Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 74 of 91
Found at i:26906979 original size:14 final size:14
Alignment explanation
Indices: 26906962--26907010 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
26906952 TTTATTTTCT
26906962 TATTTTATTTTTAA
1 TATTTTATTTTTAA
*
26906976 TATTTTAAATTTTAA
1 TATTTT-ATTTTTAA
*
26906991 -ATTTTTTTATTTAA
1 TATTTTATT-TTTAA
26907005 TATTTT
1 TATTTT
26907011 TAATTTGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.03
14 16 0.55
15 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTATTTTTAA
Found at i:26907025 original size:29 final size:28
Alignment explanation
Indices: 26906963--26907018 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
26906953 TTATTTTCTT
*
26906963 ATTTTATTTTTAATATTTTAAATTTTAA
1 ATTTTATTTTTAATATTTTAAATTTGAA
* *
26906991 ATTTTTTTATTTAATATTTTTAATTTGA
1 ATTTTATT-TTTAATATTTTAAATTTGA
26907019 TGATTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTTATTTTTAATATTTTAAATTTGAA
Found at i:26916999 original size:2 final size:2
Alignment explanation
Indices: 26916992--26917074 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
26916982 AAACTATTAA
*
26916992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26917034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26917075 AACTGTAATG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26918876 original size:52 final size:52
Alignment explanation
Indices: 26918723--26918879 Score: 224
Period size: 52 Copynumber: 3.0 Consensus size: 52
26918713 ACACATGACG
* ** * * *
26918723 GTGATAGTAGTGTACTGTGTGAGTGCACACATTGGTGATATATGCCATGGGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
** * *
26918775 ACGATAGTGGTGTGTTGTGTGAGTACACACACTGATAATATATGCCATGTGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
26918827 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
26918879 G
1 G
26918880 ATGTGAGAGT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 91 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (52 bp):
GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
Found at i:26918903 original size:36 final size:35
Alignment explanation
Indices: 26918854--26918968 Score: 126
Period size: 36 Copynumber: 3.2 Consensus size: 35
26918844 TGTGAGTGCA
26918854 CACACTGATGATATATGCCATGTGCGATGT-GAGAGTG
1 CACA-TGATGATAT-TGCCATGTGCGATGTGGA-AGTG
* *
26918891 CACATGATGATATTGCCTTGTGCGATGAGGAAGTG
1 CACATGATGATATTGCCATGTGCGATGTGGAAGTG
* * *
26918926 CACAGGATGAT-TCTAGCTATGTGCGGTGTGGAAGTG
1 CACATGATGATAT-T-GCCATGTGCGATGTGGAAGTG
26918962 CACATGA
1 CACATGA
26918969 GCTGGTGAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
34 1 0.01
35 28 0.42
36 34 0.51
37 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (35 bp):
CACATGATGATATTGCCATGTGCGATGTGGAAGTG
Found at i:26919231 original size:72 final size:73
Alignment explanation
Indices: 26919133--26919275 Score: 182
Period size: 73 Copynumber: 2.0 Consensus size: 73
26919123 AATTCTTTAA
* * * * *
26919133 CTTGATAGCCTTGGTTTTCGCTGCAGC-GAAATTCATTCTCGCTGCAACAAGAAACTCTCGGGT-
1 CTTGATAGCCTAGATTTTCGCTGCAGCAAAAATGCATTCTCGCTACAACAAGAAACTCTCGGGTG
26919196 GTTGGGGG
66 GTTGGGGG
* * * *
26919204 CTTGACTAGCCTAGATTTTTGCTGCAGCAAAAATGCATTCTCGCTACAGCGAGGAACTCTCGGGT
1 CTTGA-TAGCCTAGATTTTCGCTGCAGCAAAAATGCATTCTCGCTACAACAAGAAACTCTCGGGT
26919269 GGTTGGG
65 GGTTGGG
26919276 TAAAATGCCT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
71 5 0.08
72 19 0.32
73 30 0.50
74 6 0.10
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (73 bp):
CTTGATAGCCTAGATTTTCGCTGCAGCAAAAATGCATTCTCGCTACAACAAGAAACTCTCGGGTG
GTTGGGGG
Found at i:26946809 original size:2 final size:2
Alignment explanation
Indices: 26946802--26946938 Score: 105
Period size: 2 Copynumber: 68.0 Consensus size: 2
26946792 CTTTGCATAC
* * *
26946802 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * ** * *
26946844 AC AT AT AT NT CCT TT GAT -T CT TT GC AT AC AT AT AT AT AT AT AC
1 AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
26946887 AT AC AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26946929 AT AT AT AT AT
1 AT AT AT AT AT
26946939 TCATGACCTT
Statistics
Matches: 105, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
1 1 0.01
2 102 0.97
3 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:26946898 original size:71 final size:70
Alignment explanation
Indices: 26946782--26946922 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 70
26946772 CGCACCAACA
26946782 TCCTTTGATTCTTTGCATACATATATATATATACATACATATATATATATATATATATACATACA
1 TCCTTTGATTCTTTGCATACATATATATATATACATACATATATATATATATATATATACATACA
26946847 TATAT
66 TATAT
26946852 NTCCTTTGATTCTTTGCATACATATATATATATACATACATATATATATATATATATATACATAC
1 -TCCTTTGATTCTTTGCATACATATATATATATACATACATATATATATATATATATATACATAC
26946917 ATATAT
65 ATATAT
26946923 ATATATATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (70 bp):
TCCTTTGATTCTTTGCATACATATATATATATACATACATATATATATATATATATATACATACA
TATAT
Found at i:26950014 original size:27 final size:27
Alignment explanation
Indices: 26949983--26950042 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
26949973 TTTCTGACGG
*
26949983 ATAATCTAAACTAGATTTTATTGTGTT
1 ATAATCTAAACTAGATTTCATTGTGTT
26950010 ATAATCTAAACTAGATTTCATTGTGTT
1 ATAATCTAAACTAGATTTCATTGTGTT
26950037 ATAATC
1 ATAATC
26950043 CTATGCGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (27 bp):
ATAATCTAAACTAGATTTCATTGTGTT
Found at i:26955914 original size:21 final size:20
Alignment explanation
Indices: 26955874--26955916 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
26955864 AAAAAACATC
*
26955874 AAAAAATATTTTTTTAATTT
1 AAAAAATATTTTATTAATTT
26955894 AAAAAATATTAATTATT-ATTT
1 AAAAAATATT--TTATTAATTT
26955915 AA
1 AA
26955917 TTAAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAAAATATTTTATTAATTT
Found at i:26955941 original size:26 final size:24
Alignment explanation
Indices: 26955881--26955941 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
26955871 ATCAAAAAAT
* *
26955881 ATTTTTTTAATTTAAAAAATATTA
1 ATTTTTTTAATTAAAAAAATATAA
26955905 ATTATTATTTAATTAAAATACAATATAA
1 ATT-TT-TTTAATTAAAA-A-AATATAA
26955933 ATTTTTTTA
1 ATTTTTTTA
26955942 GATAGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 3 0.10
25 2 0.06
26 14 0.45
27 3 0.10
28 9 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTTTTAATTAAAAAAATATAA
Found at i:26957973 original size:2 final size:2
Alignment explanation
Indices: 26957966--26957990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26957956 TAAATTTGAG
26957966 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26957991 GGTAACTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26971501 original size:2 final size:2
Alignment explanation
Indices: 26971494--26971532 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26971484 GATAAAAGAA
* *
26971494 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26971533 AAGAAGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:26986403 original size:181 final size:181
Alignment explanation
Indices: 26986168--26986774 Score: 759
Period size: 181 Copynumber: 3.4 Consensus size: 181
26986158 AAAATGGAAA
* * * * *
26986168 AAAAGAGATCATAACAGTTTCCTTAGTTTATGAATCTCCATGAATACAATCCATTTTCTAAAAAT
1 AAAA-AGATCATAACAGTCTCCTTAATTTATGAATCACCATGAACACAATCCATTTACTAAAAAT
* * * * *
26986233 TTAAAACCATTGATGAATCACTCCTCAACATCATCACTTTCATCACATCTAAGTATTAAACTCGT
65 TTAAAACCATTGATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAACTTGT
* * * * * * *
26986298 ATTGATATGAATAACTTGCACAGGGATTGTTATTCACGACAATTCACAAAAT
130 ACTAACATGAATAACTTGCAAAGGGATAGTTGTTCATGACAATTCACAAAAT
* * * * *
26986350 AAAAAGATCATAACAGTTTTCTTAATTTATGAATCACCATGAACACAATCCATTAACTGAAAATC
1 AAAAAGATCATAACAGTCTCCTTAATTTATGAATCACCATGAACACAATCCATTTACTAAAAATT
*
26986415 TAAAACCATTGATGAATCACTCCTCAACACCATTGCTTTGATCACATCCAAGTATTAAACTTGTA
