Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 180 of 318
Found at i:56474621 original size:31 final size:31
Alignment explanation
Indices: 56474509--56474621 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 31
56474499 CATCATGTGT
*
56474509 ACAAGAGAGCTACGAGATGTATACCATGTAG
1 ACAAGAGAGCTACGGGATGTATACCATGTAG
* * * * *
56474540 ACAAGAGAGCTACGGGATAAATGTAGCTAGGT-C
1 ACAAGAGAGCTACGGGAT--GTATA-CCATGTAG
* * * * *
56474573 ACATGTGTGATATGGGATGTATACCATGTAG
1 ACAAGAGAGCTACGGGATGTATACCATGTAG
56474604 ACAAGAGAGCTACGGGAT
1 ACAAGAGAGCTACGGGAT
56474622 AAATGTAGCT
Statistics
Matches: 57, Mismatches: 21, Indels: 8
0.66 0.24 0.09
Matches are distributed among these distances:
30 4 0.07
31 33 0.58
33 16 0.28
34 4 0.07
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.21
Consensus pattern (31 bp):
ACAAGAGAGCTACGGGATGTATACCATGTAG
Found at i:56477951 original size:93 final size:93
Alignment explanation
Indices: 56477792--56477963 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
56477782 GCCCATAAGT
*** *
56477792 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATGAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
56477857 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
56477885 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
56477950 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
56477964 CAAATATCCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:56477959 original size:46 final size:46
Alignment explanation
Indices: 56477784--56477959 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
56477774 TGTAACCCGC
* *** *
56477784 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * *
56477830 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
56477880 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
56477923 CCATAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
56477960 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 62 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:56480386 original size:30 final size:30
Alignment explanation
Indices: 56480342--56480430 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
56480332 CAAAGATAAC
56480342 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
56480371 GAGAAACCCAGAATAAAGGAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
56480401 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
56480431 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.19
30 37 0.77
31 2 0.04
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:56480398 original size:15 final size:15
Alignment explanation
Indices: 56480342--56480421 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
56480332 CAAAGATAAC
*
56480342 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
56480356 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
56480371 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
56480386 AAGGAATCCAGAATA
1 AAGAAATCCAGAATA
* *
56480401 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
56480416 AAGAAA
1 AAGAAA
56480422 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:56480430 original size:15 final size:15
Alignment explanation
Indices: 56480353--56480430 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
56480343 AGAAAACCGA
56480353 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
56480368 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
*
56480382 AATAAAGGAATCC-AG
1 -ATAAAGAAATCCAAG
* *
56480397 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
56480413 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
56480428 ATA
1 ATA
56480431 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.08
15 43 0.86
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:56483747 original size:10 final size:10
Alignment explanation
Indices: 56483732--56483795 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
56483722 AAACTACAAA
56483732 ATATTTTTAT
1 ATATTTTTAT
56483742 ATATTTTTAT
1 ATATTTTTAT
56483752 -T-TTTTT-T
1 ATATTTTTAT
56483759 ATACTTTTTA-
1 ATA-TTTTTAT
*
56483769 ATAATTCTTA-
1 AT-ATTTTTAT
56483779 ATAATTTTTAT
1 AT-ATTTTTAT
56483790 A-ATTTT
1 ATATTTT
56483796 GTTGGAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
7 1 0.02
8 6 0.13
9 6 0.13
10 31 0.67
11 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:56483766 original size:9 final size:9
Alignment explanation
Indices: 56483734--56483816 Score: 62
Period size: 9 Copynumber: 8.8 Consensus size: 9
56483724 ACTACAAAAT
56483734 ATTTTTATA
1 ATTTTTATA
*
56483743 TATTTTTATT
1 -ATTTTTATA
*
56483753 TTTTTTATA
1 ATTTTTATA
*
56483762 CTTTTTAATA
1 ATTTTT-ATA
*
56483772 ATTCTTAATA
1 ATT-TTTATA
56483782 ATTTTTATA
1 ATTTTTATA
56483791 ATTTTGT-TGGA
1 ATTTT-TAT--A
56483802 ATTTTTA-A
1 ATTTTTATA
56483810 ATTTTTA
1 ATTTTTA
56483817 AAAATTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
8 8 0.13
9 23 0.38
10 21 0.35
11 8 0.13
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:56486015 original size:9 final size:10
Alignment explanation
Indices: 56485985--56486016 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56485975 GTTGGACCTA
56485985 ATTGTAAAAT
1 ATTGTAAAAT
56485995 ATTGTAAAAT
1 ATTGTAAAAT
56486005 ATTGT-AAAT
1 ATTGTAAAAT
56486014 ATT
1 ATT
56486017 CACATGACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (10 bp):
ATTGTAAAAT
Found at i:56494814 original size:20 final size:21
Alignment explanation
Indices: 56494778--56494825 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
56494768 ATTTTGATAT
*
56494778 ACATGATTTGATATGATATGC
1 ACATGATATGATATGATATGC
56494799 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
56494819 ACATGAT
1 ACATGAT
56494826 GTATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:56494918 original size:24 final size:23
Alignment explanation
Indices: 56494872--56494935 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
56494862 GGAGGAAGTG
* *
56494872 CAAAAGGGCTTTACCCCAGTTTAC
1 CAAAAAGGCTTT-GCCCAGTTTAC
*
56494896 CGAAAAAGGCTTTGCCCAGTTTAT
1 C-AAAAAGGCTTTGCCCAGTTTAC
*
56494920 CAAAAAGGGTTTGCCC
1 CAAAAAGGCTTTGCCC
56494936 CATTATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.40
24 11 0.31
25 10 0.29
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
CAAAAAGGCTTTGCCCAGTTTAC
Found at i:56494932 original size:23 final size:24
Alignment explanation
Indices: 56494886--56494935 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
56494876 AGGGCTTTAC
56494886 CCCAGTTTACCGAAAAAGGCTTTG
1 CCCAGTTTACCGAAAAAGGCTTTG
* *
56494910 CCCAGTTTATC-AAAAAGGGTTTG
1 CCCAGTTTACCGAAAAAGGCTTTG
56494933 CCC
1 CCC
56494936 CATTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (24 bp):
CCCAGTTTACCGAAAAAGGCTTTG
Found at i:56494937 original size:24 final size:25
Alignment explanation
Indices: 56494873--56494937 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
56494863 GAGGAAGTGC
*
56494873 AAAAGGGCTTTACCCCAGTTTACCGA
1 AAAAGGG-TTTGCCCCAGTTTACCGA
* *
56494899 AAAAGGCTTTG-CCCAGTTTATC-A
1 AAAAGGGTTTGCCCCAGTTTACCGA
56494922 AAAAGGGTTTGCCCCA
1 AAAAGGGTTTGCCCCA
56494938 TTATTAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 11 0.32
24 14 0.41
25 3 0.09
26 6 0.18
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
AAAAGGGTTTGCCCCAGTTTACCGA
Found at i:56494941 original size:22 final size:22
Alignment explanation
Indices: 56494898--56494952 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
56494888 CAGTTTACCG
56494898 AAAAAGGCTTTGCCCAGTTTATC
1 AAAAAGGCTTTGCCCAG-TTATC
* *
56494921 AAAAAGGGTTTGCCCCA-TTATT
1 AAAAAGGCTTTG-CCCAGTTATC
56494943 AAAAGAGGCT
1 AAAA-AGGCT
56494953 AGGCCTCCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (22 bp):
AAAAAGGCTTTGCCCAGTTATC
Found at i:56495222 original size:30 final size:32
Alignment explanation
Indices: 56495186--56495250 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
56495176 TGATATGAGT
*
56495186 TGTGAATTAT-AAAATGCTTCGGCCCAGTA-A
1 TGTGAATTATGAAAAGGCTTCGGCCCAGTATA
* *
56495216 TGTGAATTATGAAGAGGCTTCGGCCTAGTATA
1 TGTGAATTATGAAAAGGCTTCGGCCCAGTATA
56495248 TGT
1 TGT
56495251 TGAGATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 10 0.33
31 16 0.53
32 4 0.13
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (32 bp):
TGTGAATTATGAAAAGGCTTCGGCCCAGTATA
Found at i:56505084 original size:20 final size:20
Alignment explanation
Indices: 56505028--56505084 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
56505018 AAGTTTATGC
* *
56505028 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGGTAAG
*
56505048 TAAGTAAATTGAATGGTAAG
1 TAAGTAAATGGAATGGTAAG
*
56505068 TAAGTAAATGGAGTGGT
1 TAAGTAAATGGAATGGT
56505085 TTATAATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (20 bp):
TAAGTAAATGGAATGGTAAG
Found at i:56508992 original size:79 final size:82
Alignment explanation
Indices: 56508881--56509065 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
56508871 GCTCCTCGTT
* *
56508881 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTT-GGGATCTTAACCC
* *
56508944 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
56508961 CAAATGCCTTCGGG-CTTATCCCGGAAT-TAGTATCTCGCACAAATGCCTTGGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
* *
56509024 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
