Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 191 of 214
Found at i:55939875 original size:18 final size:18
Alignment explanation
Indices: 55939848--55940133 Score: 242
Period size: 18 Copynumber: 15.6 Consensus size: 18
55939838 CACGAAATTT
55939848 ATTTTT-AAAACACGAAA
1 ATTTTTGAAAACACGAAA
55939865 ATTTTTGAAAACACGAAA
1 ATTTTTGAAAACACGAAA
* *
55939883 ATTTTTG-TAACAAGAGAA
1 ATTTTTGAAAACACGA-AA
* *
55939901 TTTTTTGAAAACACGAGGATT
1 ATTTTTGAAAACACGA--A-A
* *
55939922 TTTTTTGAAAACACAAAA
1 ATTTTTGAAAACACGAAA
**
55939940 ATTGGTG-AAACACGAGAA
1 ATTTTTGAAAACACGA-AA
* * * *
55939958 TTTTTTTGACAACGCGAGA
1 -ATTTTTGAAAACACGAAA
*
55939977 ATTTTTAAAAACACGAAA
1 ATTTTTGAAAACACGAAA
** *
55939995 ATTTGCG-AAGCACGAGAA
1 ATTTTTGAAAACACGA-AA
*
55940013 TTTTTTGAAAACACGAAA
1 ATTTTTGAAAACACGAAA
*
55940031 ATTTTTTAAAACACGAAA
1 ATTTTTGAAAACACGAAA
55940049 ATTTTTG-AAACACGGAAA
1 ATTTTTGAAAACAC-GAAA
* *
55940067 TTTTTTGAAAACACGAAT
1 ATTTTTGAAAACACGAAA
55940085 ATTTTTG-AAACACCGAAA
1 ATTTTTGAAAACA-CGAAA
55940103 ATTTTTTTGAAAACACGAAA
1 A--TTTTTGAAAACACGAAA
*
55940123 AATTTTGAAAA
1 ATTTTTGAAAA
55940134 ATGGAATTTT
Statistics
Matches: 214, Mismatches: 39, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
17 37 0.17
18 112 0.52
19 25 0.12
20 20 0.09
21 20 0.09
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAA
Found at i:55939912 original size:54 final size:54
Alignment explanation
Indices: 55939779--55940108 Score: 303
Period size: 54 Copynumber: 6.0 Consensus size: 54
55939769 CGTGATCCAA
* ** * * * *
55939779 TTGAAACATGAGAATTTTTTTG-AAACAC-AAAAACTTTGGAAATATGAGAA-TT
1 TTGAAACACGAGAA-TTTTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTT
* *
55939831 TTAAGAACACGA-AATTTATTTTTAAAACACGAAAATTTTTGAAAACACGAAAATTT
1 TTGA-AACACGAGAA-TT-TTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTT
* * ** * *
55939887 TTGTAACAAGAGAATTTTTTGAAAACACGAGGATTTTTTTTGAAAACACAAAAATTG
1 TTGAAACACGAGAATTTTTTGAAAACACGA--A-AATTTTTGAAAACACGAAAATTT
* * * * *
55939944 GTGAAACACGAGAATTTTTTTGACAACGCGAGAATTTTTAAAAACACGAAAATTT
1 TTGAAACACGAGAA-TTTTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTT
** * *
55939999 GCGAAGCACGAGAATTTTTTGAAAACACGAAAATTTTTTAAAACACGAAAATTT
1 TTGAAACACGAGAATTTTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTT
*
55940053 TTGAAACACG-GAAATTTTTTGAAAACACGAATATTTTTG-AAACACCGAAAATTT
1 TTGAAACACGAG-AATTTTTTGAAAACACGAAAATTTTTGAAAACA-CGAAAATTT
55940107 TT
1 TT
55940109 TTGAAAACAC
Statistics
Matches: 227, Mismatches: 39, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
52 8 0.04
53 16 0.07
54 98 0.43
55 54 0.24
56 7 0.03
57 30 0.13
58 14 0.06
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (54 bp):
TTGAAACACGAGAATTTTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTT
Found at i:55940182 original size:37 final size:37
Alignment explanation
Indices: 55939839--55940183 Score: 178
Period size: 36 Copynumber: 9.4 Consensus size: 37
55939829 TTTTAAGAAC
*
55939839 ACGAAATTTATTTTT-AAAACACGAAAATTTTTGAAAA
1 ACGAAATTT-TTTTTGAAAACACGAAAAATTTTGAAAA
* * * **
55939876 CACGAAA--ATTTTTG-TAACAAGAGAATTTTTTGAAAA
1 -ACGAAATTTTTTTTGAAAACACGA-AAAATTTTGAAAA
* * *
55939912 CACGAGGATTTTTTTTGAAAACAC-AAAAATTGGTGAAAC
1 -ACGA-AATTTTTTTTGAAAACACGAAAAATT-TTGAAAA
* * * * *
55939951 ACGAGAA-TTTTTTTGACAACGCGAGAATTTTTAAAAA
1 ACGA-AATTTTTTTTGAAAACACGAAAAATTTTGAAAA
* ** * **
55939988 CACGAAA--ATTTGCG-AAGCACGAGAATTTTTTGAAAA
1 -ACGAAATTTTTTTTGAAAACACGA-AAAATTTTGAAAA
* * *
55940024 CACGAAA-ATTTTTT-AAAACACGAAAATTTTTGAAAC
1 -ACGAAATTTTTTTTGAAAACACGAAAAATTTTGAAAA
* *
55940060 ACGGAAA--TTTTTTGAAAACACGAATATTTTTGAAACA