66 TAAAACCATTGATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAACTTGTA
* ** * *
26986480 CTAACATGAATAACTTGTAAAAAGATCGTTGTTCATGGCAATTCACAAAAT
131 CTAACATGAATAACTTGCAAAGGGATAGTTGTTCATGACAATTCACAAAAT
* * * ** * *
26986531 AAAGAGATCATAACAATCTCCTTAATTTATGAGTTGCCATGAACACGATCCATTTACTAGAAATT
1 AAAAAGATCATAACAGTCTCCTTAATTTATGAATCACCATGAACACAATCCATTTACTAAAAATT
* * * *
26986596 TAAAACCATTAATGAATCACTGCTCAACACCATCGTTTTGATCACATCCATGTATTAAACTTGTA
66 TAAAACCATTGATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAACTTGTA
* ** * *
26986661 CTAACCTGAATAACCCGCAAAGGAATCAG--GTTCATGACAATCCACAAAAT
131 CTAACATGAATAACTTGCAAAGGGAT-AGTTGTTCATGACAATTCACAAAAT
* * *
26986711 AAAAAGATCATAACAGTCTTCTTAATTTATAAATCACCATGAACACAATCCATTTACTAGAAAT
1 AAAAAGATCATAACAGTCTCCTTAATTTATGAATCACCATGAACACAATCCATTTACTAAAAAT
26986775 CTAAGATATA
Statistics
Matches: 364, Mismatches: 60, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
180 75 0.21
181 284 0.78
182 5 0.01
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (181 bp):
AAAAAGATCATAACAGTCTCCTTAATTTATGAATCACCATGAACACAATCCATTTACTAAAAATT
TAAAACCATTGATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAACTTGTA
CTAACATGAATAACTTGCAAAGGGATAGTTGTTCATGACAATTCACAAAAT
Found at i:26987797 original size:53 final size:53
Alignment explanation
Indices: 26987712--26987818 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
26987702 ACTCATGATC
* * * **
26987712 TTTGCAAGTTATTCTGAATTACCTTCATTTCCTTGTGTGACATAATTATTCCA
1 TTTGCAACTCATTCTGAATTACCTTCAATTCCTTGTAAGACATAATTATTCCA
* *
26987765 TTTGCAACTCATTTTGAATTACCTTCAATTCCTTGTAAGACATAGTTATTCCA
1 TTTGCAACTCATTCTGAATTACCTTCAATTCCTTGTAAGACATAATTATTCCA
26987818 T
1 T
26987819 GTTTATTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (53 bp):
TTTGCAACTCATTCTGAATTACCTTCAATTCCTTGTAAGACATAATTATTCCA
Found at i:26988266 original size:25 final size:27
Alignment explanation
Indices: 26988208--26988265 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 27
26988198 TATTAAAAAG
*
26988208 ATATATTAACAAATCAAAAATAATTAT
1 ATATGTTAACAAATCAAAAATAATTAT
26988235 ATGTATGTTAACAAATCAAAAATAATTAT
1 A--TATGTTAACAAATCAAAAATAATTAT
26988264 AT
1 AT
26988266 GAAGAGCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
29 26 0.93
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (27 bp):
ATATGTTAACAAATCAAAAATAATTAT
Found at i:26991048 original size:2 final size:2
Alignment explanation
Indices: 26991041--26991067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26991031 TTTCTAAACT
26991041 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
26991068 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26997126 original size:3 final size:3
Alignment explanation
Indices: 26997120--26997145 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26997110 CAAAAAAAAC
26997120 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
26997146 GGTAAAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:26998126 original size:4 final size:4
Alignment explanation
Indices: 26998117--26998141 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26998107 AATGAAACCA
26998117 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
26998142 TAGATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:27005962 original size:17 final size:18
Alignment explanation
Indices: 27005940--27005973 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27005930 AAATAATAAC
27005940 ATATATT-AATTTTTTTA
1 ATATATTAAATTTTTTTA
27005957 ATATATTAAATTTTTTT
1 ATATATTAAATTTTTTT
27005974 TTCAATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATTAAATTTTTTTA
Found at i:27010513 original size:2 final size:2
Alignment explanation
Indices: 27010506--27010540 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27010496 TGTCAATTAC
27010506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27010541 CTCAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27016948 original size:2 final size:2
Alignment explanation
Indices: 27016941--27016980 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
27016931 NNNNNNNNNN
*
27016941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27016981 CATACATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27017111 original size:38 final size:38
Alignment explanation
Indices: 27017018--27017131 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
27017008 CACACTCAAC
* * *** *
27017018 TCATGTGCACTCCCTACACGCATAAGGCAATATCATTA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
*
27017056 CCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
* *
27017094 TCATGTGCATTCCCTACTCGCGCATTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
27017132 CACGCACTCC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (38 bp):
TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
Found at i:27020057 original size:143 final size:143
Alignment explanation
Indices: 27019885--27020188 Score: 452
Period size: 143 Copynumber: 2.1 Consensus size: 143
27019875 TTCTTAAAAA
*
27019885 TAAAATGTATTTTTATTTTTAATCATTCTAGAATTTTACTTTAATAACTAAAAATTATTTTTG-G
1 TAAAAT-TATTTCTATTTTTAATCATTCTAGAATTTT--TTTAATAACTAAAAATTATTTTTGAG
*
27019949 GA-TTTTAAAATTTTTTAGAATTTCTAAG-AATAAAAAATTATTTTATGTTTTTCAAAATTTATA
63 GATTTTTAAAA-ATTTTAGAATTTCTAAGTAATAAAAAATTATTTTATGTTTTTCAAAATTTATA
27020012 GATTTTTTTCAAAAATT
127 GATTTTTTTCAAAAATT
* ** * * **
27020029 TAAAATTATTTCTATTTTTTATTGTTCTAGAATTTTTTTAATAATTAGAAATTATTTTTGATTAT
1 TAAAATTATTTCTATTTTTAATCATTCTAGAATTTTTTTAATAACTAAAAATTATTTTTGAGGAT
* *
27020094 TTTTAAAAATTTTAGAATTTCTAAGTATTAAAAAATTATTTTATGTTTTTCTAAATTTATAGATT
66 TTTTAAAAATTTTAGAATTTCTAAGTAATAAAAAATTATTTTATGTTTTTCAAAATTTATAGATT
27020159 TTTTTCAAAAATT
131 TTTTTCAAAAATT
27020172 TAAAATTATTTCTATTT
1 TAAAATTATTTCTATTT
27020189 CTTCTAATTT
Statistics
Matches: 146, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
141 22 0.15
142 17 0.12
143 101 0.69
144 6 0.04
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (143 bp):
TAAAATTATTTCTATTTTTAATCATTCTAGAATTTTTTTAATAACTAAAAATTATTTTTGAGGAT
TTTTAAAAATTTTAGAATTTCTAAGTAATAAAAAATTATTTTATGTTTTTCAAAATTTATAGATT
TTTTTCAAAAATT
Found at i:27020150 original size:46 final size:45
Alignment explanation
Indices: 27019961--27020156 Score: 112
Period size: 48 Copynumber: 4.2 Consensus size: 45
27019951 TTTTAAAATT
* * *
27019961 TTTTAGAATTTCTAAGAATAAAAAATTATTTTATGTTTTTCAAAA
1 TTTTAGAATTTCTAAGTATTAAAAATTATTTTATGTTTTTCTAAA
* * ** * * **
27020006 TTTATAGATTTTTTTCAAAAATTTAAAATTATTTCTAT-TTTTTAT-TG
1 TTT-TAGA-ATTTCT-AAGTATTAAAAATTATTT-TATGTTTTTCTAAA
* * * *
27020053 TTCTAGAATTTTTTTAA-TAATTAGAAATTATTTT-TGATTATTTTTAAAAA
1 TTTTAGAA--TTTCTAAGT-ATTAAAAATTATTTTATG-TT-TTTCT--AAA
27020103 TTTTAGAATTTCTAAGTATTAAAAAATTATTTTATGTTTTTCTAAA
1 TTTTAGAATTTCTAAGTATT-AAAAATTATTTTATGTTTTTCTAAA
27020149 TTTATAGA
1 TTT-TAGA
27020157 TTTTTTTCAA
Statistics
Matches: 113, Mismatches: 21, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
44 1 0.01
45 4 0.04
46 30 0.27
47 19 0.17
48 33 0.29
49 17 0.15
50 9 0.08
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (45 bp):
TTTTAGAATTTCTAAGTATTAAAAATTATTTTATGTTTTTCTAAA
Found at i:27020194 original size:48 final size:45
Alignment explanation
Indices: 27019982--27020195 Score: 141
Period size: 48 Copynumber: 4.5 Consensus size: 45
27019972 CTAAGAATAA
*
27019982 AAAATTATTTTATGTTTTTCAAAATTTATAGATTTTTTTCAAAAATTT
1 AAAATTATTTTA--TTTTTCTAAATTTATAGATTTTTTT-AAAAATTT
* * *
27020030 AAAATTATTTCTATTTTT-T-ATTGTTCTAGAATTTTTTTAATAA-TT
1 AAAATTATTT-TATTTTTCTAAAT-TTATAG-ATTTTTTTAAAAATTT
* * * ** *
27020075 AGAAATTATTTTTGATTATTTTTAAAAATTT-TAGA-ATTTCTAAGTATTAA
1 A-AAATTA-TTTT-ATT-TTTCT--AAATTTATAGATTTTTTTAAAAATT-T
27020125 AAAATTATTTTATGTTTTTCTAAATTTATAGATTTTTTTCAAAAATTT
1 AAAATTATTTTA--TTTTTCTAAATTTATAGATTTTTTT-AAAAATTT
27020173 AAAATTATTTCTATTTCTTCTAA
1 AAAATTATTT-TATTT-TTCTAA