56509041 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56509066 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.04
79 53 0.59
80 33 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:56509065 original size:40 final size:40
Alignment explanation
Indices: 56508881--56509065 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
56508871 GCTCCTCGTT
* *
56508881 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
56508921 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
56508961 CAAATGCCTTCGGG-CTTATCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
56509000 CAAATGCCTT-GGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
56509041 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56509066 CATCATTCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 3 0.02
39 31 0.25
40 78 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:56513785 original size:40 final size:40
Alignment explanation
Indices: 56513741--56513926 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
56513731 GCTCCTCGTT
*
56513741 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
56513781 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
56513821 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAT-TCGCA
* * * * *
56513861 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AATTCGCA
56513902 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56513927 CATCATTCAA
Statistics
Matches: 129, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 4 0.03
40 111 0.86
41 13 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:56523998 original size:40 final size:40
Alignment explanation
Indices: 56523954--56524139 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
56523944 GCTCCTCGTT
*
56523954 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
56523994 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
56524034 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAT-TCGCA
* * * * *
56524074 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AATTCGCA
56524115 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56524140 CATCATTCAA
Statistics
Matches: 129, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 4 0.03
40 111 0.86
41 13 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:56530190 original size:79 final size:81
Alignment explanation
Indices: 56530073--56530255 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
56530063 GCTCCTCGTT
* **
56530073 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
56530137 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
56530153 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
56530216 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
56530233 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
56530256 GACATCATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 54 0.61
80 32 0.36
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:56530194 original size:39 final size:39
Alignment explanation
Indices: 56530073--56530255 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 39
56530063 GCTCCTCGTT
* *
56530073 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCA
*
56530113 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* *
56530153 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* * * * *
56530192 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCA
56530233 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
56530256 GACATCATTC
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.02
39 35 0.29
40 69 0.57
41 16 0.13
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:56531222 original size:20 final size:20
Alignment explanation
Indices: 56531166--56531222 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
56531156 AAGTTTATGC
* *
56531166 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGGTAAG
*
56531186 TAAGTAAATTGAATGGTAAG
1 TAAGTAAATGGAATGGTAAG
*
56531206 TAAGTAAATGGAGTGGT
1 TAAGTAAATGGAATGGT
56531223 TTATAATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (20 bp):
TAAGTAAATGGAATGGTAAG
Found at i:56535134 original size:79 final size:82
Alignment explanation
Indices: 56535023--56535207 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
56535013 GCTCCTCGTT
* *
56535023 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
56535086 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
56535103 CAAATGCCTTCGGG-CTTATCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
56535166 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
56535183 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56535208 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:56535207 original size:40 final size:40
Alignment explanation
Indices: 56535023--56535207 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
56535013 GCTCCTCGTT
* *
56535023 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
56535063 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
56535103 CAAATGCCTTCGGG-CTTATCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
56535142 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
56535183 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56535208 CATCATTCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 79 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:56546810 original size:24 final size:23
Alignment explanation
Indices: 56546783--56546844 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
56546773 TGAGCTAAAT
56546783 AGGAAACTCATAAGAGTTTTAATC
1 AGGAAACTCATAAGAGTTTTAA-C
* *
56546807 AGGAAGCTTAT-AGAG-TTTAAC
1 AGGAAACTCATAAGAGTTTTAAC
*
56546828 AGGTAACTC-TGAAGAGT
1 AGGAAACTCAT-AAGAGT
56546845 CATTATCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.03
21 7 0.23
22 9 0.30
23 4 0.13
24 9 0.30
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (23 bp):
AGGAAACTCATAAGAGTTTTAAC
Found at i:56550985 original size:40 final size:40
Alignment explanation
Indices: 56550923--56551100 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
56550913 CAACCAAGTA
* * * *
56550923 CCTTCGGGATTTA-ACCGGATATAGCT-ACCCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
*
56550962 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
56551002 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * * *
56551042 CCTTCGGGACTTAGCCCGGGA-CTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCC-GGATATAGTAACTCGCACGAATG
56551082 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
56551101 TTATCATCCA
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 14 0.11
40 108 0.86
41 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:56562827 original size:30 final size:30
Alignment explanation
Indices: 56562793--56562889 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
56562783 TAAACTAAAA
*
56562793 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
56562823 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
56562853 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
56562882 ATGAGCTA
1 -TGAGCTA
56562890 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:56565200 original size:27 final size:27
Alignment explanation
Indices: 56565167--56565434 Score: 195
Period size: 27 Copynumber: 9.9 Consensus size: 27
56565157 TTAGTTTACC
*
56565167 AAATTACTAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATACCCCTGATTTGTA
* * * *
56565194 AAGTTACCAAAATACCCCTAATTTGTG
1 AAATTACTAAAATACCCCTGATTTGTA
* *
56565221 AAATTACTGAAATA-CCCTCGACTTGTA
1 AAATTACTAAAATACCCCT-GATTTGTA
* * * * **
56565248 ACATTACCAAAATACCCTTGGTTTACA
1 AAATTACTAAAATACCCCTGATTTGTA
* * *
56565275 AAATTACCAAAATATCCCTGGTTTGTA
1 AAATTACTAAAATACCCCTGATTTGTA
* * *
56565302 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACTAAAATACCCCTGATTTGTA
* * *
56565329 AAATTA-TCGAAATA-CCCTCAGTTTGCA
1 AAATTACT-AAAATACCCCTGA-TTTGTA
56565356 AAATTACTAAAATA-CCCTCGATTTGTA
1 AAATTACTAAAATACCCCT-GATTTGTA
* * *
56565383 AAATTAATGAAATA-CCCTCGACTTGTTA
1 AAATTACTAAAATACCCCT-GATTTG-TA
* * *
56565411 AAATTACCAAAGTACCCCCGATTT
1 AAATTACTAAAATACCCCTGATTT
56565435 ACAGAATTAC
Statistics
Matches: 188, Mismatches: 45, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
26 9 0.05
27 155 0.82
28 21 0.11
29 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACTAAAATACCCCTGATTTGTA
Found at i:56565234 original size:54 final size:54
Alignment explanation
Indices: 56565167--56565428 Score: 253
Period size: 54 Copynumber: 4.8 Consensus size: 54
56565157 TTAGTTTACC
* * *
56565167 AAATTACTAAAATACCC-CTGGTTTGTAAAGTTACCAAAATACCCCTAATTTGTG
1 AAATTACTGAAATACCCTC-GGTTTGTAAAATTACCAAAATACCCCTAATTTGTA
** * * ** **
56565221 AAATTACTGAAATACCCTCGACTTGTAACATTACCAAAATACCCTTGGTTTACA
1 AAATTACTGAAATACCCTCGGTTTGTAAAATTACCAAAATACCCCTAATTTGTA
** *
56565275 AAATTACCAAAATATCCCT-GGTTTGTAAAATTACCAAAATACCCCTAATTTGTG
1 AAATTACTGAAATA-CCCTCGGTTTGTAAAATTACCAAAATACCCCTAATTTGTA
* * * *
56565329 AAATTA-TCGAAATACCCTCAGTTTGCAAAATTACTAAAATA-CCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGGTTTGTAAAATTACCAAAATACCCCT-AATTTGTA
* ** *
56565383 AAATTAATGAAATACCCTCGACTTGTTAAAATTACCAAAGTACCCC
1 AAATTACTGAAATACCCTCGGTTTG-TAAAATTACCAAAATACCCC
56565429 CGATTTACAG
Statistics