1 AC-GAAATTTTTTTTGAAAACACGAAAAATTTTGAAA-A
* *
55940097 CCGAAAATTTTTTTGAAAACACGAAAAATTTTGAAAA
1 ACGAAATTTTTTTTGAAAACACGAAAAATTTTGAAAA
* * * * * *
55940134 ATGGAATTTTTTTTGAAGACATG-AGAATTTTGAAAG
1 ACGAAATTTTTTTTGAAAACACGAAAAATTTTGAAAA
*
55940170 ACGAAATCTTTTTT
1 ACGAAATTTTTTTT
55940184 ATTTTTATTT
Statistics
Matches: 239, Mismatches: 51, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
35 24 0.10
36 99 0.41
37 49 0.21
38 51 0.21
39 12 0.05
40 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (37 bp):
ACGAAATTTTTTTTGAAAACACGAAAAATTTTGAAAA
Found at i:55940183 original size:74 final size:73
Alignment explanation
Indices: 55939849--55940146 Score: 202
Period size: 74 Copynumber: 4.1 Consensus size: 73
55939839 ACGAAATTTA
* * * **
55939849 TTTTT-AAAACACGAAAATTTTTGAAA-ACACGAAAATTTTTGT--AACAAGAGAATTTTTTGAA
1 TTTTTGAAAACACGAATATTTTTGAAACAC-CGAAAATTTTTTTAAAACACGA-AAAATTTTGAA
**
55939910 AACACGAGGATTT
64 AA-AC--GGAAAT
* * ** * * * * *
55939923 TTTTTGAAAACACAAAAATTGGTGAAACA-CGAGAATTTTTTTGACAACGCG-AGAATTTTTAAA
1 TTTTTGAAAACACGAATATTTTTGAAACACCGAAAATTTTTTT-AAAACACGAAAAATTTTGAAA
* *
55939986 AACACGAAAA
65 AAC-GGAAAT
** * *
55939996 TTTGCG-AAGCACGAGA-ATTTTTTGAAA-ACACGAAAA-TTTTTTAAAACACGAAAATTTTTGA
1 TTTTTGAAAACACGA-ATA-TTTTTGAAACAC-CGAAAATTTTTTTAAAACACGAAAAATTTTGA
*
55940057 AACACGGAAAT
63 AAAACGGAAAT
55940068 TTTTTGAAAACACGAATATTTTTGAAACACCGAAAATTTTTTTGAAAACACGAAAAATTTTGAAA
1 TTTTTGAAAACACGAATATTTTTGAAACACCGAAAATTTTTTT-AAAACACGAAAAATTTTGAAA
* *
55940133 AATGGAATT
65 AACGGAAAT
55940142 TTTTT
1 TTTTT
55940147 TGAAGACATG
Statistics
Matches: 172, Mismatches: 37, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
72 38 0.22
73 48 0.28
74 54 0.31
75 27 0.16
76 1 0.01
77 4 0.02
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (73 bp):
TTTTTGAAAACACGAATATTTTTGAAACACCGAAAATTTTTTTAAAACACGAAAAATTTTGAAAA
ACGGAAAT
Found at i:55940891 original size:24 final size:25
Alignment explanation
Indices: 55940855--55940904 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
55940845 GGACCTGCTA
*
55940855 GCCTGCCAAGCTGTT-GGGCTGTTG
1 GCCTGCCAAGCTGTTAGGCCTGTTG
55940879 GCCTG-CAAGGCTGTTAGGCCTGTTG
1 GCCTGCCAA-GCTGTTAGGCCTGTTG
55940904 G
1 G
55940905 GCAGCTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 11 0.48
25 9 0.39
ACGTcount: A:0.10, C:0.24, G:0.38, T:0.28
Consensus pattern (25 bp):
GCCTGCCAAGCTGTTAGGCCTGTTG
Found at i:55941045 original size:7 final size:7
Alignment explanation
Indices: 55941033--55941100 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
55941023 CGACTATTAA
55941033 TTTTTCT
1 TTTTTCT
55941040 TTTTTC-
1 TTTTTCT
55941046 -TTTTCT
1 TTTTTCT
*
55941052 TTTTTCA
1 TTTTTCT
55941059 TTTTTCAT
1 TTTTTC-T
55941067 TTTTT-T
1 TTTTTCT
*
55941073 TCTTTCT
1 TTTTTCT
55941080 TCTTCTTCT
1 T-TT-TTCT
**
55941089 TCCTTCT
1 TTTTTCT
55941096 TTTTT
1 TTTTT
55941101 TTCTTCTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
5 5 0.11
6 5 0.11
7 26 0.55
8 6 0.13
9 5 0.11
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:55941106 original size:19 final size:20
Alignment explanation
Indices: 55941072--55941115 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
55941062 TTCATTTTTT
55941072 TTCTTTCTTCTTCTTCTTCC
1 TTCTTTCTTCTTCTTCTTCC
*
55941092 TTCTTT-TTTTTCTTCTTCC
1 TTCTTTCTTCTTCTTCTTCC
*
55941111 CTCTT
1 TTCTT
55941116 CACCCTAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTTCTTCTTCTTCTTCC
Found at i:55941471 original size:30 final size:29
Alignment explanation
Indices: 55941455--55941611 Score: 206
Period size: 30 Copynumber: 5.2 Consensus size: 29
