Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 176 of 230
Found at i:52691719 original size:20 final size:23
Alignment explanation
Indices: 52691689--52691733 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
52691679 AGAAAAAGAG
52691689 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
52691710 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
52691732 AA
1 AA
52691734 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:52695100 original size:35 final size:32
Alignment explanation
Indices: 52694931--52695090 Score: 239
Period size: 32 Copynumber: 4.9 Consensus size: 32
52694921 AGAAATGACA
* *
52694931 CATTTCTTACAGGGAATCTTTCCTGTTCACGT
1 CATTTCTTGCAGGGAATCTCTCCTGTTCACGT
52694963 CATTTCTTGCAGGGAATCTCTCCTGTTCACGT
1 CATTTCTTGCAGGGAATCTCTCCTGTTCACGT
*
52694995 CATTTCTTGCAGGGAATCTCTCATGTTCACGT
1 CATTTCTTGCAGGGAATCTCTCCTGTTCACGT
52695027 CATTTCTTGCAGGGAATCTCTCCTGTTCACGCAT
1 CATTTCTTGCAGGGAATCTCTCCTGTTCACG--T
* * *
52695061 TATTTTGTTGCAGGGAATCTTTCCTGTTCA
1 CA-TTTCTTGCAGGGAATCTCTCCTGTTCA
52695091 TGTATTATTT
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
32 91 0.77
34 2 0.02
35 25 0.21
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (32 bp):
CATTTCTTGCAGGGAATCTCTCCTGTTCACGT
Found at i:52697098 original size:20 final size:18
Alignment explanation
Indices: 52697048--52697099 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
52697038 CTACAAGATA
52697048 AACATTAAATTAA-ATTT
1 AACATTAAATTAATATTT
52697065 AACATTAAGA-TAATCACTTT
1 AACATTAA-ATTAAT-A-TTT
*
52697085 AATATTAAATTAATA
1 AACATTAAATTAATA
52697100 AAATACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (18 bp):
AACATTAAATTAATATTT
Found at i:52704089 original size:21 final size:21
Alignment explanation
Indices: 52704065--52704104 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52704055 GATTTAAAAT
52704065 TGAAATTAGTAAAT-AAATAAA
1 TGAAA-TAGTAAATGAAATAAA
*
52704086 TGAAATATTAAATGAAATA
1 TGAAATAGTAAATGAAATA
52704105 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (21 bp):
TGAAATAGTAAATGAAATAAA
Found at i:52704097 original size:12 final size:12
Alignment explanation
Indices: 52704082--52704110 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
52704072 AGTAAATAAA
52704082 TAAATGAAATAT
1 TAAATGAAATAT
52704094 TAAATGAAATAT
1 TAAATGAAATAT
52704106 TAAAT
1 TAAAT
52704111 AAAACAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (12 bp):
TAAATGAAATAT
Found at i:52718959 original size:25 final size:26
Alignment explanation
Indices: 52718922--52718982 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
52718912 GTTGTAAATC
* * *
52718922 AAAAAAATATCTTTAGA-AATTTTCT
1 AAAATAATCTCTTCAGAGAATTTTCT
52718947 AAAATAATCTCTTCAGAGAATTTTCT
1 AAAATAATCTCTTCAGAGAATTTTCT
*
52718973 GAAATAATCT
1 AAAATAATCT
52718983 TTCTCTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (26 bp):
AAAATAATCTCTTCAGAGAATTTTCT
Found at i:52719192 original size:25 final size:25
Alignment explanation
Indices: 52719138--52719192 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
52719128 TAAATATTAA
*
52719138 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
52719163 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
52719187 TATTAA
1 T-TTAA
52719193 AATAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:52721905 original size:16 final size:16
Alignment explanation
Indices: 52721885--52721919 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52721875 AGTAAACCAT
*
52721885 AAAAACCCTAAACCTA
1 AAAAACCATAAACCTA
*
52721901 AAAAATCATAAACCTA
1 AAAAACCATAAACCTA
52721917 AAA
1 AAA
52721920 CAAAAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAACCATAAACCTA
Found at i:52721934 original size:22 final size:22
Alignment explanation
Indices: 52721891--52721934 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
52721881 CCATAAAAAC
* * *
52721891 CCTAAACCTAAAAAATCATAAA
1 CCTAAAACAAAAAAACCATAAA
*
52721913 CCTAAAACAAAAAAACCCTAAA
1 CCTAAAACAAAAAAACCATAAA
52721935 AAATGGTCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.61, C:0.25, G:0.00, T:0.14
Consensus pattern (22 bp):
CCTAAAACAAAAAAACCATAAA
Found at i:52723804 original size:21 final size:21
Alignment explanation
Indices: 52723780--52723832 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
52723770 CATTGTTTCT
52723780 AATCTCACCGCTACAGT-ATCC
1 AATCTCACCGCTACAGTAAT-C
*
52723801 AATCTCACCGCTACAGTAATT
1 AATCTCACCGCTACAGTAATC
52723822 AATCTCACCGC
1 AATCTCACCGC
52723833 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAATC
Found at i:52725076 original size:31 final size:29
Alignment explanation
Indices: 52725041--52725105 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
52725031 GTGACCACTT
*
52725041 CGTAACAAAACAATAATATAAGTGACTAAAA
1 CGTAACAAAAC-A-AACATAAGTGACTAAAA
* *
52725072 CGTAACATATCAAACATAAGTGACTAAAA
1 CGTAACAAAACAAACATAAGTGACTAAAA
*
52725101 TGTAA
1 CGTAA
52725106 TATGAGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.67
30 1 0.03
31 9 0.30
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (29 bp):
CGTAACAAAACAAACATAAGTGACTAAAA
Found at i:52725127 original size:31 final size:29
Alignment explanation
Indices: 52725041--52725128 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
52725031 GTGACCACTT
*
52725041 CGTAACAAAACAATAATATAAGTGACTAAAA
1 CGTAACATAAC-A-AATATAAGTGACTAAAA
* *
52725072 CGTAACATATCAAACATAAGTGACTAAAA
1 CGTAACATAACAAATATAAGTGACTAAAA
* * *
52725101 TGTAATATGAGACAAATAAAAGTGACTA
1 CGTAACAT-A-ACAAATATAAGTGACTA
52725129 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 22 0.47
30 2 0.04
31 23 0.49
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (29 bp):
CGTAACATAACAAATATAAGTGACTAAAA
Found at i:52726893 original size:20 final size:20
Alignment explanation
Indices: 52726868--52726914 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
52726858 AAAAATAAAT
52726868 AAAAATATTAAAATTTAATG
1 AAAAATATTAAAATTTAATG
* *
52726888 AAAAATATTAAAATTTCATT
1 AAAAATATTAAAATTTAATG
52726908 AAAAATA
1 AAAAATA
52726915 GAAAAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATATTAAAATTTAATG
Found at i:52726953 original size:10 final size:10
Alignment explanation
Indices: 52726940--52726991 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
52726930 AAATAGTAAC
52726940 AAAATTATAA
1 AAAATTATAA
52726950 AAAATTATAA
1 AAAATTATAA
***
52726960 ATTTTTAT-A
1 AAAATTATAA
52726969 AAAATTATAAA
1 AAAATTAT-AA
52726980 AAAATTATAA
1 AAAATTATAA
52726990 AA
1 AA
52726992 TGCATCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 6 0.18
10 19 0.56
11 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTATAA
Found at i:52726987 original size:20 final size:19
Alignment explanation
Indices: 52726842--52726991 Score: 69
Period size: 20 Copynumber: 7.7 Consensus size: 19
52726832 GACATGTGAC
52726842 AAAAATTATAAAAAGTA-AA
1 AAAAATTATAAAAA-TATAA
* *
52726861 AATAA--ATAAAAATAT-T
1 AAAAATTATAAAAATATAA
* *
52726877 AAAATTTAATGAAAAATAT-T
1 AAAAATT-AT-AAAAATATAA
* *
52726897 AAAATTTCATTAAAAATAGAA
1 AAAAATT-A-TAAAAATATAA
*
52726918 AAGAAATTATACAAATAGTAA
1 AA-AAATTATAAAAATA-TAA
*
52726939 CAAAATTATAAAAA-ATTATA
1 AAAAATTATAAAAATA-TA-A
***
52726959 AATTTTTATAAAAATTATAA
1 AAAAATTATAAAAA-TATAA
52726979 AAAAATTATAAAA
1 AAAAATTATAAAA
52726992 TGCATCAAAA
Statistics
Matches: 99, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.05
17 7 0.07
19 9 0.09
20 64 0.65
21 9 0.09
22 5 0.05
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTATAAAAATATAA
Found at i:52732277 original size:25 final size:25
Alignment explanation
Indices: 52732249--52732298 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
52732239 GTGTGACACA
*
52732249 TGGCTATGTGACACGGTCATGTGTC
1 TGGCCATGTGACACGGTCATGTGTC
52732274 TGGCCATGTGACACGGTCATGTGTC
1 TGGCCATGTGACACGGTCATGTGTC
52732299 CCCTGTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (25 bp):
TGGCCATGTGACACGGTCATGTGTC
Found at i:52732296 original size:13 final size:13
Alignment explanation
Indices: 52732254--52732296 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
52732244 ACACATGGCT
52732254 ATGTGACACGGTC
1 ATGTGACACGGTC
* * *
52732267 ATGTGTC-TGGCC
1 ATGTGACACGGTC
52732279 ATGTGACACGGTC
1 ATGTGACACGGTC
52732292 ATGTG
1 ATGTG
52732297 TCCCCTGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.28
Consensus pattern (13 bp):
ATGTGACACGGTC
Found at i:52737373 original size:10 final size:10
Alignment explanation
Indices: 52737358--52737386 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
52737348 ATTGCGTGTT
52737358 TGAATAGAAA
1 TGAATAGAAA
52737368 TGAATAG-AA
1 TGAATAGAAA
52737377 TGAATAGAAA
1 TGAATAGAAA
52737387 AAGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:52737685 original size:26 final size:26
Alignment explanation
Indices: 52737648--52737716 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
52737638 TTCTCGAAAC
52737648 TTTATT-GAGGGTAAAATCGTCAAAAT
1 TTTATTAG-GGGTAAAATCGTCAAAAT
52737674 TTTATTAGGGGTAAAATCGTCAAAAT
1 TTTATTAGGGGTAAAATCGTCAAAAT
*
52737700 TTT-TCCAGGGGTAAAAT
1 TTTAT-TAGGGGTAAAAT
52737717 TGAGATGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 1 0.03
26 38 0.95
27 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (26 bp):
TTTATTAGGGGTAAAATCGTCAAAAT
Found at i:52746467 original size:19 final size:19
Alignment explanation
Indices: 52746443--52746485 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
52746433 GTTTAATTTT
*
52746443 TATTTTTAT-AATTTTTATA
1 TATTTTT-TGAATCTTTATA
52746462 TATTTTTTGAATCTTTATA
1 TATTTTTTGAATCTTTATA
52746481 TATTT
1 TATTT
52746486 ATTTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTGAATCTTTATA
Found at i:52746490 original size:21 final size:21
Alignment explanation
Indices: 52746456--52746508 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
52746446 TTTTATAATT
52746456 TTTATATA-TT-TTTTGAATC
1 TTTATATATTTATTTTGAATC
** *
52746475 TTTATATATTTATTTTTCATT
1 TTTATATATTTATTTTGAATC