Matches: 165, Mismatches: 35, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
53 8 0.05
54 135 0.82
55 19 0.12
56 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.30
Consensus pattern (54 bp):
AAATTACTGAAATACCCTCGGTTTGTAAAATTACCAAAATACCCCTAATTTGTA
Found at i:56565306 original size:81 final size:79
Alignment explanation
Indices: 56565167--56565445 Score: 263
Period size: 81 Copynumber: 3.4 Consensus size: 79
56565157 TTAGTTTACC
* * ** * * *
56565167 AAATTACTAAAATACCCCTGGTTTGTAAAGTTACCAAAATACCCCTAATTTGTGAAATTACTGAA
1 AAATTACCAAAATACCCCCGGTTTACAAAATTACCAAAATA-CCCTGATTTGTAAAATTACTGAA
56565232 ATACCCTCGACTTGT
65 ATACCCTCGACTTGT
** * **
56565247 AACATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATATCCCTGGTTTGTAAAATTACCAA
1 AA-ATTACCAAAATACCCCCGGTTTACAAAATTACCAAAATA-CCCTGATTTGTAAAATTACTGA
* *
56565312 AATACCC-CTAATTTGT
64 AATACCCTC-GACTTGT
* * * * * * *
56565328 GAAATTATCGAAATACCCTCAGTTTGCAAAATTACTAAAATACCCTCGATTTGTAAAATTAATGA
1 -AAATTACCAAAATACCCCCGGTTTACAAAATTACCAAAATACCCT-GATTTGTAAAATTACTGA
56565393 AATACCCTCGACTTGTT
64 AATACCCTCGACTTG-T
* * *
56565410 AAAATTACCAAAGTACCCCCGATTTACAGAATTACC
1 -AAATTACCAAAATACCCCCGGTTTACAAAATTACC
56565446 GTTTTACCCT
Statistics
Matches: 158, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
80 7 0.04
81 121 0.77
82 30 0.19
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (79 bp):
AAATTACCAAAATACCCCCGGTTTACAAAATTACCAAAATACCCTGATTTGTAAAATTACTGAAA
TACCCTCGACTTGT
Found at i:56565362 original size:108 final size:108
Alignment explanation
Indices: 56565160--56565373 Score: 324
Period size: 108 Copynumber: 2.0 Consensus size: 108
56565150 GAATACTTTA
* * *
56565160 GTTTACCAAATTACTAAAATACCCCTGGTTTGTAAAGTTACCAAAATACCCCTAATTTGTGAAAT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAAT
* *
56565225 TACTGAAATACCCTCGACTTGTAACATTACCAAAATACCCTTG
66 TACTGAAATACCCTCGACTTGCAAAATTACCAAAATACCCTTG
*
56565268 GTTTACAAAATTACCAAAATATCCCTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAAT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAAT
* *
56565333 TA-TCGAAATACCCTC-AGTTTGCAAAATTACTAAAATACCCT
66 TACT-GAAATACCCTCGA-CTTGCAAAATTACCAAAATACCCT
56565374 CGATTTGTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 2 0.02
108 94 0.98
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (108 bp):
GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAAT
TACTGAAATACCCTCGACTTGCAAAATTACCAAAATACCCTTG
Found at i:56565480 original size:27 final size:27
Alignment explanation
Indices: 56565221--56565481 Score: 98
Period size: 27 Copynumber: 9.6 Consensus size: 27
56565211 CTAATTTGTG
* * * **
56565221 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCAATTTACA
* * ***
56565248 ACATTACCAAAATACCCTTGGTTTACA
1 AAATTACCGAAATACCCTCAATTTACA
* ** **
56565275 AAATTACCAAAATATCCCT-GGTTTGTA
1 AAATTACCGAAATA-CCCTCAATTTACA
* ***
56565302 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCGAAATACCCTC-AATTTACA
* * *
56565329 AAATTATCGAAATACCCTCAGTTTGCA
1 AAATTACCGAAATACCCTCAATTTACA
** * **
56565356 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCAATTTACA
** * *
56565383 AAATTAATGAAATACCCTCGACTTGT-TA
1 AAATTACCGAAATACCCTC-AATT-TACA
* *
56565411 AAATTACC-AAAGTACCCCCGATTTACA
1 AAATTACCGAAA-TACCCTCAATTTACA
* ***
56565438 GAATTACCGTTTTACCCTCAATTTACA
1 AAATTACCGAAATACCCTCAATTTACA
**
56565465 AAATTATTGAAATACCC
1 AAATTACCGAAATACCC
56565482 CTGTAGGGTA
Statistics
Matches: 178, Mismatches: 47, Indels: 18
0.73 0.19 0.07
Matches are distributed among these distances:
26 4 0.02
27 152 0.85
28 21 0.12
29 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCAATTTACA
Found at i:56565496 original size:27 final size:27
Alignment explanation
Indices: 56565473--56565607 Score: 198
Period size: 27 Copynumber: 5.0 Consensus size: 27
56565463 CAAAATTATT
56565473 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
56565500 GAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
56565527 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
56565554 GAAATACCCCTGTAGGATAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* ** *
56565581 GAGATACCTTTGTAGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
56565608 ATTTTGCCCC
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 96 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:56565846 original size:25 final size:25
Alignment explanation
Indices: 56565812--56565878 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
56565802 AGGAAGTGCT
*
56565812 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
56565837 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
56565862 AAAAGGGTTTTACCCCA
1 AAAAGGGCTTTGCCCCA
56565879 AATATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:56574086 original size:26 final size:26
Alignment explanation
Indices: 56574057--56574130 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 26
56574047 ATACTATGAG
56574057 TTGGCTTCAAGCCATGATATAGCACT
1 TTGGCTTCAAGCCATGATATAGCACT
* * * *
56574083 TTGGGTGCGAG--AT-AAACT-G-A-T
1 TTGGCTTCAAGCCATGATA-TAGCACT
56574104 TTGGCTTCAAGCCATGATATAGCACT
1 TTGGCTTCAAGCCATGATATAGCACT
56574130 T
1 T
56574131 CGAGTGGGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 14
0.60 0.15 0.25
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 6 0.18
24 6 0.18
25 1 0.03
26 10 0.30
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (26 bp):
TTGGCTTCAAGCCATGATATAGCACT
Found at i:56574166 original size:47 final size:47
Alignment explanation
Indices: 56574057--56574158 Score: 168
Period size: 47 Copynumber: 2.2 Consensus size: 47
56574047 ATACTATGAG
* * *
56574057 TTGGCTTCAAGCCATGATATAGCACTTTGGGTGCGAGATAAACTGAT
1 TTGGCTTCAAGCCATGATATAGCACTTCGAGTGCGAGATAAACCGAT
*
56574104 TTGGCTTCAAGCCATGATATAGCACTTCGAGTGGGAGATAAACCGAT
1 TTGGCTTCAAGCCATGATATAGCACTTCGAGTGCGAGATAAACCGAT
56574151 TTGGCTTC
1 TTGGCTTC
56574159 GGGCCATGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (47 bp):
TTGGCTTCAAGCCATGATATAGCACTTCGAGTGCGAGATAAACCGAT
Found at i:56575503 original size:21 final size:18
Alignment explanation
Indices: 56575477--56575520 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
56575467 TTTTAAAATT
56575477 ATAAAAAGATATAAATGAATA
1 ATAAAAAGATA-AAAT-AA-A
*
56575498 ATAAAATGATAAAATAAA
1 ATAAAAAGATAAAATAAA
56575516 ATAAA
1 ATAAA
56575521 TAATAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 4 0.18
21 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
ATAAAAAGATAAAATAAA
Found at i:56575519 original size:29 final size:28
Alignment explanation
Indices: 56575470--56575525 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
56575460 TCTAAAGTTT
* *
56575470 TAAAATTATAAAAAGATATAAATGAATAA
1 TAAAATGATAAAAAGAAATAAAT-AATAA
56575499 TAAAATGATAAAATA-AAATAAATAATA
1 TAAAATGATAAAA-AGAAATAAATAATA
56575526 GTTAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
TAAAATGATAAAAAGAAATAAATAATAA
Found at i:56575531 original size:29 final size:29
Alignment explanation
Indices: 56575469--56575531 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
56575459 ATCTAAAGTT
* *
56575469 TTAAAATTATAAAAAGATATAAATGAATA
1 TTAAAATGATAAAAAGAAATAAATGAATA
*
56575498 ATAAAATGATAAAATA-AAATAAAT-AATA
1 TTAAAATGATAAAA-AGAAATAAATGAATA
56575526 GTTAAA
1 -TTAAA
56575532 TATTAGGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
29 23 0.82
30 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (29 bp):
TTAAAATGATAAAAAGAAATAAATGAATA
Found at i:56575703 original size:79 final size:76
Alignment explanation
Indices: 56575603--56575750 Score: 183
Period size: 79 Copynumber: 1.9 Consensus size: 76
56575593 TCAAGGATAC
* *
56575603 AATAATATAATAATAATTAAATAAGCAT-AA-AAAAGAAAATATAATTATAGTAATAATAACATT
1 AATAATAGAATAATAATTAAATAA--ATAAATAAAAGAAAATATAATGATAGTAATAATAACATT
56575666 AAATTAACTAATTT
64 -AATTAACTAATTT
* * * *
56575680 AATAATAGAATGATAATGATAAATTAATAAATAAAAGAAAATATAATGATAGTAGTAATAATATT
1 AATAATAGAATAATAAT--TAAATAAATAAATAAAAGAAAATATAATGATAGTAATAATAACATT
56575745 AATTAA
64 AATTAA
56575751 TTTAGTAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
77 17 0.28
78 8 0.13
79 36 0.59
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (76 bp):
AATAATAGAATAATAATTAAATAAATAAATAAAAGAAAATATAATGATAGTAATAATAACATTAA
TTAACTAATTT
Found at i:56578682 original size:92 final size:95
Alignment explanation
Indices: 56578559--56578735 Score: 288
Period size: 92 Copynumber: 1.9 Consensus size: 95
56578549 TGTATGTGAC
* * *
56578559 AAGTTTGGGTAATTGTATTGTAAGTCTGGTAATACTCTGTAACCCTATTTCGGCATTGAATATGA
1 AAGTTTGGGTAATTGTATTGTAAGTCCGGTAATACTCTATAACCCTATTTCGGCATTGAATACGA
56578624 GTGAGG-GTGTTACA-TTTTATTGGTATCA
66 GTGAGGAGTGTTACACTTTTATTGGTATCA
**
56578652 AAGTTT-GGTAATTGTATTGTAAGTCCGGTAATACTCTATAACCCTATTTCGGTGTTGAATACGA
1 AAGTTTGGGTAATTGTATTGTAAGTCCGGTAATACTCTATAACCCTATTTCGGCATTGAATACGA
56578716 GTGAGGAGTGTTACACTTTT
66 GTGAGGAGTGTTACACTTTT
56578736 CTAGACAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
92 59 0.77
93 14 0.18
94 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (95 bp):
AAGTTTGGGTAATTGTATTGTAAGTCCGGTAATACTCTATAACCCTATTTCGGCATTGAATACGA
GTGAGGAGTGTTACACTTTTATTGGTATCA
Found at i:56585173 original size:23 final size:24
Alignment explanation
Indices: 56585147--56585196 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
