTCAATTTGGTAT
1 TTGGTCGGTCATAGACACTTCAACATTCTTTGAATTTTCTTTTTTCATAGAGTTCAATTTGGTAT
1907067 AAATCCATG-ACTT
66 AAATCCATGAACTT
1907080 TTGGTC-GTCATAGACACTTCAACATTCTTTGAATTTTCCCTTTTTTCATAGAGTTCAATTTGGT
1 TTGGTCGGTCATAGACACTTCAACATTCTTTGAATTTT--CTTTTTTCATAGAGTTCAATTTGGT
1907144 ATAAATCCATGAACTT
64 ATAAATCCATGAACTT
1907160 TTG
1 TTG
1907163 TACCTCTTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
75 27 0.35
76 9 0.12
79 35 0.45
80 7 0.09
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (79 bp):
TTGGTCGGTCATAGACACTTCAACATTCTTTGAATTTTCTTTTTTCATAGAGTTCAATTTGGTAT
AAATCCATGAACTT
Found at i:1913070 original size:11 final size:10
Alignment explanation
Indices: 1913055--1913090 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
1913045 AAAAAAACAT
1913055 AAATACAAAA
1 AAATACAAAA
1913065 ACAATACCAAAA
1 A-AATA-CAAAA
1913077 AAATACAAAA
1 AAATACAAAA
1913087 AAAT
1 AAAT
1913091 GAAACGGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
11 8 0.33
12 6 0.25
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATACAAAA
Found at i:1918374 original size:17 final size:18
Alignment explanation
Indices: 1918352--1918385 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1918342 AAATTATGAT
1918352 TTGATAT-AAAAATATTC
1 TTGATATCAAAAATATTC
*
1918369 TTGATATCATAAATATT
1 TTGATATCAAAAATATT
1918386 AACTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TTGATATCAAAAATATTC
Found at i:1926175 original size:22 final size:23
Alignment explanation
Indices: 1926125--1926175 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
1926115 TTTGACGTAT
* *
1926125 CTCCTTTCTCTATAGTGATTTGG
1 CTCCTCTCTCTATAGTGATTTGC
1926148 CT-CTCTCTCTAT-GTG-TTGTGC
1 CTCCTCTCTCTATAGTGATT-TGC
1926169 CTCCTCT
1 CTCCTCT
1926176 AGAAACTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.29
22 13 0.54
23 2 0.08
ACGTcount: A:0.08, C:0.29, G:0.16, T:0.47
Consensus pattern (23 bp):
CTCCTCTCTCTATAGTGATTTGC
Found at i:1933041 original size:20 final size:20
Alignment explanation
Indices: 1932985--1933049 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
1932975 ATTATATTGT
*
1932985 ATCAAGACTCATTCAAGATTA
1 ATCAAGATTCA-TCAAGATTA
1933006 ATCAAGAACTTC--CAAGATTA
1 ATCAAG-A-TTCATCAAGATTA
*
1933026 TTCAAGATTCATCAAGATTCA
1 ATCAAGATTCATCAAGATT-A
1933047 ATC
1 ATC
1933050 TTTCTTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 20 0.56
21 9 0.25
22 1 0.03
23 2 0.06
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (20 bp):
ATCAAGATTCATCAAGATTA
Found at i:1933459 original size:43 final size:43
Alignment explanation
Indices: 1933410--1933748 Score: 290
Period size: 44 Copynumber: 7.7 Consensus size: 43
1933400 TCAAAAATTA
* *
1933410 ATCTAAATTTAAAGGTTCGTATTTTAAAATTTTAGAAATTCAC
1 ATCTAAATTTAAAGGTTCGCATTTGAAAATTTTAGAAATTCAC
* * * *
1933453 ATCTAAA-TTACGAATGTTCGCATTTAAAAATTTTAGATATTCAA
1 ATCTAAATTTA--AAGGTTCGCATTTGAAAATTTTAGAAATTCAC
* * *** * *
1933497 ATCTAAATTGAAAGATTTTTATTTGAAAATTTTAGAGATTTAC
1 ATCTAAATTTAAAGGTTCGCATTTGAAAATTTTAGAAATTCAC
* * *
1933540 ATCTAAATTTCAAGGATTCCCATTTGAACAATTTTAGATATTCAC
1 ATCTAAATTTAAAGG-TTCGCATTTGAA-AATTTTAGAAATTCAC
*
1933585 ATATAAATTTCAAAGG-TCGCATTTGAAAATTTTAGAAATTCAC
1 ATCTAAATTT-AAAGGTTCGCATTTGAAAATTTTAGAAATTCAC
* * ** * * *
1933628 ATGTAAAATTCAAATATT-TCATTTGAAAAATTTTAGAGATTTAC
1 ATCT-AAATTTAAAGGTTCGCATTTG-AAAATTTTAGAAATTCAC
* *
1933672 ATCTAAATTTCAAAGGTTCGCAATTGAAAATTTTA-AAGATTCAT
1 ATCTAAATTT-AAAGGTTCGCATTTGAAAATTTTAGAA-ATTCAC
* ** *
1933716 ATCTAAATTCAAAAATTCTCATTTGAAAGATTT
1 ATCTAAATTTAAAGGTTCGCATTTGAAA-ATTT
1933749 AAAGATTCTT
Statistics
Matches: 235, Mismatches: 48, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
42 3 0.01
