Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 97 of 204
Found at i:29467741 original size:17 final size:17
Alignment explanation
Indices: 29467721--29467757 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29467711 AATTTTTGAA
29467721 TTAGTAAATTCTGTGAT
1 TTAGTAAATTCTGTGAT
* *
29467738 TTAGTGAATTTTGTGAT
1 TTAGTAAATTCTGTGAT
29467755 TTA
1 TTA
29467758 AAAAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (17 bp):
TTAGTAAATTCTGTGAT
Found at i:29469038 original size:46 final size:46
Alignment explanation
Indices: 29468985--29469170 Score: 318
Period size: 46 Copynumber: 4.0 Consensus size: 46
29468975 CCATGGAAAA
* *
29468985 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
* *
29469031 TTGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
29469077 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
* *
29469123 TTGTGAAAAGTAGGTATGATATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
29469169 TT
1 TT
29469171 ATAGCATTGT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 134 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
Found at i:29472797 original size:22 final size:23
Alignment explanation
Indices: 29472772--29472821 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
29472762 ATTTGTTTGT
* *
29472772 CTTTTTTTG-TTTTCTTTATTTA
1 CTTTTTTAGTTTTTATTTATTTA
29472794 CTTTTTTAGTTTTTATTTATTTA
1 CTTTTTTAGTTTTTATTTATTTA
29472817 -TTTTT
1 CTTTTT
29472822 CCTTTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (23 bp):
CTTTTTTAGTTTTTATTTATTTA
Found at i:29472808 original size:15 final size:16
Alignment explanation
Indices: 29472790--29472847 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 16
29472780 GTTTTCTTTA
29472790 TTTACTTT-TTTAGTT
1 TTTACTTTATTTAGTT
29472805 TTTA-TTTATTTA-TT
1 TTTACTTTATTTAGTT
*
29472819 TTTCCTTTATTT-G-T
1 TTTACTTTATTTAGTT
29472833 TTTA-TTTATTT-GTT
1 TTTACTTTATTTAGTT
29472847 T
1 T
29472848 ATTATTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
15 15 0.41
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTACTTTATTTAGTT
Found at i:29472852 original size:24 final size:22
Alignment explanation
Indices: 29472773--29472861 Score: 58
Period size: 24 Copynumber: 3.8 Consensus size: 22
29472763 TTTGTTTGTC
*
29472773 TTTTTTTGTTT-TCTTTATTTA-
1 TTTTTTTATTTGT-TTTATTTAT
* *
29472794 CTTTTTTAGTTTTTATTTATTTAT
1 TTTTTTTA-TTTGT-TTTATTTAT
29472818 TTTTCCTTTATTTGTTTTATTTAT
1 TTTT--TTTATTTGTTTTATTTAT
29472842 TTGTTTATTA-TTGATTTTAT
1 TT-TTT-TTATTTG-TTTTAT
29472862 AATATTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.11
22 3 0.05
23 13 0.24
24 23 0.42
25 6 0.11
26 4 0.07
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTTTATTTGTTTTATTTAT
Found at i:29472858 original size:28 final size:28
Alignment explanation
Indices: 29472804--29472858 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
29472794 CTTTTTTAGT
* *
29472804 TTTTATTTATTTATTTTTCCTTTATTTG
1 TTTTATTTATTTATTTTTCATTGATTTG
*
29472832 TTTTATTTATTTGTTTATT-ATTGATTT
1 TTTTATTTATTTATTT-TTCATTGATTT
29472859 TATAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTATTTATTTATTTTTCATTGATTTG
Found at i:29472881 original size:13 final size:13
Alignment explanation
Indices: 29472863--29472888 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29472853 TGATTTTATA
29472863 ATATTTTAAATGT
1 ATATTTTAAATGT
29472876 ATATTTTAAATGT
1 ATATTTTAAATGT
29472889 TTTCTAATAT
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:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATGT
Found at i:29472926 original size:21 final size:19
Alignment explanation
Indices: 29472893--29472969 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 19
29472883 AAATGTTTTC
29472893 TAATATATTTTTTTAAAAT
1 TAATATATTTTTTTAAAAT
*
29472912 TACATATATTTTTTTAATAT
1 TA-ATATATTTTTTTAAAAT
*
29472932 T-AT-TATTTTTTAAAAATT
1 TAATATATTTTTTTAAAA-T
29472950 TAA-ATATTATTTTTAAAAT
1 TAATATATT-TTTTTAAAAT
29472969 T
1 T
29472970 TTAAATATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.22
18 4 0.08
19 9 0.18
20 25 0.51
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATATATTTTTTTAAAAT
Found at i:29472960 original size:22 final size:22
Alignment explanation
Indices: 29472932--29472987 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
29472922 TTTTTAATAT
29472932 TATTATTTTTTAAAAATTTAAA
1 TATTATTTTTTAAAAATTTAAA
*
29472954 TATTA-TTTTTAAAATTTTAAA
1 TATTATTTTTTAAAAATTTAAA
29472975 TATTATTTTTTAA
1 TATTATTTTTTAA
29472988 TATTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTTTTTAAAAATTTAAA
Found at i:29472970 original size:20 final size:18
Alignment explanation
Indices: 29472897--29472984 Score: 79
Period size: 20 Copynumber: 4.6 Consensus size: 18
29472887 GTTTTCTAAT
29472897 ATATTTTTTTAAAATTACA
1 ATATTTTTTTAAAATTA-A
*
29472916 TATATTTTTTTAATATT-A
1 -ATATTTTTTTAAAATTAA
* *
29472934 TTATTTTTTAAAAATTTAA
1 ATATTTTTTTAAAA-TTAA
29472953 ATATTATTTTTAAAATTTTAA
1 ATATT-TTTTTAAAA--TTAA
29472974 ATATTATTTTT
1 ATATT-TTTTT
29472985 TAATATTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.19
18 3 0.05
19 5 0.09
20 23 0.40
21 16 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTTTTTAAAATTAA
Found at i:29472972 original size:21 final size:21
Alignment explanation
Indices: 29472923--29472984 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 21
29472913 ACATATATTT
29472923 TTTTAATATTATTATTTTTTAAAA
1 TTTTAA-A-TATTA-TTTTTAAAA
*
29472947 ATTTAAATATTATTTTTAAAA
1 TTTTAAATATTATTTTTAAAA
29472968 TTTTAAATATTATTTTT
1 TTTTAAATATTATTTTT
29472985 TAATATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 25 0.69
22 5 0.14
23 1 0.03
24 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAATATTATTTTTAAAA
Found at i:29472996 original size:22 final size:21
Alignment explanation
Indices: 29472932--29472996 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
29472922 TTTTTAATAT
29472932 TATTATTTTTTAAAAATTTAAA
1 TATTATTTTTT-AAAATTTAAA
29472954 TATTA-TTTTTAAAATTTTAAA
1 TATTATTTTTTAAAA-TTTAAA
*
29472975 TATTATTTTTTAATATTATAAA
1 TATTATTTTTTAAAATT-TAAA
29472997 ACATTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
20 4 0.10
21 18 0.46
22 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATTTTTTAAAATTTAAA
Found at i:29473084 original size:22 final size:21
Alignment explanation
Indices: 29473059--29473126 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
29473049 TTTTATAATC
*
29473059 TTTTAAATGTATATTTTAAAAA
1 TTTTAAATATAT-TTTTAAAAA
* *
29473081 TTTTAAAATTTATTTTTTAAAA
1 TTTT-AAATATATTTTTAAAAA
*
29473103 TTTTAAATATAATTTTTTAAAA
1 TTTTAAATAT-ATTTTTAAAAA
29473125 TT
1 TT
29473127 ATTTTTAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
21 5 0.12
22 29 0.71
23 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
TTTTAAATATATTTTTAAAAA
Found at i:29477735 original size:2 final size:2
Alignment explanation
Indices: 29477728--29477762 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29477718 TACGAGAACT
29477728 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
29477763 TCAGTCGTTA
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:29479985 original size:44 final size:44
Alignment explanation
Indices: 29479934--29480147 Score: 304
Period size: 44 Copynumber: 4.9 Consensus size: 44
29479924 TTGAAGTAAA
*
29479934 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCAGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCAGTCC
* *
29479978 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCAATCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCAGTCC
* * * **
29480022 AATTGTTGATTAAATGTTGTCTAAATATTGATTGAATGTTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCAGTCC
* * *
29480066 AATTGTTGATTAAATGTTGTCCAAATGTTGATTTAATGCTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCAGTCC
* *
29480110 AATTG-TGATTGAATGCTGTCCAAATGTTGATTAAATGC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGC
29480148 TGTCTGAATG
Statistics
Matches: 153, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 30 0.20
44 123 0.80
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (44 bp):
AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCAGTCC
Found at i:29480046 original size:11 final size:11
Alignment explanation
Indices: 29480032--29480095 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
29480022 AATTGTTGAT
29480032 TAAATGTTGTC
1 TAAATGTTGTC
*
29480043 TAAATATTGAT-
1 TAAATGTTG-TC
*
29480054 TGAATGTTGTC
1 TAAATGTTGTC
* *
29480065 CAATTGTTGAT-
1 TAAATGTTG-TC
29480076 TAAATGTTGTC
1 TAAATGTTGTC
*
29480087 CAAATGTTG
1 TAAATGTTG
29480096 ATTTAATGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
10 2 0.05
11 36 0.90
12 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.44
Consensus pattern (11 bp):
TAAATGTTGTC
Found at i:29480087 original size:88 final size:88
Alignment explanation
Indices: 29479934--29480151 Score: 339
Period size: 88 Copynumber: 2.5 Consensus size: 88
29479924 TTGAAGTAAA
*
29479934 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCAGTCCAATTGTTGATTAAATGCTGTC
1 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCTGTCCAATTGTTGATTAAATGCTGTC
29479999 CAAATGTTGATTTAATGCAATCC
66 CAAATGTTGATTTAATGCAATCC
* * * *
29480022 AATTGTTGATTAAATGTTGTCTAAATATTGATTGAATGTTGTCCAATTGTTGATTAAATGTTGTC
1 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCTGTCCAATTGTTGATTAAATGCTGTC
**
29480087 CAAATGTTGATTTAATGCTGTCC
66 CAAATGTTGATTTAATGCAATCC
* * *
29480110 AATTG-TGATTGAATGCTGTCCAAATGTTGATTAAATGCTGTC
1 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCTGTC
29480152 TGAATGTTGG
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 31 0.26
88 86 0.74
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (88 bp):
AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCTGTCCAATTGTTGATTAAATGCTGTC
CAAATGTTGATTTAATGCAATCC
Found at i:29480170 original size:22 final size:22
Alignment explanation
Indices: 29479937--29480160 Score: 261
Period size: 22 Copynumber: 10.2 Consensus size: 22
29479927 AAGTAAAAAT
29479937 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * *
29479959 TATTGATTGAATGCAGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
29479981 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* ** *
29480003 TGTTGATTTAATGCAATCCAAT
1 TGTTGATTAAATGCTGTCCAAA
* *
29480025 TGTTGATTAAATGTTGTCTAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * *
29480047 TATTGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
29480069 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* *
29480091 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
29480113 TG-TGATTGAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
**
29480134 TGTTGATTAAATGCTGTCTGAA
1 TGTTGATTAAATGCTGTCCAAA
29480156 TGTTG
1 TGTTG
29480161 GATAATTGCT
Statistics
Matches: 168, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
21 19 0.11
22 149 0.89
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (22 bp):
TGTTGATTAAATGCTGTCCAAA
Found at i:29484936 original size:21 final size:18
Alignment explanation
Indices: 29484896--29484939 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
29484886 AAATTGCAAA
*