56585137 CCTATACTTG
56585147 TGATGTATGAAATGTG-GTGAAAA
1 TGATGTATGAAATGTGTGTGAAAA
* * * *
56585170 TGATTTGTGATATGTGTGTTAAAA
1 TGATGTATGAAATGTGTGTGAAAA
56585194 TGA
1 TGA
56585197 GGTTAATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (24 bp):
TGATGTATGAAATGTGTGTGAAAA
Found at i:56586171 original size:27 final size:27
Alignment explanation
Indices: 56586141--56586226 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
56586131 ATGAATGCTT
56586141 GATGATTAAGCTGAAGATATTTGGTAA
1 GATGATTAAGCTGAAGATATTTGGTAA
* * * *
56586168 GATGA-TAA-CTTTAA-ATATGAATGCT-T
1 GATGATTAAGC-TGAAGATAT--TTGGTAA
56586194 GATGATTAAGCTGAAGATATTTGGTAA
1 GATGATTAAGCTGAAGATATTTGGTAA
56586221 GATGAT
1 GATGAT
56586227 AATCTTGGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 5 0.11
26 14 0.32
27 20 0.45
28 5 0.11
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (27 bp):
GATGATTAAGCTGAAGATATTTGGTAA
Found at i:56586185 original size:53 final size:53
Alignment explanation
Indices: 56586120--56586228 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
56586110 AGATATGGTC
56586120 TAACTTTAAATATGAATGCTTGATGATTAAGCTGAAGATATTTGGTAAGATGA
1 TAACTTTAAATATGAATGCTTGATGATTAAGCTGAAGATATTTGGTAAGATGA
56586173 TAACTTTAAATATGAATGCTTGATGATTAAGCTGAAGATATTTGGTAAGATGA
1 TAACTTTAAATATGAATGCTTGATGATTAAGCTGAAGATATTTGGTAAGATGA
56586226 TAA
1 TAA
56586229 TCTTGGTATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.36
Consensus pattern (53 bp):
TAACTTTAAATATGAATGCTTGATGATTAAGCTGAAGATATTTGGTAAGATGA
Found at i:56588568 original size:24 final size:24
Alignment explanation
Indices: 56588519--56588568 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
56588509 GGAGTTTCGA
*
56588519 TTTTTTTTTTAGCTCATTTAATTTTT
1 TTTTTTTTTTAG--CATTTAAGTTTT
56588545 TTTTTTTTTTAG-ATTTGAAGTTTT
1 TTTTTTTTTTAGCATTT-AAGTTTT
56588569 CTAAATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
26 12 0.55
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (24 bp):
TTTTTTTTTTAGCATTTAAGTTTT
Found at i:56590916 original size:46 final size:46
Alignment explanation
Indices: 56590863--56590955 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
56590853 CTTAATTGCA
* *
56590863 ATTAAGAGTTTTAGTTTTATTTATTTTCTTTATTATATCAGGTTTT
1 ATTAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTT
* *
56590909 ATTAAGAGTTTTGGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 ATTAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTT
56590955 A
1 A
56590956 ATTTCCTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (46 bp):
ATTAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTT
Found at i:56593124 original size:20 final size:19
Alignment explanation
Indices: 56593093--56593164 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
56593083 AATTACACCA
56593093 AAAATATTTAAAATAATTTT
1 AAAAT-TTTAAAATAATTTT
56593113 CAAAATTTTAAAATAATTTTT
1 -AAAATTTTAAAATAA-TTTT
*
56593134 AAAA-TTCAAAAT-ATTTAT
1 AAAATTTTAAAATAATTT-T
*
56593152 AAAATTTAAAAAT
1 AAAATTTTAAAAT
56593165 TCTAAAGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 14 0.30
20 14 0.30
21 9 0.20
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTTAAAATAATTTT
Found at i:56593146 original size:19 final size:19
Alignment explanation
Indices: 56593098--56593162 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 19
56593088 CACCAAAAAT
*
56593098 ATTTAAAATAATTTTCAAA
1 ATTTAAAATAATTTTTAAA
56593117 ATTTTAAAATAATTTTTAAA
1 A-TTTAAAATAATTTTTAAA
* *
56593137 ATTCAAAAT-ATTTATAAA
1 ATTTAAAATAATTTTTAAA
56593155 ATTTAAAA
1 ATTTAAAA
56593163 ATTCTAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 15 0.37
19 8 0.20
20 18 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTAAAATAATTTTTAAA
Found at i:56593154 original size:18 final size:19
Alignment explanation
Indices: 56593102--56593162 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
56593092 AAAAATATTT
*
56593102 AAAATAATTT-TCAAAATTTT
1 AAAATAATTTAT-AAAA-TTC
*
56593122 AAAATAATTTTTAAAATTC
1 AAAATAATTTATAAAATTC
*
56593141 AAAAT-ATTTATAAAATTT
1 AAAATAATTTATAAAATTC
56593159 AAAA
1 AAAA
56593163 ATTCTAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 15 0.41
19 7 0.19
20 14 0.38
21 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATAATTTATAAAATTC
Found at i:56594682 original size:20 final size:20
Alignment explanation
Indices: 56594645--56594684 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56594635 TAAAAAATAC
*
56594645 TTTTAAAAATATTTTTAAAT
1 TTTTAAAAATATTATTAAAT
56594665 TTTTAAAAA-ATTGATTAAAT
1 TTTTAAAAATATT-ATTAAAT
56594685 GTTATGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTAAAAATATTATTAAAT
Found at i:56597111 original size:19 final size:19
Alignment explanation
Indices: 56597073--56597126 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 19
56597063 ATATATTTGC
*
56597073 TAATGTATAAATGATTAATGA
1 TAATGTA-ATATG-TTAATGA
56597094 TAATGTAATATGTTAATGA
1 TAATGTAATATGTTAATGA
56597113 TAATGTAATATGTT
1 TAATGTAATATGTT
56597127 TGAATTCGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 21 0.66
20 4 0.12
21 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.43
Consensus pattern (19 bp):
TAATGTAATATGTTAATGA
Found at i:56597763 original size:32 final size:32
Alignment explanation
Indices: 56597719--56597784 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
56597709 TTTACTTTCC
* * *
56597719 ATTTAGCTCTCACGAGTTTCTATTTAACTCAT
1 ATTTAGCACTCACGAGCTTCGATTTAACTCAT
*
56597751 ATTTAGCACTCACGAGCTTCGGTTTAACTCAT
1 ATTTAGCACTCACGAGCTTCGATTTAACTCAT
56597783 AT
1 AT
56597785 GAGTTTCCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (32 bp):
ATTTAGCACTCACGAGCTTCGATTTAACTCAT
Found at i:56597866 original size:42 final size:42
Alignment explanation
Indices: 56597794--56597903 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 42
56597784 TGAGTTTCCG
* ** * * * *
56597794 TTCAACCCTAATGGGTTCCCGTTCAGCTCTTTTGAACTTCTG
1 TTCAACCCTTATGGGTTTTCATTCACCTCTTATGAACTTCTA
* **
56597836 TTTAACCCTTATGGGTTTTCATTCACCTCTTATGGGCTTCTA
1 TTCAACCCTTATGGGTTTTCATTCACCTCTTATGAACTTCTA
*
56597878 TTCAACCTTTATGGG-TTTCTATTCAC
1 TTCAACCCTTATGGGTTTTC-ATTCAC
56597904 TTATGTGCTT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.07
42 51 0.93
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (42 bp):
TTCAACCCTTATGGGTTTTCATTCACCTCTTATGAACTTCTA
Found at i:56597869 original size:21 final size:21
Alignment explanation
Indices: 56597843--56597903 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
56597833 CTGTTTAACC
56597843 CTTATGGGTTT-TCATTCACCT
1 CTTATGGGTTTCT-ATTCACCT
*
56597864 CTTATGGGCTTCTATTCAACCT
1 CTTATGGGTTTCTATTC-ACCT
56597886 -TTATGGGTTTCTATTCAC
1 CTTATGGGTTTCTATTCAC
56597904 TTATGTGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 29 0.81
22 5 0.14
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (21 bp):
CTTATGGGTTTCTATTCACCT
Found at i:56601532 original size:16 final size:16
Alignment explanation
Indices: 56601511--56601554 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
56601501 ATATTGATAA
56601511 ATTAAAAAATTAAAAC
1 ATTAAAAAATTAAAAC
** *
56601527 ATTAAATCATTAAATC
1 ATTAAAAAATTAAAAC
56601543 ATTAAAACAATT
1 ATTAAAA-AATT
56601555 TTATAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAAAAATTAAAAC
Found at i:56601537 original size:8 final size:8
Alignment explanation
Indices: 56601519--56601548 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56601509 AAATTAAAAA
*
56601519 ATTAAAAC
1 ATTAAATC
56601527 ATTAAATC
1 ATTAAATC
56601535 ATTAAATC
1 ATTAAATC
56601543 ATTAAA
1 ATTAAA
56601549 ACAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTAAATC
Found at i:56601751 original size:20 final size:20
Alignment explanation
Indices: 56601726--56601763 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56601716 TTACTTTCAA
56601726 AATTAAGTTTTGGCATAAGG
1 AATTAAGTTTTGGCATAAGG
* *
56601746 AATTAATTTTTGGTATAA
1 AATTAAGTTTTGGCATAA
56601764 AAAGATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (20 bp):
AATTAAGTTTTGGCATAAGG
Found at i:56602401 original size:21 final size:21
Alignment explanation
Indices: 56602377--56602484 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 21
56602367 CAAAACCATA
*
56602377 CAAAAAAAATTGAGGTAATAC
1 CAAAAAATATTGAGGTAATAC
*
56602398 CAAAAAATATT-ACAGT-ATAC
1 CAAAAAATATTGA-GGTAATAC
56602418 CAAAAAATA-TGAGG-AAGTAC
1 CAAAAAATATTGAGGTAA-TAC
* * *
56602438 C--AAAATTTTGAGGGAAAAC
1 CAAAAAATATTGAGGTAATAC
* **
56602457 C-AAAAATATAGAAGAAAATAC
1 CAAAAAATATTG-AGGTAATAC
56602478 CAAAAAA
1 CAAAAAA
56602485 ACATGAGAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
18 5 0.07
19 11 0.16
20 28 0.41
21 19 0.28
22 5 0.07
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (21 bp):
CAAAAAATATTGAGGTAATAC
Found at i:56602404 original size:19 final size:20
Alignment explanation
Indices: 56602380--56602442 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
56602370 AACCATACAA
56602380 AAAAAAT-TGAGGTAATACC
1 AAAAAATATGAGGTAATACC
* *
56602399 AAAAAATATTACAGT-ATACC
1 AAAAAATATGA-GGTAATACC
56602419 AAAAAATATGAGG-AAGTACC
1 AAAAAATATGAGGTAA-TACC
56602439 AAAA
1 AAAA
56602443 TTTTGAGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 9 0.25