27020196 TTTTTAAAGT
Statistics
Matches: 130, Mismatches: 16, Indels: 40
0.70 0.09 0.22
Matches are distributed among these distances:
45 5 0.04
46 22 0.17
47 27 0.21
48 48 0.37
49 20 0.15
50 4 0.03
51 2 0.02
52 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (45 bp):
AAAATTATTTTATTTTTCTAAATTTATAGATTTTTTTAAAAATTT
Found at i:27027549 original size:2 final size:2
Alignment explanation
Indices: 27027537--27027565 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
27027527 ATATGAAAGC
27027537 CA CA C- CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
27027566 TTATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27028200 original size:19 final size:20
Alignment explanation
Indices: 27028165--27028249 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
27028155 ATCATGGTAG
* *
27028165 GAACACATTCATGATGGGAA
1 GAACACGTTCATTATGGGAA
27028185 GAACA-GTTCATTATGGGAA
1 GAACACGTTCATTATGGGAA
**
27028204 G-ACTACGCCCATTATGGGAA
1 GAAC-ACGTTCATTATGGGAA
* * *
27028224 GAACACCTTCATCATGAGAA
1 GAACACGTTCATTATGGGAA
*
27028244 TAACAC
1 GAACAC
27028250 ATTAATCTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.04
19 14 0.27
20 34 0.65
21 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
GAACACGTTCATTATGGGAA
Found at i:27029370 original size:96 final size:96
Alignment explanation
Indices: 27029206--27029397 Score: 312
Period size: 96 Copynumber: 2.0 Consensus size: 96
27029196 ATCACTCACT
27029206 AGACAATGCAACAAGAAACTGCACTTCTTTTCTTCCAATATATTTTGAGTAAAAGTTTCCCAAAC
1 AGACAATGCAACAAGAAACTGCACTTCTTTTCTTCCAATATATTTTGAGTAAAAGTTTCCCAAAC
** *
27029271 ATTTCTAGATGTTAATAAATTTGGTGATGGC
66 ATTTCTAGACATTAATAAATGTGGTGATGGC
* * * * *
27029302 AGACAATGCAACAAGAAATTGCACTTCTTTTCTTCCAATATTTTTTGAGTGACAGTTTCTCAAAC
1 AGACAATGCAACAAGAAACTGCACTTCTTTTCTTCCAATATATTTTGAGTAAAAGTTTCCCAAAC
27029367 ATTTCTAGACATTAATAAATGTGGTGATGGC
66 ATTTCTAGACATTAATAAATGTGGTGATGGC
27029398 TACTATAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (96 bp):
AGACAATGCAACAAGAAACTGCACTTCTTTTCTTCCAATATATTTTGAGTAAAAGTTTCCCAAAC
ATTTCTAGACATTAATAAATGTGGTGATGGC
Found at i:27037529 original size:24 final size:25
Alignment explanation
Indices: 27037500--27037547 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
27037490 TTTTATTTTA
*
27037500 AATTAAATAAATTTTA-TAATTAAT
1 AATTAAATAAATATTATTAATTAAT
*
27037524 AATTAAATAACTATTATTAATTAA
1 AATTAAATAAATATTATTAATTAA
27037548 AATATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAAATAAATATTATTAATTAAT
Found at i:27038190 original size:20 final size:20
Alignment explanation
Indices: 27038167--27038204 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27038157 GGAAACACAA
27038167 TTATT-TAATTTTGGCCTAAT
1 TTATTGTAATTTT-GCCTAAT
*
27038187 TTATTGTCATTTTGCCTA
1 TTATTGTAATTTTGCCTA
27038205 TGTTATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (20 bp):
TTATTGTAATTTTGCCTAAT
Found at i:27055260 original size:26 final size:26
Alignment explanation
Indices: 27055221--27055271 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
27055211 CTTAGTTAAC
*
27055221 TTTTGAGACGTTACTGGTTGTTATTT
1 TTTTGAGACCTTACTGGTTGTTATTT
*
27055247 TTTTGTGACCTTACTGGTTGTTATT
1 TTTTGAGACCTTACTGGTTGTTATT
27055272 GGAATGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.10, G:0.22, T:0.55
Consensus pattern (26 bp):
TTTTGAGACCTTACTGGTTGTTATTT
Found at i:27076012 original size:2 final size:2
Alignment explanation
Indices: 27076005--27076036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27075995 AAGCTGAACC
27076005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27076037 GATGCACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27092478 original size:27 final size:25
Alignment explanation
Indices: 27092426--27092488 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 25
27092416 TGGTATCTTT
27092426 TTAATTTAAATAAATTGAAAACTTA
1 TTAATTTAAATAAATTGAAAACTTA
*
27092451 TTAATTTAATATTAAAATTTAAAA-TTA
1 TTAATTTAA-A-T-AAATTGAAAACTTA
27092478 TTAATATTAAA
1 TTAAT-TTAAA
27092489 ATATACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.27
26 1 0.03
27 10 0.30
28 13 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTAATTTAAATAAATTGAAAACTTA
Found at i:27092484 original size:22 final size:23
Alignment explanation
Indices: 27092456--27092499 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27092446 ACTTATTAAT
*
27092456 TTAATATTAAAATTTA-AAATTA
1 TTAATATTAAAATATACAAATTA
27092478 TTAATATTAAAATATACAAATT
1 TTAATATTAAAATATACAAATT
27092500 TGTATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATATTAAAATATACAAATTA
Found at i:27099888 original size:18 final size:18
Alignment explanation
Indices: 27099865--27099900 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27099855 GTATTCCTTC
27099865 TTAGAAAATCTTCAGAAA
1 TTAGAAAATCTTCAGAAA
27099883 TTAGAAAATCTTCAGAAA
1 TTAGAAAATCTTCAGAAA
27099901 GGAAGGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAGAAAATCTTCAGAAA
Found at i:27105299 original size:2 final size:2
Alignment explanation
Indices: 27105292--27105323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27105282 TAACTAGGAT
27105292 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27105324 AAGTGCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27121913 original size:2 final size:2
Alignment explanation
Indices: 27121906--27121938 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27121896 GCATGCATGT
27121906 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27121939 TAACTCCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27123708 original size:18 final size:18
Alignment explanation
Indices: 27123674--27123708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27123664 CAACAACTAC
**
27123674 CATTAAAACATGGAAAAG
1 CATTAAAACATCCAAAAG
27123692 CATTAAAACATCCAAAA
1 CATTAAAACATCCAAAA
27123709 TTCATCAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (18 bp):
CATTAAAACATCCAAAAG
Found at i:27138698 original size:171 final size:173
Alignment explanation
Indices: 27138320--27138763 Score: 419
Period size: 171 Copynumber: 2.6 Consensus size: 173
27138310 TCATGCAATG
* * * *
27138320 AACCAGGGGC-ATCCCTGCTGTCCTTCTTATGGTCTGACATG-GTCTCAACTTCCTTCTCATAAA
1 AACCA-GGGCAATCCTTGC-GTCCTTATCATGGTCTGGCA-GCGTCTCAACTTCCTTCTCATAAA
* *
27138383 CATACAAATTTTCAGAAGGTTCTGTAGATTCC-AA--AGACAGTCCAATACCTATCTCTTTCTTA
63 TATACAAATTTTCAGAAGGTTCTGTAGATTCCAAATTAGACAGTCAAATACCTATCTCTTTCTTA
* * * **
27138445 TTTTGAAAGGGCACAGCCGCATAAATGGGAAGGTCCTCATGTGATG
128 TTCTGAAAGGACACAGCCGCATAAATGGGAAGGTCCTCAAGTGACA
* * * * * *
27138491 CACCAGGGCAATCCTTGCTGTCCTTGTTACGGTCTGGCAGCGTCTCAACTTCCTTCTGACAAATA
1 AACCAGGGCAATCCTTGC-GTCCTTATCATGGTCTGGCAGCGTCTCAACTTCCTTCTCATAAATA
* * * * *
27138556 TACAAAATTTCAGAAGGTTTTGTAGATTCCAAATTAGA-AGGTTAAATACCTGTCTCTTTTTTAT
65 TACAAATTTTCAGAAGGTTCTGTAGATTCCAAATTAGACA-GTCAAATACCTATCTCTTTCTTAT
* ** * *
27138620 TCTGCAAGGATGCAGTCC-CATCAAT-GGACAGGTGCTCAAGTGACA
129 TCTGAAAGGACACAG-CCGCATAAATGGGA-AGGTCCTCAAGTGACA
* * *
27138665 AACCAGGG-AGATCCTTGC-T-CTTATCATGGTCTGGCA-CATTCTCAAATTCCTTCTCATTAAT
1 AACCAGGGCA-ATCCTTGCGTCCTTATCATGGTCTGGCAGC-GTCTCAACTTCCTTCTCATAAAT
**
27138726 ATACAAATTTTTCA-AAGGTTCTGTAGATAGCAAATTAG
64 ATACAAA-TTTTCAGAAGGTTCTGTAGATTCCAAATTAG
27138764 GTTTGTCAAT
Statistics
Matches: 225, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
170 6 0.03
171 138 0.61
172 8 0.04
173 5 0.02
174 66 0.29
175 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (173 bp):
AACCAGGGCAATCCTTGCGTCCTTATCATGGTCTGGCAGCGTCTCAACTTCCTTCTCATAAATAT
ACAAATTTTCAGAAGGTTCTGTAGATTCCAAATTAGACAGTCAAATACCTATCTCTTTCTTATTC
TGAAAGGACACAGCCGCATAAATGGGAAGGTCCTCAAGTGACA
Found at i:27145807 original size:27 final size:27
Alignment explanation
Indices: 27145740--27145807 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
27145730 TAATCAAATT
* *
27145740 AATCGA-TCAGTTAAAGTTTCATTTTC