29484896 AAAAATATAAAATTTATT
1 AAAAATATAAAACTTATT
29484914 AAAAATAATAGAAACTTATT
1 AAAAAT-ATA-AAACTTATT
*
29484934 TAAAAT
1 AAAAAT
29484940 TTATGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 3 0.14
20 13 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAATATAAAACTTATT
Found at i:29485747 original size:30 final size:30
Alignment explanation
Indices: 29485713--29485772 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
29485703 ATTTTTTTCT
29485713 ATTTTTAATA-ACTTTTTTGCAATTATTATA
1 ATTTTTAATATACTTTTTTGCAATT-TTATA
*
29485743 ATTTTTAATATATTTTTTTGCAATTTTATA
1 ATTTTTAATATACTTTTTTGCAATTTTATA
29485773 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTTTAATATACTTTTTTGCAATTTTATA
Found at i:29485763 original size:31 final size:33
Alignment explanation
Indices: 29485713--29485790 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 33
29485703 ATTTTTTTCT
*
29485713 ATTTTTAATA-ACTTTTTTGCAATTAT-TA-TA
1 ATTTTTAATATATTTTTTTGCAATTATATATTA
*
29485743 ATTTTTAATATATTTTTTTGCAATTTTATATTA
1 ATTTTTAATATATTTTTTTGCAATTATATATTA
*
29485776 AATTTTAATAT-TTTT
1 ATTTTTAATATATTTT
29485791 ATAATTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 10 0.24
31 14 0.33
32 6 0.14
33 12 0.29
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (33 bp):
ATTTTTAATATATTTTTTTGCAATTATATATTA
Found at i:29485844 original size:26 final size:27
Alignment explanation
Indices: 29485815--29485874 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
29485805 GTTCTTATAA
* *
29485815 TTTTTATTATTTTTAAAAATTCT-ACT
1 TTTTTATAATTTTTAAAAATTCTAAAT
*
29485841 TTTTTATAATTTTTGAAAATTCTAAAT
1 TTTTTATAATTTTTAAAAATTCTAAAT
29485868 TTTTTAT
1 TTTTTAT
29485875 GACTTTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTATAATTTTTAAAAATTCTAAAT
Found at i:29488675 original size:27 final size:28
Alignment explanation
Indices: 29488627--29488689 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
29488617 TATACGGAAT
** * *
29488627 GAAT-CCTTCCATGGAAGGCTCTGAAGG
1 GAATGCCTTCCATGGAAAACTCTAAAAG
29488654 GAATGCCTT-CATGGAAAACTCTAAAAG
1 GAATGCCTTCCATGGAAAACTCTAAAAG
29488681 GAATGCCTT
1 GAATGCCTT
29488690 GACAGCGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (28 bp):
GAATGCCTTCCATGGAAAACTCTAAAAG
Found at i:29494700 original size:44 final size:44
Alignment explanation
Indices: 29494637--29494731 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
29494627 CCTATTAGCT
* ** *
29494637 AATACCATACACAAGCAGACTTTATACCTTTCGCACATTGGTGA
1 AATACTATACACAAGCAGACTTTATACAATTCACACATTGGTGA
* *
29494681 AATACTATACACAAGCAGACTTTATGCAATTCACCCATTGGTGA
1 AATACTATACACAAGCAGACTTTATACAATTCACACATTGGTGA
29494725 AATACTA
1 AATACTA
29494732 AACTTACACA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (44 bp):
AATACTATACACAAGCAGACTTTATACAATTCACACATTGGTGA
Found at i:29500463 original size:7 final size:7
Alignment explanation
Indices: 29500451--29500475 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29500441 AAGTTTTATA
29500451 GGTTTAG
1 GGTTTAG
29500458 GGTTTAG
1 GGTTTAG
29500465 GGTTTAG
1 GGTTTAG
29500472 GGTT
1 GGTT
29500476 CAAAATAATC
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:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:29510878 original size:501 final size:499
Alignment explanation
Indices: 29509929--29510906 Score: 1393
Period size: 501 Copynumber: 1.9 Consensus size: 499
29509919 CCAGTCAGGC
* * *
29509929 TCATCTTCTTCCCCTCTTTCCTGGTCTTTTGATCCAACTTTGGCAACAGTGTCCATGGTCAGAAA
1 TCATCTTCTTCCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCATGGTCAGAAA
* * * *
29509994 AGGAGTTTGCTTGTCAACTTTGTCTTCTGCTATCAGGTCTTCATATTTCTCCAAAGGCTTAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCAAAGGCTTAGAAG
*
29510059 TTTCATGATGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTTTGCATCCTCC
131 TTTCATGATGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTCC
* *
29510124 TCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGATTCATCTTCTTG
196 TCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGATGCATCTTCTAG
*
29510189 CCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAAAGGAGCTTGCT
261 CCCTCTTTCCTGATCTTTCGATCCAACTTTGACAACAGCATCCACTGTCAGCAAAGGAGCTTGCT
* * ** * *
29510254 TATCAACTTCGTCTTCGGCTACCTGGTCTTCATGTTTCTCTGAAGGCTCAGAAGTTTCATGGTGA
326 TATCAACTTCGTCTTCGACTACCAGGTCTTCACATTTCTCCGAAGGCTCAGAAATTTCATGGTGA
* *
29510319 ACACCTCCTTCATTTGCAGAAGTTCTAACAGAATCAAGTTCTTTTGCATCCTCCTCCTCTTCTAG
391 ACACCTCCTTCATCTGCAGAAGTTCTAACAGAATCAAGTTC-TTTGCAT-CGCCTCCTCTTCTAG
29510384 TTTTAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
454 TTTTAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
* *
29510430 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACT-GTCAGCA
1 TCATCTTCTTCCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCA-TGGTCAGAA
* **
29510494 AAGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAA
65 AAGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCAAAGGCTTAGAA
* *
29510559 GTTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCCTCCTC
130 GTTTCATGATGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCT-
*
29510624 CCTCTCTTCTCGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGATGCATCTT
194 -C-CTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGATGCATCTT
* * * * * * **
29510689 CTAGCCTTCTTTCCTGTTCTTTTGATTCAACTTTTACAAGAGTGTTGTCCACTGTCAGCAAAGGA
257 CTAGCCCTCTTTCCTGATCTTTCGATCCAACTTTGACAACA--G-CATCCACTGTCAGCAAAGGA
* * * *
29510754 GCTTGCTTATCAACTTTGT-TCTCTACTATCAGGTCTTCACATTTCTCCGAAGGCTTAGAAATTT
319 GCTTGCTTATCAACTTCGTCT-TCGACTACCAGGTCTTCACATTTCTCCGAAGGCTCAGAAATTT
** * * * * * *
29510818 CATGGTGAATGCCTCCTTTATCTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCCTCCTCCCCC
383 CATGGTGAACACCTCCTTCATCTGCAGAAGTTCTAACAGAATCAAGTTCTT-TGCAT-CGCCTCC
* *
29510883 TTTTCTAGTTTCAGATCCTCCCTT
446 TCTTCTAGTTTTAGATCCTCCCTT
29510907 ACTTCTGATT
Statistics
Matches: 421, Mismatches: 47, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
501 176 0.42
502 1 0.00
503 1 0.00
504 93 0.22
506 4 0.01
507 146 0.35
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (499 bp):
TCATCTTCTTCCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCATGGTCAGAAA
AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCAAAGGCTTAGAAG
TTTCATGATGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTCC
TCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGATGCATCTTCTAG
CCCTCTTTCCTGATCTTTCGATCCAACTTTGACAACAGCATCCACTGTCAGCAAAGGAGCTTGCT
TATCAACTTCGTCTTCGACTACCAGGTCTTCACATTTCTCCGAAGGCTCAGAAATTTCATGGTGA
ACACCTCCTTCATCTGCAGAAGTTCTAACAGAATCAAGTTCTTTGCATCGCCTCCTCTTCTAGTT
TTAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
Found at i:29510932 original size:255 final size:252
Alignment explanation
Indices: 29509929--29510906 Score: 1435
Period size: 252 Copynumber: 3.9 Consensus size: 252
29509919 CCAGTCAGGC
* * * * *
29509929 TCATCTTCTTCCCCTCTTTCCTGGTCTTTTGATCCAACTTTGGCAACAGTGTCCA-TGGTCAGAA
1 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACT-GTCAGCA
* * * * *
29509993 AAGGAGTTTGCTTGTCAACTTTGTCTTCTGCTATCAGGTCTTCATATTTCTCCAAAGGCTTAGAA
65 AAGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCGAAGGCTTAGAA
* *
29510058 GTTTCATGATGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTTTGCATCCT-
130 GTTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTC
29510122 --CCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
195 CCCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
*
29510178 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAA
1 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACTGTCAGCAA
* * * ** * *
29510243 AGGAGCTTGCTTATCAACTTCGTCTTCGGCTACCTGGTCTTCATGTTTCTCTGAAGGCTCAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCGAAGGCTTAGAAG
* * *
29510308 TTTCATGGTGAACACCTCCTTCATTTGCAGAAGTTCTAACAGAATCAAGTTCTTTTGCATCCTCC
131 TTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTCC
* *
29510373 TCCTCTTCTAGTTTTAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
196 CCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
29510430 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACTGTCAGCAA
1 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACTGTCAGCAA
* *
29510495 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCGAAGGCTTAGAAG
*
29510560 TTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCCTCCTCC
131 TTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTCC
* *
29510625 CTCTCTTCTCGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
196 CCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
* * * * * * ** * *
29510682 GCATCTTCTAGCCTTCTTTCCTGTTCTTTTGATTCAACTTTTACAAGAGTGTTGTCCACTGTCAG
1 TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACA--G-CGTCCACTGTCAG
* *
29510747 CAAAGGAGCTTGCTTATCAACTTTGT-TCTCTACTATCAGGTCTTCACATTTCTCCGAAGGCTTA
63 CAAAGGAGCTTGCTTATCAACTTTGTCT-TCTGCTACCAGGTCTTCACATTTCTCCGAAGGCTTA
* ** * * *
29510811 GAAATTTCATGGTGAATGCCTCCTTTATCTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCCTC
127 GAAGTTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATC
*
29510876 CTCCCCCTTTTCTAGTTTCAGATCCTCCCTT
192 CTCCCCCTCTTCTAGTTTCAGATCCTCCCTT
29510907 ACTTCTGATT
Statistics
Matches: 665, Mismatches: 56, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
249 172 0.26
250 1 0.00
252 332 0.50
254 2 0.00
255 158 0.24
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (252 bp):
TCATCTTCTTGCCCTCTTTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACTGTCAGCAA
AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACATTTCTCCGAAGGCTTAGAAG
TTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCATCCTCC
CCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
Found at i:29514745 original size:21 final size:20
Alignment explanation
Indices: 29514711--29514751 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29514701 TTCACAAATT
*
29514711 AAATAAATATATTTATATTC
1 AAATAAATAAATTTATATTC
*
29514731 AAATAAAATAAATTTGTATTC
1 AAAT-AAATAAATTTATATTC
29514752 TTTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATAAATAAATTTATATTC
Found at i:29518923 original size:29 final size:29
Alignment explanation
Indices: 29518881--29518937 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
29518871 AGATGACATA
29518881 TTAGTCTTTTAATTGGTTTGCTCATTTCC
1 TTAGTCTTTTAATTGGTTTGCTCATTTCC
29518910 TTAGTCTTTTAATTGGTTTGCTCATTTC
1 TTAGTCTTTTAATTGGTTTGCTCATTTC
29518938 TGATTAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.56
Consensus pattern (29 bp):
TTAGTCTTTTAATTGGTTTGCTCATTTCC
Found at i:29521262 original size:2 final size:2
Alignment explanation
Indices: 29521255--29521281 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29521245 CATCTTATGC
29521255 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 A
29521282 AAAAGACTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29523326 original size:2 final size:2
Alignment explanation
Indices: 29523321--29523369 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
29523311 ACTATAGATA
* *
29523321 AT AT AT AT -T AT GAT AT GT GT 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 AT AT AT AT AT AT AT AT