55941445 GGCTGAAACA
55941455 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAA-G
*
55941485 TAAGTTTGAGAAAGTTTAGGGGTCAAAAG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAAG
* *
55941514 TTAATTTCGAGAAAGTTTAGGGGTTAAAATG
1 -TAATTTTGAGAAAGTTTAGGGGTCAAAA-G
**
55941545 TAATTTTGAGAAAGTTTAGTAGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAA-G
* *
55941575 TAATTTTGAGAAAGTTTAGGGGTTAAAATT
1 TAATTTTGAGAAAGTTTAGGGGTCAAAA-G
55941605 TAATTTT
1 TAATTTT
55941612 TTTTATTTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
29 1 0.01
30 111 0.98
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
TAATTTTGAGAAAGTTTAGGGGTCAAAAG
Found at i:55941609 original size:60 final size:60
Alignment explanation
Indices: 55941455--55941611 Score: 244
Period size: 60 Copynumber: 2.6 Consensus size: 60
55941445 GGCTGAAACA
* * *
55941455 TAATTTTGAGAAAGTTTAGGGGTCAAAATGTAAGTTTGAGAAAGTTTAGGGGTCAAAAGT
1 TAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGAGTCAAAAGT
* *
55941515 TAATTTCGAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGTAGTCAAAA-T
1 TAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGAGTCAAAAGT
*
55941574 GTAATTTTGAGAAAGTTTAGGGGTTAAAATTTAATTTT
1 -TAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTT
55941612 TTTTATTTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 1 0.01
60 88 0.99
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
TAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGAGTCAAAAGT
Found at i:55941621 original size:9 final size:9
Alignment explanation
Indices: 55941607--55941642 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55941597 TTAAAATTTA
55941607 ATTTTTTTT
1 ATTTTTTTT
55941616 A-TTTTTTT
1 ATTTTTTTT
55941624 ATTTTTTTT
1 ATTTTTTTT
55941633 ATTTTTTTT
1 ATTTTTTTT
55941642 A
1 A
55941643 AAAACACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:55941622 original size:8 final size:8
Alignment explanation
Indices: 55941609--55941640 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
55941599 AAAATTTAAT
55941609 TTTTTTTA
1 TTTTTTTA
55941617 TTTTTTTA
1 TTTTTTTA
55941625 TTTTTTTTA
1 -TTTTTTTA
55941634 TTTTTTT
1 TTTTTTT
55941641 TAAAAACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTTA
Found at i:55941629 original size:17 final size:17
Alignment explanation
Indices: 55941607--55941640 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55941597 TTAAAATTTA
55941607 ATTTTTTTTATTTTTTT
1 ATTTTTTTTATTTTTTT
55941624 ATTTTTTTTATTTTTTT
1 ATTTTTTTTATTTTTTT
55941641 TAAAAACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (17 bp):
ATTTTTTTTATTTTTTT
Found at i:55942066 original size:77 final size:77
Alignment explanation
Indices: 55941775--55943805 Score: 2162
Period size: 78 Copynumber: 26.3 Consensus size: 77
55941765 TTTATTTTTA
* * * * *
55941775 TTTGAAAAACAGAAA-TT--GAAAATACCTCGGCGTGTGGCCCAAGGCTCAACTCACCTCTCACA
1 TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGT-GACCGAGGCTCAACTCACCTCTCGCA
*
55941837 ATATGAATTGATT
65 ATATGAGTTGATT
* * **
55941850 TTTGAAAAACAGAAA-TT-GAAAAATACCTC-G-ACGTGACTCGAGGCTCAACTCATTTCTCGCA
1 TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGTGAC-CGAGGCTCAACTCACCTCTCGCA
55941911 ATATGAGTTGATTTTT
65 ATATGAGTTGA---TT
*
55941927 TTTGAAAATACA-AAATTTAAAAGAAATAACTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTGAAAA-ACAGAAATTTAAAA-AAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCG
* *
55941991 CAGTATGAGTTGGTT
63 CAATATGAGTTGATT
* * *
55942006 TTTGAAAAACAGGAATTTGAAAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAT
1 TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAA
55942071 TATGAGTTGA-T
66 TATGAGTTGATT
* * *
55942082 TTTAAAAAACCAGAAATATAAAAGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGC
1 TTTGAAAAA-CAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGC
55942147 AATATGAGTTGATT
64 AATATGAGTTGATT
* *
55942161 TTTGAAAAACACAAATATAAAAGAAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCGC
*
55942224 ATTATGAGTTGATT
64 AATATGAGTTGATT
* * *
55942238 TTTGAAAACCAGAAATGTGAAAGAAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAAT-TTAAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCGC
*
55942301 ATTATGAGTTGA-T
64 AATATGAGTTGATT
* *
55942314 TTTAAAAAATAGAAATTTAAAAGAAATACCTCGGCA--TGACCCGAGGCTCAACTCA----TCGC
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCGC
*
55942373 ATTATGAGTTGA-T
64 AATATGAGTTGATT
* * * *
55942386 TTTAAAAAACAGAAATTTAAAAGAAAGACCTCGGCATGTGTCTGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55942451 ATATGAGTTGATT
65 ATATGAGTTGATT
* * *
55942464 TTCGAAAAACAGAAATTTAAAAGAAATACCTCAGCATG-GTCCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55942528 ATATGAGTTGATTT
65 ATATGAGTTGA-TT
* *
55942542 TTTGAAAAACATAAATTTAAAAGAAATACCTCGGCATG-GTCCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55942606 ATATGAGTTGATT
65 ATATGAGTTGATT
* * * * *
55942619 TTCGAAAAATAAAAATTT--TAAAATACCTCGGCATG-GTCCGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAA
55942681 TATGAGTTGATTT
66 TATGAGTTGA-TT
* ** * *
55942694 TTTGAAAAACATAAATTTAAAAGAAATACCTCGGCATG-GTTCGAGGTTCAAATCACCTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55942758 ATATGAGTTGATTTT
65 ATATGAGTTGA--TT
* * *
55942773 TTTGAAAAAAAAAATAGAAATTTAAAAGAAATACCTCAGC--GTGACCCAAGGCTCAACTCACCT
1 TTTG-----AAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCT
* *
55942836 CTCGTATTATGAGTTGATT
59 CTCGCAATATGAGTTGATT
*
55942855 TTTGAAAAAAAAAACAGAAA-TT--AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTC
1 TTTG-----AAAAACAGAAATTTAAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTC
* *
55942915 TCGTATTATGAGTTGATT
60 TCGCAATATGAGTTGATT
*
55942933 TTTGAAAAAAAACAGAAATTT--AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTC
1 TTTG---AAAAACAGAAATTTAAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTC
* *
55942994 GTATTATGAGTTGATT
62 GCAATATGAGTTGATT
*
55943010 TTTGAAAAAAACAGAAA-TT--AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCG
1 TTTG--AAAAACAGAAATTTAAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCG
* *
55943070 TATTATGAGTTGATT
63 CAATATGAGTTGATT
*
55943085 TTTGAAAAAAAAACAGAAATTT--AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT
1 TTTG----AAAAACAGAAATTTAAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCT
*
55943146 CGCATTATGAGTTGATT
61 CGCAATATGAGTTGATT
*** * *
55943163 TAAAAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGTA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55943228 ATATGAGTTGATT
65 ATATGAGTTGATT
* * * *
55943241 TTTGAAAAACAGAAATATAAAAGAAATACATCGGCATGTGACCGAGGCTCAACTCGCTTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55943306 ATATGAGTTGATT
65 ATATGAGTTGATT
** * * * * **
55943319 TTAAAAAAAAATAGAAATTT--AAAAGTACCTCGGGATGTGGCCCGAGGCTCAACTCACCTAGCG
1 TT--TGAAAAACAGAAATTTAAAAAAATACCTCGGCATGT-GACCGAGGCTCAACTCACCTCTCG
55943382 CAATATGAGTTGA-T
63 CAATATGAGTTGATT
* * * *
55943396 TTTGAAAAATAGGAATTTTAAAAAATACCTCGGTATGTGACCTGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGTGACC-GAGGCTCAACTCACCTCTCGCA
55943461 ATATGAGTTGATT
65 ATATGAGTTGATT
* *
55943474 TTTGAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGACCGATGCTCAACTCA-CTCTCGCA