1 AATCGATTCGGTTAAAATTTCATTTTC
* *
27145766 AATCGATTTGTTTAAAATTTCATTTTC
1 AATCGATTCGGTTAAAATTTCATTTTC
** *
27145793 GGTCGGTTCGGTTAA
1 AATCGATTCGGTTAA
27145808 TTTTTACAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.44
Consensus pattern (27 bp):
AATCGATTCGGTTAAAATTTCATTTTC
Found at i:27146158 original size:2 final size:2
Alignment explanation
Indices: 27146151--27146195 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
27146141 CTAAAAGCAT
27146151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27146192 TA TA
1 TA TA
27146196 CTATTACACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27151260 original size:14 final size:15
Alignment explanation
Indices: 27151228--27151265 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27151218 ATCCTGAGAA
*
27151228 TTTACATTGGAGCTG
1 TTTAGATTGGAGCTG
27151243 TTTAGATTGGAG-TG
1 TTTAGATTGGAGCTG
27151257 TTTATGATT
1 TTTA-GATT
27151266 TGCTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (15 bp):
TTTAGATTGGAGCTG
Found at i:27157820 original size:25 final size:23
Alignment explanation
Indices: 27157792--27157872 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 23
27157782 ATTTTATTAT
27157792 TAAAATTTAAAATTAATAATTATAA
1 TAAAATTTAAAA-TAATAA-TATAA
* *
27157817 TAAAAATATCAAAT-ATAATA-AA
1 T-AAAATTTAAAATAATAATATAA
*
27157839 TAAAATTTAACAAAAATAATATATA
1 TAAAATTTAA-AATAATAATATA-A
27157864 TAAAATTTA
1 TAAAATTTA
27157873 TTATCATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 7 0.15
22 5 0.11
23 8 0.17
24 5 0.11
25 12 0.26
26 9 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAATTTAAAATAATAATATAA
Found at i:27159089 original size:2 final size:2
Alignment explanation
Indices: 27159082--27159117 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
27159072 GTACTTAGAG
*
27159082 TA TA TA TA TA TA AA TA CTA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T
27159118 TCTTACTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:27159099 original size:23 final size:23
Alignment explanation
Indices: 27159073--27159116 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
27159063 TTCATGACTG
27159073 TACT-TAGAGTATATATATATAAA
1 TACTATAGA-TATATATATATAAA
*
27159096 TACTATATATATATATATATA
1 TACTATAGATATATATATATA
27159117 TTCTTACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (23 bp):
TACTATAGATATATATATATAAA
Found at i:27179728 original size:17 final size:17
Alignment explanation
Indices: 27179696--27179734 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27179686 TTTAAGTCCC
*
27179696 AATAAAAAAAAAATAAT
1 AATAAAAAAAAAATAAA
* *
27179713 AATAAAAAATATATAAA
1 AATAAAAAAAAAATAAA
27179730 AATAA
1 AATAA
27179735 TAGAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAAAAAAATAAA
Found at i:27182020 original size:24 final size:24
Alignment explanation
Indices: 27181982--27182038 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27181972 AATATAAAAT
* *
27181982 GATATGGTCCCTAGATCATGGATC
1 GATATGATCCATAGATCATGGATC
*
27182006 GATATGATCCATAGATGATGGATC
1 GATATGATCCATAGATCATGGATC
*
27182030 TATATGATC
1 GATATGATC
27182039 GAAAAGGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (24 bp):
GATATGATCCATAGATCATGGATC
Found at i:27196936 original size:2 final size:2
Alignment explanation
Indices: 27196929--27196958 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27196919 TTTCTATAAG
27196929 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27196959 GATTANTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27199356 original size:2 final size:2
Alignment explanation
Indices: 27199338--27199426 Score: 137
Period size: 2 Copynumber: 45.0 Consensus size: 2
27199328 AACTCTACTT
* *
27199338 TA TA TC TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27199380 TA TA NT- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27199421 TA TA TA
1 TA TA TA
27199427 AAGTTTTATA
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.03
2 77 0.96
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27201539 original size:16 final size:15
Alignment explanation
Indices: 27201513--27201542 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27201503 GTCATCTACC
27201513 TAATATATATATTTT
1 TAATATATATATTTT
27201528 TAATATTATATATTT
1 TAATA-TATATATTT
27201543 AGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATATATATTTT
Found at i:27201982 original size:15 final size:15
Alignment explanation
Indices: 27201960--27202005 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
27201950 ATAATTACAG
27201960 ATAATATGATTATAA
1 ATAATATGATTATAA
*
27201975 ATAATATGATTGTAA
1 ATAATATGATTATAA
*
27201990 ATAACATGATTATAA
1 ATAATATGATTATAA
27202005 A
1 A
27202006 AAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (15 bp):
ATAATATGATTATAA
Found at i:27202247 original size:27 final size:27
Alignment explanation
Indices: 27202203--27202269 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
27202193 TATCTCTTAA
* *
27202203 ATATATTTTTAATGTCATATTTTTAT-TT
1 ATAT-TTTTTATTATCAT-TTTTTATATT
*
27202231 TTATTTTTTATTATCATTTTTTATATT
1 ATATTTTTTATTATCATTTTTTATATT
*
27202258 ATATATTTTATT
1 ATATTTTTTATT
27202270 TTAATTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 7 0.21
27 23 0.70
28 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (27 bp):
ATATTTTTTATTATCATTTTTTATATT
Found at i:27202316 original size:15 final size:14
Alignment explanation
Indices: 27202296--27202377 Score: 51
Period size: 15 Copynumber: 5.6 Consensus size: 14
27202286 TAATACATAA
27202296 ATTTTAATTTCTTAT
1 ATTTTAATTT-TTAT
* *
27202311 ATTTTATTTTATTTT
1 ATTTTAATTT-TTAT
*
27202326 AATTTCTAATTCTTAT
1 -ATTT-TAATTTTTAT
* *
27202342 ATTAT-ATATTT-T
1 ATTTTAATTTTTAT
*
27202354 ATTTTAATATTTTTT
1 ATTTTAAT-TTTTAT
27202369 ATTTTAATT
1 ATTTTAATT
27202378 ATGGTATTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
14 5 0.10
15 24 0.47
16 7 0.14
17 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTAATTTTTAT
Found at i:27202379 original size:33 final size:33
Alignment explanation
Indices: 27202295--27202361 Score: 104
Period size: 31 Copynumber: 2.1 Consensus size: 33
27202285 ATAATACATA
27202295 AATTT-TAATTTCTTATATT-T-TATTTTATTTT
1 AATTTCTAA-TTCTTATATTATATATTTTATTTT
27202326 AATTTCTAATTCTTATATTATATATTTTATTTT
1 AATTTCTAATTCTTATATTATATATTTTATTTT
27202359 AAT
1 AAT
27202362 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 15 0.45
32 4 0.12
33 14 0.42
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (33 bp):
AATTTCTAATTCTTATATTATATATTTTATTTT
Found at i:27213162 original size:13 final size:13
Alignment explanation
Indices: 27213144--27213168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27213134 ACAGCAAGAA
27213144 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
27213157 TTTTTCTTTTTT
1 TTTTTCTTTTTT
27213169 AACAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:27216838 original size:11 final size:11
Alignment explanation
Indices: 27216796--27216849 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
27216786 CCATATTTCT
27216796 ATTTT-TTAAA
1 ATTTTATTAAA
27216806 ATTTTTATTTAAA
1 A-TTTTA-TTAAA
*
27216819 A-TATATTAAGA
1 ATTTTATTAA-A
27216830 ATTTT-TTAAA
1 ATTTTATTAAA
27216840 ATTTTATTAA
1 ATTTTATTAA
27216850 TCATTTATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 11 0.31
11 17 0.47
12 2 0.06
13 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTATTAAA
Found at i:27217158 original size:25 final size:25
Alignment explanation
Indices: 27217128--27217177 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27217118 TACACTAATA
27217128 TTAGTTAATATAAATTAAGAAGATT
1 TTAGTTAATATAAATTAAGAAGATT
27217153 TTAGTTAATATAAATTAAGAAGATT
1 TTAGTTAATATAAATTAAGAAGATT
27217178 GATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (25 bp):
TTAGTTAATATAAATTAAGAAGATT