20 25 0.69
21 2 0.06
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (20 bp):
AAAAAATATGAGGTAATACC
Found at i:56602581 original size:19 final size:20
Alignment explanation
Indices: 56602555--56602597 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
56602545 TCATGGATGC
*
56602555 ATACCAAAAAGTATGAGGAA
1 ATACAAAAAAGTATGAGGAA
*
56602575 ATACAAAAAATTATGAGGAA
1 ATACAAAAAAGTATGAGGAA
56602595 ATA
1 ATA
56602598 AATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (20 bp):
ATACAAAAAAGTATGAGGAA
Found at i:56602726 original size:20 final size:19
Alignment explanation
Indices: 56602676--56602732 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
56602666 TGAAAGTACA
*
56602676 AAAAATGATGAGCGAATAAC
1 AAAAATGATGAG-GGATAAC
*
56602696 AAACAA-CATGAGAGGATAAC
1 AAA-AATGATGAG-GGATAAC
56602716 AAAAATGATGAGGGATA
1 AAAAATGATGAGGGATA
56602733 CCAATTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 7 0.23
20 22 0.71
21 2 0.06
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (19 bp):
AAAAATGATGAGGGATAAC
Found at i:56602837 original size:106 final size:106
Alignment explanation
Indices: 56602652--56602864 Score: 399
Period size: 106 Copynumber: 2.0 Consensus size: 106
56602642 TATGAGGGAA
*
56602652 TACGAAAAAATATTTGAAAGTACAAAAAATGATGAGCGAATAACAAACAACATGAGAGGATAACA
1 TACGAAAAAATATTTGAAAGTACAAAAAATGATGAGAGAATAACAAACAACATGAGAGGATAACA
56602717 AAAATGATGAGGGATACCAATTTTTGGTTCTTCTAAATAAT
66 AAAATGATGAGGGATACCAATTTTTGGTTCTTCTAAATAAT
*
56602758 TACGAAAAAATATTTGAAAGTACAAAAAATTATGAGAGAATAACAAACAACATGAGAGGATAACA
1 TACGAAAAAATATTTGAAAGTACAAAAAATGATGAGAGAATAACAAACAACATGAGAGGATAACA
*
56602823 AAAATGGTGAGGGATACCAATTTTTGGTTCTTCTAAATAAT
66 AAAATGATGAGGGATACCAATTTTTGGTTCTTCTAAATAAT
56602864 T
1 T
56602865 TTTCCATTTA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (106 bp):
TACGAAAAAATATTTGAAAGTACAAAAAATGATGAGAGAATAACAAACAACATGAGAGGATAACA
AAAATGATGAGGGATACCAATTTTTGGTTCTTCTAAATAAT
Found at i:56603121 original size:22 final size:22
Alignment explanation
Indices: 56603069--56603124 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
56603059 AGGAATATCC
56603069 AAAATTATGAG-GAA-ATACAA
1 AAAATTATGAGAGAATATACAA
* *
56603089 AAAATTA--AGAGAATGTATAA
1 AAAATTATGAGAGAATATACAA
56603109 AAAATTATGAGAGAAT
1 AAAATTATGAGAGAAT
56603125 TGTTAGTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 18 0.60
22 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (22 bp):
AAAATTATGAGAGAATATACAA
Found at i:56605644 original size:43 final size:43
Alignment explanation
Indices: 56605597--56605685 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 43
56605587 GTAATTCGAT
* *
56605597 ATCGAAGCCTCTATCCCAGATAGGGTCTTACACGAAATCTCAA
1 ATCGAAGCCTCTATCCCAGACACGGTCTTACACGAAATCTCAA
* * * * * *
56605640 ATCGAGGCCTGTGTCCCAGACACGGTCTTACATGATATTTCAA
1 ATCGAAGCCTCTATCCCAGACACGGTCTTACACGAAATCTCAA
56605683 ATC
1 ATC
56605686 AAATTTGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
ATCGAAGCCTCTATCCCAGACACGGTCTTACACGAAATCTCAA
Found at i:56612744 original size:43 final size:43
Alignment explanation
Indices: 56612686--56612770 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
56612676 GTAATTCGAT
56612686 ATCGAAGCCTCTGTCCCAGACAAGGCCTTACACGAAATCTCAA
1 ATCGAAGCCTCTGTCCCAGACAAGGCCTTACACGAAATCTCAA
* * * * *
56612729 ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATCTCA
1 ATCGAAGCCTCTGTCCCAGACAAGGCCTTACACGAAATCTCA
56612771 GATCAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
ATCGAAGCCTCTGTCCCAGACAAGGCCTTACACGAAATCTCAA
Found at i:56617325 original size:47 final size:47
Alignment explanation
Indices: 56617271--56617558 Score: 414
Period size: 47 Copynumber: 6.1 Consensus size: 47
56617261 TTAGGATTTT
** *
56617271 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
56617318 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
56617365 ATGTGGTGAATATAAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
56617412 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* ** *
56617459 ATGTGATGAATGTGAGCATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
56617506 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
56617553 ATGTGA
1 ATGTGA
56617559 AATATATATA
Statistics
Matches: 212, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 212 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:56617373 original size:25 final size:25
Alignment explanation
Indices: 56617298--56617373 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
56617288 GTGTATATAT
56617298 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
56617323 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
56617345 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
56617370 GTGA
1 GTGA
56617374 ATATAAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:56617524 original size:141 final size:141
Alignment explanation
Indices: 56617270--56617558 Score: 488
Period size: 141 Copynumber: 2.0 Consensus size: 141
56617260 TTTAGGATTT
** *
56617270 TATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
* *
56617335 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATAAACATGCATATATGTGATAAG
66 ATACATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATAAACATGCATATATGTGATAAA
56617400 GCCGAATGGCC
131 GCCGAATGGCC
56617411 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
* * *
56617476 ATATATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGGTAAA
66 ATACATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATAAACATGCATATATGTGATAAA
*
56617541 GCCGAATGGTC
131 GCCGAATGGCC
*
56617552 AATGTGA
1 TATGTGA
56617559 AATATATATA
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.28
Consensus pattern (141 bp):
TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
ATACATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATAAACATGCATATATGTGATAAA
GCCGAATGGCC
Found at i:56617609 original size:94 final size:93
Alignment explanation
Indices: 56617291--56617614 Score: 366
Period size: 94 Copynumber: 3.4 Consensus size: 93
56617281 TGTGAATGTG
* * * * *
56617291 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCC
1 TATATATGTGATAAGGCCGAATGGCCTATGTG-TGAATATGAACATGCATATATGTGATAAAGCC
* * * *
56617356 GAATGGCCAATGTGGTGAATATAAACATG
65 GAATGGCCAATGTGATGAATATGAGCATA
* * *
56617385 CATATATGTGATAAGGCCGAATGGCCTATGTGATGAATGTGAACATGCATATATGTGATAAGGCC
1 TATATATGTGATAAGGCCGAATGGCCTATGTG-TGAATATGAACATGCATATATGTGATAAAGCC
*
56617450 GAATGGCCAATGTGATGAATGTGAGCATA
65 GAATGGCCAATGTGATGAATATGAGCATA
* * *
56617479 TATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGGTAAAGCC
1 TATATATGTGATAAGGCCGAATGGCCTATGT-GTGAATATGAACATGCATATATGTGATAAAGCC
* *
56617544 GAATGGTCAATGTGAAATATATATATGAG-ATA
65 GAATGGCCAATGTG--AT-GA-ATATGAGCATA
* * *
56617576 TGTATATGTGGTAAAGCCGAATGG-CTA-GTGTGAAATATG
1 TATATATGTGATAAGGCCGAATGGCCTATGTGTG-AATATG
56617615 TAGGCGATGT
Statistics
Matches: 201, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
94 158 0.79
95 9 0.04
96 4 0.02
97 24 0.12
98 6 0.03
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (93 bp):
TATATATGTGATAAGGCCGAATGGCCTATGTGTGAATATGAACATGCATATATGTGATAAAGCCG
AATGGCCAATGTGATGAATATGAGCATA
Found at i:56617908 original size:37 final size:37
Alignment explanation
Indices: 56617763--56617907 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
56617753 GGAAATATAT
*
56617763 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
56617800 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
56617837 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
56617874 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
56617908 TCGTCTGAGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:56623943 original size:20 final size:20
Alignment explanation
Indices: 56623919--56623976 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
56623909 CAAAAAAAAA
56623919 ATGAGGGAATACCAAAAATT
1 ATGAGGGAATACCAAAAATT
* * *
56623939 CTGA-GGAAGTTCCAAATATT
1 ATGAGGGAA-TACCAAAAATT
* *
56623959 ATGAGAGAATATCAAAAA
1 ATGAGGGAATACCAAAAA
56623977 AATCTGCAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (20 bp):
ATGAGGGAATACCAAAAATT
Found at i:56624032 original size:20 final size:20
Alignment explanation
Indices: 56624009--56624154 Score: 77
Period size: 20 Copynumber: 7.3 Consensus size: 20
56623999 GAGGATGTAT
56624009 AAAAAATTATGAGAGAATAC
1 AAAAAATTATGAGAGAATAC
* *
56624029 AAAAAAATATGAGGGAATAC
1 AAAAAATTATGAGAGAATAC
* * **
56624049 CAAAAACTCCGAG-GAAGTAC
1 AAAAAATTATGAGAGAA-TAC
* * * *
56624069 TAAAAGTTATGAGGGAATAT
1 AAAAAATTATGAGAGAATAC
* *
56624089 AAGAAAA-TCTGA-AAAATTAC
1 AA-AAAATTATGAGAGAA-TAC
* *
56624109 CAAAAA-TATGAG-GATGTACC
1 AAAAAATTATGAGAGA-ATA-C
*
56624129 AAAAAATTATAAGAGAATAC
1 AAAAAATTATGAGAGAATAC
56624149 AAAAAA
1 AAAAAA
56624155 AAATAGTGAG
Statistics
Matches: 92, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
19 16 0.17
20 61 0.66
21 13 0.14
22 2 0.02
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAAATTATGAGAGAATAC
Found at i:56624033 original size:118 final size:120
Alignment explanation
Indices: 56623902--56624158 Score: 360
Period size: 118 Copynumber: 2.1 Consensus size: 120
56623892 TGTTTCAACA
* * *
56623902 AGAATACCAAAAAAAAAATGAGGGAATACCAAAAATTCTGAGGAAGTTCCAAATA-TTATGAGAG