1 TTTGAAAAACAGAAATTTAAAA-AAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCA
55943538 ATATGAGTTGA-T
65 ATATGAGTTGATT
* * * *
55943550 TTTAAAAAACATAGAAATTT--AAAAGTACCTCGGGATGTGGCCCGAGGCTCAACTCACCTCTCG
1 TTTGAAAAAC--AGAAATTTAAAAAAATACCTCGGCATGT-GACCGAGGCTCAACTCACCTCTCG
55943613 CAATATGAGTTGA-T
63 CAATATGAGTTGATT
* * * *
55943627 TTTGACAAATAGGAATTTTAAAAAAAATACCTC-GTATGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTGAAAAACA-GAAATTT-AAAAAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCG
*
55943691 TAATATGAGTTGATT
63 CAATATGAGTTGATT
* * * * *
55943706 TTTGAAAAAAACAGAAA-TT-GAAAAGTACCTCGGGATGTGGCCGAGGCTCAACTCACTTCTCGC
1 TTTG--AAAAACAGAAATTTAAAAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGC
55943769 AATATGAGTTGATT
64 AATATGAGTTGATT
*
55943783 TTTGAAAAACAGAAATTGAAAAA
1 TTTGAAAAACAGAAATTTAAAAA
55943806 TATTTCTTGA
Statistics
Matches: 1740, Mismatches: 145, Indels: 140
0.86 0.07 0.07
Matches are distributed among these distances:
72 51 0.03
73 16 0.01
74 99 0.06
75 141 0.08
76 134 0.08
77 474 0.27
78 601 0.35
79 77 0.04
80 23 0.01
81 8 0.00
82 57 0.03
83 2 0.00
84 57 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (77 bp):
TTTGAAAAACAGAAATTTAAAAAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATT
Found at i:55943805 original size:155 final size:155
Alignment explanation
Indices: 55941775--55943804 Score: 2197
Period size: 155 Copynumber: 13.1 Consensus size: 155
55941765 TTTATTTTTA
* * * * *
55941775 TTTGAAAAACAGAAA-TT--GA-AAATACCTCGGCGTGTGGCCCAAGGCTCAACTCACCTCTCAC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * * * * *
55941836 AATATGAATTGATTTTTG--AAAAACAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAAC
66 AATATGAGTTGATTTTTGAAAAAAACAGAAATTTAAAAATACCTCGGCATGGCCCGAGGCTCAAC
**
55941899 TCATTTCTCGCAATATGAGTTGATTTTT
131 TCACCTCTCGCAATATGAGTTGA---TT
*
55941927 TTTGAAAATACA-AAATTTAAAAGAAATAACTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTGAAAA-ACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
* * * *
55941991 CAGTATGAGTTGGTTTTTG--AAAAACAGGAATTTGAAAAAATACCTCGGCATGTGACCGAGGCT
65 CAATATGAGTTGATTTTTGAAAAAAACAGAAATTT--AAAAATACCTCGGCATG-GCCCGAGGCT
*
55942054 CAACTCACCTCTCGCATTATGAGTTGA-T
127 CAACTCACCTCTCGCAATATGAGTTGATT
* * *
55942082 TTTAAAAAACCAGAAATATAAAAGAAATACCTCGGCATGTGA-CCGAGGCTCAACTCACTTCTCG
1 TTTGAAAAA-CAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
* ** *
55942146 CAATATGAGTTGATTTTTGAAAAACACA-AATATAAAAGAAATACCTCGGCATGACCCGAGGCTC
65 CAATATGAGTTGATTTTTGAAAAAAACAGAA-ATTTAA-AAATACCTCGGCATGGCCCGAGGCTC
*
55942210 AACTCACCTCTCGCATTATGAGTTGATT
128 AACTCACCTCTCGCAATATGAGTTGATT
* * *
55942238 TTTGAAAACCAGAAATGTGAAAGAAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * *
55942301 ATTATGAGTTGA-TTTT--AAAAAATAGAAATTTAAAAGAAATACCTCGGCATGACCCGAGGCTC
66 AATATGAGTTGATTTTTGAAAAAAACAGAAATTT--AA-AAATACCTCGGCATGGCCCGAGGCTC
*
55942363 AACTCA----TCGCATTATGAGTTGA-T
128 AACTCACCTCTCGCAATATGAGTTGATT
* * * *
55942386 TTTAAAAAACAGAAATTTAAAAGAAAGACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * *
55942450 AATATGAGTTGATTTTCG--AAAAACAGAAATTTAAAAGAAATACCTCAGCATGGTCCGAGGCTC
66 AATATGAGTTGATTTTTGAAAAAAACAGAAATTT--AA-AAATACCTCGGCATGGCCCGAGGCTC
55942513 AACTCACCTCTCGCAATATGAGTTGATTT
128 AACTCACCTCTCGCAATATGAGTTGA-TT
* *
55942542 TTTGAAAAACATAAATTTAAAAGAAATACCTCGGCATG-G-TCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * * *
55942605 AATATGAGTTGATTTTCGAAAAATA-A-AAATTTTAAAATACCTCGGCATGGTCCGAGGCTCAAC
66 AATATGAGTTGATTTTTGAAAAAAACAGAAATTTAAAAATACCTCGGCATGGCCCGAGGCTCAAC
55942668 TCACCTCTCGCAATATGAGTTGATTT