29523363 AT AT AT A
1 AT AT AT A
29523370 AAAAAGTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29527816 original size:231 final size:231
Alignment explanation
Indices: 29527544--29528252 Score: 1330
Period size: 231 Copynumber: 3.1 Consensus size: 231
29527534 GTTAAGCAGA
* *
29527544 GTTGAATCATTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTAAGAGGTATAA
1 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
*
29527609 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAA
66 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
*
29527674 CTGAATCCAAAGAGAAGCTTAGCAAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
131 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
*
29527739 AAAGAACGAGAGAGAGCAGTGTCTTTGACGAAAAGG
196 AAAGAACGAGAGAGGGCAGTGTCTTTGACGAAAAGG
29527775 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
1 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
*
29527840 AGAAAGGCTTGAGGAGGCATCTAGGTATCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
66 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
29527905 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
131 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
* *
29527970 AAAGAACGAGAGAGGGCAGTGTCTTTGATGGAAAGG
196 AAAGAACGAGAGAGGGCAGTGTCTTTGACGAAAAGG
29528006 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
1 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
29528071 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
66 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
29528136 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
131 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
29528201 AAAGAACGAGAGAGGGCAGTGTCTTTGAC-AGAAAGG
196 AAAGAACGAGAGAGGGCAGTGTCTTTGACGA-AAAGG
29528237 GTTGAATCTTTGGATC
1 GTTGAATCTTTGGATC
29528253 ACCTTGAAGA
Statistics
Matches: 466, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
231 466 1.00
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.23
Consensus pattern (231 bp):
GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
AAAGAACGAGAGAGGGCAGTGTCTTTGACGAAAAGG
Found at i:29528423 original size:462 final size:460
Alignment explanation
Indices: 29527544--29528473 Score: 1238
Period size: 462 Copynumber: 2.0 Consensus size: 460
29527534 GTTAAGCAGA
29527544 GTTGAATCATTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTAAGAGGTATAA
1 GTTGAATCATTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTAAGAGGTATAA
29527609 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAA
66 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAA
29527674 CTGAATCCAAAGAGAAGCTTAGCAAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
131 CTGAATCCAAAGAGAAGCTTAGCAAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
**
29527739 AAAGAACGAGAGAGAGCAGTGTCTTTGACGAAAAGGGTTGAATCTTTGGATCTTATTGAAGGACA
196 AAAGAACGAGAGAGAGCAGTGTCTTTGACGAAAAGGGTTGAATCTTTGGATCACATTGAAGGACA
* * ** *
29527804 GCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAAGGCTTGAGGAGGCATCTAGGTATC
261 GCGACTCCAGAAACAGAAAGAGCTTGAGAGGTATAAAGAAAGGCTTGAGGAAGCATCTAGGTATC
* * * *** *
29527869 AAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAGCTGAATCCAAAGAGAAGCTTAGCGAAGTT
326 AAATACACTTAGAAGAGCAAGCTTGGCAGAGGAAAAAGGAATCCAAAGAGAAACTTAGC-AAGTT
* * *
29527934 TGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAG-TAAAGAACGAGAGAGGGCAG-TGTCTTTG
390 TG-AATGCGCTTGAAACAGCAAAATCTGAATTG-GCTAAAGAACGAGAGAGGACAGCT-TCTTTA
29527997 ATGGAA-AGG
452 AT-GAAGAGG
* *
29528006 GTTGAATCTTTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTGAGAGGTATAA
1 GTTGAATCATTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTAAGAGGTATAA
*
29528071 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAG
66 AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAA
*
29528136 CTGAATCCAAAGAGAAGCTTAGCGAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
131 CTGAATCCAAAGAGAAGCTTAGCAAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
* *
29528201 AAAGAACGAGAGAGGGCAGTGTCTTTGAC-AGAAAGGGTTGAATCTTTGGATCACCTTGAA-GAG
196 AAAGAACGAGAGAGAGCAGTGTCTTTGACGA-AAAGGGTTGAATCTTTGGATCACATTGAAGGA-
* * * * * * *
29528264 CAGTGGCTCCAGAAACAGGATGAGGTTGAGA-G-ATACAAGAAAATGCTTGAGGAAGCATGTAGG
259 CAGCGACTCCAGAAACAGAAAGAGCTTGAGAGGTATA-AAG-AAAGGCTTGAGGAAGCATCTAGG
* * * ****
29528327 -AGTCAAAGT-CAGTTAGAAGAGCAAG-TTGGGCATATGAAAAAGGAATTTGGAGAGAAACTTGA
322 TA-TCAAA-TACACTTAGAAGAGCAAGCTT-GGCAGAGGAAAAAGGAATCCAAAGAGAAACTT--
* * ** *
29528389 AGC-AGCTTTTG-ATGC-TTTAGAAACTGTGAAATCTGAATTGGCTAAAGAACGTGAGAGGACAG
382 AGCAAG--TTTGAATGCGCTT-GAAACAGCAAAATCTGAATTGGCTAAAGAACGAGAGAGGACAG
29528451 CTTCTTTAATGAAGAGG
444 CTTCTTTAATGAAGAGG
29528468 GTTGAA
1 GTTGAA
29528474 CAGTGGGCTC
Statistics
Matches: 411, Mismatches: 42, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
460 3 0.01
461 16 0.04
462 383 0.93
463 2 0.00
464 7 0.02
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (460 bp):
GTTGAATCATTGGATCTTATTGAAGGACAGCGATTCCTGATGCAGAAAGAGCTTAAGAGGTATAA
AGAAAGGCTTGAGGAGGCATCTAGGTGTCAAATACACTTGGAAGAGCAAGCTTTGCAGAGGGAAA
CTGAATCCAAAGAGAAGCTTAGCAAAGTTTGCAATGCGCTTGAAGCAGCAAAATCTGAATTGAGT
AAAGAACGAGAGAGAGCAGTGTCTTTGACGAAAAGGGTTGAATCTTTGGATCACATTGAAGGACA
GCGACTCCAGAAACAGAAAGAGCTTGAGAGGTATAAAGAAAGGCTTGAGGAAGCATCTAGGTATC
AAATACACTTAGAAGAGCAAGCTTGGCAGAGGAAAAAGGAATCCAAAGAGAAACTTAGCAAGTTT
GAATGCGCTTGAAACAGCAAAATCTGAATTGGCTAAAGAACGAGAGAGGACAGCTTCTTTAATGA
AGAGG
Found at i:29537076 original size:13 final size:14
Alignment explanation
Indices: 29537057--29537089 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
29537047 TGCATAAACA
29537057 TCCACATGTTCAAC
1 TCCACATGTTCAAC
29537071 -CCACATGTTCAAC
1 TCCACATGTTCAAC
29537084 TCCACA
1 TCCACA
29537090 GCTCTCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.30, C:0.39, G:0.06, T:0.24
Consensus pattern (14 bp):
TCCACATGTTCAAC
Found at i:29544536 original size:124 final size:124
Alignment explanation
Indices: 29544340--29544566 Score: 382
Period size: 124 Copynumber: 1.8 Consensus size: 124
29544330 TAATTTCGAG
* * *
29544340 TTGACGTTTATGATCAAATAGTATAAAAGCGCTTTTAGTAGGATGCTATTTGAGAACAATTAGTG
1 TTGACGTTTATGAGCAAATAGTATAAAAGCGCTTCTAGCAGGATGCTATTTGAGAACAATTAGTG
29544405 AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT
66 AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT
* * * *
29544464 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTATGAGCAAATAGTATAAAAGCGCTTCTAGCAGGATGCTATTTGAGAACAATTAGTG
*
29544529 AAAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAG
66 AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
29544567 TATGTTTAGG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 95 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (124 bp):
TTGACGTTTATGAGCAAATAGTATAAAAGCGCTTCTAGCAGGATGCTATTTGAGAACAATTAGTG
AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT
Found at i:29548698 original size:20 final size:20
Alignment explanation
Indices: 29548661--29548698 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29548651 TTTATTTTTA
*
29548661 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
29548681 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
29548699 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:29552274 original size:24 final size:24
Alignment explanation
Indices: 29552237--29552299 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29552227 ATTATCATAA
*
29552237 TCAAATACATATGCATAAACAAAT
1 TCAAATACAAATGCATAAACAAAT
* * *
29552261 TTAGATACAAATGCATACACAAAT
1 TCAAATACAAATGCATAAACAAAT
*
29552285 TCAAATACAGATGCA
1 TCAAATACAAATGCA
29552300 GACGCTGATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (24 bp):
TCAAATACAAATGCATAAACAAAT
Found at i:29552867 original size:28 final size:27
Alignment explanation
Indices: 29552809--29552871 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
29552799 TTAATTAGGG
* *
29552809 TCCTAGCTTAAATACATGTTTAATATG
1 TCCTAGCTTAAATACATGTTTAAGATA
*
29552836 TCCTAGCTT-AATGCATGATTTTAAGATA
1 TCCTAGCTTAAATACATG--TTTAAGATA
29552864 TCCTAGCT
1 TCCTAGCT
29552872 GCTGTCGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.23
27 9 0.29
28 15 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (27 bp):
TCCTAGCTTAAATACATGTTTAAGATA
Found at i:29558710 original size:125 final size:126
Alignment explanation
Indices: 29558258--29558725 Score: 812
Period size: 129 Copynumber: 3.7 Consensus size: 126
29558248 CGTCTCTGGT
* * * * *
29558258 CAAATAATATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
*
29558323 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATTTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
29558384 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
*
29558449 TGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTTTTTTCTGATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAT-AA--TTTTTTTTCTGATGTTTCTGAG
29558513 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
29558578 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTCTGATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
* * *
29558638 TAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCCCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
29558703 TGGACGCGATTTTGCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
29558726 CAAGTTTGGG
Statistics
Matches: 328, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
125 106 0.32
126 96 0.29
127 2 0.01
128 2 0.01
129 122 0.37
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (126 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCACTCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
Found at i:29559163 original size:25 final size:25
Alignment explanation
Indices: 29559135--29559185 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
29559125 ATATTGAGTT
*
29559135 ATATGTACAATTATTAAGCCAAAAA
1 ATATGTAAAATTATTAAGCCAAAAA
29559160 ATATGTAAAATTATTAAGCCAAAAA
1 ATATGTAAAATTATTAAGCCAAAAA
29559185 A
1 A
29559186 ATTTAGGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (25 bp):
ATATGTAAAATTATTAAGCCAAAAA
Found at i:29559231 original size:11 final size:10
Alignment explanation
Indices: 29559187--29559460 Score: 62
Period size: 9 Copynumber: 28.6 Consensus size: 10
29559177 GCCAAAAAAA
29559187 TTTAGGTTAG
1 TTTAGGTTAG
29559197 TTTAGGGTT--
1 TTTA-GGTTAG
* *
29559206 TTTA-ATTAA
1 TTTAGGTTAG
29559215 TTTAGGTTAGG
1 TTTAGGTTA-G
29559226 TTTAGGGTT--
1 TTTA-GGTTAG
*
29559235 TTTA-GTTAA
1 TTTAGGTTAG
29559244 TTTAGGTTAGG
1 TTTAGGTTA-G
*
29559255 TTTAGG--GG
1 TTTAGGTTAG
*
29559263 TTTTA-GTTAA
1 -TTTAGGTTAG
*
29559273 TTTAGGTTAA
1 TTTAGGTTAG
*
29559283 ATTAGGGTT--
1 TTTA-GGTTAG
*
29559292 TTTA-ATTAG
1 TTTAGGTTAG
29559301 TTTAGGTTAGG
1 TTTAGGTTA-G
29559312 TTTAGGGTT--
1 TTTA-GGTTAG
*
29559321 TTTA-GTTAA
1 TTTAGGTTAG
29559330 TTTAGGTTAG
1 TTTAGGTTAG
*
29559340 ATTAGGGTT--
1 TTTA-GGTTAG
*
29559349 TTTA-GTTAA
1 TTTAGGTTAG
29559358 TTTAGGTTAGG
1 TTTAGGTTA-G
29559369 TTTAGGGTT--
1 TTTA-GGTTAG
* *
29559378 TTTA-ATTAA
1 TTTAGGTTAG
29559387 TTTAGGTTAG
1 TTTAGGTTAG
*
29559397 ATTAGGGTT--
1 TTTA-GGTTAG
* *
29559406 TTTA-ATTAA
1 TTTAGGTTAG
29559415 TTTAGGTTAG
1 TTTAGGTTAG