43 89 0.38
44 109 0.46
45 30 0.13
46 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (43 bp):
ATCTAAATTTAAAGGTTCGCATTTGAAAATTTTAGAAATTCAC
Found at i:1933520 original size:87 final size:85
Alignment explanation
Indices: 1933409--1933727 Score: 302
Period size: 87 Copynumber: 3.6 Consensus size: 85
1933399 TTCAAAAATT
* * *
1933409 AATCTAAATTTAAAGGTTCGTATTTTAAAATTTTAGAAATTCACATCTAAATTACGAATGTTCGC
1 AATCTAAATTCAAA-GTTCGTATTTGAAAATTTTAGAAATTCACATCTAAATT-C-AATGTTCCC
1933474 ATTT-AAAAATTTTAGATATTCA
63 ATTTGAAAAATTTTAGATATTCA
* ** * * *
1933496 AATCTAAATTGAAAGATTTTTATTTGAAAATTTTAGAGATTTACATCTAAATTTCAAGGATTCCC
1 AATCTAAATTCAAAG-TTCGTATTTGAAAATTTTAGAAATTCACATCTAAA-TTCAATG-TTCCC
*
1933561 ATTTGAACAATTTTAGATATTCA
63 ATTTGAAAAATTTTAGATATTCA
* * * * * * *
1933584 CATATAAATTTCAAAGGTCGCATTTGAAAATTTTAGAAATTCACATGTAAAATTCAAATATT-TC
1 AATCTAAA-TTCAAAGTTCGTATTTGAAAATTTTAGAAATTCACATCT-AAATTC-AATGTTCCC
* *
1933648 ATTTGAAAAATTTTAGAGATTTA
63 ATTTGAAAAATTTTAGATATTCA
* * * *
1933671 CATCTAAATTTCAAAGGTTCGCAATTGAAAATTTTA-AAGATTCATATCTAAATTCAA
1 AATCTAAA-TTCAAA-GTTCGTATTTGAAAATTTTAGAA-ATTCACATCTAAATTCAA
1933728 AAATTCTCAT
Statistics
Matches: 193, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
86 6 0.03
87 95 0.49
88 81 0.42
89 11 0.06
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (85 bp):
AATCTAAATTCAAAGTTCGTATTTGAAAATTTTAGAAATTCACATCTAAATTCAATGTTCCCATT
TGAAAAATTTTAGATATTCA
Found at i:1933610 original size:88 final size:89
Alignment explanation
Indices: 1933410--1933748 Score: 370
Period size: 88 Copynumber: 3.9 Consensus size: 89
1933400 TCAAAAATTA
* * * * *
1933410 ATCTAAATTT-AAAGGTTCGTATTTTAAAATTTTAGAAATTCACATCTAAATTACGAATG-TTCG
1 ATCTAAATTTCAAAGGTTCGCATTTGAAAATTTTAGAAATTCACATCTAAATTTC-AAAGATTCT
*
1933473 CATTT-AAAAATTTTAGATATTCAA
65 CATTTGAAAAATTTTAGATATTCAC
* * *** * * * *
1933497 ATCTAAA-TTGAAAGATTTTTATTTGAAAATTTTAGAGATTTACATCTAAATTTCAAGGATTCCC
1 ATCTAAATTTCAAAGGTTCGCATTTGAAAATTTTAGAAATTCACATCTAAATTTCAAAGATTCTC
*
1933561 ATTTGAACAATTTTAGATATTCAC
66 ATTTGAAAAATTTTAGATATTCAC
* * * *
1933585 ATATAAATTTCAAAGG-TCGCATTTGAAAATTTTAGAAATTCACATGTAAAATTCAAATATT-TC
1 ATCTAAATTTCAAAGGTTCGCATTTGAAAATTTTAGAAATTCACATCTAAATTTCAAAGATTCTC
* *
1933648 ATTTGAAAAATTTTAGAGATTTAC
66 ATTTGAAAAATTTTAGATATTCAC
* * *
1933672 ATCTAAATTTCAAAGGTTCGCAATTGAAAATTTTA-AAGATTCATATCTAAA-TTCAAAAATTCT
1 ATCTAAATTTCAAAGGTTCGCATTTGAAAATTTTAGAA-ATTCACATCTAAATTTCAAAGATTCT
*
1933735 CATTTGAAAGATTT
65 CATTTGAAAAATTT
1933749 AAAGATTCTT
Statistics
Matches: 212, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
86 5 0.02
87 100 0.47
88 101 0.48
89 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (89 bp):
ATCTAAATTTCAAAGGTTCGCATTTGAAAATTTTAGAAATTCACATCTAAATTTCAAAGATTCTC
ATTTGAAAAATTTTAGATATTCAC
Found at i:1933756 original size:23 final size:23
Alignment explanation
Indices: 1933730--1933800 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
1933720 AAATTCAAAA
*
1933730 ATTCTCATTTGAAAGATTTAAAG
1 ATTCTCATATGAAAGATTTAAAG
* *
1933753 ATTCTTATATGATAAG-TTCAAAG
1 ATTCTCATATGA-AAGATTTAAAG
* * *
1933776 ATTCCCATATAAAAGATTTACAG
1 ATTCTCATATGAAAGATTTAAAG
1933799 AT
1 AT
1933801 ATTCATTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (23 bp):
ATTCTCATATGAAAGATTTAAAG
Found at i:1933791 original size:46 final size:43
Alignment explanation
Indices: 1933703--1933800 Score: 106
Period size: 46 Copynumber: 2.2 Consensus size: 43
1933693 AATTGAAAAT
* * * *
1933703 TTTAAAGATTCATATCTAAATTCAAAAATTCTCATTTGAAAGA
1 TTTAAAGATTCATATATAAATTCAAAAATTCCCATATAAAAGA
* *
1933746 TTTAAAGATTCTTATATGATAAGTTCAAAGATTCCCATATAAAAGA
1 TTTAAAGATTC--ATAT-ATAAATTCAAAAATTCCCATATAAAAGA