131 TCACCTCTCGCAATATGAGTTGA-TT
* ** * *
55942694 TTTGAAAAACATAAATTTAAAAGAAATACCTCGGCATG-G-TTCGAGGTTCAAATCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * * * *
55942757 AATATGAGTTGATTTTTTTGAAAAAAAAAATAGAAATTTAAAAGAAATACCTCAGCGTGACCCAA
66 AATATGAGTTGA--TTTTTG---AAAAAAACAGAAATTT--AA-AAATACCTCGGCATGGCCCGA
* *
55942822 GGCTCAACTCACCTCTCGTATTATGAGTTGATT
123 GGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *** * *
55942855 TTTGAAAAA-AAAAACAGAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTC
1 TTTGAAAAACAGAAATTTAAA--AGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
* * * * *
55942917 GTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCTC
64 GCAATATGAGTTGATTTTTG-AAAAAAACAGAAATTTAAAAATACCTCGGCATGGCCCGAGGCTC
* *
55942982 AACTCACCTCTCGTATTATGAGTTGATT
128 AACTCACCTCTCGCAATATGAGTTGATT
*
55943010 TTTGAAAAAAACAGAAA-TT--AA-AAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTC
1 TTTG--AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
* * * * *
55943069 GTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATTTAAAAATACCTCAGCGTGACCCGAGGCT
64 GCAATATGAGTTGATTTTTG--AAAAAAACAGAAATTTAAAAATACCTCGGCATGGCCCGAGGCT
*
55943134 CAACTCACCTCTCGCATTATGAGTTGATT
127 CAACTCACCTCTCGCAATATGAGTTGATT
*** * *
55943163 TAAAAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGT
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * *
55943227 AATATGAGTTGATTTTTG--AAAAACAGAAATATAAAAGAAATACATCGGCATGTGACCGAGGCT
66 AATATGAGTTGATTTTTGAAAAAAACAGAAAT-T-TAA-AAATACCTCGGCATG-GCCCGAGGCT
* *
55943290 CAACTCGCTTCTCGCAATATGAGTTGATT
127 CAACTCACCTCTCGCAATATGAGTTGATT
** * * * **
55943319 TTAAAAAAAAATAGAAATTTAAAAG---TACCTCGGGATGTGGCCCGAGGCTCAACTCACCTAGC
1 TT--TGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
* * * * *
55943381 GCAATATGAGTTGA-TTTTGAAAAATA-GGAATTTTAAAAAATACCTCGGTATGTGACCTGAGGC
64 GCAATATGAGTTGATTTTTGAAAAAAACAGAAATTT-AAAAATACCTCGGCATG-G-CCCGAGGC
55943444 TCAACTCACCTCTCGCAATATGAGTTGATT
126 TCAACTCACCTCTCGCAATATGAGTTGATT
* *
55943474 TTTGAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGA-CCGATGCTCAACTCA-CTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
* * *
55943537 AATATGAGTTGA-TTTT-AAAAAACATAGAAATTTAAAAGTACCTCGGGATGTGGCCCGAGGCTC
66 AATATGAGTTGATTTTTGAAAAAA-ACAGAAATTTAAAAATACCTCGGCA--TGGCCCGAGGCTC
55943600 AACTCACCTCTCGCAATATGAGTTGA-T
128 AACTCACCTCTCGCAATATGAGTTGATT
* * * * *
55943627 TTTGACAAATAGGAATTTTAAAAAAAATACCTC-GTATGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTGAAAAACA-GAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
* * * * *
55943691 TAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAAGTACCTCGGGATGTGGCCGAGGCTCA
65 CAATATGAGTTGATTTTTGAAAAAAACAGAAATTTAAAAATACCTCGGCATG-GCCCGAGGCTCA
*
55943756 ACTCACTTCTCGCAATATGAGTTGATT
129 ACTCACCTCTCGCAATATGAGTTGATT
*
55943783 TTTGAAAAACAGAAATTGAAAA
1 TTTGAAAAACAGAAATTTAAAA
55943805 ATATTTCTTG
Statistics
Matches: 1642, Mismatches: 156, Indels: 157
0.84 0.08 0.08
Matches are distributed among these distances:
148 32 0.02
149 49 0.03
150 52 0.03
151 19 0.01
152 211 0.13
153 162 0.10
154 177 0.11
155 380 0.23
156 317 0.19
157 36 0.02
158 56 0.03
159 37 0.02
160 14 0.01
161 13 0.01
162 87 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (155 bp):
TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTTTGAAAAAAACAGAAATTTAAAAATACCTCGGCATGGCCCGAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATT
Found at i:55950861 original size:36 final size:36
Alignment explanation
Indices: 55950778--55950870 Score: 134
Period size: 35 Copynumber: 2.6 Consensus size: 36