29559425 ATTTAGGGTT--
1 -TTTA-GGTTAG
* *
29559435 TTTA-ATTAA
1 TTTAGGTTAG
29559444 TTTAGGTTAG
1 TTTAGGTTAG
29559454 ATTTAGG
1 -TTTAGG
29559461 GTTTTTAATT
Statistics
Matches: 196, Mismatches: 26, Indels: 83
0.64 0.09 0.27
Matches are distributed among these distances:
7 19 0.10
8 2 0.01
9 69 0.35
10 45 0.23
11 45 0.23
12 16 0.08
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (10 bp):
TTTAGGTTAG
Found at i:29559238 original size:29 final size:29
Alignment explanation
Indices: 29559185--29559489 Score: 465
Period size: 29 Copynumber: 10.7 Consensus size: 29
29559175 AAGCCAAAAA
29559185 AATTTAGGTTA-GTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
29559213 AATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
29559242 AATTTAGGTTAGGTTTAGGGGTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
**
29559271 AATTTAGGTTA-AATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
29559299 AGTTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
29559328 AATTTAGGTTA-GATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
29559356 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
29559385 AATTTAGGTTA-GATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
29559413 AATTTAGGTTAGATTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
29559442 AATTTAGGTTAGATTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
29559471 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGGTTTAGG
29559490 TTAGGGTTTT
Statistics
Matches: 254, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
28 88 0.35
29 166 0.65
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (29 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAATT
Found at i:29559289 original size:57 final size:57
Alignment explanation
Indices: 29559185--29559489 Score: 495
Period size: 57 Copynumber: 5.3 Consensus size: 57
29559175 AAGCCAAAAA
* *
29559185 AATTTAGGTTA-GTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATT
* * *
29559242 AATTTAGGTTAGGTTTAGGGGTTTTAGTTAATTTAGGTTAAATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
* * *
29559299 AGTTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
29559356 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
*
29559413 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGATTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGA-TTAGGGTTTTTAATT
*
29559471 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGGTTTAGG
29559490 TTAGGGTTTT
Statistics
Matches: 231, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
57 173 0.75
58 58 0.25
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (57 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
Found at i:29559330 original size:86 final size:87
Alignment explanation
Indices: 29559185--29559489 Score: 492
Period size: 86 Copynumber: 3.6 Consensus size: 87
29559175 AAGCCAAAAA
29559185 AATTTAGGTTAG-TTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
1 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
*
29559249 GTTAGGTTTAGGGGTTTTAGTT
66 GTTAGGTTTAGGGTTTTTAGTT
* *
29559271 AATTTAGGTTA-AATTAGGGTTTTTAATTAGTTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
1 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
*
29559335 GTTA-GATTAGGGTTTTTAGTT
66 GTTAGGTTTAGGGTTTTTAGTT
* * *
29559356 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAG
1 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
* *
29559420 GTTAGATTTAGGGTTTTTAATT
66 GTTAGGTTTAGGGTTTTTAGTT
*
29559442 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGG
29559490 TTAGGGTTTT
Statistics
Matches: 201, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
85 52 0.26
86 143 0.71
87 6 0.03
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (87 bp):
AATTTAGGTTAGATTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAG
GTTAGGTTTAGGGTTTTTAGTT
Found at i:29559727 original size:21 final size:21
Alignment explanation
Indices: 29559702--29559761 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
29559692 TCCTCTAGCT
*
29559702 TCCGGCGGTGGTTGTTCTTCC
1 TCCGGTGGTGGTTGTTCTTCC
*
29559723 TCCGGTGGTGATTGTGGTTCTTCC
1 TCCGGTGGTG---GTTGTTCTTCC
29559747 TCCGGTGGTGGTTGT
1 TCCGGTGGTGGTTGT
29559762 GGTTCTTCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.39
24 20 0.61
ACGTcount: A:0.02, C:0.22, G:0.37, T:0.40
Consensus pattern (21 bp):
TCCGGTGGTGGTTGTTCTTCC
Found at i:29559747 original size:24 final size:24
Alignment explanation
Indices: 29559715--29559770 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
29559705 GGCGGTGGTT
29559715 GTTCTTCCTCCGGTGGTGATTGTG
1 GTTCTTCCTCCGGTGGTGATTGTG
*
29559739 GTTCTTCCTCCGGTGGTGGTTGTG
1 GTTCTTCCTCCGGTGGTGATTGTG
29559763 GTTCTTCC
1 GTTCTTCC
29559771 GGTTCGGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.02, C:0.23, G:0.32, T:0.43
Consensus pattern (24 bp):
GTTCTTCCTCCGGTGGTGATTGTG
Found at i:29559771 original size:21 final size:21
Alignment explanation
Indices: 29559700--29559773 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
29559690 CTTCCTCTAG
* **
29559700 CTTCCGGCGGTGGTTGTTCTT
1 CTTCCGGTGGTGGTTGTGGTT
* *
29559721 CCTCCGGTGGTGATTGTGGTT
1 CTTCCGGTGGTGGTTGTGGTT
29559742 CTTCCTCCGGTGGTGGTTGTGGTT
1 C-T--TCCGGTGGTGGTTGTGGTT
29559766 CTTCCGGT
1 CTTCCGGT
29559774 TCGGCATCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 23 0.53
23 1 0.02
24 19 0.44
ACGTcount: A:0.01, C:0.23, G:0.35, T:0.41
Consensus pattern (21 bp):
CTTCCGGTGGTGGTTGTGGTT
Found at i:29560069 original size:18 final size:18
Alignment explanation
Indices: 29560025--29560070 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29560015 TATTCGGAAA
* *
29560025 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
29560043 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
29560061 AGGAAACATA
1 AGGATACATA
29560071 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:29560690 original size:7 final size:7
Alignment explanation
Indices: 29560680--29560704 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29560670 TTATATACAT
29560680 AATACTA
1 AATACTA
29560687 AATACTA
1 AATACTA
29560694 AATACTA
1 AATACTA
29560701 AATA
1 AATA
29560705 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29561839 original size:30 final size:31
Alignment explanation
Indices: 29561786--29561849 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
29561776 GCCATTGATG
29561786 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
29561817 AAAATATAAAAAAA-TTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
29561847 AAA
1 AAA
29561850 TGGATTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:29561931 original size:21 final size:22
Alignment explanation
Indices: 29561895--29561944 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
29561885 AAATATGGGT
29561895 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
29561917 TTGAGAGAA-TTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
29561938 TTGAGAG
1 TTGAGAG
29561945 GAAAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:29563327 original size:21 final size:22
Alignment explanation
Indices: 29563283--29563328 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29563273 TTGGCACCAC
* **
29563283 AAAATAAAAAATTACTTTTTAA
1 AAAATAAAAAATTAATTTAAAA
29563305 AAAATAAAAAA-TAATTTAAAA
1 AAAATAAAAAATTAATTTAAAA
29563326 AAA
1 AAA
29563329 TGGGTTGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAAAAAATTAATTTAAAA
Found at i:29570798 original size:18 final size:17
Alignment explanation
Indices: 29570770--29570804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29570760 ATTATTAAGA
*
29570770 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29570787 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29570805 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29571025 original size:44 final size:45
Alignment explanation
Indices: 29570962--29571059 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
29570952 CTATTACACC
*
29570962 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * *
29571006 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
29571051 TCCATTACA
1 TCCATTACA
29571060 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
43 1 0.02
44 22 0.46
45 25 0.52
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:29571130 original size:9 final size:9
Alignment explanation
Indices: 29571113--29571206 Score: 91
Period size: 9 Copynumber: 10.4 Consensus size: 9
29571103 GTAGTGATTC
29571113 AATTCGGTT
1 AATTCGGTT
*
29571122 AATTTGGTT
1 AATTCGGTT
* *
29571131 AATTTGGGT
1 AATTCGGTT
29571140 AATTCGGTT
1 AATTCGGTT
*
29571149 AATTCGGGT
1 AATTCGGTT
* *
29571158 AATCCGATT
1 AATTCGGTT
*
29571167 AATTCAGTT
1 AATTCGGTT
*
29571176 AATTTTGG-T
1 AA-TTCGGTT
*
29571185 AATTCGGGT
1 AATTCGGTT
29571194 AATTCGGTT
1 AATTCGGTT
29571203 AATT
1 AATT
29571207 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
8 4 0.06
9 61 0.90
10 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29571208 original size:27 final size:27
Alignment explanation
Indices: 29571113--29571208 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
29571103 GTAGTGATTC
*
29571113 AATTCGGTTAA-TTTGGTTAATTTGGGT
1 AATTCGGTTAATTTTGG-TAATTCGGGT
** * **
29571140 AATTCGGTTAATTCGGGTAATCCGATT
1 AATTCGGTTAATTTTGGTAATTCGGGT
*
29571167 AATTCAGTTAATTTTGGTAATTCGGGT
1 AATTCGGTTAATTTTGGTAATTCGGGT
29571194 AATTCGGTTAATTTT
1 AATTCGGTTAATTTT
29571209 TAACCAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
27 52 0.95
28 3 0.05
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (27 bp):
AATTCGGTTAATTTTGGTAATTCGGGT
Found at i:29572777 original size:22 final size:24
Alignment explanation
Indices: 29572735--29572778 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
29572725 CAATTTTGAC
29572735 AAAAAAAATCATATATCAATTTTT
1 AAAAAAAATCATATATCAATTTTT
*
29572759 AAAAAAAA-CAT-TATTAATTT
1 AAAAAAAATCATATATCAATTT
29572779 CAAGTAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAAAAAATCATATATCAATTTTT
Found at i:29573544 original size:17 final size:17
Alignment explanation
Indices: 29573491--29573546 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
29573481 TAATTATTTG
29573491 AAATATTTCACATATAA
1 AAATATTTCACATATAA
* * **
29573508 AAA-AATT-ATAT-TTG
1 AAATATTTCACATATAA
29573522 AAATATTTCACATATAA
1 AAATATTTCACATATAA
29573539 AAATATTT
1 AAATATTT
29573547 GAAATATCAT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 6 0.21
17 12 0.43
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATATTTCACATATAA
Found at i:29575198 original size:18 final size:17
Alignment explanation
Indices: 29575167--29575201 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29575157 GATTTAGGGT
29575167 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
29575184 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
29575202 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:29577857 original size:25 final size:24
Alignment explanation
Indices: 29577816--29577862 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
29577806 AAAAAATATT
29577816 AAATATATATATATTTTAATTTTTA
1 AAATATATATATATTTT-ATTTTTA
*