1 AGAATA-C-AAAAAAAAATGAGGGAATACCAAAAACTCCGAGGAAGTACCAAA-AGTTATGAGAG
* * *
56623966 AATATCAAAAAAATCTGCAAAATTACC-AAAA-ATGAGGATGTA-TAAAAAATTATGAG
63 AATAT-AAAAAAATCTGAAAAATTACCAAAAATATGAGGATGTACCAAAAAATTATAAG
* * *
56624022 AGAATACAAAAAAATATGAGGGAATACCAAAAACTCCGAGGAAGTACTAAAAGTTATGAGGGAAT
1 AGAATACAAAAAAAAATGAGGGAATACCAAAAACTCCGAGGAAGTACCAAAAGTTATGAGAGAAT
*
56624087 ATAAGAAAATCTGAAAAATTACCAAAAATATGAGGATGTACCAAAAAATTATAAG
66 ATAAAAAAATCTGAAAAATTACCAAAAATATGAGGATGTACCAAAAAATTATAAG
56624142 AGAATACAAAAAAAAAT
1 AGAATACAAAAAAAAAT
56624159 AGTGAGAGAA
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
117 20 0.16
118 56 0.46
119 12 0.10
120 34 0.28
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (120 bp):
AGAATACAAAAAAAAATGAGGGAATACCAAAAACTCCGAGGAAGTACCAAAAGTTATGAGAGAAT
ATAAAAAAATCTGAAAAATTACCAAAAATATGAGGATGTACCAAAAAATTATAAG
Found at i:56624054 original size:40 final size:41
Alignment explanation
Indices: 56624010--56624155 Score: 90
Period size: 40 Copynumber: 3.7 Consensus size: 41
56624000 AGGATGTATA
56624010 AAAAATTATGAGAGAA-TACAAAAAAATATGAGGGAATACC
1 AAAAATTATGAGAGAAGTACAAAAAAATATGAGGGAATACC
* ** * ** *
56624050 AAAAACTCCGAG-GAAGTACTAAAAGTTATGAGGGAATA-T
1 AAAAATTATGAGAGAAGTACAAAAAAATATGAGGGAATACC
* * * * * *
56624089 AAGAAAATCTGA-AAAATTAC-CAAAAATATGA-GGATGTACC
1 AA-AAATTATGAGAGAAGTACAAAAAAATATGAGGGA-ATACC
*
56624129 AAAAAATTATAAGAGAA-TACAAAAAAA
1 -AAAAATTATGAGAGAAGTACAAAAAAA
56624156 AATAGTGAGA
Statistics
Matches: 77, Mismatches: 21, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
38 3 0.04
39 15 0.19
40 49 0.64
41 10 0.13
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.18
Consensus pattern (41 bp):
AAAAATTATGAGAGAAGTACAAAAAAATATGAGGGAATACC
Found at i:56624110 original size:60 final size:57
Alignment explanation
Indices: 56623928--56624155 Score: 183
Period size: 60 Copynumber: 3.8 Consensus size: 57
56623918 AATGAGGGAA
* * *
56623928 TACCAAAAATTCTGAGGAAGTTCCAAATATTATGAGAGAATATCAAAAAAATCTGCAAAAT
1 TACCAAAAA-TC-GAGGAAGTACTAAA-ATTATGAGAGAATAT-AAAAAAATCTGAAAAAT
* * * **
56623989 TACCAAAAAT-GAGGATGTA-TAAAAAATTATGAGAGAATACAAAAAAATATGAGGGAA-
1 TACCAAAAATCGAGGAAGTACT--AAAATTATGAGAGAATATAAAAAAATCTGA-AAAAT
* *
56624046 TACCAAAAACTCCGAGGAAGTACTAAAAGTTATGAGGGAATATAAGAAAATCTGAAAAAT
1 TACCAAAAA-T-CGAGGAAGTACTAAAA-TTATGAGAGAATATAAAAAAATCTGAAAAAT
* * * * *
56624106 TACCAAAAATATGAGGATGTACCAAAAAATTATAAGAGAATACAAAAAAA
1 TACCAAAAAT-CGAGGAAGTA-C-TAAAATTATGAGAGAATATAAAAAAA
56624156 AATAGTGAGA
Statistics
Matches: 133, Mismatches: 23, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
57 19 0.14
58 24 0.18
59 18 0.14
60 58 0.44
61 14 0.11
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.21
Consensus pattern (57 bp):
TACCAAAAATCGAGGAAGTACTAAAATTATGAGAGAATATAAAAAAATCTGAAAAAT
Found at i:56624659 original size:17 final size:17
Alignment explanation
Indices: 56624637--56624670 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56624627 TATTGAAAAC
56624637 TGTGAGGAAATACCACA
1 TGTGAGGAAATACCACA
56624654 TGTGAGGAAATACCACA
1 TGTGAGGAAATACCACA
56624671 AATTTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (17 bp):
TGTGAGGAAATACCACA
Found at i:56624686 original size:20 final size:20
Alignment explanation
Indices: 56624661--56624713 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
56624651 ACATGTGAGG
* *
56624661 AAATACCACAAATTTTAAGA
1 AAATACCAAAAATTCTAAGA
56624681 AAATACCAAAAATTCTAAGA
1 AAATACCAAAAATTCTAAGA
* *
56624701 GAATATCAAAAAT
1 AAATACCAAAAAT
56624714 ATTTGAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (20 bp):
AAATACCAAAAATTCTAAGA
Found at i:56625140 original size:21 final size:21
Alignment explanation
Indices: 56625019--56625193 Score: 79
Period size: 20 Copynumber: 8.8 Consensus size: 21
56625009 TTTTTAAAAC
* *
56625019 AATACCAAAAATTATAAG-GG
1 AATACCAAAAATTATGAGTGA
* *
56625039 AATA-CAAAAAATGTGAG-GA
1 AATACCAAAAATTATGAGTGA
** ** *
56625058 AGCACCAAAAAAAATGAG-GT
1 AATACCAAAAATTATGAGTGA
** *
56625078 AATATAAAAAATTATGA-TGG
1 AATACCAAAAATTATGAGTGA
*
56625098 AATATCAAAAA--ATGCAAG-GA
1 AATACCAAAAATTATG--AGTGA
*
56625118 AATACTAAAAATTATGAGTGA
1 AATACCAAAAATTATGAGTGA
*
56625139 AATACCAAAAATTATGAAT-A
1 AATACCAAAAATTATGAGTGA
* *
56625159 AGTACCAAAAA--A--AGAGA
1 AATACCAAAAATTATGAGTGA
56625176 TAATACCAAAAATTATGA
1 -AATACCAAAAATTATGA
56625194 TAGGTTATCA
Statistics
Matches: 115, Mismatches: 26, Indels: 26
0.69 0.16 0.16
Matches are distributed among these distances:
16 1 0.01
17 1 0.01
18 14 0.12
19 13 0.11
20 63 0.55
21 19 0.17
22 4 0.03
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (21 bp):
AATACCAAAAATTATGAGTGA
Found at i:56625164 original size:20 final size:19
Alignment explanation
Indices: 56625118--56625193 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 19
56625108 AATGCAAGGA
* *
56625118 AATACTAAAAATTATGAGT
1 AATACCAAAAATTATGAAT
56625137 GAAATACCAAAAATTATGAAT
1 --AATACCAAAAATTATGAAT
*
56625158 AAGTACCAAAAA--AAGAGAT
1 AA-TACCAAAAATTATGA-AT
56625177 AATACCAAAAATTATGA
1 AATACCAAAAATTATGA
56625194 TAGGTTATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 12 0.26
19 6 0.13
20 12 0.26
21 17 0.36
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (19 bp):
AATACCAAAAATTATGAAT
Found at i:56625514 original size:23 final size:24
Alignment explanation
Indices: 56625488--56625536 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
56625478 TGTGTATACT
*
56625488 AAAAAATTCTAAAAATAT-ATAAA
1 AAAAAATTATAAAAATATAATAAA
* *
56625511 AAAAAATTATGAAGATATAATAAA
1 AAAAAATTATAAAAATATAATAAA
56625535 AA
1 AA
56625537 TATGAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAATTATAAAAATATAATAAA
Found at i:56625540 original size:19 final size:18
Alignment explanation
Indices: 56625497--56625556 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
56625487 TAAAAAATTC
*
56625497 TAAAAATAT-ATAAA-AA
1 TAAAAATATGAAAAATAA
* *
56625513 -AAAATTATGAAGATATAA
1 TAAAAATATGAA-AAATAA
*
56625531 TAAAAATATGAAAAATAC
1 TAAAAATATGAAAAATAA
56625549 TAAAAATA
1 TAAAAATA
56625557 AGAGAGATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 2 0.06
18 14 0.41
19 10 0.29
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (18 bp):
TAAAAATATGAAAAATAA
Found at i:56625602 original size:19 final size:20
Alignment explanation
Indices: 56625580--56625633 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
56625570 AGATTATAAG
*
56625580 ATATATTAATTATTATG-AA
1 ATATATAAATTATTATGAAA
**
56625599 ATATATAAAAAATTATGAAA
1 ATATATAAATTATTATGAAA
*
56625619 ATATATCAATTATTA
1 ATATATAAATTATTA
56625634 ACTTATAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
ATATATAAATTATTATGAAA
Found at i:56627041 original size:6 final size:6
Alignment explanation
Indices: 56627030--56627056 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56627020 AAAAGCATTT
56627030 AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AAT
56627057 CATCATTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:56627534 original size:72 final size:71
Alignment explanation
Indices: 56627448--56627629 Score: 195
Period size: 71 Copynumber: 2.5 Consensus size: 71
56627438 AATAATGAAT
* * **
56627448 TGTGCCCTGAGCTAG-CTGGTAAAACTGACAAATGAGTGTACCAAGCACTAATTGGTATAACTGA
1 TGTGCCCTGCGCTAGTC-GGTAAAACTGA-AAATGAGTGTACCAAGCACTAATTGATATAACCAA
56627512 CAAATAAA
64 CAAATAAA
* ** ** * **
56627520 TGTGCCTTGCGCTAGTCGGTAAAACCAAAAATGAGTGTGTCTAGCACTGGTTGATATAACCAACA
1 TGTGCCCTGCGCTAGTCGGTAAAACTGAAAATGAGTGTACCAAGCACTAATTGATATAACCAACA
56627585 AATAAA
66 AATAAA
* * *
56627591 TGCGCCCTACGCTGGTCGGTAAAACTGAAACATGAGTGT
1 TGTGCCCTGCGCTAGTCGGTAAAACTGAAA-ATGAGTGT
56627630 TCATTCATTC
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
71 59 0.66
72 30 0.33
73 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (71 bp):
TGTGCCCTGCGCTAGTCGGTAAAACTGAAAATGAGTGTACCAAGCACTAATTGATATAACCAACA
AATAAA
Found at i:56628152 original size:107 final size:107
Alignment explanation
Indices: 56628025--56628227 Score: 352
Period size: 107 Copynumber: 1.9 Consensus size: 107
56628015 TCAGCTATAG
56628025 AAAAACACTTATTCGCCTATAATATCAACATTAAAATCGACATAAACACTTATTTAATCCGAACA
1 AAAAACACTTATTCGCCTATAATATCAACATTAAAATCGACATAAACACTTATTTAATCCGAACA
56628090 TTTAATTTAACAAAAACATAATAGAAATGTCTAGCTTTGGAA
66 TTTAATTTAACAAAAACATAATAGAAATGTCTAGCTTTGGAA
* ** *
56628132 AAAAACACTTATTCGCCTATAATATCAGCATTAAAATTTACATAAACACTTATTTAATCCTAACA
1 AAAAACACTTATTCGCCTATAATATCAACATTAAAATCGACATAAACACTTATTTAATCCGAACA
* *
56628197 TTTAATTTAACATAAACATTATAGAAATGTC
66 TTTAATTTAACAAAAACATAATAGAAATGTC
56628228 CTCAACTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 90 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (107 bp):
AAAAACACTTATTCGCCTATAATATCAACATTAAAATCGACATAAACACTTATTTAATCCGAACA
TTTAATTTAACAAAAACATAATAGAAATGTCTAGCTTTGGAA
Found at i:56628214 original size:18 final size:18
Alignment explanation
Indices: 56628166--56628268 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 18
56628156 TCAGCATTAA
*
56628166 AATTT-ACATAAACACTT
1 AATTTAACATAAACATTT
*
56628183 -ATTTAATCCT-AACATTT
1 AATTTAA-CATAAACATTT
56628200 AATTTAACATAAACATTAT
1 AATTTAACATAAACATT-T
* *
56628219 AGAAATGTCCTCAACTTTAACATTT
1 ---AAT-T--T-AACATAAACATTT
56628244 AATTTAACATAAACATTT