52746496 TTTATATTATTTA
1 TTTATA-TATTTA
52746509 ATGTGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.29
20 2 0.07
21 12 0.43
22 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTATATATTTATTTTGAATC
Found at i:52750724 original size:13 final size:13
Alignment explanation
Indices: 52750703--52750755 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
52750693 TGAGTTCGGT
52750703 TATATTGTTTTAA
1 TATATTGTTTTAA
* *
52750716 TATACTGTTATAA
1 TATATTGTTTTAA
52750729 TTATATTGTTTTAA
1 -TATATTGTTTTAA
*
52750743 TATAATGTTTTAA
1 TATATTGTTTTAA
52750756 CTTTTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:52750732 original size:27 final size:27
Alignment explanation
Indices: 52750702--52750787 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
52750692 ATGAGTTCGG
52750702 TTATATTGTTTTAATATACTGTTATAA
1 TTATATTGTTTTAATATACTGTTATAA
* *
52750729 TTATATTGTTTTAATATAATGTTTTAA
1 TTATATTGTTTTAATATACTGTTATAA
* ** *
52750756 CTTTTA-AATTTTAGTATACTGTTATAA
1 -TTATATTGTTTTAATATACTGTTATAA
*
52750783 ATATA
1 TTATA
52750788 CATTTAATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 3 0.06
27 41 0.85
28 4 0.08
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (27 bp):
TTATATTGTTTTAATATACTGTTATAA
Found at i:52750811 original size:15 final size:15
Alignment explanation
Indices: 52750791--52750824 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52750781 AAATATACAT
*
52750791 TTAATTTGTAACACA
1 TTAATTTCTAACACA
52750806 TTAATTTCTAACACA
1 TTAATTTCTAACACA
52750821 TTAA
1 TTAA
52750825 ATTTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAATTTCTAACACA
Found at i:52750968 original size:13 final size:13
Alignment explanation
Indices: 52750952--52751061 Score: 86
Period size: 13 Copynumber: 8.6 Consensus size: 13
52750942 TACTGTTTTA
52750952 ATAATATATTGTT
1 ATAATATATTGTT
52750965 ATAA-A-A-T-TT
1 ATAATATATTGTT
*
52750974 ATAATATACTGTT
1 ATAATATATTGTT
* * *
52750987 TTAATATACTATT
1 ATAATATATTGTT
52751000 ATAAATATACTT-TT
1 AT-AATATA-TTGTT
*
52751014 TTAATATATTGTT
1 ATAATATATTGTT
* *
52751027 TTAATATACTGTT
1 ATAATATATTGTT
52751040 ATAATTATATTGTT
1 ATAA-TATATTGTT
*
52751054 TTAATATA
1 ATAATATA
52751062 ATTTTTTAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
11 2 0.03
12 4 0.05
13 45 0.56
14 20 0.25
15 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (13 bp):
ATAATATATTGTT
Found at i:52751030 original size:40 final size:40
Alignment explanation
Indices: 52750975--52751070 Score: 133
Period size: 40 Copynumber: 2.4 Consensus size: 40
52750965 ATAAAATTTA
*
52750975 TAATATACTGTTTTAATATACTATTATAAATATACTT-TTT
1 TAATATATTGTTTTAATATACTATTATAAATATA-TTGTTT
* *
52751015 TAATATATTGTTTTAATATACTGTTATAATTATATTGTTT
1 TAATATATTGTTTTAATATACTATTATAAATATATTGTTT
52751055 TAATATAATT-TTTTAA
1 TAATAT-ATTGTTTTAA
52751071 CTTTTAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.04
40 46 0.90
41 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (40 bp):
TAATATATTGTTTTAATATACTATTATAAATATATTGTTT
Found at i:52751056 original size:27 final size:26
Alignment explanation
Indices: 52750975--52751070 Score: 111
Period size: 27 Copynumber: 3.6 Consensus size: 26
52750965 ATAAAATTTA
* *
52750975 TAATATACTGTTTTAATATACTATTAT
1 TAATATACTGTTTTAATATATTGTT-T
* *
52751002 AAATATACTTTTTTAATATATTGTTT
1 TAATATACTGTTTTAATATATTGTTT
*
52751028 TAATATACTGTTATAATTATATTGTTT
1 TAATATACTGTTTTAA-TATATTGTTT
* *
52751055 TAATATAATTTTTTAA
1 TAATATACTGTTTTAA
52751071 CTTTTAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.24
27 44 0.76
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TAATATACTGTTTTAATATATTGTTT
Found at i:52751068 original size:13 final size:13
Alignment explanation
Indices: 52750975--52751070 Score: 88
Period size: 13 Copynumber: 7.2 Consensus size: 13
52750965 ATAAAATTTA
*
52750975 TAATATACTGTTT
1 TAATATACTTTTT
*
52750988 TAATATACTATTAT
1 TAATATACT-TTTT
*
52751002 AAATATACTTTTT
1 TAATATACTTTTT
52751015 TAATATA-TTGTTT
1 TAATATACTT-TTT
* *
52751028 TAATATACTGTTA
1 TAATATACTTTTT
52751041 TAATTATA-TTGTTT
1 TAA-TATACTT-TTT
*
52751055 TAATATAATTTTT
1 TAATATACTTTTT
52751068 TAA
1 TAA
52751071 CTTTTAAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
12 2 0.03
13 44 0.65
14 22 0.32
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (13 bp):
TAATATACTTTTT
Found at i:52751126 original size:15 final size:15
Alignment explanation
Indices: 52751106--52751139 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52751096 AAATATACAT
*
52751106 TTAATTTGTAACACA
1 TTAATTTCTAACACA
52751121 TTAATTTCTAACACA
1 TTAATTTCTAACACA
52751136 TTAA
1 TTAA
52751140 ATTTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAATTTCTAACACA
Found at i:52751344 original size:40 final size:40
Alignment explanation
Indices: 52751300--52751387 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
52751290 TATAATATCC
*
52751300 TGTTTTAATATACTATTATAAATATACTT-TTTTAATATAT
1 TGTTTTAATATACTATTATAAATATA-TTGTTTTAATATAA
*
52751340 TGTTTTAATATACTATTATAATTATATTGTTTTAATATAA
1 TGTTTTAATATACTATTATAAATATATTGTTTTAATATAA
52751380 TGTTTTAA
1 TGTTTTAA
52751388 CTTTTAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.04
40 43 0.96
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (40 bp):
TGTTTTAATATACTATTATAAATATATTGTTTTAATATAA
Found at i:52751373 original size:27 final size:26
Alignment explanation
Indices: 52751320--52751378 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
52751310 TACTATTATA
* *
52751320 AATATACTTTTTTAATATATTGTTTT
1 AATATACTATTATAATATATTGTTTT
52751346 AATATACTATTATAATTATATTGTTTT
1 AATATACTATTATAA-TATATTGTTTT
52751373 AATATA
1 AATATA
52751379 ATGTTTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
AATATACTATTATAATATATTGTTTT
Found at i:52751378 original size:317 final size:315
Alignment explanation
Indices: 52750703--52751441 Score: 1381
Period size: 317 Copynumber: 2.3 Consensus size: 315
52750693 TGAGTTCGGT
52750703 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
1 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
52750768 AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAATTTCTAACACATTAAATTTTAGT
66 AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAATTTCTAACACATTAAATTTTAGT
52750833 TTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTAACTAAATAATTAA
131 TTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTAACTAAATAATTAA
* *
52750898 TATTGTTAATTTTTTTTATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAATATATTG
196 TATTGTTAATTTTTTTGATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAATATACTG
52750963 TTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAA
261 TTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAA
*
52751018 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATTTTTTAACTTTTAAATTTT
1 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
52751083 AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAATTTCTAACACATTAAATTTTAGT
66 AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAATTTCTAACACATTAAATTTTAGT
*
52751148 TTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTTTAATGTTATTAACTAAATAAT
131 TTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTATAATG---TTAACTAAATAAT
52751213 TAATATTGTTAA-TTTTTTGATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAATATA
193 TAATATTGTTAATTTTTTTGATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAATATA
*
52751277 CTGTTATAAAATTTATAATATCCTGTTTTAATATACTATTATAAATATACTTTTTTAA
258 CTGTTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAA
*
52751335 TATATTGTTTTAATATACTATTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
1 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
*
52751400 AATATACTGTTATAAATATACATTTAATTTGTAACACATTAA
66 AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAA
52751442 ATGTTGATGT
Statistics
Matches: 413, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
315 177 0.43
317 211 0.51
318 25 0.06
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.51
Consensus pattern (315 bp):
TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAAATTTT
AGTATACTGTTATAAATATACATTTAATTTGTAACACATTAATTTCTAACACATTAAATTTTAGT
TTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTAACTAAATAATTAA
TATTGTTAATTTTTTTGATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAATATACTG
TTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAA
Found at i:52751384 original size:13 final size:13
Alignment explanation
Indices: 52751254--52751387 Score: 96
Period size: 13 Copynumber: 10.2 Consensus size: 13
52751244 ATTTTTAATG
52751254 TAATATACTGTTTT
1 TAATATACTG-TTT
*
52751268 AATAATATACTGTTA
1 --TAATATACTGTTT
*
52751283 TAA-A-A-T-TTA
1 TAATATACTGTTT
*
52751292 TAATATCCTGTTT
1 TAATATACTGTTT
*
52751305 TAATATACTATTAT
1 TAATATACTGTT-T
* *
52751319 AAATATACTTTTT
1 TAATATACTGTTT
*
52751332 TAATATATTGTTT
1 TAATATACTGTTT
* *
52751345 TAATATACTATTA
1 TAATATACTGTTT
*
52751358 TAATTATATTGTTT
1 TAA-TATACTGTTT
*
52751372 TAATATAATGTTT
1 TAATATACTGTTT
52751385 TAA
1 TAA
52751388 CTTTTAAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
9 6 0.06
10 2 0.02
11 1 0.01
12 2 0.02
13 51 0.54
14 21 0.22
15 2 0.02
16 10 0.11
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:52754679 original size:25 final size:25
Alignment explanation
Indices: 52754645--52754692 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
52754635 TTAGGACTTG
52754645 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
52754670 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
52754693 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:52754785 original size:16 final size:16
Alignment explanation
Indices: 52754764--52754797 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52754754 ATATAAATTC
52754764 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
52754780 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
52754796 AA
1 AA