29577841 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TATTTTATTTT
29577863 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATATATATATATTTTATTTTTA
Found at i:29578008 original size:68 final size:68
Alignment explanation
Indices: 29577929--29578138 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
29577919 TCAAGTTTGT
* *
29577929 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAAATAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
29577994 AAA
66 AAA
29577997 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
29578062 AAA
66 AAA
*
29578065 TTTACTAATCAAATGTTAGATTTCATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
29578128 AAT
66 AAA
29578131 TTTACTAA
1 TTTACTAA
29578139 CAATTAATTT
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 110 0.80
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:29578039 original size:9 final size:9
Alignment explanation
Indices: 29578027--29578054 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29578017 TTTTATTACA
29578027 ACAATTAAT
1 ACAATTAAT
29578036 ACAATTAAT
1 ACAATTAAT
29578045 ACAATTAAT
1 ACAATTAAT
29578054 A
1 A
29578055 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:29578148 original size:16 final size:16
Alignment explanation
Indices: 29578127--29578168 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29578117 AATAATTTGA
*
29578127 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
29578143 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
29578159 TAGTTTTAAT
1 TAATTTTAAT
29578169 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:29578152 original size:22 final size:23
Alignment explanation
Indices: 29578142--29578203 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
29578132 TTACTAACAA
* * *
29578142 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
29578164 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
29578187 TTAATTTTA-ATTAAAAA
1 TTAATTTTATATAAAAAA
29578204 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:29580110 original size:18 final size:17
Alignment explanation
Indices: 29580073--29580146 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
29580063 TAAATTTCAT
*
29580073 AAAAT-TATAAAAATTG
1 AAAATATATAAAAATTC
29580089 AAAATATATAAACAATTC
1 AAAATATATAAA-AATTC
* *
29580107 AAAAGATATTTTAAAAA-TA
1 -AAA-ATA-TATAAAAATTC
*
29580126 AAAAAATATAAAAATTC
1 AAAATATATAAAAATTC
29580143 AAAA
1 AAAA
29580147 ATTTAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
16 12 0.26
17 13 0.28
18 7 0.15
19 4 0.09
20 5 0.11
21 5 0.11
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAATATATAAAAATTC
Found at i:29585630 original size:43 final size:43
Alignment explanation
Indices: 29585569--29585654 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
29585559 TCAAATATGT
*
29585569 TAGTTATTCATTTCATGTAAACATCAATAACAAAGATGAGCTC
1 TAGTTATTCATATCATGTAAACATCAATAACAAAGATGAGCTC
*
29585612 TAGTTATTCATATCATGTAAACATCAATAACAAATATGAGCTC
1 TAGTTATTCATATCATGTAAACATCAATAACAAAGATGAGCTC
29585655 ATCAAATGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (43 bp):
TAGTTATTCATATCATGTAAACATCAATAACAAAGATGAGCTC
Found at i:29585946 original size:24 final size:24
Alignment explanation
Indices: 29585903--29585978 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
29585893 TATAAAGGGA
29585903 AGCTCACAAAGAGC-CTTTAACAGGT
1 AGCTC-CAAAGAGCAC-TTAACAGGT
* *
29585928 AGCTCCAAAGAGCACTTAATAGGA
1 AGCTCCAAAGAGCACTTAACAGGT
* *
29585952 AGCTCCGAAGAGCACTTAACGGGT
1 AGCTCCAAAGAGCACTTAACAGGT
29585976 AGC
1 AGC
29585979 ACCGGGTAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 38 0.86
25 6 0.14
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
AGCTCCAAAGAGCACTTAACAGGT
Found at i:29586694 original size:2 final size:2
Alignment explanation
Indices: 29586687--29586720 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29586677 AGATATTTTC
29586687 AT AT AT AT 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 AT AT AT AT
29586721 TCATAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29587253 original size:9 final size:9
Alignment explanation
Indices: 29587239--29587342 Score: 138
Period size: 9 Copynumber: 11.4 Consensus size: 9
29587229 TTTGGTTAAA
29587239 AATTACCCG
1 AATTACCCG
29587248 AATTACCCG
1 AATTACCCG
29587257 AATTACCCG
1 AATTACCCG
*
29587266 AATTAACCG
1 AATTACCCG
29587275 AATTACCCG
1 AATTACCCG
*
29587284 AATTAACCG
1 AATTACCCG
*
29587293 AATTAACCG
1 AATTACCCG
*
29587302 AATTAACCG
1 AATTACCCG
29587311 AATTA-CCG
1 AATTACCCG
*
29587319 AAAAATACCCG
1 --AATTACCCG
29587330 AATTACCCG
1 AATTACCCG
29587339 AATT
1 AATT
29587343 TTTTTATTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
8 3 0.03
9 77 0.89
10 4 0.05
11 3 0.03
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:29589148 original size:28 final size:28
Alignment explanation
Indices: 29589108--29589164 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29589098 TCGGTGGTGT
29589108 AAAGCTTTGTGTCAAGTTGGAGACCCAC
1 AAAGCTTTGTGTCAAGTTGGAGACCCAC
29589136 AAAGCTTTGTGTCAAGTTGGAGACCCAC
1 AAAGCTTTGTGTCAAGTTGGAGACCCAC
29589164 A
1 A
29589165 GAATACCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (28 bp):
AAAGCTTTGTGTCAAGTTGGAGACCCAC
Found at i:29590100 original size:43 final size:43
Alignment explanation
Indices: 29590046--29590315 Score: 310
Period size: 43 Copynumber: 6.3 Consensus size: 43
29590036 TCTTTTAAAG
* * *
29590046 CGCCGCTATAGACTATGGTCTTTAACGGCGCTTAGATAAAAAA
1 CGCCACTATAGACTATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * * *
29590089 CGCCGCGATAGACCATGGTCTTTAGCGGCGCTTATACAAAAAA
1 CGCCACTATAGACTATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * *
29590132 TGCCACTATAGA-TCGTGGTCTTTAGCGGCGCTTATACAAAAAA
1 CGCCACTATAGACT-ATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * * *
29590175 CGCCACTATAGA-TCGTGGTCTTTAGCGGCGTTTGGATAAAAAA
1 CGCCACTATAGACT-ATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * *
29590218 CGCCACTATAGACCATGGTCTTCAGCGGCGCTTGGACAAAAAA
1 CGCCACTATAGACTATGGTCTTTAGCGGCGCTTAGACAAAAAA
* * *
29590261 CGCCACTATAGACGATGGTCTTTAGCGCCGCTTAGGCAAAAAAA
1 CGCCACTATAGACTATGGTCTTTAGCGGCGCTTAGAC-AAAAAA
*
29590305 CACCACTATAG
1 CGCCACTATAG
29590316 GCCGTGTTCT
Statistics
Matches: 198, Mismatches: 26, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
43 182 0.92
44 16 0.08
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (43 bp):
CGCCACTATAGACTATGGTCTTTAGCGGCGCTTAGACAAAAAA
Found at i:29590216 original size:129 final size:130
Alignment explanation
Indices: 29590051--29590329 Score: 373
Period size: 129 Copynumber: 2.2 Consensus size: 130
29590041 TAAAGCGCCG
** * * *
29590051 CTATAGACTATGGTCTTTAACGGCGCTTAGATAAAAAACGCCGCGATAGACCATGGTCTTTAGCG
1 CTATAGACCGTGGTCTTTAGCGGCGCTTAGATAAAAAACGCCACGATAGACCATGGTCTTCAGCG
* * * * *
29590116 GCGCTTATACAAAAAATGCCACTATAGATCG-TGGTCTTTAGCGGCGCTTATAC-AAAAAACGCC
66 GCGCTTAGACAAAAAACGCCACTATAGA-CGATGGTCTTTAGCGCCGCTTAGACAAAAAAACACC
29590179 A
130 A
* * * *
29590180 CTATAGATCGTGGTCTTTAGCGGCGTTTGGATAAAAAACGCCACTATAGACCATGGTCTTCAGCG
1 CTATAGACCGTGGTCTTTAGCGGCGCTTAGATAAAAAACGCCACGATAGACCATGGTCTTCAGCG
* *
29590245 GCGCTTGGACAAAAAACGCCACTATAGACGATGGTCTTTAGCGCCGCTTAGGCAAAAAAACACCA
66 GCGCTTAGACAAAAAACGCCACTATAGACGATGGTCTTTAGCGCCGCTTAGACAAAAAAACACCA
* *
29590310 CTATAGGCCGTGTTCTTTAG
1 CTATAGACCGTGGTCTTTAG
29590330 TGACGTTTAC
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
128 2 0.02
129 100 0.78
130 27 0.21
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (130 bp):
CTATAGACCGTGGTCTTTAGCGGCGCTTAGATAAAAAACGCCACGATAGACCATGGTCTTCAGCG
GCGCTTAGACAAAAAACGCCACTATAGACGATGGTCTTTAGCGCCGCTTAGACAAAAAAACACCA
Found at i:29590787 original size:21 final size:21
Alignment explanation
Indices: 29590763--29590817 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
29590753 TTTCGTTGAA
29590763 CCTCAGCTTCTCTCGCTGCTG
1 CCTCAGCTTCTCTCGCTGCTG
29590784 CCTCAGCTTCTCTCGCTGCTG
1 CCTCAGCTTCTCTCGCTGCTG
*
29590805 CCTCTGCTTCTCT
1 CCTCAGCTTCTCT
29590818 TGTTGCCGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.04, C:0.44, G:0.16, T:0.36
Consensus pattern (21 bp):
CCTCAGCTTCTCTCGCTGCTG
Found at i:29590809 original size:108 final size:108
Alignment explanation
Indices: 29590687--29590900 Score: 299
Period size: 108 Copynumber: 2.0 Consensus size: 108
29590677 CTTTAATTCC
*
29590687 CTCGCTGTAGCCTCTGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTACT-GCTGGAGTTCTTCAT
1 CTCGCTGTAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAG-TACTAGCTGGAGTTCTTCAT
*
29590751 A-CTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCCTCAGCTTCT
65 ATCTTT-GTTGAACCTCAGCTTCTCTCGATGCTGCCTCAGCTTCT
* * **
29590795 CTCGCTGCT-GCCTCTGCTTCTCTTGTTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCAT
1 CTCGCTG-TAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCAT
* * *
29590859 ATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTT
65 ATCTTTGTTGAACCTCAGCTTCTCTCGATGCTGCCTCAGCTT
29590901 TAAGTTGTGT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
107 2 0.02
108 87 0.93
109 5 0.05
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.39
Consensus pattern (108 bp):
CTCGCTGTAGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATA
TCTTTGTTGAACCTCAGCTTCTCTCGATGCTGCCTCAGCTTCT
Found at i:29590831 original size:21 final size:21
Alignment explanation
Indices: 29590768--29590834 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
29590758 TTGAACCTCA
* * *
29590768 GCTTCTCTCGCTGCTGCCTCA
1 GCTTCTCTCGCTGCCGCATCT
* *
29590789 GCTTCTCTCGCTGCTGCCTCT
1 GCTTCTCTCGCTGCCGCATCT
* *
29590810 GCTTCTCTTGTTGCCGCATCT
1 GCTTCTCTCGCTGCCGCATCT
29590831 GCTT
1 GCTT
29590835 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.03, C:0.39, G:0.19, T:0.39
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCGCATCT
Found at i:29593758 original size:11 final size:11
Alignment explanation
Indices: 29593742--29593769 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29593732 TACTCATTCT
29593742 AAGTAATATGA
1 AAGTAATATGA
29593753 AAGTAATATGA
1 AAGTAATATGA
29593764 AAGTAA
1 AAGTAA
29593770 ATTAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (11 bp):
AAGTAATATGA
Found at i:29595108 original size:14 final size:14
Alignment explanation
Indices: 29595089--29595156 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
29595079 ATGATCGTTG
29595089 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
29595103 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
29595118 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
*
29595131 -AACCTTAAATCTC
1 AAACCCTAAATCTC
*
29595144 AAACCTTAAATCT
1 AAACCCTAAATCT
29595157 ATACCCCGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
14 16 0.36
15 17 0.39
16 2 0.05
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:29595702 original size:41 final size:41
Alignment explanation
Indices: 29595652--29595970 Score: 178
Period size: 41 Copynumber: 7.8 Consensus size: 41
29595642 GGTAAATGCG
*
29595652 TTAGCGGTGCTTAGATACAAACGCCGCTAAAG-GCCGAAAAA
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCCG-AAAA
* * * * * **
29595693 TTAGTGGTGCTCAGATAAAAACGTCACTAAAGATCCGAGCA