Found at i:27224783 original size:23 final size:23
Alignment explanation
Indices: 27224757--27224800 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27224747 ATACAATAAC
*
27224757 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
27224780 CTTATCCTAATAGAATTAGGA
1 CTTATCCTAATAGAATTAGGA
27224801 TTTGTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:27228130 original size:26 final size:26
Alignment explanation
Indices: 27228098--27228165 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 26
27228088 ATAAGAACTT
27228098 ATTTAATTCAAAATAATAATA-TAAAA
1 ATTTAATTCAAAATAA-AATATTAAAA
*
27228124 ATTTAATTACATATAATAAAATATTAATA
1 ATTTAATT-CA-A-AATAAAATATTAAAA
*
27228153 ATTT-ATTTAAAAT
1 ATTTAATTCAAAAT
27228166 TTTTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 3 0.08
26 9 0.25
27 3 0.08
28 8 0.22
29 13 0.36
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTAATTCAAAATAAAATATTAAAA
Found at i:27228329 original size:18 final size:20
Alignment explanation
Indices: 27228286--27228335 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27228276 GATAATGAAT
*
27228286 TATTATATAGTGAATTATTA
1 TATTATATAGTGAATTATGA
*
27228306 TTTTATATAGTG-ATTATGAA
1 TATTATATAGTGAATTATG-A
27228326 TTATTATATA
1 -TATTATATA
27228336 ATGGTCCAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
TATTATATAGTGAATTATGA
Found at i:27233500 original size:2 final size:2
Alignment explanation
Indices: 27233493--27233522 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
27233483 GTAGATCTTG
*
27233493 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
27233523 GTGCACGTGT
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:27237440 original size:5 final size:5
Alignment explanation
Indices: 27237430--27237467 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
27237420 TGCTTATAAA
27237430 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
27237468 TCCTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:27242991 original size:2 final size:2
Alignment explanation
Indices: 27242984--27243012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27242974 TGATAAAAAG
27242984 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
27243013 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:27245934 original size:26 final size:26
Alignment explanation
Indices: 27245894--27246013 Score: 100
Period size: 26 Copynumber: 4.5 Consensus size: 26
27245884 CAAAATATTT
* *
27245894 TATAATATTATAATTAAAATATAATA
1 TATAATATAAAAATTAAAATATAATA
* *
27245920 TATAATATGAAAATTATAAA-ATAAAA
1 TATAATATAAAAATTA-AAATATAATA
* *
27245946 TAAAATATAAGAAATTAAAATTTATATAA
1 TATAATATAA-AAATTAAAATATA-AT-A
* *
27245975 TATAGGTA-AAAAATTAAAATAAAATA
1 TATA-ATATAAAAATTAAAATATAATA
*
27246001 TATAATACAAAAA
1 TATAATATAAAAA
27246014 ATTATATTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.03
26 40 0.53
27 13 0.17
28 12 0.16
29 6 0.08
30 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (26 bp):
TATAATATAAAAATTAAAATATAATA
Found at i:27245937 original size:21 final size:20
Alignment explanation
Indices: 27245893--27245955 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 20
27245883 TCAAAATATT
27245893 TTATAATATTATAAT-TAAAA
1 TTATAATA-TATAATATAAAA
27245913 -TATAATATATAATATGAAAA
1 TTATAATATATAATAT-AAAA
*
27245933 TTATAA-A-ATAAAATAAAA
1 TTATAATATATAATATAAAA
27245951 -TATAA
1 TTATAA
27245956 GAAATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 14 0.36
20 5 0.13
21 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TTATAATATATAATATAAAA
Found at i:27246034 original size:27 final size:27
Alignment explanation
Indices: 27245905--27246031 Score: 73
Period size: 26 Copynumber: 4.7 Consensus size: 27
27245895 ATAATATTAT
* * **
27245905 AATTAAAATATAATATATAATATGAAA
1 AATTAAAATAAAATATAAAATACAAAA
* * *
27245932 ATTATAAAAT-AAA-ATAAAATATAAGA
1 AAT-TAAAATAAAATATAAAATACAAAA
** * *
27245958 AATTAAAAT-TTATATAATATAGGTAAAA
1 AATTAAAATAAAATATAAAATA--CAAAA
*
27245986 AATTAAAATAAAATATATAATACAAAA
1 AATTAAAATAAAATATAAAATACAAAA
* *
27246013 AATTATATTAAAA-ATAAAA
1 AATTAAAATAAAATATAAAA
27246032 ATAATAATGA
Statistics
Matches: 77, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
25 7 0.09
26 24 0.31
27 19 0.25
28 19 0.25
29 8 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (27 bp):
AATTAAAATAAAATATAAAATACAAAA
Found at i:27246303 original size:15 final size:15
Alignment explanation
Indices: 27246279--27246327 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
27246269 TTTTTCATAC
*
27246279 AATCACATTACTTGT
1 AATCATATTACTTGT
* *
27246294 AATCATATTATTTGC
1 AATCATATTACTTGT
*
27246309 AATTATATTAC-TGT
1 AATCATATTACTTGT
27246323 AATCA
1 AATCA
27246328 CATTGAATTG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (15 bp):
AATCATATTACTTGT
Found at i:27265800 original size:2 final size:2
Alignment explanation
Indices: 27265789--27265820 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27265779 AGAGAAAAGA
27265789 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27265821 ANGAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27265853 original size:56 final size:55
Alignment explanation
Indices: 27265767--27265877 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 55
27265757 ATTTTTAATT
27265767 GAAAGAAAATAAAGAGAAAAGAATATTATATATATATATATATATATATATATAA
1 GAAAGAAAATAAAGAGAAAAGAATATTATATATATATATATATATATATATATAA
27265822 NGAAAGAAAATAAAGA-AGAAAGAATATTATATATATATATATATATATATATATAA
1 -GAAAGAAAATAAAGAGA-AAAGAATATTATATATATATATATATATATATATATAA
27265878 AGTTACAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 1 0.02
56 53 0.98
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (55 bp):
GAAAGAAAATAAAGAGAAAAGAATATTATATATATATATATATATATATATATAA
Found at i:27265856 original size:2 final size:2
Alignment explanation
Indices: 27265845--27265876 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27265835 AGAAGAAAGA
27265845 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27265877 AAGTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27275413 original size:20 final size:19
Alignment explanation
Indices: 27275377--27275415 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
27275367 TTTACGGGGT
27275377 TTTTTTTTTTCTTTTTTTC
1 TTTTTTTTTTCTTTTTTTC
*
27275396 TTTTTTTTTTGTTATTTTTC
1 TTTTTTTTTTCTT-TTTTTC
27275416 AAATGGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTCTTTTTTTC
Found at i:27276815 original size:14 final size:14
Alignment explanation
Indices: 27276796--27276830 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
27276786 CTATCTCCAT
27276796 ATTTTTTCATTTTG
1 ATTTTTTCATTTTG
*
27276810 ATTTTTGCATTTTG
1 ATTTTTTCATTTTG
27276824 ATTTTTT
1 ATTTTTT
27276831 ACACAACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.06, G:0.09, T:0.71
Consensus pattern (14 bp):
ATTTTTTCATTTTG
Found at i:27292162 original size:2 final size:2
Alignment explanation
Indices: 27292157--27292199 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
27292147 TCTTTCTCTC
27292157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27292198 TA
1 TA
27292200 CNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27292282 original size:2 final size:2
Alignment explanation
Indices: 27292275--27292300 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27292265 NNNNNNNNNN
27292275 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
27292301 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:27292305 original size:2 final size:2
Alignment explanation
Indices: 27292300--27292339 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27292290 TCTCTCTCTC
27292300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27292340 CTTATTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27294924 original size:45 final size:45
Alignment explanation
Indices: 27294863--27294956 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