52754798 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:52759735 original size:12 final size:13
Alignment explanation
Indices: 52759718--52759746 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52759708 GCATTACTCT
52759718 TTTTATTT-TTTA
1 TTTTATTTGTTTA
52759730 TTTTATTTGTTTA
1 TTTTATTTGTTTA
52759743 TTTT
1 TTTT
52759747 TAGTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTATTTGTTTA
Found at i:52759964 original size:29 final size:30
Alignment explanation
Indices: 52759931--52759991 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
52759921 TGCATATTTC
* *
52759931 TATACTTTATATAC-TTTATAATTTATATA
1 TATACGTTATATACTTTTATAATATATATA
52759960 TATACGTTATATACATTTTTATAATATATATA
1 TATACGTTATATAC--TTTTATAATATATATA
52759992 CATATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
32 14 0.52
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (30 bp):
TATACGTTATATACTTTTATAATATATATA
Found at i:52760679 original size:109 final size:109
Alignment explanation
Indices: 52760488--52760815 Score: 543
Period size: 109 Copynumber: 3.0 Consensus size: 109
52760478 TCAAAAAGGA
* * * * *
52760488 AAAAATTTCTAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTA
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
52760553 GGTTTCGATTTTTCTCGTTCGACCAAATGGCCAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATGGCCAAATATCCTTTT
52760597 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
*
52760662 GGTTTCGATTTTTCTCGTTCGACCAAATGACCAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATGGCCAAATATCCTTTT
* *
52760706 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
52760771 GGTTTCGA--TTTCTCGTTGGACCAAATAGCCAAATATCCTCTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATGGCCAAATATCCTTTT
52760813 AAA
1 AAA
52760816 TCTTAATCCA
Statistics
Matches: 207, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
107 33 0.16
109 174 0.84
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
GGTTTCGATTTTTCTCGTTCGACCAAATGGCCAAATATCCTTTT
Found at i:52766569 original size:16 final size:16
Alignment explanation
Indices: 52766548--52766578 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52766538 CATTACAACC
52766548 CGTTGCAAGGGGTATA
1 CGTTGCAAGGGGTATA
*
52766564 CGTTGCCAGGGGTAT
1 CGTTGCAAGGGGTAT
52766579 TAATTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (16 bp):
CGTTGCAAGGGGTATA
Found at i:52772423 original size:44 final size:44
Alignment explanation
Indices: 52772113--52772713 Score: 213
Period size: 44 Copynumber: 13.8 Consensus size: 44
52772103 TAACAAGTCC
* * * *
52772113 TATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
* * * * * **
52772157 TATTTCCCTAAACAGTAGTGAAGCAGATCAAAGAC-G-ACGAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTA-G-ATCT
* * * * ***
52772201 TATCT-TCTCGAG-A-TAGTAGGAAGTATATTTAAGCCACCAG-TC-
1 TATCTCCCT-GAGCAGTAGT-GG-AGTAGATTGAAGACTGTAGATCT
* * * *
52772243 TATCTCCCTGAGCAGCAGTGCAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
* * * * * * *
52772287 TATCTCCTTAAGCAGTAGTAGAGCAGATCGAAGACAG-CGAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAG-ATCT
* * * * *** *
52772331 TATCT-TCTCGAG-A-TAGTAGGAAGCAGATTTAAGCCACCAG-TCC
1 TATCTCCCT-GAGCAGTAGT-GG-AGTAGATTGAAGACTGTAGATCT
* * *
52772374 TATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
* * *
52772418 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGT-GAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAG-ATCT
* * * *** *
52772462 TATCTTCCC-GAG-A-TAGTAGGAAGCAGATTTAAGCCACCAG-TCC
1 TATC-TCCCTGAGCAGTAGT-GG-AGTAGATTGAAGACTGTAGATCT
* * *
52772505 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
* * * * *
52772549 TATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGAC-G-ATGAATTT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTA-G-ATCT
* * * * * *** *
52772593 TATCT-TCT-AG-AGATAGTAGAAAGCAGATTTAAGCCACCAG-TCC
1 TATCTCCCTGAGCAG-TAGT-G-GAGTAGATTGAAGACTGTAGATCT
* * * * *
52772636 TATCTCCCAGAGCAGCATTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
* *
52772680 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGA
52772714 TGACGAATCT
Statistics
Matches: 391, Mismatches: 125, Indels: 82
0.65 0.21 0.14
Matches are distributed among these distances:
41 2 0.01
42 43 0.11
43 85 0.22
44 238 0.61
45 19 0.05
46 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGACTGTAGATCT
Found at i:52772574 original size:87 final size:87
Alignment explanation
Indices: 52772235--52772583 Score: 212
Period size: 87 Copynumber: 4.0 Consensus size: 87
52772225 ATATTTAAGC
* * *
52772235 CACCAGT-CTATCTCCCTGAGCAGCAGTGCAGTAGGTTGAAGATTGTAGATCTTATC-TCCTTAA
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGATTGAAGACTGTAGATCTTATCTTCC-TAA
* *
52772298 GCAGTAGTAGAGCAGATCGAAGA
65 GCAGTAGTGGAGCAGATTGAAGA
* * * * * * * * *** * *
52772321 CAGCGAATCTTATCT-TCTCGAG-A-TAGTAGGAAGCAGATTTAAGCCACCAG-TCCTATCTCCC
1 CA-CCAGTCCTATCTCCCT-GAGCAGCAGT-GG-AGTAGATTGAAGACTGTAGATCTTATCTTCC
* * * *
52772382 TGAGTAGTAGTGGAGTAGGTTGAAGA
62 TAAGCAGTAGTGGAGCAGATTGAAGA
**** * * * * * **
52772408 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGT-GAATCTTATCTTCCCG
1 CACCAG-TCCTATCTCCCTGAGCAGCAGTGGAGTAGATTGAAGACTGTAG-ATCTTATCTTCCTA
* *
52772472 AG-A-TAGTAGGAAGCAGATTTAAGC
64 AGCAGTAGT-GG-AGCAGATTGAAGA
* *
52772496 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTTCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGATTGAAGACTGTAGATCTTATCTTCCTAAG
*
52772561 CAGTAGTGGAGCAGATCGAAGA
66 CAGTAGTGGAGCAGATTGAAGA
52772583 C
1 C
52772584 GATGAATTTT
Statistics
Matches: 187, Mismatches: 59, Indels: 33
0.67 0.21 0.12
Matches are distributed among these distances:
86 11 0.06
87 115 0.61
88 53 0.28
89 8 0.04
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGATTGAAGACTGTAGATCTTATCTTCCTAAG
CAGTAGTGGAGCAGATTGAAGA
Found at i:52772799 original size:131 final size:131
Alignment explanation
Indices: 52772108--52772778 Score: 1076
Period size: 131 Copynumber: 5.1 Consensus size: 131
52772098 CATCATAACA
* * *
52772108 AGTCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATTTCCCTAAACAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * * *
52772173 AGTGAAGCAGATCAAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGTATATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCAC
52772238 C
131 C
* *
52772239 AGT-CTATCTCCCTGAGCAGCAGTGCAGTAGGTTGAAGATTGTAGATCTTATCTCCTTAAGCAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
*
52772303 AGTAGAGCAGATCGAAGAC-AGCGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGACGA-CGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCA
52772367 CC
130 CC
* *
52772369 AGTCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* ** *
52772434 AGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCAC
52772499 C
131 C
*
52772500 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTTCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * * *
52772565 AGTGGAGCAGATCGAAGACGATGAATTTTATCTTCTAGAGATAGTAGAAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCAC
52772630 C
131 C
* *
52772631 AGTCCTATCTCCCAGAGCAGCATTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * *
52772696 AGTGGAGCAGATTGAAGATGACGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCAC
52772761 C
131 C
*
52772762 AGTCCTATGTCCCTGAG
1 AGTCCTATCTCCCTGAG
52772779 TTGCAGTAGA
Statistics
Matches: 497, Mismatches: 40, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
129 1 0.00
130 118 0.24
131 378 0.76
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (131 bp):
AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCAC
C
Found at i:52774430 original size:12 final size:13
Alignment explanation
Indices: 52774415--52774443 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52774405 TTGCATTACT
52774415 TTTTATTT-TTTA
1 TTTTATTTGTTTA
52774427 TTTTATTTGTTTA
1 TTTTATTTGTTTA
52774440 TTTT
1 TTTT
52774444 TTAGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTATTTGTTTA
Found at i:52774641 original size:16 final size:17
Alignment explanation
Indices: 52774615--52774650 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
52774605 ATATATATGC
*
52774615 ATACTTCTATACTTTAT
1 ATACTTCTATAATTTAT
52774632 ATACTT-TATAATTTAT
1 ATACTTCTATAATTTAT
52774648 ATA
1 ATA
52774651 TATACGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATACTTCTATAATTTAT
Found at i:52774660 original size:29 final size:30
Alignment explanation
Indices: 52774622--52774682 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
52774612 TGCATACTTC
* *
52774622 TATACTTTATATAC-TTTATAATTTATATA
1 TATACGTTATATACTTTTATAATATATATA
52774651 TATACGTTATATACATTTTTATAATATATATA
1 TATACGTTATATAC--TTTTATAATATATATA
52774683 CATATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
32 14 0.52
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (30 bp):
TATACGTTATATACTTTTATAATATATATA
Found at i:52774782 original size:16 final size:15
Alignment explanation
Indices: 52774750--52774783 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
52774740 TACCTACTTG
52774750 TATTTTATATATATA
1 TATTTTATATATATA
*
52774765 TATTTTATAATCTATA
1 TATTTTAT-ATATATA
52774781 TAT
1 TAT
52774784 ATCTACATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTATATATATA
Found at i:52779018 original size:29 final size:29
Alignment explanation
Indices: 52778976--52779033 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
52778966 ATGAATTATG
*
52778976 AAGTTTTATGGTAGAAATGGAAAGGTTGT
1 AAGTTTTATGGTAGAAATAGAAAGGTTGT
52779005 AAGTTTTATGGTAGAAATAGAAAGGTTGT
1 AAGTTTTATGGTAGAAATAGAAAGGTTGT
52779034 TGATAGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.34
Consensus pattern (29 bp):
AAGTTTTATGGTAGAAATAGAAAGGTTGT
Found at i:52779733 original size:24 final size:25
Alignment explanation
Indices: 52779687--52779733 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
52779677 TGGCCCTCTT
*
52779687 GAGCTTCCTGTTATATAGTTCTTGC
1 GAGCTTCCTGTTATATAGCTCTTGC
52779712 GAGCTT-CTCGTTA-ATAGCTCTT