*
1933792 TTTACAGAT
1 TTTAAAGAT
1933801 ATTCATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 11 0.24
45 4 0.09
46 30 0.67
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (43 bp):
TTTAAAGATTCATATATAAATTCAAAAATTCCCATATAAAAGA
Found at i:1934072 original size:25 final size:26
Alignment explanation
Indices: 1934028--1934079 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1934018 CATTCGAGGA
1934028 TCTCATCTTGAAAGGGTTT-CTCATT
1 TCTCATCTTGAAAGGGTTTCCTCATT
*
1934053 TCTCATCTTTGAAA-GTTTTCCTCATT
1 TCTCATC-TTGAAAGGGTTTCCTCATT
1934079 T
1 T
1934080 AAGGATTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (26 bp):
TCTCATCTTGAAAGGGTTTCCTCATT
Found at i:1934239 original size:25 final size:26
Alignment explanation
Indices: 1934209--1934261 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1934199 ATTCTCTCTA
* *
1934209 AATGATGCAAATGCAA-GTTCTAAAC
1 AATGATGCAAATCCAATATTCTAAAC
*
1934234 AATGATGTAAATCCAATATTCTAAAC
1 AATGATGCAAATCCAATATTCTAAAC
1934260 AA
1 AA
1934262 CAATTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (26 bp):
AATGATGCAAATCCAATATTCTAAAC
Found at i:1936079 original size:21 final size:21
Alignment explanation
Indices: 1936045--1936084 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1936035 AATTTTTAAG
1936045 AATTTCATCTTTCAATAATTAC
1 AATTTCATCTTTCAA-AATTAC
*
1936067 AATTT-ATTTTTCAAAATT
1 AATTTCATCTTTCAAAATT
1936085 TTATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTCATCTTTCAAAATTAC
Found at i:1936093 original size:10 final size:10
Alignment explanation
Indices: 1936080--1936123 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1936070 TTATTTTTCA
1936080 AAATTTTATT
1 AAATTTTATT
1936090 AAATTTTATTTT
1 AAATTTTA--TT
1936102 AAATTTTATT
1 AAATTTTATT
* *
1936112 TATTTTTATT
1 AAATTTTATT
1936122 AA
1 AA
1936124 TCAAATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.66
12 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AAATTTTATT
Found at i:1936105 original size:12 final size:12
Alignment explanation
Indices: 1936080--1936112 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1936070 TTATTTTTCA
1936080 AAATTTTA--TT
1 AAATTTTATTTT
1936090 AAATTTTATTTT
1 AAATTTTATTTT
1936102 AAATTTTATTT
1 AAATTTTATTT
1936113 ATTTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AAATTTTATTTT
Found at i:1936108 original size:22 final size:22
Alignment explanation
Indices: 1936080--1936121 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1936070 TTATTTTTCA
1936080 AAATTTTATTAAATTTTATTTT
1 AAATTTTATTAAATTTTATTTT
* *
1936102 AAATTTTATTTATTTTTATT
1 AAATTTTATTAAATTTTATT
1936122 AATCAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AAATTTTATTAAATTTTATTTT
Found at i:1936769 original size:18 final size:18
Alignment explanation
Indices: 1936748--1936785 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1936738 ATCAGATAAG
1936748 AAAACAAAATAA-ATAAAT
1 AAAA-AAAATAAGATAAAT
*
1936766 AAAAAAATTAAGATAAAT
1 AAAAAAAATAAGATAAAT
1936784 AA
1 AA
1936786 TAAAGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAAAATAAGATAAAT
Found at i:1936793 original size:13 final size:12
Alignment explanation
Indices: 1936775--1936843 Score: 54
Period size: 13 Copynumber: 5.7 Consensus size: 12
1936765 TAAAAAAATT
1936775 AAGATAAATAATA
1 AAGATAAATAA-A
* *
1936788 AAGATATATAAC
1 AAGATAAATAAA
1936800 AAGA-AAAT-AA
1 AAGATAAATAAA
*
1936810 AGGATAAATACAA
1 AAGATAAATA-AA
1936823 AAGATAGAATAGAA
1 AAGATA-AATA-AA
1936837 AA-ATAAA
1 AAGATAAA
1936844 AATAATAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
10 4 0.09
11 7 0.16
12 6 0.13
13 20 0.44
14 8 0.18
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.17