27294853 ATTAAATTTA
* * * *
27294863 AATAATACTAAATAATATTCTTTGTTACATTTATTATATTCAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
* * * *
27294908 AATAATATTAAGTAATATGCTTTATAATATTTATTATAGTGAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
27294953 AATA
1 AATA
27294957 TTAATATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (45 bp):
AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
Found at i:27294972 original size:18 final size:20
Alignment explanation
Indices: 27294949--27294986 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
27294939 TATTATAGTG
27294949 AAATAATA-TTA-ATATTTT
1 AAATAATATTTAGATATTTT
27294967 AAATAATATTTAGATATTTT
1 AAATAATATTTAGATATTTT
27294987 TATTTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATAATATTTAGATATTTT
Found at i:27295388 original size:13 final size:13
Alignment explanation
Indices: 27295370--27295400 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
27295360 ATATTGAAAG
27295370 ATTTTGACTCAAT
1 ATTTTGACTCAAT
27295383 ATTTTGACTCAAT
1 ATTTTGACTCAAT
27295396 ATTTT
1 ATTTT
27295401 TTTGTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (13 bp):
ATTTTGACTCAAT
Found at i:27300610 original size:58 final size:58
Alignment explanation
Indices: 27300544--27300656 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
27300534 TTTTTTTGGG
*
27300544 GTTACTCCCCTCCCTCCCTTTCTTTACAGTCAATATAGAAGTTTATCATGTTTTCATA
1 GTTACTCCCCTCCCTCCCTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTCATA
27300602 GTTACTCCCCTCCCTCCCTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTC
1 GTTACTCCCCTCCCTCCCTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTC
27300657 GTAGCTCTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (58 bp):
GTTACTCCCCTCCCTCCCTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTCATA
Found at i:27316681 original size:6 final size:5
Alignment explanation
Indices: 27316645--27316684 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
27316635 CTGAAATCCA
* *
27316645 AAAAG AAGAG GAAAG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
27316685 TGGGAGAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:27317079 original size:7 final size:7
Alignment explanation
Indices: 27317069--27317093 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27317059 CGTTTTTTCT
27317069 TTTTAAA
1 TTTTAAA
27317076 TTTTAAA
1 TTTTAAA
27317083 TTTTAAA
1 TTTTAAA
27317090 TTTT
1 TTTT
27317094 TCTTAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:27339940 original size:14 final size:14
Alignment explanation
Indices: 27339921--27339950 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27339911 AATAGGAACC
27339921 AAGGTTTGACCATT
1 AAGGTTTGACCATT
*
27339935 AAGGTTTGAGCATT
1 AAGGTTTGACCATT
27339949 AA
1 AA
27339951 AAGAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (14 bp):
AAGGTTTGACCATT
Found at i:27351505 original size:7 final size:7
Alignment explanation
Indices: 27351493--27351517 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27351483 AAGACTCTGA
27351493 AGAGACG
1 AGAGACG
27351500 AGAGACG
1 AGAGACG
27351507 AGAGACG
1 AGAGACG
27351514 AGAG
1 AGAG
27351518 GCATATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.44, T:0.00
Consensus pattern (7 bp):
AGAGACG
Found at i:27353535 original size:19 final size:20
Alignment explanation
Indices: 27353499--27353537 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27353489 TGACCCATTC
* *
27353499 TAATTTTTGATTAGTAAAAA
1 TAATTTTAGAATAGTAAAAA
27353519 TAATTTTAGAATA-TAAAAA
1 TAATTTTAGAATAGTAAAAA
27353538 AGTATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATTTTAGAATAGTAAAAA
Found at i:27353757 original size:26 final size:26
Alignment explanation
Indices: 27353697--27353763 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
27353687 TTATTTTATT
27353697 TTTAAAATATTAA--TAATTTATAAA
1 TTTAAAATATTAATTTAATTTATAAA
* * *
27353721 --TAACATTTTAATTTAATTTTTAAA
1 TTTAAAATATTAATTTAATTTATAAA
27353745 TTTAAAATATTAATTTAAT
1 TTTAAAATATTAATTTAAT
27353764 ATAATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 9 0.26
24 10 0.29
26 15 0.44
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAAAATATTAATTTAATTTATAAA
Found at i:27358307 original size:26 final size:26
Alignment explanation
Indices: 27358259--27358316 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
27358249 ACGTTATTTT
*
27358259 AAAAAAAATTATTACACATTATAGTG
1 AAAAAAAATTATTACACACTATAGTG
** *
27358285 AAAAAAAATTATTACATGCTATATTG
1 AAAAAAAATTATTACACACTATAGTG
27358311 AAAAAA
1 AAAAAA
27358317 TTTTATCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (26 bp):
AAAAAAAATTATTACACACTATAGTG
Found at i:27360180 original size:51 final size:51
Alignment explanation
Indices: 27360104--27360314 Score: 210
Period size: 51 Copynumber: 4.1 Consensus size: 51
27360094 ATACTTGAAG
* * * * *
27360104 CGAAGATATTATGTGTTCGTGATCAAAATTAGGTCGTAAAGACCCTTAAAA
1 CGAAGATATCAAGTGTTCGTAATCAAGATTAAGTCGTAAAGACCCTTAAAA
* * * *
27360155 CGAAGATATCAAATGTTCGTAATCAAGATTAAGTCGTAAAAATCCTTAAAG
1 CGAAGATATCAAGTGTTCGTAATCAAGATTAAGTCGTAAAGACCCTTAAAA
* * * * * *
27360206 CAAAGATATCAAGTGTTCATGAA-CAAGATTAAGTCATTAAGATCCTTGAAGA
1 CGAAGATATCAAGTGTTCGT-AATCAAGATTAAGTCGTAAAGACCCTT-AAAA
* ** * *
27360258 -GAAGATATCAAGTGTTCGTGATCAAGATTAAGTCGTGCAGACCCTTGAAG
1 CGAAGATATCAAGTGTTCGTAATCAAGATTAAGTCGTAAAGACCCTTAAAA
27360308 CGAAGAT
1 CGAAGAT
27360315 CAAGCAAAGT
Statistics
Matches: 129, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
50 2 0.02
51 123 0.95
52 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (51 bp):
CGAAGATATCAAGTGTTCGTAATCAAGATTAAGTCGTAAAGACCCTTAAAA
Found at i:27360314 original size:102 final size:102
Alignment explanation
Indices: 27360097--27360314 Score: 258
Period size: 102 Copynumber: 2.1 Consensus size: 102
27360087 ATCACAAATA
* * * * * *
27360097 CTTGAAGCGAAGATATTATGTGTTCGTGATCAAAATTAGGTCGTAAAGACCCTTAAAACGAAGAT
1 CTTGAAGCGAAGATATCAAGTGTTCATGAACAAAATTAAGTCATAAAGACCCTTAAAACGAAGAT
*
27360162 ATCAAATGTTCGTAATCAAGATTAAGTCGTAAAAATC
66 ATCAAATGTTCGTAATCAAGATTAAGTCGTAAAAACC
* * * * * *
27360199 CTTAAAGCAAAGATATCAAGTGTTCATGAACAAGATTAAGTCATTAAGATCCTTGAAGA-GAAGA
1 CTTGAAGCGAAGATATCAAGTGTTCATGAACAAAATTAAGTCATAAAGACCCTT-AAAACGAAGA
* * ** *
27360263 TATCAAGTGTTCGTGATCAAGATTAAGTCGTGCAGACC
65 TATCAAATGTTCGTAATCAAGATTAAGTCGTAAAAACC
27360301 CTTGAAGCGAAGAT
1 CTTGAAGCGAAGAT
27360315 CAAGCAAAGT
Statistics
Matches: 95, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
102 92 0.97
103 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (102 bp):
CTTGAAGCGAAGATATCAAGTGTTCATGAACAAAATTAAGTCATAAAGACCCTTAAAACGAAGAT
ATCAAATGTTCGTAATCAAGATTAAGTCGTAAAAACC
Found at i:27362336 original size:2 final size:2
Alignment explanation
Indices: 27362323--27362361 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
27362313 GCTTTTATTC
*
27362323 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27362362 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27363011 original size:2 final size:2
Alignment explanation
Indices: 27363004--27363032 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27362994 ACATCACTAT
27363004 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27363033 TATATGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27372083 original size:18 final size:17
Alignment explanation
Indices: 27372060--27372110 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
27372050 ATTACTTTTG
27372060 TTTCTTTTCTTCTTCTTT
1 TTTCTTTTCTT-TTCTTT
27372078 TTTC-TTTCTTTCTCTTT
1 TTTCTTTTCTTT-TCTTT
27372095 TTTCTTTT-TTTTCTTT
1 TTTCTTTTCTTTTCTTT
27372111 CTCCCTCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.19
17 18 0.58
18 7 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTCTTTTCTTT
Found at i:27372085 original size:22 final size:24
Alignment explanation