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCCGAAAA
* * * **
29595734 TTAGCGGCGCTTAGACAAAAACGCCGCTAAA-TGCCAGAGTA
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCC-GAAAA
* * * * * * * **
29595775 TTAGTGGCGCTCAAATAAAAACGCCACTAAAAATCCGAGCA
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCCGAAAA
* * * * **
29595816 TTAGCGGCGCTGAGAGAAAATCGCCGCTAAAG-GCCAGAAGT
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCC-GAAAA
* * * * *
29595857 TTAGCGGCG-TTCATATAAAAACGCCGCTAAAGATCTGAGAA
1 TTAGCGGTGCTT-AGATAAAAACGCCGCTAAAGAGCCGAAAA
* * * * * **
29595898 TTAGCGGCGCTCAGATAAAAACACCACTAAAGATCCGAGCA
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCCGAAAA
* ** *
29595939 TTAGCGGCGCACAAATAAAAACGCCGCTAAAG
1 TTAGCGGTGCTTAGATAAAAACGCCGCTAAAG
29595971 GTTTAAAAAT
Statistics
Matches: 216, Mismatches: 55, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
40 5 0.02
41 204 0.94
42 7 0.03
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (41 bp):
TTAGCGGTGCTTAGATAAAAACGCCGCTAAAGAGCCGAAAA
Found at i:29595747 original size:82 final size:82
Alignment explanation
Indices: 29595652--29595970 Score: 336
Period size: 82 Copynumber: 3.9 Consensus size: 82
29595642 GGTAAATGCG
* * * *
29595652 TTAGCGGTGCTTAGATACAAACGCCGCTAAAGGCC-GAAAAATTAGTGGTGCTCAGATAAAAACG
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAG-AAAATTAGTGGCGCTCAAATAAAAACG
*
29595716 TCACTAAAGATCCGAGCA
65 CCACTAAAGATCCGAGCA
* * **
29595734 TTAGCGGCGCTTAGACAAAAACGCCGCTAAATGCCAGAGTATTAGTGGCGCTCAAATAAAAACGC
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAAAATTAGTGGCGCTCAAATAAAAACGC
*
29595799 CACTAAAAATCCGAGCA
66 CACTAAAGATCCGAGCA
* * * ** * * *
29595816 TTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAAGTTTAGCGGCGTTCATATAAAAACGC
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAAAATTAGTGGCGCTCAAATAAAAACGC
* * *
29595881 CGCTAAAGATCTGAGAA
66 CACTAAAGATCCGAGCA
* * * * ** * *
29595898 TTAGCGGCGCTCAGATAAAAACACCACTAAAGATCC-GAGCATTAGCGGCGCACAAATAAAAACG
1 TTAGCGGCGCTTAGATAAAAACGCCGCTAAAG-GCCAGAAAATTAGTGGCGCTCAAATAAAAACG
*
29595962 CCGCTAAAG
65 CCACTAAAG
29595971 GTTTAAAAAT
Statistics
Matches: 199, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
82 196 0.98
83 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (82 bp):
TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAAAATTAGTGGCGCTCAAATAAAAACGC
CACTAAAGATCCGAGCA
Found at i:29595846 original size:123 final size:123
Alignment explanation
Indices: 29595733--29595971 Score: 311
Period size: 123 Copynumber: 1.9 Consensus size: 123
29595723 AGATCCGAGC
* *
29595733 ATTAGCGGCGCTT-AGACAAAAACGCCGCTAAATG-CCAGAGTATTAGTGGCGCTCAAATAAAAA
1 ATTAGCGGCG-TTCAGACAAAAACGCCGCTAAA-GACCAGAGAATTAGCGGCGCTCAAATAAAAA
*
29595796 CGCCACTAAAAATCCGAGCATTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAAG
64 CACCACTAAAAATCCGAGCATTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAAG
* * * * * *
29595856 TTTAGCGGCGTTCATATAAAAACGCCGCTAAAGATCTGAGAATTAGCGGCGCTCAGATAAAAACA
1 ATTAGCGGCGTTCAGACAAAAACGCCGCTAAAGACCAGAGAATTAGCGGCGCTCAAATAAAAACA
* ** * * *
29595921 CCACTAAAGATCCGAGCATTAGCGGCGCACAAATAAAAACGCCGCTAAAGG
66 CCACTAAAAATCCGAGCATTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGG
29595972 TTTAAAAATC
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 3 0.03
123 96 0.97
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (123 bp):
ATTAGCGGCGTTCAGACAAAAACGCCGCTAAAGACCAGAGAATTAGCGGCGCTCAAATAAAAACA
CCACTAAAAATCCGAGCATTAGCGGCGCTGAGAGAAAATCGCCGCTAAAGGCCAGAAG
Found at i:29596123 original size:40 final size:40
Alignment explanation
Indices: 29596049--29596124 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
29596039 AATTTCTATT
* *
29596049 TTTAGCGGCGCTTCTTCGAAATCGCCGCGGATGCTCTACC
1 TTTAGCGGCGCTTCTGCGAAATCGCCGCGAATGCTCTACC
* *
29596089 TTTAGCGGCGCTT-TGGCTAAATCGCCGCTAATGCTC
1 TTTAGCGGCGCTTCT-GCGAAATCGCCGCGAATGCTC
29596125 GATTTTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 30 0.97
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGCTTCTGCGAAATCGCCGCGAATGCTCTACC
Found at i:29598370 original size:22 final size:22
Alignment explanation
Indices: 29598342--29598407 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
29598332 ATCTCACCAC
29598342 ATAGTTTGTGGTATACCTAATA
1 ATAGTTTGTGGTATACCTAATA
* *
29598364 ATAGTTT-T--TATA-GT-A-C
1 ATAGTTTGTGGTATACCTAATA
29598380 A-AGTTTGTGGTATACCTAATA
1 ATAGTTTGTGGTATACCTAATA
29598401 ATAGTTT
1 ATAGTTT
29598408 TTATAGTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
15 5 0.15
16 2 0.06
17 1 0.03
18 5 0.15
19 5 0.15
20 1 0.03
21 2 0.06
22 12 0.36
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.44
Consensus pattern (22 bp):
ATAGTTTGTGGTATACCTAATA
Found at i:29598394 original size:37 final size:37
Alignment explanation
Indices: 29598344--29598418 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
29598334 CTCACCACAT
29598344 AGTTTGTGGTATACCTAATAATAGTTTTTATAGTACA
1 AGTTTGTGGTATACCTAATAATAGTTTTTATAGTACA
29598381 AGTTTGTGGTATACCTAATAATAGTTTTTATAGTACA
1 AGTTTGTGGTATACCTAATAATAGTTTTTATAGTACA
29598418 A
1 A
29598419 CCATTTACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (37 bp):
AGTTTGTGGTATACCTAATAATAGTTTTTATAGTACA
Found at i:29604142 original size:18 final size:16
Alignment explanation
Indices: 29604110--29604151 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
29604100 AATCATTATT
29604110 TAATTAATTTAATATC
1 TAATTAATTTAATATC
29604126 TAATTATATTGTAATAT-
1 TAATTA-ATT-TAATATC
29604143 TAACTTAAT
1 TAA-TTAAT
29604152 CAATAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 8 0.35
18 9 0.39
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTAATTTAATATC
Found at i:29605529 original size:15 final size:16
Alignment explanation
Indices: 29605509--29605540 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29605499 ACAATAATTC
29605509 TAAAAATTT-TAAAAA
1 TAAAAATTTATAAAAA
29605524 TAAAAATTTATAAAAA
1 TAAAAATTTATAAAAA
29605540 T
1 T
29605541 TCAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAATTTATAAAAA
Found at i:29608857 original size:115 final size:114
Alignment explanation
Indices: 29608499--29608875 Score: 456
Period size: 114 Copynumber: 3.3 Consensus size: 114
29608489 AAAATAAGCA
** **
29608499 TTAGCGGCGTTTTTTATCCAAA-CGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGGGC
1 TTAGCGGCGTTTTTGGT--AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGACC
* * * ** *
29608562 ATTCAGGGATTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
64 TTTCGGGGATTTAGCGGCGTTTTTAATAAAGCACCGCTAATGCTCAGGGCT
* * * *
29608613 TTAGTGGCATTTTTGAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTTTGACCT
1 TTAGCGGCGTTTTTG-GTAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGACCT
* *
29608677 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATTCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAATAAAGCACCGCTAATGCTCAGGGCT
* * * *
29608727 TTTGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAACATTAGCCCAATGACGCCGTTTTCTGACCTT
1 TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGACCTT
* * * *
29608792 TCGGGGGCTTTAGCGGCATTTTTAATACAA-CACCGCTAATGCTCTGGGAT
66 TC-GGGGATTTAGCGGCGTTTTTAATA-AAGCACCGCTAATGCTCAGGGCT
*
29608842 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAA
1 TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAA
29608876 TTATTTGTCT
Statistics
Matches: 227, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
112 3 0.01
113 7 0.03
114 145 0.64
115 70 0.31
116 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGACCTT
TCGGGGATTTAGCGGCGTTTTTAATAAAGCACCGCTAATGCTCAGGGCT
Found at i:29609368 original size:16 final size:16
Alignment explanation
Indices: 29609347--29609383 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
29609337 TTCGCTGTAT
29609347 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29609363 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29609379 TGGAA
1 TGGAA
29609384 AATCAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.19
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:29609642 original size:14 final size:15
Alignment explanation
Indices: 29609598--29609644 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
29609588 TCATATTTAA
*
29609598 AAATA-ATTATTATT
1 AAATATATTATAATT
29609612 AAATATATTATAATT
1 AAATATATTATAATT
29609627 AAA-ATA-TATAATT
1 AAATATATTATAATT
*
29609640 TAATA
1 AAATA
29609645 AAATTCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.31
14 9 0.31
15 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATATTATAATT
Found at i:29609762 original size:14 final size:15
Alignment explanation
Indices: 29609713--29609764 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29609703 ATAAAATATA
29609713 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
29609728 TATTAAATATATTAT
1 AATTAAATATATTAT
29609743 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
29609756 AATTTAATA
1 AATTAAATA
29609765 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:29610090 original size:66 final size:66
Alignment explanation
Indices: 29610013--29610211 Score: 226
Period size: 66 Copynumber: 3.2 Consensus size: 66
29610003 TAAAATTCTT
*
29610013 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAGATAATTTG
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
29610078 A
66 A
** * * * *
29610079 AATAATTAATATT-AAATAT--ATTT--T--AAT--TAAAATAT-ATAATTTAATA-A-AATTCT
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATT-T
*
29610132 -T
65 GA
29610133 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
29610198 A
66 A
29610199 AATAATTAATATT
1 AATAATTAATATT
29610212 AAATATATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
54 17 0.16
55 6 0.06
56 8 0.08
57 11 0.10
59 4 0.04
61 4 0.04
63 11 0.10
64 8 0.08
65 6 0.06
66 30 0.29
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (66 bp):
AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
A
Found at i:29610121 original size:18 final size:17
Alignment explanation
Indices: 29610094--29610128 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29610084 TTAATATTAA
*
29610094 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29610112 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29610129 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29610237 original size:59 final size:59
Alignment explanation
Indices: 29610050--29610238 Score: 192
Period size: 59 Copynumber: 3.2 Consensus size: 59
29610040 CTCAAATCAT
*
29610050 AATATATGATACTGTAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
* * * ** *
29610109 AATATAT-A-A-TTTAATA-A-AATTCT-TAATAATTAATATTCTTATATGAATTTACTCAAATC
1 AATATATGATACTATAAAAGATAATT-TGAAATAATTAATATT-AAATAT--ATTT--T--AATT
*
29610168 AT
58 AA
29610170 AATATATGATACTATAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
29610229 AATATATGAT
1 AATATATGAT
29610239 TTACTAAAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
54 17 0.17
55 6 0.06
56 5 0.05
57 5 0.05
58 1 0.01
59 22 0.22
61 12 0.12
62 1 0.01
63 5 0.05
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.42
Consensus pattern (59 bp):
AATATATGATACTATAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
Found at i:29610260 original size:120 final size:120
Alignment explanation
Indices: 29609600--29610249 Score: 1142
Period size: 120 Copynumber: 5.4 Consensus size: 120
29609590 ATATTTAAAA
* *
29609600 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
* *
29609665 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAAC
*
29609720 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
*
29609785 TCTTATATGAATTTACTCAAATCATAATATATGATACTCTAAAAGATAATTTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAAC
*
29609840 ATAATTATTATTAAACATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
*
29609905 TCTTATATGAATTTACTCAAATCATAATATATGATACTCTAAAAGATAATTTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAAC
*
29609960 ATAATTATTATTAAACATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
*
29610025 TCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAGATAATTTGAA-
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT-AAC
*
29610080 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
29610145 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA-
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT-AAC
* * *
29610200 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTACTAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
29610250 TAAAATAATT
Statistics
Matches: 517, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
120 515 1.00
121 2 0.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAAC
Found at i:29610322 original size:26 final size:28
Alignment explanation
Indices: 29610292--29610350 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
29610282 TGAATTTGTC
*
29610292 TAATTTAA-AATAAT-TATTATTACATA
1 TAATTTAATAATAATATATAATTACATA
*
29610318 TAATTTAATAATAATATATAATTTCATA
1 TAATTTAATAATAATATATAATTACATA
*
29610346 AAATT
1 TAATT
29610351 CTTGATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 8 0.29
27 6 0.21
28 14 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATTTAATAATAATATATAATTACATA
Found at i:29610348 original size:47 final size:46
Alignment explanation
Indices: 29610297--29610440 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
29610287 TTGTCTAATT
29610297 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
29610344 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
29610388 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
29610435 TAAAAT
1 TAAAAT
29610441 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:29610360 original size:91 final size:91
Alignment explanation
Indices: 29610265--29610472 Score: 337
Period size: 91 Copynumber: 2.3 Consensus size: 91
29610255 TAATTATAAC
* * *
29610265 TAATAAATTTTCTTATATGAATTTGT-CTAATTTAAAATAATTATTATTACATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATAC-AATTTAAAATAATTAATATTAAATATAATTTAATAA
*
29610329 TAATATATAATTTCATAAAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
29610356 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
29610421 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
29610447 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
29610473 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
91 88 0.81
92 21 0.19
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:29610432 original size:44 final size:43
Alignment explanation
Indices: 29610292--29610432 Score: 115
Period size: 44 Copynumber: 3.1 Consensus size: 43
29610282 TGAATTTGTC
* *
29610292 TAATTTAAAATAATTATTATTACATATAATTTAATAATAATATA
1 TAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATA
** * * * *
29610336 TAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTATA
1 TAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATATA
*
29610383 CAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATA
1 TAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATA
29610427 TAATTT
1 TAATTT
29610433 CATAAAATTC
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 30 0.42
45 7 0.10
46 7 0.10
47 22 0.31
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (43 bp):
TAATTTAAAATAATTAATATTAAATATAATTTAATAATATATA
Found at i:29610447 original size:47 final size:47
Alignment explanation
Indices: 29610315--29610453 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
29610305 TTATTATTAC
* *
29610315 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
29610362 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
29610406 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
29610453 A
1 A
29610454 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:29614865 original size:22 final size:22
Alignment explanation
Indices: 29614802--29614867 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
29614792 TATTGTTCAA
* *
29614802 ACATGAGAGCTTAGTACGTGAA
1 ACATGAGAGCTTAGTACGTTAG
29614824 ACATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
*
29614846 CCATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
29614868 TTTTACTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (22 bp):
ACATGAGAGCTTAGTACGTTAG
Found at i:29618526 original size:87 final size:87
Alignment explanation
Indices: 29618375--29618540 Score: 251
Period size: 87 Copynumber: 1.9 Consensus size: 87
29618365 GACCACAGTT
* * * *
29618375 GAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
*
29618440 AAAGGCTGCAGCGAAAGAATCA
66 AAACGCTGCAGCGAAAGAATCA
* * *
29618462 GAGGTTCAAAATAAATATGAAGAACTCCAGCTACAACTTAAAACAGATGCAGCATCGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
*
29618527 AGACGCTGCAGCGA
66 AAACGCTGCAGCGA
29618541 GGGAAGCAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (87 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
AAACGCTGCAGCGAAAGAATCA
Found at i:29618529 original size:21 final size:21
Alignment explanation
Indices: 29618505--29618550 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
29618495 CAACTTAAAA
* *
29618505 CAGATGCAGCATCGAGAGAAG
1 CAGACGCAGCAGCGAGAGAAG
* *
29618526 CAGACGCTGCAGCGAGGGAAG
1 CAGACGCAGCAGCGAGAGAAG
29618547 CAGA
1 CAGA
29618551 GTAGAGCAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.37, T:0.07
Consensus pattern (21 bp):
CAGACGCAGCAGCGAGAGAAG
Found at i:29618574 original size:87 final size:87
Alignment explanation
Indices: 29618375--29618577 Score: 210
Period size: 87 Copynumber: 2.3 Consensus size: 87
29618365 GACCACAGTT
* * * * * *
29618375 GAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGC
1 GAGGTACAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
* *
29618440 AAAGGCTGCAGCGAAAGAATCA
66 AAACGCTGCAGCGAAAGAAGCA
* * * * *
29618462 GAGGTTCAAAATAAATATGAAGAACTCCAGCTACAACTTAAAACAGATGCAGCATCGAGAGAAGC
1 GAGGTACAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
* **
29618527 AGACGCTGCAGCGAGGGAAGCA
66 AAACGCTGCAGCGAAAGAAGCA
* ** *
29618549 GA-GTAGAGCAGAAAGTACGACGAACTCCA
1 GAGGTACAAAAGAAA-TACGAAGAACTCCA
29618578 ACAACAGTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 7 0.07
87 89 0.93
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (87 bp):
GAGGTACAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAACAGAGGCAGCAGCGAGAGAAGC
AAACGCTGCAGCGAAAGAAGCA
Found at i:29618975 original size:43 final size:43
Alignment explanation
Indices: 29618903--29619177 Score: 358
Period size: 43 Copynumber: 6.4 Consensus size: 43
29618893 AAACAAATAA
* * *
29618903 CGGCGTCTGTGTAAAAA-CGCCGCTAAAAGAACATGACCTTTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCT-AAAGAACATGATCTTTAG
* * * * *
29618946 TGGCGTTTGAGGAAGAAGCGCCACTAAAGAACATGATTTTTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
29618989 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
* *
29619032 CGG-GATTTGTGGAAAAAACGCCGCT-AAGAACCATGATCTTTAA
1 CGGCG-TTTGTGGAAAAAGCGCCGCTAAAGAA-CATGATCTTTAG
*
29619075 CGGAGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
* * * *
29619118 TGGCGTTTGTTGAAAAAGCGCCACTAAAGAACATGACCTTTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
29619161 CGGCGTTTGTAGGAAAA
1 CGGCGTTTGT-GGAAAA
29619178 CGCTGCTAAA
Statistics
Matches: 202, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
42 6 0.03
43 179 0.89
44 17 0.08
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (43 bp):
CGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTTTAG
Found at i:29619804 original size:9 final size:10
Alignment explanation
Indices: 29619781--29619843 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
29619771 AGAAGTTAGA
29619781 AAAAAATTAT
1 AAAAAATTAT
*
29619791 AAAAAATTGT
1 AAAAAATTAT
29619801 AAAAAATTAT
1 AAAAAATTAT
*
29619811 AAAATA-TAT
1 AAAAAATTAT
*
29619820 -AGAAA-TAT
1 AAAAAATTAT
*
29619828 AGAAAAAATAT
1 A-AAAAATTAT
29619839 AAAAA
1 AAAAA
29619844 TTTTATAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
8 6 0.14
9 3 0.07
10 31 0.70
11 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:29619814 original size:28 final size:28
Alignment explanation
Indices: 29619783--29619842 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
29619773 AAGTTAGAAA
*
29619783 AAAAT-TATA-AAAAATTGTAAAAAATTAT
1 AAAATATATAGAAAAATAG-AAAAAA-TAT
*
29619811 AAAATATATAGAAATATAGAAAAAATAT
1 AAAATATATAGAAAAATAGAAAAAATAT
29619839 AAAA
1 AAAA
29619843 ATTTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.43
29 10 0.36
30 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAATATATAGAAAAATAGAAAAAATAT
Found at i:29620110 original size:10 final size:10
Alignment explanation
Indices: 29620092--29620203 Score: 59
Period size: 10 Copynumber: 11.1 Consensus size: 10
29620082 TTGATGCATA
29620092 TTATAATTTT
1 TTATAATTTT
*
29620102 TTATGA-TTT
1 TTATAATTTT
**
29620111 TTATAAAATT
1 TTATAATTTT
*
29620121 TTACAATTTT
1 TTATAATTTT
*
29620131 TTATATTTTT
1 TTATAATTTT
*
29620141 TTATGATATTT
1 TTATAAT-TTT
* *
29620152 ATATATAGTTT
1 TTATA-ATTTT
* *
29620163 TTCTAA-GTT
1 TTATAATTTT
*
29620172 TTAGTAA-ATT
1 TTA-TAATTTT
*
29620182 TTAAATATTTT
1 TTATA-ATTTT
29620193 TTATAATTTT
1 TTATAATTTT
29620203 T
1 T
29620204 ATTAAAGTTT
Statistics
Matches: 75, Mismatches: 21, Indels: 12
0.69 0.19 0.11
Matches are distributed among these distances:
9 13 0.17
10 43 0.57
11 18 0.24
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
TTATAATTTT
Found at i:29620114 original size:19 final size:19
Alignment explanation
Indices: 29620092--29620154 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
29620082 TTGATGCATA
29620092 TTATAATTTTTTATGATTT
1 TTATAATTTTTTATGATTT
** **
29620111 TTATAAAATTTTACAATTTT
1 TTATAATTTTTTATGA-TTT
* *
29620131 TTATATTTTTTTATGATAT
1 TTATAATTTTTTATGATTT
29620150 TTATA
1 TTATA
29620155 TATAGTTTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATAATTTTTTATGATTT
Found at i:29620152 original size:29 final size:30
Alignment explanation
Indices: 29620078--29620152 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
29620068 ATTAAAGGGC
* *
29620078 TTTTTTGATGCATA-TTATAATTTTTTATGA
1 TTTTTTTATG-ATATTTACAATTTTTTATGA
* **
29620108 TTTTTATAAAAT-TTTACAATTTTTTAT-A
1 TTTTTTTATGATATTTACAATTTTTTATGA
29620136 TTTTTTTATGATATTTA
1 TTTTTTTATGATATTTA
29620153 TATATAGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
28 10 0.29