Consensus pattern (12 bp):
AAGATAAATAAA
Found at i:1937494 original size:8 final size:9
Alignment explanation
Indices: 1937456--1937495 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
1937446 CATGTTTTTA
1937456 CTTTTTCAT
1 CTTTTTCAT
1937465 CTTTTTCAT
1 CTTTTTCAT
1937474 -TTCTTT-AT
1 CTT-TTTCAT
1937482 CTTTTTC-T
1 CTTTTTCAT
1937490 CTTTTT
1 CTTTTT
1937496 TTTCTTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (9 bp):
CTTTTTCAT
Found at i:1939583 original size:38 final size:38
Alignment explanation
Indices: 1939532--1939607 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1939522 TATTATAATA
*
1939532 TGTAGGCTTGAGAAATAACCCACTAGACATAAAACATG
1 TGTAGGCCTGAGAAATAACCCACTAGACATAAAACATG
* *
1939570 TGTAGGCCTGAGAAATAACCCAGTAGAGATAAAACATG
1 TGTAGGCCTGAGAAATAACCCACTAGACATAAAACATG
1939608 AGAGTCACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (38 bp):
TGTAGGCCTGAGAAATAACCCACTAGACATAAAACATG
Found at i:1945555 original size:2 final size:2
Alignment explanation
Indices: 1945548--1945576 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1945538 ATTTGAACAA
1945548 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1945577 CCCCTGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1949514 original size:25 final size:25
Alignment explanation
Indices: 1949460--1949513 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1949450 ATAGTAAAGC
* *
1949460 AAAAATCTGCATAATCAACGTAGTT
1 AAAAATCTGCACAATCAACATAGTT
*
1949485 AAAAATTTGCACAATCAACATA-TT
1 AAAAATCTGCACAATCAACATAGTT
1949509 AAAAA
1 AAAAA
1949514 AATCACCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (25 bp):
AAAAATCTGCACAATCAACATAGTT
Found at i:1951827 original size:3 final size:3
Alignment explanation
Indices: 1951819--1951849 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1951809 CAAATGCACG
*
1951819 ACA ACA ACA ACA ACA ACA ACA ACC ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1951850 ACTTAGCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1952239 original size:2 final size:2
Alignment explanation
Indices: 1952234--1952261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1952224 AAGCCCCCCT
1952234 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1952262 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1956320 original size:3 final size:3
Alignment explanation
Indices: 1956312--1956355 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1956302 CAAATATTAA
* *
1956312 AAT AAT AAT AAT AAT AAC AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1956356 CTATTGTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1957122 original size:3 final size:3
Alignment explanation
Indices: 1957116--1957153 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1957106 TATTATTGAC
1957116 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1957154 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1957158 original size:3 final size:3
Alignment explanation
Indices: 1957152--1957177 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1957142 AATAATAATA
1957152 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1957178 ATTTTTTAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1957719 original size:18 final size:18
Alignment explanation
Indices: 1957670--1957719 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1957660 ACTTTTTTAG
*
1957670 ATTTATCATATATA-AAA
1 ATTTATCAAATATATAAA
1957687 ATTTGAT-AAAT-TATAAA
1 ATTT-ATCAAATATATAAA
1957704 ATTTATCAAATATATA
1 ATTTATCAAATATATA
1957720 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 6 0.21
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTTATCAAATATATAAA
Done.