55950768 CACGAGGATT
* * *
55950778 TTTTTTGAAAACACAAAAATTGGTGAAACACGAGAA
1 TTTTTTGAAAACACGAAAATTTGCGAAACACGAGAA
* *
55950814 -TTTTTAAAAACACGAAAATTTGCGAAGCACGAGAA
1 TTTTTTGAAAACACGAAAATTTGCGAAACACGAGAA
55950849 TTTTTTGAAAACACGAAAATTT
1 TTTTTTGAAAACACGAAAATTT
55950871 TTTAAAACAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 30 0.60
36 20 0.40
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (36 bp):
TTTTTTGAAAACACGAAAATTTGCGAAACACGAGAA
Found at i:55950946 original size:37 final size:35
Alignment explanation
Indices: 55950704--55950945 Score: 131
Period size: 37 Copynumber: 6.7 Consensus size: 35
55950694 CACGAAATTT
*
55950704 TTTTTAAAACA-CGAAATTTTTTGAAAACACGAAA
1 TTTTTGAAACACCGAAATTTTTTGAAAACACGAAA
* * *
55950738 TTTTTTGTAACA-AGAGAATTTTTTTGAAAACACGAGGATTT
1 -TTTTTGAAACACCGA-AA-TTTTTTGAAAACACGA--A--A
* * **
55950779 TTTTTGAAA-ACACAAAAATTGGTG-AAACACGAGAA
1 TTTTTGAAACAC-CGAAATTTTTTGAAAACACGA-AA
* * ** *
55950814 TTTTT-AAAAACACGAAAATTTGCG-AAGCACGAGAA
1 TTTTTGAAACAC-CGAAATTTTTTGAAAACACGA-AA
55950849 TTTTTTGAAA-ACACGAAAATTTTTT-AAAACACGAAAA
1 -TTTTTGAAACAC-CG-AAATTTTTTGAAAACACG-AAA
* **
55950886 GTTTTTCAAACATGGAAATTTTTTGAAAACACGAATA
1 -TTTTTGAAACACCGAAATTTTTTGAAAACACGAA-A
55950923 TTTTTGAAACACCGAAATTTTTT
1 TTTTTGAAACACCGAAATTTTTT
55950946 TTTTGAAAAC
Statistics
Matches: 164, Mismatches: 26, Indels: 33
0.74 0.12 0.15
Matches are distributed among these distances:
34 3 0.02
35 38 0.23
36 43 0.26
37 53 0.32
38 10 0.06
39 6 0.04
40 10 0.06
41 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTTGAAACACCGAAATTTTTTGAAAACACGAAA
Found at i:55950967 original size:23 final size:22
Alignment explanation
Indices: 55950923--55950967 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55950913 AACACGAATA
*
55950923 TTTTTGAAACACCGAAATTTTT
1 TTTTTGAAACACCGAAAATTTT
*
55950945 TTTTTGAAA-ACACGAAAAATTT
1 TTTTTGAAACAC-CGAAAATTTT
55950967 T
1 T
55950968 GAAAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
TTTTTGAAACACCGAAAATTTT
Found at i:55950969 original size:18 final size:18
Alignment explanation
Indices: 55950651--55950972 Score: 185
Period size: 18 Copynumber: 17.6 Consensus size: 18
55950641 ATGAGAATTT
*
55950651 TTTTTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
55950668 CTTTTG-AAATACGAGAA
1 TTTTTGAAAACACGAAAA
*
55950685 -TTTT-AAGAACACGAAATT
1 TTTTTGAA-AACACGAAA-A
* *
55950703 TTTTTTAAAACACGAAAT
1 TTTTTGAAAACACGAAAA
*
55950721 TTTTTGAAAACACGAAAT
1 TTTTTGAAAACACGAAAA
* **
55950739 TTTTTGTAACAAGA-GAATT
1 TTTTTG-AA-AACACGAAAA
**
55950758 TTTTTGAAAACACGAGGATTT
1 TTTTTGAAAACACGA--A-AA
*
55950779 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACGAAAA
** *
55950797 TTGGTG-AAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
55950814 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
** * *
55950832 TTTGCG-AAGCACGAGAAT
1 TTTTTGAAAACACGA-AAA
55950850 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
55950868 TTTTTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
55950886 GTTTTT-CAAACATGGAAAT
1 -TTTTTGAAAACA-CGAAAA
*
55950905 TTTTTGAAAACACGAATA
1 TTTTTGAAAACACGAAAA
*
55950923 TTTTTG-AAACACCGAAATTTTT
1 TTTTTGAAAACA-CGAAA----A
55950945 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
55950963 ATTTTGAAAA
1 TTTTTGAAAA
55950973 ATGGAATTTT
Statistics
Matches: 239, Mismatches: 43, Indels: 45
0.73 0.13 0.14
Matches are distributed among these distances:
16 5 0.02
17 47 0.20
18 102 0.43
19 47 0.20
20 6 0.03
21 16 0.07
22 11 0.05
23 5 0.02
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:55950986 original size:20 final size:22