Indices: 27372055--27372113 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
27372045 TATATATTAC
*
27372055 TTTTGTTTCTTT-TC-TTCTTCTT
1 TTTTCTTTCTTTCTCTTTCTTCTT
*
27372077 TTTTCTTTCTTTCTCTTTTTTC-T
1 TTTTCTTTCTTTCTCTTTCTTCTT
27372100 TTTT-TTTCTTTCTC
1 TTTTCTTTCTTTCTC
27372114 CCTCCTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 21 0.64
23 7 0.21
24 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTCTTTCTTTCTCTTTCTTCTT
Found at i:27372089 original size:26 final size:26
Alignment explanation
Indices: 27372060--27372112 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
27372050 ATTACTTTTG
27372060 TTTCT-TTTCTTCTTCTTTTTTCTTTC
1 TTTCTCTTTCTTCTT-TTTTTTCTTTC
*
27372086 TTTCTCTTTTTTCTTTTTTTTCTTTC
1 TTTCTCTTTCTTCTTTTTTTTCTTTC
27372112 T
1 T
27372113 CCCTCCTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTCTCTTTCTTCTTTTTTTTCTTTC
Found at i:27372344 original size:12 final size:12
Alignment explanation
Indices: 27372327--27372367 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
27372317 CGAGCGAAAG
27372327 AAAAAAAGAAG-
1 AAAAAAAGAAGA
27372338 AAAAAAA-AAGA
1 AAAAAAAGAAGA
*
27372349 AACAAAAGAAGA
1 AAAAAAAGAAGA
*
27372361 AACAAAA
1 AAAAAAA
27372368 CAAAAGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 3 0.11
11 13 0.48
12 11 0.41
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:27372358 original size:22 final size:21
Alignment explanation
Indices: 27372323--27372367 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
27372313 AAGGCGAGCG
27372323 AAAGAAAAAAAGAAGAAAAAA
1 AAAGAAAAAAAGAAGAAAAAA
*
27372344 AAAGAAACAAAAGAAGAAACAA
1 AAAGAAA-AAAAGAAGAAAAAA
27372366 AA
1 AA
27372368 CAAAAGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAAGAAGAAAAAA
Found at i:27372921 original size:21 final size:21
Alignment explanation
Indices: 27372888--27372927 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27372878 AAATTAAAAT
*
27372888 AATTTTTAAAATTAAAAATTA
1 AATTATTAAAATTAAAAATTA
* *
27372909 AATTATTATAATTTAAAAT
1 AATTATTAAAATTAAAAAT
27372928 AAAAAAATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATTAAAATTAAAAATTA
Found at i:27387045 original size:2 final size:2
Alignment explanation
Indices: 27387038--27387063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27387028 CTCAAATCTC
27387038 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27387064 TATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27398798 original size:26 final size:28
Alignment explanation
Indices: 27398751--27398811 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
27398741 ATTTTTAATT
*
27398751 TAATTTATTTTTAAATAGTAAT-ATTTA
1 TAATTTATTTTTAAATAGTAATGATTGA
*
27398778 TAATTTA-TTTTAAATATTAATGATTGA
1 TAATTTATTTTTAAATAGTAATGATTGA
27398805 TAATTTA
1 TAATTTA
27398812 AATATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (28 bp):
TAATTTATTTTTAAATAGTAATGATTGA
Found at i:27406911 original size:18 final size:18
Alignment explanation
Indices: 27406888--27406943 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
27406878 TGTTAAATGA
27406888 AAAAAAATTATAATATTT
1 AAAAAAATTATAATATTT
*
27406906 AAAAAAATCTCTAAATTATTT
1 AAAAAAAT-TAT-AA-TATTT
* *
27406927 AAATAAATTATTATATT
1 AAAAAAATTATAATATT
27406944 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 12 0.39
19 3 0.10
20 4 0.13
21 12 0.39
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAAAATTATAATATTT
Found at i:27406944 original size:21 final size:22
Alignment explanation
Indices: 27406894--27406945 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
27406884 ATGAAAAAAA
*
27406894 ATTATAATATTTAAAAAAATCT
1 ATTATATTATTTAAAAAAATCT
* * *
27406916 -CTAAATTATTTAAATAAAT-T
1 ATTATATTATTTAAAAAAATCT
27406936 ATTATATTAT
1 ATTATATTAT
27406946 ATTTTAAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTATATTATTTAAAAAAATCT
Found at i:27410520 original size:18 final size:18
Alignment explanation
Indices: 27410486--27410520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27410476 TATTTTTTAA
**
27410486 ATAAAATTAAATTATAAT
1 ATAAAATTAAAAAATAAT
27410504 ATAAAATTAAAAAATAA
1 ATAAAATTAAAAAATAA
27410521 CGATCATCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATTAAAAAATAAT
Found at i:27419843 original size:22 final size:22
Alignment explanation
Indices: 27419815--27419860 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27419805 CTGCCCTTCC
27419815 GCTGAGACCCTGACAGATACAT
1 GCTGAGACCCTGACAGATACAT
27419837 GCTGAGACCCTGACAGATACAT
1 GCTGAGACCCTGACAGATACAT
27419859 GC
1 GC
27419861 ACATAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.17
Consensus pattern (22 bp):
GCTGAGACCCTGACAGATACAT
Found at i:27422698 original size:38 final size:38
Alignment explanation
Indices: 27422596--27422718 Score: 135
Period size: 38 Copynumber: 3.3 Consensus size: 38
27422586 AATTTGTATT
27422596 TTTTTTATAATAATA-CTAAAACTATTAACAACT-ATTA
1 TTTTTTATAATAATACCTAAAACTATTAA-AACTAATTA
* * * * ** *
27422633 TATTTTGTAATAATGCTTGTAACTATTAAAATTAATTA
1 TTTTTTATAATAATACCTAAAACTATTAAAACTAATTA
*
27422671 TTTTTTATAATAATACCTAAAAATATTAAAACTAATT-
1 TTTTTTATAATAATACCTAAAACTATTAAAACTAATTA
*
27422708 TTTTTTGTAAT
1 TTTTTTATAAT
27422719 GGCTCCGAGG
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
37 25 0.37
38 43 0.63
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTTTATAATAATACCTAAAACTATTAAAACTAATTA
Found at i:27431909 original size:142 final size:142
Alignment explanation
Indices: 27431698--27432143 Score: 531
Period size: 142 Copynumber: 3.0 Consensus size: 142
27431688 TCGCCTACCA
* * *
27431698 AAAATTAAACAGTTTATTTTACCCAAAATCATATATCCTGTTCAT-CTCTATATGCGCACATCGA
1 AAAATTAAACAGTTTATTTTACCCAAAATCATATATCTTGTTCATCCTC-ATATGCGCACACCAA
* *
27431762 AAGTGTTAAATGTTATAAACTTGA-TAATGCAATAGTTACAT-AGTTTGAAAAATATAAAAGATT
65 AAGTGTTAAATGTTATAAACATGACT-ATGCAATAATTACATGAGTTTG-AAAATATAAAAGATT
27431825 TTTTATTTTTAAATG
128 TTTTATTTTTAAATG
*
27431840 AAAATTAAACAGGTTATTTTACCCAAAATCATATATCTTGTTCATCCTCATATGCGCACACCAAA
1 AAAATTAAACAGTTTATTTTACCCAAAATCATATATCTTGTTCATCCTCATATGCGCACACCAAA
* * *
27431905 AGTGTTAAATGTTATAAACATGACTATGCAATAATTACATGATTTTGACAATATAAAAGGTTTTT
66 AGTGTTAAATGTTATAAACATGACTATGCAATAATTACATGAGTTTGAAAATATAAAAGATTTTT
27431970 TATTTTTAAATG
131 TATTTTTAAATG
* * * * *
27431982 AAAATTAAATAATTTATTTTA-CCAAAAACTATATATCTTATTCATCTTCATATGCGCACACCTG
1 AAAATTAAACAGTTTATTTTACCCAAAATC-ATATATCTTGTTCATCCTCATATGCG--CA-C--
* * * *
27432046 ATCACTAGTTGAAATGTATTAAATGTTATAAACGTGACTATGCAATAATTACATGATTTTGACAA
60 A-C-C-A----AAA-GTGTTAAATGTTATAAACATGACTATGCAATAATTACATGAGTTTGAAAA
*
27432111 TATAAAAGGTTTTTTTATTTTTAAATG
117 TATAAAA-GATTTTTTATTTTTAAATG
27432138 AAAATT
1 AAAATT
27432144 GTTAATTAAA
Statistics
Matches: 268, Mismatches: 18, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
141 7 0.03
142 163 0.61
143 9 0.03
144 2 0.01
145 1 0.00
147 1 0.00
148 1 0.00
149 1 0.00
150 1 0.00
154 3 0.01
155 55 0.21
156 24 0.09
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (142 bp):
AAAATTAAACAGTTTATTTTACCCAAAATCATATATCTTGTTCATCCTCATATGCGCACACCAAA
AGTGTTAAATGTTATAAACATGACTATGCAATAATTACATGAGTTTGAAAATATAAAAGATTTTT
TATTTTTAAATG
Found at i:27439733 original size:15 final size:15
Alignment explanation
Indices: 27439713--27439744 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27439703 CAGGAGCTCT
27439713 TTACCTGGTTTATTC
1 TTACCTGGTTTATTC
*
27439728 TTACCTTGTTTATTC
1 TTACCTGGTTTATTC
27439743 TT
1 TT
27439745 TGCCACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.09, T:0.59
Consensus pattern (15 bp):
TTACCTGGTTTATTC
Found at i:27443655 original size:22 final size:22
Alignment explanation
Indices: 27443618--27443684 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
27443608 CATCCCTTTT
27443618 TTTTAATATTTT--TTTATATTA
1 TTTT-ATATTTTAATTTATATTA
*
27443639 TTTTATATTTTAATTTATTTTA
1 TTTTATATTTTAATTTATATTA