1 AATTTAACATAAACATTT
*
56628262 AAGTTAA
1 AATTTAA
56628269 TCATTTAACA
Statistics
Matches: 66, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
16 4 0.06
17 9 0.14
18 31 0.47
19 2 0.03
21 1 0.02
22 6 0.09
23 1 0.02
25 2 0.03
26 10 0.15
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTTAACATAAACATTT
Found at i:56631955 original size:36 final size:36
Alignment explanation
Indices: 56631907--56632006 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 36
56631897 AGCTAGCTAG
* *
56631907 TAAAACCAACAAATGAGTGTGCCTAGCACTGGCCGG
1 TAAAACCGACAAATGAGTGTGCCTAGCACTGGCCGA
* * * * * *
56631943 TATAACTGACAAATAAATGTGTCCT-GCGCTGGTCGA
1 TAAAACCGACAAATGAGTGTG-CCTAGCACTGGCCGA
* *
56631979 TAAAACCGAAAAATGAGTGTGCCCAGCA
1 TAAAACCGACAAATGAGTGTGCCTAGCA
56632007 TTGGTTGATA
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
35 2 0.04
36 42 0.89
37 3 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (36 bp):
TAAAACCGACAAATGAGTGTGCCTAGCACTGGCCGA
Found at i:56632041 original size:72 final size:72
Alignment explanation
Indices: 56631907--56632070 Score: 168
Period size: 72 Copynumber: 2.3 Consensus size: 72
56631897 AGCTAGCTAG
* * ** *** *
56631907 TAAAACC-AACAAATGAGTGTGCCTAGCACTGGCCGGTATAACTGACAAATAAATGTGTCCTGCG
1 TAAAACCGAA-AAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCA
**
56631971 CTGGTCGA
65 CTAATCGA
* **
56631979 TAAAACCGAAAAATGAGTGTGCCCAGCATTGGTTGATATAACCAACAAATAAATGCACCCTGCAC
1 TAAAACCGAAAAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCAC
*
56632044 TAATCGG
66 TAATCGA
* *
56632051 TAAAACTGACAAATGAGTGT
1 TAAAACCGAAAAATGAGTGT
56632071 TCATTCATTC
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 73 0.97
73 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (72 bp):
TAAAACCGAAAAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCAC
TAATCGA
Found at i:56632639 original size:107 final size:105
Alignment explanation
Indices: 56632455--56632673 Score: 348
Period size: 107 Copynumber: 2.1 Consensus size: 105
56632445 TTAGATATAA
* *
56632455 CCAGCTTTAGAAAAACACTTATTTAGCTATAATATCAGCAATAAAATTGACATAAACAATTATTT
1 CCAGCTTTAGAAAAACACTTATTCACCTATAATATCAGCAATAAAATTGACATAAACAATTATTT
*
56632520 AATCCTAACATTTAATTTAACATAAACATAATAGAAATGT
66 AATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
* * * *
56632560 CCAGCTTTGGAAAAATACACTTATTCACCTATAATATCAGCATTAAAATTTACATAAACACTTAT
1 CCAGCTTTAG-AAAA-ACACTTATTCACCTATAATATCAGCAATAAAATTGACATAAACAATTAT
56632625 TTAATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
64 TTAATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
*
56632667 CTAGCTT
1 CCAGCTT
56632674 GGACAACACT
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 9 0.09
106 4 0.04
107 91 0.88
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.33
Consensus pattern (105 bp):
CCAGCTTTAGAAAAACACTTATTCACCTATAATATCAGCAATAAAATTGACATAAACAATTATTT
AATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
Found at i:56632761 original size:22 final size:22
Alignment explanation
Indices: 56632702--56632763 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
56632692 GCTTTAGATG
*
56632702 ACATTTAGAACATATTTTGGACA
1 ACATTTA-AACATACTTTGGACA
56632725 ACATTTAAA-AGTACTTT-GACA
1 ACATTTAAACA-TACTTTGGACA
*
56632746 GCATTTGAAACATACTTT
1 ACATTT-AAACATACTTT
56632764 TGCTAGCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 10 0.29
22 16 0.47
23 8 0.24
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
ACATTTAAACATACTTTGGACA
Found at i:56646967 original size:15 final size:15
Alignment explanation
Indices: 56646949--56646980 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56646939 AAATCGAGTA
56646949 AATTAATTTGATGCT
1 AATTAATTTGATGCT
56646964 AATTAATTTGATGCT
1 AATTAATTTGATGCT
56646979 AA
1 AA
56646981 CCTGAATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (15 bp):
AATTAATTTGATGCT
Found at i:56647605 original size:5 final size:5
Alignment explanation
Indices: 56647595--56647619 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56647585 ACTCAATTAA
56647595 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
56647620 TATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:56648431 original size:34 final size:34
Alignment explanation
Indices: 56648391--56648458 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
56648381 TAATCAATAT
56648391 TTAAAGTGTAAGTTAATTGATTTAAGAAGAAGCG
1 TTAAAGTGTAAGTTAATTGATTTAAGAAGAAGCG
*
56648425 TTAAAGTGTAAGTTATTTGATTTAAGAAGAAGCG
1 TTAAAGTGTAAGTTAATTGATTTAAGAAGAAGCG
56648459 GTTATGAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (34 bp):
TTAAAGTGTAAGTTAATTGATTTAAGAAGAAGCG
Found at i:56648935 original size:28 final size:29
Alignment explanation
Indices: 56648881--56648936 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
56648871 CTGAGACAAA
* *
56648881 TTAATATTTTTATTATTAAATAGATTAAT
1 TTAATATTTTTATTATTAAAAAAATTAAT
56648910 TTAAT-TTTTTATTATTAAAAAAATTAA
1 TTAATATTTTTATTATTAAAAAAATTAA
56648937 ATGATGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAATATTTTTATTATTAAAAAAATTAAT
Found at i:56651224 original size:40 final size:40
Alignment explanation
Indices: 56651155--56651331 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
56651145 ACCCAAGTAT
*
56651155 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
56651194 CTTCGGGTCTTAGCCCAGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
56651234 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
56651274 CTTCAGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
56651314 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
56651332 TTATCATCCG
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 100 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:56653920 original size:25 final size:24
Alignment explanation
Indices: 56653867--56653931 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
56653857 TTTTCCCTCA
* *
56653867 TATTATTTATTTTAAATTGTTTCAT
1 TATTATTTATTTT-AATGGTTTCAG
56653892 TATTATTTATTTTAA-GGCTTTCACG
1 TATTATTTATTTTAATGG-TTTCA-G
*
56653917 TATTATGTATTTTAA
1 TATTATTTATTTTAA
56653932 ACTATTATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 7 0.20
25 27 0.77
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (24 bp):
TATTATTTATTTTAATGGTTTCAG
Found at i:56654128 original size:26 final size:26
Alignment explanation
Indices: 56654095--56654155 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
56654085 CTTTTATATG
56654095 TTATTTTAAAAT-ATTATATATATTAT
1 TTATTTTAAAATGATT-TATATATTAT
** * *
56654121 TTATTTTAACTTGCTTTGTATATTAT
1 TTATTTTAAAATGATTTATATATTAT
56654147 TTATTTTAA
1 TTATTTTAA
56654156 TTTGTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAAATGATTTATATATTAT
Found at i:56654174 original size:26 final size:26
Alignment explanation
Indices: 56654113--56654176 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
56654103 AAATATTATA
*
56654113 TATATTATTTATTTTAACTTGCTTTG
1 TATATCATTTATTTTAACTTGCTTTG
* *
56654139 TATATTATTTATTTTAATTTG-TTT-
1 TATATCATTTATTTTAACTTGCTTTG
56654163 TACGTATCATTTAT
1 TA--TATCATTTAT
56654177 CTCAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 29 0.85
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (26 bp):
TATATCATTTATTTTAACTTGCTTTG
Found at i:56661648 original size:24 final size:24
Alignment explanation
Indices: 56661635--56661745 Score: 114
Period size: 24 Copynumber: 4.6 Consensus size: 24
56661625 ATTATTCTGT
*
56661635 CCAAGAGACTGCCCAACATTCGGC
1 CCAACAGACTGCCCAACATTCGGC
56661659 CCAACAGACTGCCCAACATTCGGC
1 CCAACAGACTGCCCAACATTCGGC
** * * *
56661683 TTAATAGACTGCCCAGCATTCAGC
1 CCAACAGACTGCCCAACATTCGGC
* * * * *
56661707 CTAACAGACTACCCAGCATGCGGT
1 CCAACAGACTGCCCAACATTCGGC
*
56661731 CCAAGAGACTGCCCA
1 CCAACAGACTGCCCA
56661746 GGAATCTGCT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.30, C:0.36, G:0.19, T:0.15
Consensus pattern (24 bp):
CCAACAGACTGCCCAACATTCGGC
Found at i:56661740 original size:48 final size:48
Alignment explanation
Indices: 56661633--56661746 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 48
56661623 CCATTATTCT
* * * *
56661633 GTCCAAGAGACTGCCCAACATTCGGCCCAACAGACTGCCCAACATTCG
1 GTCCAAGAGACTGCCCAGCATTCAGCCCAACAGACTACCCAACATGCG
* * * *
56661681 G-CTTAATAGACTGCCCAGCATTCAGCCTAACAGACTACCCAGCATGCG
1 GTC-CAAGAGACTGCCCAGCATTCAGCCCAACAGACTACCCAACATGCG
56661729 GTCCAAGAGACTGCCCAG
1 GTCCAAGAGACTGCCCAG
56661747 GAATCTGCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.29, C:0.35, G:0.20, T:0.16
Consensus pattern (48 bp):
GTCCAAGAGACTGCCCAGCATTCAGCCCAACAGACTACCCAACATGCG
Found at i:56672060 original size:15 final size:16
Alignment explanation
Indices: 56672034--56672063 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56672024 TGTTTAAAAA
56672034 TTTTAAAGAAAATTAT
1 TTTTAAAGAAAATTAT
56672050 TTTTAAA-AAAATTA
1 TTTTAAAGAAAATTA
56672064 CATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTTAAAGAAAATTAT
Found at i:56675979 original size:40 final size:40
Alignment explanation
Indices: 56675878--56676098 Score: 250
Period size: 40 Copynumber: 5.5 Consensus size: 40
56675868 TATTCGAATG
* * *
56675878 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGACT
* * *
56675919 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