1 GAGCTTCCT-GTTATATAGCTCTT
52779734 CGGAGCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (25 bp):
GAGCTTCCTGTTATATAGCTCTTGC
Found at i:52779739 original size:24 final size:25
Alignment explanation
Indices: 52779687--52779733 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
52779677 TGGCCCTCTT
*
52779687 GAGCTTC-CTGTTATATAGTTCTTGC
1 GAGCTTCTC-GTTATATAGCTCTTGC
52779712 GAGCTTCTCGTTA-ATAGCTCTT
1 GAGCTTCTCGTTATATAGCTCTT
52779734 CGGAGCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 11 0.55
26 1 0.05
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (25 bp):
GAGCTTCTCGTTATATAGCTCTTGC
Found at i:52779826 original size:26 final size:25
Alignment explanation
Indices: 52779791--52779891 Score: 112
Period size: 26 Copynumber: 3.9 Consensus size: 25
52779781 GTAGCTCTTA
* *
52779791 TGAGCATCCCATTATATGGCTCTTTG
1 TGAGCTTCCCATTA-ATGGCTCTTTT
*
52779817 TGAGCTTCCCGATTAAAGGCTCTTTT
1 TGAGCTTCCC-ATTAATGGCTCTTTT
*
52779843 TGAGCTTCCTGATTAATGGCTCTTTT
1 TGAGCTTCC-CATTAATGGCTCTTTT
**
52779869 TGAGCTTCCTGTTTAATGGCTCT
1 TGAGCTTCC-CATTAATGGCTCT
52779892 CCGAAGCTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 63 0.94
27 4 0.06
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (25 bp):
TGAGCTTCCCATTAATGGCTCTTTT
Found at i:52779988 original size:24 final size:24
Alignment explanation
Indices: 52779961--52780022 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
52779951 TGGCTATTTA
*
52779961 GAGCTACCTGTTATTGGCTCGCAT
1 GAGCTTCCTGTTATTGGCTCGCAT
* **
52779985 GAGCTTCTTGATTA-TGGCTCTTAT
1 GAGCTTCCTG-TTATTGGCTCGCAT
52780009 GAGCTTCCTGTTAT
1 GAGCTTCCTGTTAT
52780023 ATAGCCTGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (24 bp):
GAGCTTCCTGTTATTGGCTCGCAT
Found at i:52780076 original size:25 final size:24
Alignment explanation
Indices: 52779969--52780079 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
52779959 TAGAGCTACC
*
52779969 TGTTAT-TGGCTCGCATGAGCTTCT
1 TGTTATATGGCTC-TATGAGCTTCT
* *
52779993 TGAT-TATGGCTCTTATGAGCTTCC
1 TGTTATATGGCTC-TATGAGCTTCT
* *
52780017 TGTTATATAGC-CTGGATAAGCTTCT
1 TGTTATATGGCTCT--ATGAGCTTCT
** *
52780042 CATTACATGGCTCATATGAGCTTCT
1 TGTTATATGGCTC-TATGAGCTTCT
52780067 TGTTATATGGCTC
1 TGTTATATGGCTC
52780080 GAGAGAGGAT
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
23 2 0.03
24 22 0.34
25 39 0.60
26 1 0.02
27 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (24 bp):
TGTTATATGGCTCTATGAGCTTCT
Found at i:52788327 original size:81 final size:82
Alignment explanation
Indices: 52788208--52788395 Score: 267
Period size: 81 Copynumber: 2.3 Consensus size: 82
52788198 ACCGAAGTGT
* *
52788208 AAACAGGGGCAC-AAGTGTGC-ATTCAGGGGTATCGAAGTACAAACAGGGGCATGTATGTGCAAT
1 AAACAGGGGCACGAA-TGTGCAATTCAGGGGTATCAAAGTACAAACAGGGGCACGTATGTGCAAT
*
52788271 TC-AGGGTACAAAAGTAC
65 TCAAGGGTACAAAAGTAA
* *
52788288 AAACAGGGGCACGCATGTGCAATTCAGGGGTA-CAAAAGTACAAACAGGGGCACGTATGTGTAAT
1 AAACAGGGGCACGAATGTGCAATTCAGGGGTATC-AAAGTACAAACAGGGGCACGTATGTGCAAT
52788352 TCAAGGGTACAAAAGTAA
65 TCAAGGGTACAAAAGTAA
* *
52788370 AAACAGTGGCACGTATGTGCAATTCA
1 AAACAGGGGCACGAATGTGCAATTCA
52788396 TACAACAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
80 18 0.19
81 41 0.42
82 38 0.39
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (82 bp):
AAACAGGGGCACGAATGTGCAATTCAGGGGTATCAAAGTACAAACAGGGGCACGTATGTGCAATT
CAAGGGTACAAAAGTAA
Found at i:52788331 original size:41 final size:41
Alignment explanation
Indices: 52788208--52788395 Score: 258
Period size: 41 Copynumber: 4.6 Consensus size: 41
52788198 ACCGAAGTGT
* *
52788208 AAACAGGGGCAC-AAGTGTGC-ATTCAGGGGTATC-GAAGTAC
1 AAACAGGGGCACGTA-TGTGCAATTCAGGGGTA-CAAAAGTAC
*
52788248 AAACAGGGGCATGTATGTGCAATTCA-GGGTACAAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACAAAAGTAC
*
52788288 AAACAGGGGCACGCATGTGCAATTCAGGGGTACAAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACAAAAGTAC
* * *
52788329 AAACAGGGGCACGTATGTGTAATTCAAGGGTACAAAAGTAA
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACAAAAGTAC
*
52788370 AAACAGTGGCACGTATGTGCAATTCA
1 AAACAGGGGCACGTATGTGCAATTCA
52788396 TACAACAATT
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 51 0.38
41 81 0.61
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTACAAAAGTAC
Found at i:52788337 original size:20 final size:20
Alignment explanation
Indices: 52788274--52788337 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
52788264 GTGCAATTCA
52788274 GGGTACAAAAGTACAAACAG
1 GGGTACAAAAGTACAAACAG
* ** * * *
52788294 GGGCACGCATGTGCAATTCAG
1 GGGTACAAAAGTACAA-ACAG
52788315 GGGTACAAAAGTACAAACAG
1 GGGTACAAAAGTACAAACAG
52788335 GGG
1 GGG
52788338 CACGTATGTG
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.39, C:0.17, G:0.31, T:0.12
Consensus pattern (20 bp):
GGGTACAAAAGTACAAACAG
Found at i:52800637 original size:14 final size:13
Alignment explanation
Indices: 52800618--52800648 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
52800608 TAGATTTGGC
52800618 ATTAATTAATCTTA
1 ATTAATTAA-CTTA
52800632 ATTAATTAACTTA
1 ATTAATTAACTTA
52800645 ATTA
1 ATTA
52800649 TGGCTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAATTAACTTA
Found at i:52801180 original size:215 final size:216
Alignment explanation
Indices: 52800762--52801165 Score: 605
Period size: 215 Copynumber: 1.9 Consensus size: 216
52800752 TTGGATAATT
* * * *
52800762 GTTATTTAACTCCTTAATCCCTACCTTAATTAAAACTCTACAATGGTTAGACATTTACAATTTAG
1 GTTATTTAACTCCTTAAGCCATACCTTAATTAAAACTCTACAACGATTAGACATTTACAATTTAG
* *** * *
52800827 TCCTTAAGCTTTAATAACTAGTTTATTGGCTCAATTACTTGACCACTCTTTATTATATTCACATA
66 TCCTTAAGCTTTAATAACTAGCTTATCAACTAAATTACTTGACCACTCTTTATTATATTCACAGA
* * * *
52800892 TTAACTATGTAAATATTCATATTTTATATTTATGGACTCGGTTTACGGAAATGAGGTTTCAAAAT
131 TTAACTACGTAAATATTCATAATTTATATTTACGGACTCGGTTTAAGGAAATGAGGTTTCAAAAT
52800957 CGTATTTTCCAATATCACTGA
196 CGTATTTTCCAATATCACTGA
* * *
52800978 GTTATTTAACT-C-TAAGCCATACCTTAATTAAAACTCTATAGCGATTAGACTTTTACAATTTAG
1 GTTATTTAACTCCTTAAGCCATACCTTAATTAAAACTCTACAACGATTAGACATTTACAATTTAG
*
52801041 TCCTTAAGCTTTAATTAACTAGCTTATCAACTAAATTACTTGACCACTCTTTATTATATTCATAG
66 TCCTTAAGCTTTAA-TAACTAGCTTATCAACTAAATTACTTGACCACTCTTTATTATATTCACAG
* *
52801106 ATTAACTCCGTAAATATTCATAATTTATATTTACGGACTTGGTTTAAGGAAATGAGGTTT
130 ATTAACTACGTAAATATTCATAATTTATATTTACGGACTCGGTTTAAGGAAATGAGGTTT
52801166 TGAAACTGTA
Statistics
Matches: 167, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
214 58 0.35
215 98 0.59
216 11 0.07
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (216 bp):
GTTATTTAACTCCTTAAGCCATACCTTAATTAAAACTCTACAACGATTAGACATTTACAATTTAG
TCCTTAAGCTTTAATAACTAGCTTATCAACTAAATTACTTGACCACTCTTTATTATATTCACAGA
TTAACTACGTAAATATTCATAATTTATATTTACGGACTCGGTTTAAGGAAATGAGGTTTCAAAAT
CGTATTTTCCAATATCACTGA
Found at i:52803728 original size:17 final size:17
Alignment explanation
Indices: 52803684--52803728 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
52803674 ATTTAGTCCA
*
52803684 AATCACTAGTACTCGAT
1 AATCACTAGTACTCAAT
52803701 --TCAC-A-TACTCAAT
1 AATCACTAGTACTCAAT
52803714 AATCACTAGTACTCA
1 AATCACTAGTACTCA
52803729 TTAGTACGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
13 7 0.30
14 1 0.04
15 8 0.35
16 1 0.04
17 6 0.26
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (17 bp):
AATCACTAGTACTCAAT
Found at i:52808140 original size:28 final size:28
Alignment explanation
Indices: 52808103--52808159 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
52808093 CCTGGTTGGT
52808103 TTATTGATTT-TTATCTTT-TTTATTTTTA
1 TTATTGATTTATT-T-TTTGTTTATTTTTA
*
52808131 TTATTTATTTATTTTTTGTTTATTTTTA
1 TTATTGATTTATTTTTTGTTTATTTTTA
52808159 T
1 T
52808160 CCCAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 21 0.81
29 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (28 bp):
TTATTGATTTATTTTTTGTTTATTTTTA
Found at i:52808143 original size:17 final size:16
Alignment explanation
Indices: 52808102--52808155 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
52808092 TCCTGGTTGG
* *
52808102 TTTATTGATTTTTATC
1 TTTATTTATTTTTATA
52808118 TTT-TTTATTTTTATTA
1 TTTATTTATTTTTA-TA
*
52808134 TTTATTTATTTTT-TG
1 TTTATTTATTTTTATA
52808149 TTTATTT
1 TTTATTT
52808156 TTATCCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 17 0.52
16 7 0.21
17 9 0.27
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTATA
Found at i:52809017 original size:9 final size:9
Alignment explanation
Indices: 52809000--52809036 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52808990 TGAGTTTTCG
52809000 AATTCGAAT
1 AATTCGAAT
*
52809009 AACTCGAAT
1 AATTCGAAT
52809018 AATTCGAAT
1 AATTCGAAT
52809027 AATTCGAAT
1 AATTCGAAT
52809036 A
1 A
52809037 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52815465 original size:5 final size:5
Alignment explanation
Indices: 52815457--52815482 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52815447 GAGATGGAAT
52815457 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
52815483 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:52815482 original size:26 final size:26
Alignment explanation
Indices: 52815431--52815482 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
52815421 TGAAGTTTTC
* * *
52815431 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
52815457 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
52815483 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:52816165 original size:30 final size:31
Alignment explanation
Indices: 52816126--52816185 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52816116 TGAGGTGAGA
*
52816126 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
52816157 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
52816186 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:52816355 original size:21 final size:21
Alignment explanation
Indices: 52816321--52816361 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52816311 GGGGGAAAGT
*
52816321 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