29 19 0.54
30 6 0.17
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTTTTATGATATTTACAATTTTTTATGA
Found at i:29620202 original size:9 final size:9
Alignment explanation
Indices: 29620092--29620258 Score: 59
Period size: 9 Copynumber: 17.2 Consensus size: 9
29620082 TTGATGCATA
29620092 TTATAATTTT
1 TTATAA-TTT
*
29620102 TTATGATTT
1 TTATAATTT
*
29620111 TTATAAAATT
1 TTAT-AATTT
*
29620121 TTACAATTTT
1 TTATAA-TTT
*
29620131 TTATATTTTT
1 TTATA-ATTT
29620141 TTATGATATTT
1 TTAT-A-ATTT
*
29620152 ATATATAGTTT
1 -T-TATAATTT
* *
29620163 TTCTAAGTT
1 TTATAATTT
29620172 TTAGTAAATTT
1 TTA-T-AATTT
* *
29620183 TAAATATTTT
1 T-TATAATTT
29620193 TTATAATTT
1 TTATAATTT
*
29620202 TTATTAAAGTT
1 TTA-T-AATTT
* *
29620213 TAATAACTT
1 TTATAATTT
*
29620222 TTATAACTT
1 TTATAATTT
29620231 TTAT--TTGT
1 TTATAATT-T
* *
29620239 TTTTATTTT
1 TTATAATTT
29620248 TTATAATTT
1 TTATAATTT
29620257 TT
1 TT
29620259 TTACCACATG
Statistics
Matches: 117, Mismatches: 26, Indels: 29
0.68 0.15 0.17
Matches are distributed among these distances:
7 1 0.01
8 4 0.03
9 51 0.44
10 35 0.30
11 20 0.17
12 3 0.03
13 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:29621865 original size:15 final size:15
Alignment explanation
Indices: 29621845--29621875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29621835 AATTAAACAC
29621845 TAATAAAAATGATAA
1 TAATAAAAATGATAA
*
29621860 TAATAATAATGATAA
1 TAATAAAAATGATAA
29621875 T
1 T
29621876 GAAATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
TAATAAAAATGATAA
Found at i:29630388 original size:24 final size:24
Alignment explanation
Indices: 29630361--29630407 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29630351 ACCGATGGCG
29630361 ACACCAAT-ACCATCATCAATGCTA
1 ACACCAATGACCA-CATCAATGCTA
*
29630385 ACACCAATGCCCACATCAATGCT
1 ACACCAATGACCACATCAATGCT
29630408 GATGTATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.36, G:0.06, T:0.19
Consensus pattern (24 bp):
ACACCAATGACCACATCAATGCTA
Found at i:29636646 original size:25 final size:25
Alignment explanation
Indices: 29636615--29636701 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
29636605 ACAAGCTTTA
* * *
29636615 AACGGTAAACTCTTTCGAGCTGAAT
1 AACGGTAAGCTCCTCCGAGCTGAAT
*
29636640 AATGGTAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCCTCCGAGCTGAAT
29636665 AACGGTAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCCTCCGAGCTGAAT
29636690 AACGGTAAGCTC
1 AACGGTAAGCTC
29636702 ATACGAGTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCGAGCTGAAT
Found at i:29636708 original size:25 final size:25
Alignment explanation
Indices: 29636615--29636738 Score: 131
Period size: 25 Copynumber: 5.0 Consensus size: 25
29636605 ACAAGCTTTA
* * *
29636615 AACGGTAAACTCTTTCGAGCTGAAT
1 AACGGTAAGCTCATACGAGCTGAAT
* * *
29636640 AATGGTAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCATACGAGCTGAAT
* *
29636665 AACGGTAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCATACGAGCTGAAT
* *
29636690 AACGGTAAGCTCATACGAGTTGAGT
1 AACGGTAAGCTCATACGAGCTGAAT
* * *
29636715 ATCGATAAGCTCATAAGAGCTGAA
1 AACGGTAAGCTCATACGAGCTGAA
29636739 ATCGATAACC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 85 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
AACGGTAAGCTCATACGAGCTGAAT
Found at i:29639715 original size:18 final size:18
Alignment explanation
Indices: 29639670--29639717 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
29639660 ATAATATAAA
* *
29639670 TTAAATAGTAAATTATTT
1 TTAAATATTAAAATATTT
**
29639688 AGAAAT-TTAAAATATTT
1 TTAAATATTAAAATATTT
29639705 TTAAATATTAAAA
1 TTAAATATTAAAA
29639718 ATTCCGATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAAATATTAAAATATTT
Found at i:29640601 original size:24 final size:24
Alignment explanation
Indices: 29640574--29640619 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29640564 CAGCCTCTCA
*
29640574 ATTTTCAAGTCCAAGATTCAACAC
1 ATTTTCAAGTCCAAGATCCAACAC
*
29640598 ATTTTGAAGTCCAAGATCCAAC
1 ATTTTCAAGTCCAAGATCCAAC
29640620 TTCAAATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (24 bp):
ATTTTCAAGTCCAAGATCCAACAC
Found at i:29640890 original size:140 final size:140
Alignment explanation
Indices: 29640544--29641016 Score: 586
Period size: 140 Copynumber: 3.4 Consensus size: 140
29640534 TATTTTTAAA
* * * * * *
29640544 ATTTTTGTTTTAACCAAGCGCAGCCTCTCAATTTTCAAGTCCAAGATTCAACACATTTTGAAGTC
1 ATTTTTGTTTTAACCAAGTGCAGCCTCTCAACTCTCAAGTCCAAGATCCAACAAATTTTAAAGTC
** *
29640609 CAAGATCCAACTTCAAATGTAACTACTTATTCAACTAGTTCATGCAATTTCTGTAATTTTACACT
66 CAAGATCCAACTTCAAATGTAACTACTTATTCAACTAACTCATGCAATTTTTGTAA--TTACACT
*
29640674 TCATATGCTAAT
129 TCATATACTAAT
* * * * * *
29640686 ATTTTTGTTTTAAACAAATGCAGCCTCTCAACTCTTAAGTCTAAGATTCAACAAATTCTAAAGTC
1 ATTTTTGTTTTAACCAAGTGCAGCCTCTCAACTCTCAAGTCCAAGATCCAACAAATTTTAAAGTC
* * *
29640751 CAGGATCAAACTTCAAATGTATCTACTTATTCAACTAACTCATGCAATTTTTGTAATTACACTTC
66 CAAGATCCAACTTCAAATGTAACTACTTATTCAACTAACTCATGCAATTTTTGTAATTACACTTC
* *
29640816 ATGTACTAGT
131 ATATACTAAT
* * * * *
29640826 ATTTTTGTTTTAACCAAGTGTAGCCTCTTAACTCTCAAGTCCAAGATCCAATAGATTTTTAAGTC
1 ATTTTTGTTTTAACCAAGTGCAGCCTCTCAACTCTCAAGTCCAAGATCCAACAAATTTTAAAGTC
* * ** ** * *
29640891 CAAGATCCAACTTCAAATATAACTACTTATCCAACTAACTTGTGCAAAATTTGTAATTCCACTTT
66 CAAGATCCAACTTCAAATGTAACTACTTATTCAACTAACTCATGCAATTTTTGTAATTACACTTC
29640956 ATATACTAAT
131 ATATACTAAT
* * * *
29640966 ATTTTTGTTTTAACTAAGTGAAACCTCTCAACTCTCAAGTTCAAGATCCAA
1 ATTTTTGTTTTAACCAAGTGCAGCCTCTCAACTCTCAAGTCCAAGATCCAA
29641017 ATCTATCTGG
Statistics
Matches: 283, Mismatches: 48, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
140 178 0.63
142 105 0.37
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (140 bp):
ATTTTTGTTTTAACCAAGTGCAGCCTCTCAACTCTCAAGTCCAAGATCCAACAAATTTTAAAGTC
CAAGATCCAACTTCAAATGTAACTACTTATTCAACTAACTCATGCAATTTTTGTAATTACACTTC
ATATACTAAT
Found at i:29641116 original size:22 final size:21
Alignment explanation
Indices: 29641088--29641132 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
29641078 CACATTAGCG
29641088 AACAAATATATAAATATAAATA
1 AACAAATATATAAATA-AAATA
* *
29641110 AACAAATATTTATATAAAATA
1 AACAAATATATAAATAAAATA
29641131 AA
1 AA
29641133 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AACAAATATATAAATAAAATA
Found at i:29645128 original size:81 final size:81
Alignment explanation
Indices: 29644924--29645486 Score: 439
Period size: 81 Copynumber: 6.7 Consensus size: 81
29644914 TGTTTGCAAA
* * * *
29644924 CAAAATCAAAATAAAATCTGTTAAACGGCAGGAATAAATCTCAAAACATAATTATTTAATTAAAT
1 CAAAATC-GAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACA-AATTATTCAATT--AT
* *
29644989 CTTCTCGTTTAGAAAGAAAAT
62 -TTCTCGTTTGGAAACAAAAT
* * * * *
29645010 CAAAATCGAATAAAATCTGTTAAATGACAGGACTAAATCCCGAAACAGATTATTCAATTATTTGT
1 CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACAAATTATTCAATTATTTCT
* **
29645075 CATTTGGAAGGAAAAT
66 CGTTTGGAAACAAAAT
* * * *** * * *
29645091 AAAAATCAAATAAAATCTATTAAACGGTGGGAATAAATCTCAAAATAGATTATTCAATTATTTCT
1 CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACAAATTATTCAATTATTTCT
29645156 CGTTTGGAAACAAAAT
66 CGTTTGGAAACAAAAT
* * *
29645172 CAAAATCGAATAAAATCTGTTAAACGACGGGAATAAATCCAAAAACAAATTATTCAACTATTTCT
1 CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACAAATTATTCAATTATTTCT
29645237 CGTTTGGAAACAAAAT
66 CGTTTGGAAACAAAAT
* * * * * ** *
29645253 CAAAATCGAATAAATTTTGTTAAAAGGCAGGAATAAATCTCAAAACATGTTTTATTTAATTTTAA
1 CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACA--AATTATTCAA--TT-A
* *
29645318 ATTCTCATTTGGAAACAAAATT
61 TTTCTCGTTTGGAAACAAAA-T
* * * * * * * * *
29645340 AAAAATGGAATAAAATCTGTTGAATGGC-GAGATTAAATTCCGAAAA-AATTTTATTTAATT-TT
1 CAAAATCGAATAAAATCTGTTAAACGACAG-GAATAAA-TCCCAAAACAA-ATTATTCAATTATT
29645402 AATACTCGTTTGGAAACAAAAT
63 --T-CTCGTTTGGAAACAAAAT
* * * * * * * *
29645424 AAAAAAATGGAATAAAATCTGTTGAATGGCAGGAATAGATCCCGAAATAAATTTTATTCAATT
1 --CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACAAA--TTATTCAATT
29645487 TTAAATTTTA
Statistics
Matches: 391, Mismatches: 68, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
81 193 0.49
82 3 0.01
83 7 0.02
84 14 0.04
85 57 0.15
86 71 0.18
87 40 0.10
88 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (81 bp):
CAAAATCGAATAAAATCTGTTAAACGACAGGAATAAATCCCAAAACAAATTATTCAATTATTTCT
CGTTTGGAAACAAAAT
Found at i:29645185 original size:162 final size:163
Alignment explanation
Indices: 29644925--29645365 Score: 517
Period size: 162 Copynumber: 2.7 Consensus size: 163
29644915 GTTTGCAAAC
29644925 AAAATCAAAATAAAATCTGTTAAACGGCAGGAATAAATCTCAAAACATA-ATTATTTAATTAAAT
1 AAAATC-AAATAAAATCTGTTAAACGGCAGGAATAAATCTC-AAA-ATAGATTATTTAATT-AAT
* * * **
29644989 CTTCTCGTTTAGAAAGAAAATCAAAATCGAATAAAATCTGTTAAATGACAGGACTAAATCCCGAA
62 -TTCTCGTTTGGAAACAAAATCAAAATCGAATAAAATCTGTTAAATGACAGGAATAAATCCAAAA
* * * **
29645054 ACAGATTATTCAATTATTTGTCATTTGGAAGGAAAATA
126 ACAAATTATTCAACTATTTCTCATTTGGAAACAAAATA
* ** *
29645092 AAAATCAAATAAAATCTATTAAACGGTGGGAATAAATCTCAAAATAGATTATTCAATT-ATTTCT
1 AAAATCAAATAAAATCTGTTAAACGGCAGGAATAAATCTCAAAATAGATTATTTAATTAATTTCT
* *
29645156 CGTTTGGAAACAAAATCAAAATCGAATAAAATCTGTTAAACGACGGGAATAAATCCAAAAACAAA
66 CGTTTGGAAACAAAATCAAAATCGAATAAAATCTGTTAAATGACAGGAATAAATCCAAAAACAAA
* *
29645221 TTATTCAACTATTTCTCGTTTGGAAACAAAATC
131 TTATTCAACTATTTCTCATTTGGAAACAAAATA
* * * * * * *
29645254 AAAATCGAATAAATTTTGTTAAAAGGCAGGAATAAATCTCAAAACATGTTTTATTTAATTTTAAA
1 AAAATCAAATAAAATCTGTTAAACGGCAGGAATAAATCTCAAAATA-G-ATTATTTAA--TTAAT
* * * *
29645319 TTCTCATTTGGAAACAAAATTAAAAATGGAATAAAATCTGTTGAATG
62 TTCTCGTTTGGAAACAAAA-TCAAAATCGAATAAAATCTGTTAAATG
29645366 GCGAGATTAA
Statistics
Matches: 233, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
162 126 0.54
163 3 0.01
164 10 0.04
165 13 0.06
166 33 0.14
167 25 0.11
168 23 0.10
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (163 bp):
AAAATCAAATAAAATCTGTTAAACGGCAGGAATAAATCTCAAAATAGATTATTTAATTAATTTCT
CGTTTGGAAACAAAATCAAAATCGAATAAAATCTGTTAAATGACAGGAATAAATCCAAAAACAAA
TTATTCAACTATTTCTCATTTGGAAACAAAATA
Found at i:29645392 original size:86 final size:88
Alignment explanation
Indices: 29645233--29645493 Score: 300
Period size: 86 Copynumber: 3.0 Consensus size: 88
29645223 ATTCAACTAT
* * * * * * * * *
29645233 TTCTCGTTTGGAAACAAAAT--CAAAATCGAATAAATTTTGTTAAAAGGCAGGAATAAATCTCAA
1 TTCTCATTTGGAAACAAAATAAAAAAATGGAATAAAATCTGTTGAATGGCAGGAATAAATCCCGA
* **
29645296 AACATGTTTTATTTAATTTTAAA
66 AATAAATTTTATTTAATTTTAAA
* * *
29645319 TTCTCATTTGGAAACAAAAT-TAAAAATGGAATAAAATCTGTTGAATGGC-GAGATTAAATTCCG
1 TTCTCATTTGGAAACAAAATAAAAAAATGGAATAAAATCTGTTGAATGGCAG-GAATAAATCCCG
29645382 AAA-AAATTTTATTTAATTTT-AA
65 AAATAAATTTTATTTAATTTTAAA
* * *
29645404 TACTCGTTTGGAAACAAAATAAAAAAATGGAATAAAATCTGTTGAATGGCAGGAATAGATCCCGA
1 TTCTCATTTGGAAACAAAATAAAAAAATGGAATAAAATCTGTTGAATGGCAGGAATAAATCCCGA
*
29645469 AATAAATTTTATTCAATTTTAAA
66 AATAAATTTTATTTAATTTTAAA
29645492 TT
1 TT
29645494 TTATTTTCAA
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
85 20 0.14
86 75 0.51
87 50 0.34
88 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
TTCTCATTTGGAAACAAAATAAAAAAATGGAATAAAATCTGTTGAATGGCAGGAATAAATCCCGA
AATAAATTTTATTTAATTTTAAA
Done.