56675959 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * *
56675999 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * **
56676039 ATATCCAGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
56676078 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
56676099 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 25, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 13 0.08
39 16 0.10
40 96 0.62
41 28 0.18
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:56683982 original size:40 final size:40
Alignment explanation
Indices: 56683879--56684075 Score: 234
Period size: 40 Copynumber: 4.9 Consensus size: 40
56683869 TATTCAAATG
* * *
56683879 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGACT
* * * *
56683920 ATATCCGGACTAAGATCTGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
56683960 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
56684000 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
*
56684040 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
56684076 GTTATATTAG
Statistics
Matches: 131, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 9 0.07
40 95 0.73
41 27 0.21
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:56690536 original size:30 final size:30
Alignment explanation
Indices: 56690490--56690549 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
56690480 TTCCCGAGCC
* *
56690490 TAGGGGTAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
56690520 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
56690550 CATATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:56692983 original size:21 final size:21
Alignment explanation
Indices: 56692959--56692998 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
56692949 AAACTTGTAT
56692959 AACTATCATCACAT-ATTAATA
1 AACTATCATCA-ATCATTAATA
56692980 AACTATCATCAATCATTAA
1 AACTATCATCAATCATTAA
56692999 AATACATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
AACTATCATCAATCATTAATA
Found at i:56699364 original size:27 final size:26
Alignment explanation
Indices: 56699334--56699386 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
56699324 GACCAAAATA
*
56699334 CCCCTAAAGGGTAAAATGACTGTTTTG
1 CCCCTAAAGGGT-AAATGACTGATTTG
**
56699361 CCCCTCGAGGGTAAATGACTGATTTG
1 CCCCTAAAGGGTAAATGACTGATTTG
56699387 TCTGTGACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (26 bp):
CCCCTAAAGGGTAAATGACTGATTTG
Found at i:56701059 original size:40 final size:39
Alignment explanation
Indices: 56701003--56701135 Score: 112
Period size: 37 Copynumber: 3.4 Consensus size: 39
56700993 ACACCAGTTC
* *
56701003 GACACCCAGTGCCTCATCGAATAATTCGAAGTAATAAATT
1 GACACCTAGTGTCTCATCGAATAA-TCGAAGTAATAAATT
* *
56701043 GACACCTAATGTCTCATC-AGCTGAATCGAAG---TAAATT
1 GACACCTAGTGTCTCATCGA-AT-AATCGAAGTAATAAATT
* * * * ** *
56701080 GGCACCTAGTGCCTCATCGAATTACCGAAGTAATTGACT
1 GACACCTAGTGTCTCATCGAATAATCGAAGTAATAAATT
56701119 GACACCTAGTGTCTCAT
1 GACACCTAGTGTCTCAT
56701136 AGACTCGAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
36 6 0.08
37 22 0.31
38 1 0.01
39 19 0.26
40 22 0.31
41 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
GACACCTAGTGTCTCATCGAATAATCGAAGTAATAAATT
Found at i:56701974 original size:6 final size:6
Alignment explanation
Indices: 56701963--56701991 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56701953 TTTTTTCTTT
56701963 CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
56701992 TGTTTCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:56714233 original size:28 final size:28
Alignment explanation
Indices: 56714201--56714269 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
56714191 AAATACAGTG
* *
56714201 TATACAGTAACAGTCTGGGCCTTAGCCC
1 TATACAGTAACAGTCTGGGACTAAGCCC
** *
56714229 TATACAAAAACAGTGTGGGACTAAGCCC
1 TATACAGTAACAGTCTGGGACTAAGCCC
* *
56714257 -AAACAGTATCAGT
1 TATACAGTAACAGT
56714270 ACAGTGCAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (28 bp):
TATACAGTAACAGTCTGGGACTAAGCCC
Found at i:56714462 original size:27 final size:27
Alignment explanation
Indices: 56714423--56714488 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
56714413 AGCATAGCTG
* *
56714423 CCAAAAACGGTAAATATGACAAAGCCA
1 CCAATAACAGTAAATATGACAAAGCCA
* * * * *
56714450 CCAGTAACAGTAATTGTGGCATAGCCA
1 CCAATAACAGTAAATATGACAAAGCCA
56714477 CCAATAACAGTA
1 CCAATAACAGTA
56714489 CTTCATCCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (27 bp):
CCAATAACAGTAAATATGACAAAGCCA
Found at i:56714642 original size:26 final size:27
Alignment explanation
Indices: 56714609--56714694 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
56714599 ACATACAGAA
56714609 CATA-AGGGCATAAT-CA-TCATTTTAC
1 CATACAGGG-ATAATACAGTCATTTTAC
* *
56714634 CATACAGGGGTATTACAGTCATTTTAC
1 CATACAGGGATAATACAGTCATTTTAC
* * * **
56714661 CCTACAGGGGTATTATGGTCATTTTAC
1 CATACAGGGATAATACAGTCATTTTAC
*
56714688 CCTACAG
1 CATACAG
56714695 AGGTATTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
25 7 0.13
26 6 0.11
27 40 0.75
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (27 bp):
CATACAGGGATAATACAGTCATTTTAC
Found at i:56714656 original size:27 final size:27
Alignment explanation
Indices: 56714625--56714740 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
56714615 GGCATAATCA
56714625 TCATTTTACCATACAGGGGTATTACAG
1 TCATTTTACCATACAGGGGTATTACAG
* **
56714652 TCATTTTACCCTACAGGGGTATTATGG
1 TCATTTTACCATACAGGGGTATTACAG
* * **
56714679 TCATTTTACCCTACAGAGGTATTATGG
1 TCATTTTACCATACAGGGGTATTACAG
* * *
56714706 TCATTTTA-CAAACTGGGGGTATTTCAG
1 TCATTTTACCATAC-AGGGGTATTACAG
*
56714733 TAATTTTA
1 TCATTTTA
56714741 AAATTTGAGG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
26 3 0.04
27 73 0.96
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (27 bp):
TCATTTTACCATACAGGGGTATTACAG
Found at i:56714725 original size:54 final size:54
Alignment explanation
Indices: 56714625--56714728 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
56714615 GGCATAATCA
* **
56714625 TCATTTTACCATACAGGGGTATTACAGTCATTTTACCCTACAGGGGTATTATGG
1 TCATTTTACCATACAGAGGTATTACAGTCATTTTACCAAACAGGGGTATTATGG
* ** *
56714679 TCATTTTACCCTACAGAGGTATTATGGTCATTTTA-CAAACTGGGGGTATT
1 TCATTTTACCATACAGAGGTATTACAGTCATTTTACCAAAC-AGGGGTATT
56714729 TCAGTAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 3 0.07
54 39 0.93
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (54 bp):
TCATTTTACCATACAGAGGTATTACAGTCATTTTACCAAACAGGGGTATTATGG
Found at i:56719012 original size:30 final size:30
Alignment explanation
Indices: 56718978--56719074 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
56718968 TAAACTAAAA
56718978 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
56719008 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
56719038 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
56719068 TGAGCTA
1 TGAGCTA
56719075 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:56721257 original size:30 final size:30
Alignment explanation
Indices: 56721186--56721268 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
56721176 CTTTTGTTTC
* *
56721186 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
56721217 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
56721246 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
56721269 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:56721268 original size:18 final size:18
Alignment explanation
Indices: 56721219--56721274 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56721209 CACTCTCAAA
* *
56721219 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
56721236 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
56721254 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
56721273 TT
1 TT
56721275 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:56721275 original size:12 final size:12
Alignment explanation
Indices: 56721244--56721268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56721234 TTTTTCAATC
56721244 TCATTTTCTTTT
1 TCATTTTCTTTT
56721256 TCATTTTCTTTT
1 TCATTTTCTTTT
56721268 T
1 T
56721269 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:56721286 original size:12 final size:12
Alignment explanation
Indices: 56721271--56721301 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56721261 TTCTTTTTGC
56721271 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56721283 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56721295 TTTTCAA
1 TTTTCAA
56721302 CACTCGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:56727188 original size:49 final size:50
Alignment explanation
Indices: 56727111--56727288 Score: 250
Period size: 52 Copynumber: 3.5 Consensus size: 50
56727101 ACTAGTGACT
** *
56727111 CAAGTGTGGTACTATGTGAAGGTAACTTTGAGAAG-AGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
*
56727160 AAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGC-TTGGTCA
* *
56727212 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTC-A
* *
56727263 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
56727289 GGGGTATTCG
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
49 31 0.27
50 4 0.03
51 40 0.34
52 41 0.35
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (50 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
Done.