52816342 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
52816362 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:52816413 original size:9 final size:9
Alignment explanation
Indices: 52816399--52816435 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52816389 TATAGTTTGA
52816399 TATTCGAAT
1 TATTCGAAT
52816408 TATTCGAAT
1 TATTCGAAT
* *
52816417 TATTTGAGT
1 TATTCGAAT
52816426 TATTCGAAT
1 TATTCGAAT
52816435 T
1 T
52816436 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52818714 original size:27 final size:27
Alignment explanation
Indices: 52818678--52818789 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
52818668 AATGGAAAAC
*
52818678 TGTGGCAATCTATAAAATGAAAGCCTT
1 TGTGGCAATCTATGAAATGAAAGCCTT
* * *
52818705 TGTTGCAATCTATGAAATGGATGTCC-T
1 TGTGGCAATCTATGAAATGAAAG-CCTT
* *
52818732 TGTGGCAATCTATGAAATGGAAGCTTT
1 TGTGGCAATCTATGAAATGAAAGCCTT
* * *
52818759 TGTGGC-ATATATTAAATAAAAGCCTT
1 TGTGGCAATCTATGAAATGAAAGCCTT
52818785 TGTGG
1 TGTGG
52818790 AATTCTCTGA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
26 21 0.30
27 48 0.68
28 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (27 bp):
TGTGGCAATCTATGAAATGAAAGCCTT
Found at i:52820812 original size:2 final size:2
Alignment explanation
Indices: 52820805--52820834 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
52820795 GAGCTTCCTT
*
52820805 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52820835 TCCCTATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52826241 original size:18 final size:18
Alignment explanation
Indices: 52826220--52826277 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
52826210 TGAACTTGTC
52826220 TAAAAAATTATACTTTTT
1 TAAAAAATTATACTTTTT
* *
52826238 TAAATTATTTATA-TTTTT
1 TAAA-AAATTATACTTTTT
52826256 TAAAATAATTATACTTTTT
1 TAAAA-AATTATACTTTTT
52826275 TAA
1 TAA
52826278 TTTATGTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 19 0.58
19 14 0.42
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAAAAATTATACTTTTT
Found at i:52826255 original size:19 final size:19
Alignment explanation
Indices: 52826227--52826282 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 19
52826217 GTCTAAAAAA
52826227 TTATACTTTTTTAAATTAT
1 TTATACTTTTTTAAATTAT
* *
52826246 TTATA-TTTTTTAAAATAA
1 TTATACTTTTTTAAATTAT
*
52826264 TTATACTTTTTTAATTTAT
1 TTATACTTTTTTAAATTAT
52826283 GTCCCCACGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATACTTTTTTAAATTAT
Found at i:52837891 original size:11 final size:12
Alignment explanation
Indices: 52837846--52837898 Score: 90
Period size: 12 Copynumber: 4.5 Consensus size: 12
52837836 AACAAGCTCT
52837846 TTTATTGACTCG
1 TTTATTGACTCG
*
52837858 TTTATTGGCTCG
1 TTTATTGACTCG
52837870 TTTATTGACTCG
1 TTTATTGACTCG
52837882 TTTA-TGACTCG
1 TTTATTGACTCG
52837893 TTTATT
1 TTTATT
52837899 TATTAATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 11 0.29
12 27 0.71
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (12 bp):
TTTATTGACTCG
Found at i:52838005 original size:12 final size:12
Alignment explanation
Indices: 52837977--52838028 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
52837967 TTGTTTATTA
*
52837977 TTCATTAACATTG
1 TTCATGAACA-TG
52837990 TTCATGAACATG
1 TTCATGAACATG
* *
52838002 TTCAAT-TATATG
1 TTC-ATGAACATG
52838014 TTCATGAACATG
1 TTCATGAACATG
52838026 TTC
1 TTC
52838029 GATTAAGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.59
13 11 0.34
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:52838015 original size:24 final size:23
Alignment explanation
Indices: 52837988--52838051 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
52837978 TCATTAACAT
52837988 TGTTCATGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
*
52838012 TGTTCATGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
*
52838035 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
52838052 GTGAACATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.08
23 13 0.35
24 21 0.57
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:52838062 original size:23 final size:23
Alignment explanation
Indices: 52838017--52838063 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52838007 TTATATGTTC
* *
52838017 ATGAACATGTTCGATTAAGTTAA
1 ATGAACATGTTCGATGAAATTAA
52838040 ATGAACATGTTCG-TGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
52838063 A
1 A
52838064 CAAACGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:52839777 original size:26 final size:28
Alignment explanation
Indices: 52839719--52839782 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
52839709 GTGTCATATG
52839719 AATTAA-AATAGGATAAAATAAATAATA
1 AATTAATAATAGGATAAAATAAATAATA
*
52839746 AGTTAATAATA-G-TAAAAT-AATAATTA
1 AATTAATAATAGGATAAAATAAATAA-TA
52839772 AATTAAATAAT
1 AATT-AATAAT
52839783 TATGGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 11 0.34
27 12 0.38
28 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (28 bp):
AATTAATAATAGGATAAAATAAATAATA
Found at i:52841100 original size:24 final size:23
Alignment explanation
Indices: 52841049--52841106 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
52841039 TTGTATATAC
*
52841049 AATATATAAATGAGGGAGTTGGT
1 AATATATATATGAGGGAGTTGGT
*
52841072 AATATATATATGAGTGGGGTT-GT
1 AATATATATATGAG-GGAGTTGGT
52841095 ATATATATATAT
1 A-ATATATATAT
52841107 ATGTATACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (23 bp):
AATATATATATGAGGGAGTTGGT
Found at i:52843045 original size:33 final size:34
Alignment explanation
Indices: 52843006--52843069 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
52842996 ATCTTAACCA
*
52843006 CATTGAAACTAATTCATC-ACTTA-CCATATTGGT
1 CATTGAAA-TAATGCATCAACTTAGCCATATTGGT
*
52843039 CATTGAAATCATGCATCAACTTAGCCATATT
1 CATTGAAATAATGCATCAACTTAGCCATATT
52843070 AACACACATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 13 0.48
34 7 0.26
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (34 bp):
CATTGAAATAATGCATCAACTTAGCCATATTGGT
Found at i:52851955 original size:25 final size:23
Alignment explanation
Indices: 52851922--52851982 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 23
52851912 TTTAAATAAC
*
52851922 AATATATAATAAAGATTAAAACCA
1 AATACATAATAAAGATTAAAA-CA
* **
52851946 TAATACATAATAGATTTTAAAACA
1 -AATACATAATAAAGATTAAAACA
*
52851970 AATACCTAATAAA
1 AATACATAATAAA
52851983 TCTATAATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 11 0.37
24 2 0.07
25 17 0.57
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (23 bp):
AATACATAATAAAGATTAAAACA
Found at i:52852188 original size:21 final size:21
Alignment explanation
Indices: 52852165--52852211 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
52852155 ATATAATACT
**
52852165 AATAATAATCATAGAGG-TAAT
1 AATAATAAGAATA-AGGATAAT
52852186 AATAATAAGAATAAGGATAAT
1 AATAATAAGAATAAGGATAAT
52852207 AATAA
1 AATAA
52852212 CAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.26
Consensus pattern (21 bp):
AATAATAAGAATAAGGATAAT
Found at i:52857018 original size:86 final size:86
Alignment explanation
Indices: 52856873--52857043 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 86
52856863 CTTTTGACAA
*
52856873 CCCAATGTGAGTCTAATCTTAAACTATTATATAGAATTGTTCAAACAGAAAAGCATTTAATTTAG
1 CCCAATGTGAGTCTAATCTTAAACCATTATATAGAATTGTTCAAACAGAAAAGCATTTAATTTAG
52856938 AGCATCATACCAATTGAGCAG
66 AGCATCATACCAATTGAGCAG
* *
52856959 CCCAATGTGAGTCTAATTTTAAACCATTATATATAATTGTTCAAACA-ATAAAGCATTTAATTTA
1 CCCAATGTGAGTCTAATCTTAAACCATTATATAGAATTGTTCAAACAGA-AAAGCATTTAATTTA
*
52857023 GAGCATCATAGCAATTGAGCA
65 GAGCATCATACCAATTGAGCA
52857044 TAATGTAAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 1 0.01
86 79 0.99
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (86 bp):
CCCAATGTGAGTCTAATCTTAAACCATTATATAGAATTGTTCAAACAGAAAAGCATTTAATTTAG
AGCATCATACCAATTGAGCAG
Found at i:52861329 original size:22 final size:22
Alignment explanation
Indices: 52861299--52861350 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
52861289 AATGGCTAAG
* * *
52861299 AGCCGTAAATAGGATAGCTATA
1 AGCCATAAATAGAATAGCTACA
* *
52861321 AGCTATAAATAGAATGGCTACA
1 AGCCATAAATAGAATAGCTACA
52861343 AGCCATAA
1 AGCCATAA
52861351 GTACATTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (22 bp):
AGCCATAAATAGAATAGCTACA
Found at i:52861397 original size:32 final size:33
Alignment explanation
Indices: 52861340--52861483 Score: 138
Period size: 32 Copynumber: 4.5 Consensus size: 33
52861330 TAGAATGGCT
* * * *
52861340 ACAAGCCATAAGTA-CATTAATATGATTAGCAT
1 ACAAGCCATCAGTAGCAGTAATATGATCAGCAC
* *
52861372 A-AAGCCATCAGTAGCAGTGATATGATCGGCAC
1 ACAAGCCATCAGTAGCAGTAATATGATCAGCAC
* *
52861404 ATAA-CCATCAGTAACAGTAATATGAT-AGGCAC
1 ACAAGCCATCAGTAGCAGTAATATGATCA-GCAC
* * *
52861436 A-AAGCTATCAGTAGCAGTGATATGATCAGTAC
1 ACAAGCCATCAGTAGCAGTAATATGATCAGCAC
52861468 ACAA-CCATCAGTAGCA
1 ACAAGCCATCAGTAGCA
52861484 TCGCGGCAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
31 13 0.14
32 74 0.80
33 5 0.05
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (33 bp):
ACAAGCCATCAGTAGCAGTAATATGATCAGCAC
Found at i:52861458 original size:64 final size:64
Alignment explanation
Indices: 52861340--52861480 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 64
52861330 TAGAATGGCT
* * * *
52861340 ACAAGCCATAAGT-ACATTAATATGATTAGCATAAAGCCATCAGTAGCAGTGATATGATCGGCAC
1 ACAA-CCATCAGTAACAGTAATATGATTAGCACAAAGCCATCAGTAGCAGTGATATGATCAGCAC
* * *
52861404 ATAACCATCAGTAACAGTAATATGA-TAGGCACAAAGCTATCAGTAGCAGTGATATGATCAGTAC
1 ACAACCATCAGTAACAGTAATATGATTA-GCACAAAGCCATCAGTAGCAGTGATATGATCAGCAC
52861468 ACAACCATCAGTA
1 ACAACCATCAGTA
52861481 GCATCGCGGC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 9 0.13
64 58 0.87
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (64 bp):
ACAACCATCAGTAACAGTAATATGATTAGCACAAAGCCATCAGTAGCAGTGATATGATCAGCAC
Found at i:52861695 original size:15 final size:15
Alignment explanation
Indices: 52861677--52861706 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52861667 ACAGACAAAC