* * *
27443661 TTATA-ATTTAAAATTATTATTA
1 TTTTATATTTTAATTTA-TATTA
27443683 TT
1 TT
27443685 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.18
21 13 0.34
22 18 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATATTTTAATTTATATTA
Found at i:27443685 original size:22 final size:21
Alignment explanation
Indices: 27443634--27443686 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
27443624 TATTTTTTTA
* *
27443634 TATTATT-TTATATTTTAATT
1 TATTATTATTATATTTAAAAT
27443654 TATT-TTATTATAATTTAAAAT
1 TATTATTATTAT-ATTTAAAAT
27443675 TATTATTATTAT
1 TATTATTATTAT
27443687 TTTTTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 8 0.29
21 11 0.39
22 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTATTATTATATTTAAAAT
Found at i:27444057 original size:55 final size:55
Alignment explanation
Indices: 27443986--27444098 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 55
27443976 AACGGGTAGA
* * * * *
27443986 GAGTAGGTGTTTGGAGAGAGGCC-GACGATTAGAGAGAAGAGAGAGAGAGTCCGAC
1 GAGTAAGTGTTCGGAGAGAGGCCAG-CGAATAGAGAGAAGAAAGAGAGAGGCCGAC
27444041 GAGTAAGTGTTCGGAGAGAGGCCAGCGAATAGAGAGAAGAAAGAGAGAGGCCGAC
1 GAGTAAGTGTTCGGAGAGAGGCCAGCGAATAGAGAGAAGAAAGAGAGAGGCCGAC
27444096 GAG
1 GAG
27444099 AGAGAAGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
55 51 0.98
56 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.42, T:0.12
Consensus pattern (55 bp):
GAGTAAGTGTTCGGAGAGAGGCCAGCGAATAGAGAGAAGAAAGAGAGAGGCCGAC
Found at i:27444106 original size:26 final size:25
Alignment explanation
Indices: 27444071--27444132 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 25
27444061 GCCAGCGAAT
*
27444071 AGAGAGAAGAAAGAGAGAGGCCGACG
1 AGAGAGAAGAAAGAG-GACGCCGACG
27444097 AGAGAGAAG-AA-AGGACGCCGACG
1 AGAGAGAAGAAAGAGGACGCCGACG
*
27444120 A-AGAGAGGAAAGA
1 AGAGAGAAGAAAGA
27444133 AGGTTTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 12 0.38
24 3 0.09
25 2 0.06
26 9 0.28
ACGTcount: A:0.48, C:0.11, G:0.40, T:0.00
Consensus pattern (25 bp):
AGAGAGAAGAAAGAGGACGCCGACG
Found at i:27444644 original size:23 final size:22
Alignment explanation
Indices: 27444591--27444652 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
27444581 TAATGATAGT
*
27444591 AGTAAATAAAAATAATAATAAA
1 AGTAAATAAATATAATAATAAA
*
27444613 AGAAGAATAAATATATATACATAAA
1 AGTA-AATAAATATA-ATA-ATAAA
27444638 A-TAAATAAATA-AATA
1 AGTAAATAAATATAATA
27444653 GAAAGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 17 0.50
24 4 0.12
25 6 0.18
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AGTAAATAAATATAATAATAAA
Found at i:27444965 original size:13 final size:13
Alignment explanation
Indices: 27444947--27444972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27444937 GTATATAATG
27444947 ATAATGATAAATA
1 ATAATGATAAATA
27444960 ATAATGATAAATA
1 ATAATGATAAATA
27444973 TATGAATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAATGATAAATA
Found at i:27456831 original size:3 final size:3
Alignment explanation
Indices: 27456823--27456859 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
27456813 TTAATATATG
27456823 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27456860 GTTTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27465097 original size:2 final size:2
Alignment explanation
Indices: 27465086--27465123 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
27465076 TTATCCGTAA
27465086 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27465124 AGGGGGGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27466639 original size:21 final size:20
Alignment explanation
Indices: 27466589--27466641 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
27466579 CTATTTTTAT
*
27466589 TTTTTAAAATAAAATTA-TA
1 TTTTTAAAATAAAATAATTA
27466608 TTTGATT-AAATAAAATAATTA
1 TTT--TTAAAATAAAATAATTA
27466629 TTTTTCAAAATAA
1 TTTTT-AAAATAA
27466642 TCATTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 5 0.18
20 10 0.36
21 13 0.46
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTTTAAAATAAAATAATTA
Found at i:27473086 original size:30 final size:30
Alignment explanation
Indices: 27473027--27473093 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
27473017 AATGGTTTTT
*
27473027 TATAAGAGTTTATTTGATTTAAAAATAAAAA
1 TATAA-AGTTTATTTGATCTAAAAATAAAAA
*
27473058 TATAAAGTCTTATTTGA-CTAAAACTAAAAA
1 TATAAAGT-TTATTTGATCTAAAAATAAAAA
27473088 TATAAA
1 TATAAA
27473094 AATTTGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.36
Consensus pattern (30 bp):
TATAAAGTTTATTTGATCTAAAAATAAAAA
Found at i:27473105 original size:26 final size:26
Alignment explanation
Indices: 27473069--27473132 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
27473059 ATAAAGTCTT
* *
27473069 ATTTGACTAAA-ACTAAAAATATAAAA
1 ATTTGATTAAACAATAAAAATA-AAAA
27473095 ATTTGATTAAATGCAATAAAAATAAAAA
1 ATTTGATTAAA--CAATAAAAATAAAAA
27473123 ATTT-ATTAAA
1 ATTTGATTAAA
27473133 TTTTTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 10 0.30
27 6 0.18
28 8 0.24
29 9 0.27
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
ATTTGATTAAACAATAAAAATAAAAA
Found at i:27473461 original size:17 final size:17
Alignment explanation
Indices: 27473441--27473479 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27473431 ATTTAAATAT
27473441 TTAAATATATAAAATTA
1 TTAAATATATAAAATTA
* **
27473458 TTAAATATTTAATTTTA
1 TTAAATATATAAAATTA
27473475 TTAAA
1 TTAAA
27473480 AGAAGCGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATATATAAAATTA
Found at i:27473469 original size:8 final size:8
Alignment explanation
Indices: 27473413--27473469 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
27473403 ATAAAAATAT
*
27473413 AATATTTT
1 AATATTTA
27473421 AATA-TTA
1 AATATTTA
*
27473428 ATTATTTA
1 AATATTTA
27473436 AATATTTA
1 AATATTTA
*
27473444 AATATATA
1 AATATTTA
27473452 AA-ATTATTA
1 AATA-T-TTA
27473461 AATATTTA
1 AATATTTA
27473469 A
1 A
27473470 TTTTATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
7 6 0.15
8 28 0.70
9 5 0.12
10 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATATTTA
Found at i:27477625 original size:236 final size:234
Alignment explanation
Indices: 27477200--27477669 Score: 554
Period size: 236 Copynumber: 2.0 Consensus size: 234
27477190 AATGATTGTT
* * * * * *
27477200 TGATTTCATGTATTGAACGAGATATAATTAATATTTTTGATACTGAAGTAGTTATACAATGTTTT
1 TGATTACATGTATTGAAAGAGATATAATTAATATTGTTGATACTGAAGCAGTTACACAATGCTTT
* * * *
27477265 CAAAATATGAAAACTGGTCGTGGACGATTGTAAATGATATCTTATTTTTAAAAATAATAGTATTT
66 CAAAATATGAAAACTGGTCGTGGACAATTGTAAACGATATCTTATTATT-AAAATAATAGGATTT
*
27477330 TATTGTTTGTATCTTTTTTTTTGCAATGATATTGTAATTATTATGTAAAGGAACTTTGATATACT
130 TATTGTTTGTATCTTTTTTTTTG--ATGATATTGTAATTATTATGTAAAGAAACTTTGATATACT
*
27477395 TATTTTTTACATTATAAATGATAATATTATATTAATTTATGAA
193 TATTTTTGACATT-TAAATGATAATATTATATTAATTTATGAA
* * *
27477438 TGATTACATTTATTGAAAGAGATA-AATTTAATTATTGTTGATATTGAAGCATTTACACAATGCT
1 TGATTACATGTATTGAAAGAGATATAA-TTAA-TATTGTTGATACTGAAGCAGTTACACAATGCT
* * * ** * *
27477502 TTCAAAATGTGGAAACTTGTTTTGGACAATTGT-AACGATATCTT-TATATT-AAATAATTGGCT
64 TTCAAAATATGAAAACTGGTCGTGGACAATTGTAAACGATATCTTAT-TATTAAAATAATAGGAT
* **
27477564 TTTGTTGTTTGTATCTTATTTTTTTTG-TGATGATTGTAATTATTATGTGTAGAAACTTTGATAT
128 TTTATTGTTTGTATC-T-TTTTTTTTGATGAT-ATTGTAATTATTATGTAAAGAAACTTTGATAT
* ** *
27477628 TCTTATTTTTGACATTTGGATGATAATGTTATATTAATTTAT
190 ACTTATTTTTGACATTTAAATGATAATATTATATTAATTTAT
27477670 TAAATCCACT
Statistics
Matches: 197, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
235 27 0.14
236 66 0.34
237 4 0.02
238 47 0.24
239 53 0.27
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (234 bp):
TGATTACATGTATTGAAAGAGATATAATTAATATTGTTGATACTGAAGCAGTTACACAATGCTTT
CAAAATATGAAAACTGGTCGTGGACAATTGTAAACGATATCTTATTATTAAAATAATAGGATTTT
ATTGTTTGTATCTTTTTTTTTGATGATATTGTAATTATTATGTAAAGAAACTTTGATATACTTAT
TTTTGACATTTAAATGATAATATTATATTAATTTATGAA
Done.