52861677 CAGACAAACCAGTCA
1 CAGACAAACCAGTCA
*
52861692 CAGACAAATCAGTCA
1 CAGACAAACCAGTCA
52861707 TACCAATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.30, G:0.13, T:0.10
Consensus pattern (15 bp):
CAGACAAACCAGTCA
Found at i:52861728 original size:24 final size:24
Alignment explanation
Indices: 52861653--52861731 Score: 122
Period size: 24 Copynumber: 3.3 Consensus size: 24
52861643 TGCTCAGAAT
52861653 CAGTCATACCAATCACAGACAAAC
1 CAGTCATACCAATCACAGACAAAC
* * * *
52861677 CAGACAAACCAGTCACAGACAAAT
1 CAGTCATACCAATCACAGACAAAC
52861701 CAGTCATACCAATCACAGACAAAC
1 CAGTCATACCAATCACAGACAAAC
52861725 CAGTCAT
1 CAGTCAT
52861732 TTACATCACG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.46, C:0.32, G:0.10, T:0.13
Consensus pattern (24 bp):
CAGTCATACCAATCACAGACAAAC
Found at i:52861745 original size:24 final size:24
Alignment explanation
Indices: 52861712--52861760 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
52861702 AGTCATACCA
*
52861712 ATCACAGACAAACCAGTCATTTAC
1 ATCACAGACAAACCAATCATTTAC
* *
52861736 ATCACGGACAAATCAATCATTTAC
1 ATCACAGACAAACCAATCATTTAC
52861760 A
1 A
52861761 CTCAAGGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (24 bp):
ATCACAGACAAACCAATCATTTAC
Found at i:52861854 original size:53 final size:54
Alignment explanation
Indices: 52861797--52861988 Score: 165
Period size: 53 Copynumber: 3.6 Consensus size: 54
52861787 CTCCAGAGGC
* * * *** * *
52861797 ATTACGGTCATTTAACCTTATAGGGGTATTTTGGTTATTTAACCCTAT-GGGGT
1 ATTACGGTCATTTAACCCTACAGGGGCATTACAGTCATTTAACCCTATAGGGGA
* *
52861850 ATTACGGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGA
1 ATTACGGTCATTTAACCCTACAGGGGCATTACAGTCATTTAACCCTATAGGGGA
* * ** * * *
52861904 ATTACTGTCATTTTACCCTACA-ATGCATTAC-GATCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTAACCCTACAGGGGCATTACAG-TCATTTAACCCTATAGGGGA
* * * *
52861957 ACTACAGTCATTTTACCCTATAGGGGCATTAC
1 ATTACGGTCATTTAACCCTACAGGGGCATTAC
52861989 GGTTAATTTA
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.01
53 83 0.72
54 32 0.28
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
ATTACGGTCATTTAACCCTACAGGGGCATTACAGTCATTTAACCCTATAGGGGA
Found at i:52861864 original size:27 final size:26
Alignment explanation
Indices: 52861794--52862000 Score: 171
Period size: 27 Copynumber: 7.8 Consensus size: 26
52861784 ACCCTCCAGA
* *
52861794 GGCATTACGGTCATTTAACCTTATAGG
1 GGCATTACGGTCATTTTACCCTAT-GG
* ** * *
52861821 GGTATTTTGGTTATTTAACCCTATGG
1 GGCATTACGGTCATTTTACCCTATGG
* *
52861847 GGTATTACGGTCATTTTACCCTACAGG
1 GGCATTACGGTCATTTTACCCTA-TGG
*
52861874 GGCATTACAGTCATTTTACCCTATAGG
1 GGCATTACGGTCATTTTACCCTAT-GG
* * ***
52861901 GGAATTACTGTCATTTTACCCTACAA
1 GGCATTACGGTCATTTTACCCTATGG
* * *
52861927 TGCATTACGATCATTTTACCCTACAGG
1 GGCATTACGGTCATTTTACCCTA-TGG
* *
52861954 GGCACTACAGTCATTTTACCCTATAGG
1 GGCATTACGGTCATTTTACCCTAT-GG
* *
52861981 GGCATTACGGTTAATTTACC
1 GGCATTACGGTCATTTTACC
52862001 TATCGACGGT
Statistics
Matches: 142, Mismatches: 34, Indels: 8
0.77 0.18 0.04
Matches are distributed among these distances:
26 40 0.28
27 102 0.72
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (26 bp):
GGCATTACGGTCATTTTACCCTATGG
Found at i:52861878 original size:80 final size:80
Alignment explanation
Indices: 52861777--52861988 Score: 248
Period size: 80 Copynumber: 2.7 Consensus size: 80
52861767 GGGAAAAATA
* * * * * * * *
52861777 GTCA-TTTACCCTCCAGAGGCATTACGGTCATTTAACCTTATAGGGGTATT-TTGGTTATTTAAC
1 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGAATTACT-GTCATTTAAC
*** *
52861840 CCTATGGGGTATTACG
65 CCTACAAGGCATTACG
*
52861856 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGAATTACTGTCATTTTACC
1 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGAATTACTGTCATTTAACC
*
52861921 CTACAATGCATTACG
66 CTACAAGGCATTACG
* * *
52861936 ATCATTTTACCCTACAGGGGCACTACAGTCATTTTACCCTATAGGGGCATTAC
1 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGAATTAC
52861989 GGTTAATTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 4 0.04
80 109 0.96
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (80 bp):
GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATAGGGGAATTACTGTCATTTAACC
CTACAAGGCATTACG
Found at i:52862024 original size:54 final size:55
Alignment explanation
Indices: 52861961--52862107 Score: 176
Period size: 54 Copynumber: 2.7 Consensus size: 55
52861951 AGGGGCACTA
* * *
52861961 CAGTCATTTTACCCTATAG-GGGCATTACGGTTAA-TTTACCTATCGACGGTATTT
1 CAGTAATTTTACCCTATAGAGGGCATTAC-GATAATTTTACCCATCGACGGTATTT
* * * *
52862015 CAGTAATTTTACCC-ATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTT
1 CAGTAATTTTACCCTATAGAGGGCATTACGATAATTTTACCCATCGACGGTATTT
* *
52862069 CGGTAATTTTACCCT-TAGAGGGCATTTCGATAATTTTAC
1 CAGTAATTTTACCCTATAGAGGGCATTACGATAATTTTAC
52862108 GGCCCAATCC
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
53 7 0.09
54 73 0.91
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (55 bp):
CAGTAATTTTACCCTATAGAGGGCATTACGATAATTTTACCCATCGACGGTATTT
Found at i:52862025 original size:27 final size:26
Alignment explanation
Indices: 52861995--52862107 Score: 145
Period size: 27 Copynumber: 4.2 Consensus size: 26
52861985 TTACGGTTAA
* *
52861995 TTTACCTATCGACGGTATTTCAGTAAT
1 TTTACCCATCGAGGGTATTTC-GTAAT
52862022 TTTACCCATCGAGGGTATTTCGATAAT
1 TTTACCCATCGAGGGTATTTCG-TAAT
52862049 TTTACCCATCGAGGGTATTTCGGTAAT
1 TTTACCCATCGAGGGTATTTC-GTAAT
* * *
52862076 TTTACCCTTAGAGGGCATTTCGATAAT
1 TTTACCCATCGAGGGTATTTCG-TAAT
52862103 TTTAC
1 TTTAC
52862108 GGCCCAATCC
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
26 2 0.03
27 75 0.96
28 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (26 bp):
TTTACCCATCGAGGGTATTTCGTAAT
Found at i:52864048 original size:21 final size:21
Alignment explanation
Indices: 52863990--52864042 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
52863980 TTTTTTTCCA
* *
52863990 AAACCACTTTACTTTAGGGGT
1 AAACCACTTGACTTTAAGGGT
52864011 AAACCACTTGACTTTAAGGGT
1 AAACCACTTGACTTTAAGGGT
52864032 AAACCACTTGA
1 AAACCACTTGA
52864043 ACTTAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (21 bp):
AAACCACTTGACTTTAAGGGT
Found at i:52864404 original size:24 final size:24
Alignment explanation
Indices: 52864377--52864428 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52864367 TTAGTAAGTC
*
52864377 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52864401 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52864425 AAAT
1 AAAT
52864429 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52866375 original size:24 final size:24
Alignment explanation
Indices: 52866348--52866399 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52866338 TTAGTAAGTC
*
52866348 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52866372 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52866396 AAAT
1 AAAT
52866400 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52866647 original size:15 final size:15
Alignment explanation
Indices: 52866627--52866660 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
52866617 GGGCTATTAT
52866627 ATATAAGGTTCGCAC
1 ATATAAGGTTCGCAC
52866642 ATATAAGGTTCGCAC
1 ATATAAGGTTCGCAC
52866657 ATAT
1 ATAT
52866661 TAAATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (15 bp):
ATATAAGGTTCGCAC
Found at i:52866695 original size:36 final size:34
Alignment explanation
Indices: 52866654--52866720 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
52866644 ATAAGGTTCG
52866654 CACATATTAAATCACATACTATATAACATGGGGATT
1 CACATATT--ATCACATACTATATAACATGGGGATT
**
52866690 CACATATTATGTCATACTATATAACATGGGG
1 CACATATTATCACATACTATATAACATGGGG
52866721 GCTCGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.72
36 8 0.28
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (34 bp):
CACATATTATCACATACTATATAACATGGGGATT
Found at i:52869941 original size:153 final size:151
Alignment explanation
Indices: 52869658--52870459 Score: 1226
Period size: 150 Copynumber: 5.3 Consensus size: 151
52869648 CAATTGTTCG
* *
52869658 TATTTTGGCCACTTT-TT-GTATTTTTTTCCCGGATTTTATTACTTTTAAAAAATATACTATTTT
1 TATTTCGGCC-CTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTA-TTT
52869721 TTTAATTTTTTTAATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTT
64 TTTAA-TTTTTT-ATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTT
* *
52869786 TTTTAAATAAATTTTAAAAAAAACCCT
127 TTTTAAATAAA-TTT-AAAAAAATCAT
* *
52869813 TATTTCGGCCCTATGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTT
* * * *
52869878 TACTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTTTATTTTTT
66 TAATTTTTTATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
* *
52869943 AAATAAGTTTAAAAAAACCAT
131 AAATAAATTTAAAAAAATCAT
*
52869964 TATTTCGGCCCTATGTTCGTATTTTTTATCCC-AGATTTTATTACTTTTAAAAAATATACTATTT
1 TATTTCGGCCCTTTGTTCGTATTTTTT-TCCCGA-ATTTTATTACTTTTAAAAAATATACTATTT
* * * *
52870028 TTTAATTTTTTAATTTTACATCATTTTAGTACATTATATTTGAAATGTATTAATTTGGTTTGTTT
64 TTTAATTTTTT-ATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTT
*
52870093 CTTAAATAAATTT-AAAAAATCAT
128 TTTAAATAAATTTAAAAAAATCAT
*
52870116 TATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGAATTTTATTACTTTTAAAAAATACACTATTTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTT
*
52870180 TAATTTTTTTATTTTAAATTATTTTAGTACATTATATTTAAAATGTATTAATTTAGTGTGTTTTT
66 TAA-TTTTTTATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTT
*
52870245 TAAATAAA-TT-AAAAAATCCT
130 TAAATAAATTTAAAAAAATCAT
52870265 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTT
*
52870330 TAATTTTTTGTTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
66 TAATTTTTTATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
*
52870395 AAATAAA-TTAAAAAAATCTT
131 AAATAAATTTAAAAAAATCAT
* *
52870415 TATTTCGGCCCTTTGTTTGTA-TTTTTTCCCGAATTTTCTTACTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
52870460 CAATAAAAAC
Statistics
Matches: 605, Mismatches: 33, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
149 124 0.20
150 169 0.28
151 50 0.08
152 75 0.12
153 120 0.20
154 9 0.01
155 17 0.03
156 41 0.07
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (151 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTTT
TAATTTTTTATTTTAAATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
AAATAAATTTAAAAAAATCAT
Found at i:52873303 original size:151 final size:151
Alignment explanation
Indices: 52870463--52873295 Score: 2968
Period size: 151 Copynumber: 18.8 Consensus size: 151
52870453 TTACTTTCAA
* *
52870463 TAAAAACACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA-GAATAAA
1 TAAAAA-ACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAA-AAA
* * * *
52870527 ATTAGAAAATAATATATTTTTTAAAAGTAATAAAATCCGAG--AAAAATACGAACAAATGGCCGA
64 ATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGA
* *
52870590 AATAAGGATTTTTTTTAATTTATT
129 AATAAGG-GTTTTTTAAATTTATT
*
52870614 TAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAAATAATGTAAAATTAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* *
52870679 TAAAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCGGGAAAAAAATACGAACAAAGGGCTGAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGAA
*
52870743 ATAAGGATTTATTTTTTAAATTTATT
130 ATAAGG----GTTTTTTAAATTTATT
* * * *
52870769 TTAAAAACACAGTAAATTAATACATTTCAAACATGATGTACTAAAATAATGTAAAA-TAATAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAA-AAAA
* * * * *
52870833 TATGAAAATAATA-TAT-TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGAGT
65 T-T-AAAA-AATAGTATATTTT-TTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGC
* * *
52870896 CAAAATAAGGATTTTTTTAATTTATT
126 CGAAATAAGGGTTTTTTAAATTTATT
52870922 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGT-AAATTAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * * *
52870986 TTAAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAGAAACAAATACGAACAAAAGGCCGAAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGAAA
*
52871051 TAAGGATTTTTTTTAAATTTATT
131 TAAGG--GTTTTTTAAATTTATT
* * *
52871074 T-CAAAA-ACAC------AATACATTTCATATATAATGTACTAAAATAATGTAAAATAAAAAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAAT-TAAAAAA
* * * *
52871131 TTAAAAAGTAGTATATTTTTTAAAAGTAATAAAATCCGAGATAAAAAATACGAACATAGGGCAGA
65 TTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGA-AAAAAATACGAACAAAGGGCCGA
* *
52871196 AATAAGGGTTTTTTTTAACTTATT
129 AATAAGGG-TTTTTTAAATTTATT
* *
52871220 TAAAAAATACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATAAAAAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAAT--TAAAAA
* * *
52871285 ATTAGAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCG-GAATAAAATACGAACATAGGGCCG
64 ATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCG
52871348 AAATAAGGGTTTTTTTAAATTTATT
128 AAATAAGGG-TTTTTTAAATTTATT
* *
52871373 TAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAAATAATGTAAAATAAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * * **
52871438 TAGAAAATAGTATATTTTTTTAAAAGTAATAAAATCCG-GGAAAAAATA-GAAACTTAGGGCCGA
66 TAAAAAATAGTATA-TTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACG-AACAAAGGGCCGA
52871501 AATAAGGGTTTTTTTTAAATTTATT
129 AATAAGGG--TTTTTTAAATTTATT
* *
52871526 TAAAAAACACACTATATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATAAAAAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAAT-TAAAAAA
* * * *
52871591 TTAGAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCGGGTAAAAAATA-GAACATAGGGCCGA
65 TTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGA
*
52871654 AATAAGGGTTTTTTTTAATTTATT
129 AATAAGGG-TTTTTTAAATTTATT
52871678 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATG------T--AAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * * * * *
52871735 TAAAAAATGGTATATGTTTTAAAAGTAATAAAATCTGGGAAAAAAATACGAACATAGGACCAAAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGAAA
52871800 TAAGGGTTTTTTTAAAATTTATT
131 TAAGGG-TTTTTT-AAATTTATT
*
52871823 T-AAAAACACACTAAATTAATACATTTCAAATATAATGTAATAAAATAAT-TAAAAATT-AAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGT-AAAATTAAAAAA
* * * *
52871885 TTAAAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCGAGAAAAAAATACGAAAAAATGACCAA
65 TTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGA
**** ** ** *** *
52871949 AATACGAACAATTGGT-GCTGCCTC
129 AATA--AGGGTTTTTTAAATTTATT
*** **** * * **** ** * ** ****
52871973 TGCCACTGGCACCAAAGGTGCCGC-TTGTGGCAGGCCCTCCTTCAGTATGTTTTTTTTTAACTGT
1 TAAAAAACACACTAAA-TTAATACATT-T--CA---AAT--AT-A--ATGTACTAAAATAA-TGT
**** ***** *** * * ** ** * *
52872037 CTTTTTTTTTGTATT--ATTTTGGTAAATAATAAAAAAGTAATAAAATC-CAGAAAAAAATATGA
53 -AAAATTAAAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGA
* * *
52872099 AGAAAGGGCCGAAATAAGGATTTTTTTAATTTATT
117 ACAAAGGGCCGAAATAAGGGTTTTTTAAATTTATT
*
52872134 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAAT-TAAAATTTAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * *
52872198 TTAAAAATAGTATA-TTTTTAAAAGTAATAAAAT-TCGGGAAAAAAATACGAACAAATGGCCGAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGAA
* **
52872261 ATAAGGATTTTTTTTATTTATT
130 ATAAGGGTTTTTTAAATTTATT
* * * * *
52872283 TAAAAAACAAAGTAAATTAATACATTTCAAACATGATGTACTAAAATAA--T---A-TAAAATAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * *
52872342 TAAAATAATA-TAT-TTTTATTGAAAGTAATAAAATCCGAG-AAAAAATACGAACAAAAGGCCGA
66 TAAAA-AATAGTATATTTT-TTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGA
*
52872404 AATAAGGATTTTTT-AATTTATT
129 AATAAGGGTTTTTTAAATTTATT
* *
52872426 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAATTAATGTAAAA-TAAAAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* *
52872490 TAAAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCG-GGAAAAAATACGAACAAATGGCCGAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGAA
*
52872553 ATAAGGATTTTTTTTAAATTTATT
130 ATAAGG--GTTTTTTAAATTTATT
* * * * *
52872577 TAAAAAACACAGTAAATTAATATATTTCAAACATGATGTACTAATATAATGTAAAA-TAATAAAA
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAA-AAAA
* * * * *
52872641 TACTAAAATAATA-TAT-TTTTATTGAAAGTAATAAAATCCG-GGAAAAAATATGAACAAAGAGC
65 T--TAAAA-AATAGTATATTTT-TTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGC
*
52872703 CGAAATAAGGATTTTTT-AATTTATT
126 CGAAATAAGGGTTTTTTAAATTTATT
*
52872728 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATATAAAATT-AAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * * * *
52872792 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCAGGGAAAAAAATATGAATATAGGGCCGAAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGAAA
52872857 TAAGGGTTTTTTTAAATTTATT
131 TAAGGG-TTTTTTAAATTTATT
*
52872879 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATAAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * * *
52872944 TAGAAAATAGTATATTTTTTAAAAGTAATAAAAT-TCG-GGAAAAAATACAAACATAGGGCCGAA
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGAA
* *
52873007 ACAAGGGTTTTTTTAATTTATT
130 ATAAGGGTTTTTTAAATTTATT
* *
52873029 TTAAAAACAGAAC-AAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAA-T-----A
1 TAAAAAACA-CACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAA
* * * *
52873087 --AAAAAATAGTAAATTTTTTAAAAGTAATAAAAT-TCGGGAAAAAAATATGAACATAGGGCCGA
65 TTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCT-GAGAAAAAAATACGAACAAAGGGCCGA
52873149 AATAAGGGTTTTTTAAATTTATT
129 AATAAGGGTTTTTTAAATTTATT
*
52873172 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGCAAAATTAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* *
52873237 TAAAAAATAATATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAATAAAGGG
66 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGG
52873296 AAAAAATACG
Statistics
Matches: 2286, Mismatches: 278, Indels: 236
0.82 0.10 0.08
Matches are distributed among these distances:
142 36 0.02
143 191 0.08
144 162 0.07
145 36 0.02
146 59 0.03
147 45 0.02
148 106 0.05
149 137 0.06
150 237 0.10
151 377 0.16
152 223 0.10
153 282 0.12
154 130 0.06
155 117 0.05
156 5 0.00
157 53 0.02
158 6 0.00
159 1 0.00
160 9 0.00
161 12 0.01
162 33 0.01
163 23 0.01
164 3 0.00
165 3 0.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.32
Consensus pattern (151 bp):
TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
TAAAAAATAGTATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAGGGCCGAAA
TAAGGGTTTTTTAAATTTATT
Found at i:52874101 original size:11 final size:11
Alignment explanation
Indices: 52874085--52874136 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
52874075 ATTAATCCTT
*
52874085 TCTCAATTTTC
1 TCTCAAATTTC
*
52874096 TCTCAAATTGC
1 TCTCAAATTTC
52874107 TCTC-AATTTC
1 TCTCAAATTTC
52874117 -CTTCCAAATTTC
1 TC-T-CAAATTTC
52874129 TCTCAAAT
1 TCTCAAAT
52874137 CCATATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 1 0.03
10 6 0.18
11 19 0.56
12 7 0.21
13 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAAATTTC
Found at i:52874111 original size:22 final size:22
Alignment explanation
Indices: 52874085--52874134 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
52874075 ATTAATCCTT
*
52874085 TCTCAATTTTC-TCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTGC
*
52874107 TCTCAATTTCCTTCCAAATTTC
1 TCTCAATTTCCTTCCAAATTGC
52874129 TCTCAA
1 TCTCAA
52874135 ATCCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAATTGC
Found at i:52874158 original size:51 final size:51
Alignment explanation
Indices: 52874096--52874195 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
52874086 CTCAATTTTC
52874096 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* ** * *
52874147 TCTCAATTTGCTCTCAATTTCCTTTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTT
52874196 TTAATTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:52876512 original size:49 final size:49
Alignment explanation
Indices: 52876459--52876579 Score: 224
Period size: 49 Copynumber: 2.5 Consensus size: 49
52876449 GTTTATATTA
*
52876459 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTAATATTATTTG
*
52876508 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTAATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTAATATTATTTG
52876557 ATGTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
52876580 AATATTCTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTAATATTATTTG
Found at i:52881122 original size:42 final size:42
Alignment explanation
Indices: 52880950--52881130 Score: 138
Period size: 42 Copynumber: 4.3 Consensus size: 42
52880940 TCTTCTACAA
* *
52880950 TTCATAGAGATAAGATCTGATGTTAATCCGCTCCACTGCAAC
1 TTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAAC
* ** *
52880992 TTCAG-GAAGATAGGAT-T-ATTTTCTTCAATTTGTTCCACTGCAAC
1 TTCAGAG-AGATAAGATCTGA--TT-TT-AATCCGCTCCACTGCAAC
* *** * **
52881036 TTCAGGGAGATAAGA-CTGGA-TGCGATCTGCTCTTCTGCAAC
1 TTCAGAGAGATAAGATCT-GATTTTAATCCGCTCCACTGCAAC
*
52881077 TTCAGAGAGATAAGATCTGATTTTAATCCGCTCAACTGCAAC
1 TTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAAC
*
52881119 TTCAGGGAGATA
1 TTCAGAGAGATA
52881131 GAATTATTTT
Statistics
Matches: 106, Mismatches: 22, Indels: 22
0.71 0.15 0.15
Matches are distributed among these distances:
40 1 0.01
41 31 0.29
42 41 0.39
43 3 0.03
44 28 0.26
45 1 0.01
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAAC
Found at i:52881614 original size:45 final size:45
Alignment explanation
Indices: 52881564--52881702 Score: 131
Period size: 45 Copynumber: 3.1 Consensus size: 45
52881554 CGATCTGCTT
* *
52881564 CGCTGCCAGTACAGAAAGACAAGATCTGCCATTTTCAACCTACTC
1 CGCTGCCAGTACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
* * * * * * * *
52881609 CGCTG-CTGCT-CAGGGAGACAAG-GCTGGTATCTTCGATCTACTT
1 CGCTGCCAG-TACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
* *
52881652 CGCTGTCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
1 CGCTGCCAGTACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
*
52881697 CACTGC
1 CGCTGC
52881703 TGCTCAGGGA
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
43 20 0.29
44 24 0.35
45 25 0.36
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (45 bp):
CGCTGCCAGTACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
Found at i:52881629 original size:44 final size:44
Alignment explanation
Indices: 52881580--52881714 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 44
52881570 CAGTACAGAA
*
52881580 AGACAAGATCTGCCATTTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGACAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGG
* * * * * * *
52881624 AGACAAG-GCTGGTATCTTCGATCTACTTCGCTG-T-CAATACAGGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCGCTGCTGC--T-CAGGG
*
52881668 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGG
1 AGACAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGG
52881712 AGA
1 AGA
52881715 TAAGGCTGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 20 0.29
44 25 0.36
45 20 0.29
46 1 0.01
47 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (44 bp):
AGACAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGG
Found at i:52881653 original size:88 final size:88
Alignment explanation
Indices: 52881550--52881722 Score: 283
Period size: 88 Copynumber: 2.0 Consensus size: 88
52881540 AAGACTAGTG
* * *
52881550 TCTTCGATCTGCTTCGCTGCCAGTACAGAAAGACAAGATCTGCCATTTTCAACCTACTCCGCTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTTCAACCTACTCCACTGC
52881615 TGCTCAGGGAGACAAGGCTGGTA
66 TGCTCAGGGAGACAAGGCTGGTA
* * *
52881638 TCTTCGATCTACTTCGCTGTCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTTCAACCTACTCCACTGC
*
52881703 TGCTCAGGGAGATAAGGCTG
66 TGCTCAGGGAGACAAGGCTG
52881723 AAGTTTCACC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTGGTA
Found at i:52882969 original size:8 final size:8
Alignment explanation
Indices: 52882958--52883010 Score: 65
Period size: 8 Copynumber: 6.5 Consensus size: 8
52882948 ATTTTTACTC
52882958 TTTTCATTT
1 TTTTCA-TT
52882967 TTTTCA-T
1 TTTTCATT
52882974 TTTT-ATT
1 TTTTCATT
52882981 TTTTCATT
1 TTTTCATT
52882989 TTTTCATT
1 TTTTCATT
52882997 TCATTTCATT
1 T--TTTCATT
52883007 TTTT
1 TTTT
52883011 TACGACTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.03
7 10 0.25
8 15 0.38
9 6 0.15
10 8 0.20
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:52882982 original size:14 final size:14
Alignment explanation
Indices: 52882965--52882991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52882955 CTCTTTTCAT
52882965 TTTTTTCATTTTTA
1 TTTTTTCATTTTTA
52882979 TTTTTTCATTTTT
1 TTTTTTCATTTTT
52882992 TCATTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTCATTTTTA
Found at i:52883476 original size:13 final size:13
Alignment explanation
Indices: 52883472--52883500 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52883462 TTGTTTTTTG
52883472 TTTTTTGTTCTTC
1 TTTTTTGTTCTTC
52883485 TTTTTTGTTCTT-
1 TTTTTTGTTCTTC
52883497 TTTT
1 TTTT
52883501 CCTTTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTCTTC
Found at i:52889823 original size:33 final size:33
Alignment explanation
Indices: 52889763--52889825 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
52889753 TGTAGGTATA
* * *
52889763 ATAATAATAATAATATATAATATAATAATAATT
1 ATAATAATAATAACAAATAATACAATAATAATT
*
52889796 ATAATAATAATAACAAATGATACAATAATA
1 ATAATAATAATAACAAATAATACAATAATA
52889826 GTGAAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (33 bp):
ATAATAATAATAACAAATAATACAATAATAATT
Found at i:52889825 original size:3 final size:3
Alignment explanation
Indices: 52889760--52889808 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
52889750 ATATGTAGGT
*
52889760 ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA ATT ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
52889805 ATA A
1 ATA A
52889809 CAAATGATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:52890422 original size:14 final size:14
Alignment explanation
Indices: 52890400--52890434 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52890390 TCTCCTTCTC
*
52890400 TTTTCTTTTTGTTT
1 TTTTTTTTTTGTTT
52890414 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
52890428 TGTTTTT
1 T-TTTTT
52890435 AAGAAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:52891929 original size:22 final size:22
Alignment explanation
Indices: 52891904--52891945 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
52891894 TAATTAGATA
52891904 AATT-AATAAATATAAGTTTTTT
1 AATTAAATAAATATAA-TTTTTT
52891926 AATTAAATAAATATAATTTT
1 AATTAAATAAATATAATTTT
52891946 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTAAATAAATATAATTTTTT
Found at i:52891952 original size:21 final size:22
Alignment explanation
Indices: 52891908--52891955 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
52891898 TAGATAAATT
52891908 AATAAATATAAGTTTTTTAATTA
1 AATAAATATAAGTTTTTT-ATTA
52891931 AATAAATATAA-TTTTATT-TTA
1 AATAAATATAAGTTTT-TTATTA
52891952 AATA
1 AATA
52891956 TGATAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.29
22 4 0.17
23 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATAAATATAAGTTTTTTATTA
Found at i:52897883 original size:21 final size:21
Alignment explanation
Indices: 52897854--52897894 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52897844 CTTGTTTGGT
*
52897854 GAGAAATTTGAGAGAAAATGG
1 GAGAAATTTAAGAGAAAATGG
* *
52897875 GAGAGATTTAAGGGAAAATG
1 GAGAAATTTAAGAGAAAATG
52897895 ATAAAAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (21 bp):
GAGAAATTTAAGAGAAAATGG
Found at i:52902249 original size:46 final size:46
Alignment explanation
Indices: 52902182--52902526 Score: 556
Period size: 46 Copynumber: 7.6 Consensus size: 46
52902172 TTTGAGTACT
52902182 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
52902228 TCTGAGT-AAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGA-TCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
52902274 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52902320 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
52902366 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
52902412 TCTGATCAAATGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
52902457 TTTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52902502 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
52902527 ATCATATGTA
Statistics
Matches: 281, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
43 12 0.04
44 5 0.02
45 62 0.22
46 201 0.72
47 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:52914361 original size:19 final size:19
Alignment explanation
Indices: 52914333--52914369 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
52914323 TTTTGGAGAA
52914333 TAAAAGTTT-GAGGGAAAG
1 TAAAAGTTTGGAGGGAAAG
52914351 TAAATAGTTTGGAGGGAAA
1 TAAA-AGTTTGGAGGGAAA
52914370 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.24
Consensus pattern (19 bp):
TAAAAGTTTGGAGGGAAAG
Found at i:52914707 original size:9 final size:9
Alignment explanation
Indices: 52914693--52914729 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52914683 TATAGTTTGA
52914693 TATTCGAAT
1 TATTCGAAT
52914702 TATTCGAAT
1 TATTCGAAT
*
52914711 TATTCGAGT
1 TATTCGAAT
52914720 TATTCGAAT
1 TATTCGAAT
52914729 T
1 T
52914730 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52916276 original size:19 final size:19
Alignment explanation
Indices: 52916252--52916290 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52916242 ACACTGTTAA
52916252 AATTCTCTGTTACATTGCT
1 AATTCTCTGTTACATTGCT
52916271 AATTCTCTGTTACATTGCT
1 AATTCTCTGTTACATTGCT
52916290 A
1 A
52916291 TTAAGTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (19 bp):
AATTCTCTGTTACATTGCT
Found at i:52918810 original size:15 final size:15
Alignment explanation
Indices: 52918787--52918823 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
52918777 TTCTTCTCAA
*
52918787 AAGCATTCCTAAATT
1 AAGCGTTCCTAAATT
52918802 AAGCGTTCCTAAATT
1 AAGCGTTCCTAAATT
52918817 AAGCGTT
1 AAGCGTT
52918824 AATCTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (15 bp):
AAGCGTTCCTAAATT
Done.