Alignment explanation
Indices: 55950963--55951004 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
55950953 AACACGAAAA
55950963 ATTTTGAA-AAATG-GAATTTT
1 ATTTTGAAGAAATGAGAATTTT
*
55950983 ATTTTGAAGACATGAGAATTTT
1 ATTTTGAAGAAATGAGAATTTT
55951005 GAAAGACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATTTTGAAGAAATGAGAATTTT
Found at i:55951005 original size:77 final size:75
Alignment explanation
Indices: 55950868--55951023 Score: 174
Period size: 76 Copynumber: 2.1 Consensus size: 75
55950858 AACACGAAAA
* *
55950868 TTTTTTAAAACACGAAAAGTTTTTCAAACATGGAAATTTTTTGAAAACACGAATATTTTTGAAAC
1 TTTTTTAAAACACGAAAAGATTTTCAAAAATGGAAATTTTTTGAAAACACGAATATTTTTGAAAC
*
55950933 ACCGAAATTTT
66 A-CGAAATCTT
* * * *
55950944 TTTTTTGAAAACACGAAAA-ATTTTGAAAAATGGAATTTTATTTTGAAGACATGAGA-A-TTTTG
1 TTTTTT-AAAACACGAAAAGATTTTCAAAAATGGAA-ATT-TTTTGAAAACACGA-ATATTTTTG
*
55951006 AAAGACGAAATCTT
62 AAACACGAAATCTT
55951020 TTTT
1 TTTT
55951024 ATTTTTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
76 31 0.46
77 23 0.34
78 13 0.19
79 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (75 bp):
TTTTTTAAAACACGAAAAGATTTTCAAAAATGGAAATTTTTTGAAAACACGAATATTTTTGAAAC
ACGAAATCTT
Found at i:55951731 original size:24 final size:25
Alignment explanation
Indices: 55951684--55951744 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
55951674 GCTGCTGTGA
**
55951684 TGGGCCTGCTGGCCTGCCAAGCTGT
1 TGGGCCTATTGGCCTGCCAAGCTGT
55951709 TGGG-CTATTGGCCTG-CAAGGCTGT
1 TGGGCCTATTGGCCTGCCAA-GCTGT
55951733 TGGGCCTATTGG
1 TGGGCCTATTGG
55951745 GCAGCTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 3 0.09
24 18 0.56
25 11 0.34
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (25 bp):
TGGGCCTATTGGCCTGCCAAGCTGT
Found at i:55951887 original size:7 final size:8
Alignment explanation
Indices: 55951859--55951886 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55951849 CGACTATTAA
55951859 TTTTTCAT
1 TTTTTCAT
55951867 TTTTTCAT
1 TTTTTCAT
55951875 TTTTTCAT
1 TTTTTCAT
55951883 TTTT
1 TTTT
55951887 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCAT
Found at i:55951893 original size:3 final size:3
Alignment explanation
Indices: 55951885--55951952 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
55951875 TTTTTCATTT
55951885 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
55951933 TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TT
55951953 TTTCCCTCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55952063 original size:18 final size:19
Alignment explanation
Indices: 55952040--55952075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55952030 ACCCTCTCCT
55952040 CTTCTC-CTCTTTCTTTTC
1 CTTCTCTCTCTTTCTTTTC
*
55952058 CTTCTCTCTTTTTCTTTT
1 CTTCTCTCTCTTTCTTTT
55952076 TTTTCCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
CTTCTCTCTCTTTCTTTTC
Found at i:55952349 original size:30 final size:30
Alignment explanation
Indices: 55952299--55952424 Score: 209
Period size: 30 Copynumber: 4.2 Consensus size: 30
55952289 GGCTAAAACA
*
55952299 TAATTTTGAGAAAG-TTAGGGGTCAAAAGG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* *
55952328 TAACTTTGAGAAAGTTTAGGGGTTAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
*
55952358 TAATTTTGAGAAAGTTTAGTGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
55952388 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
55952418 TAATTTT
1 TAATTTT
55952425 TTGATTTTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 13 0.15
30 76 0.85
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGGGGTCAAAATG
Found at i:55952362 original size:59 final size:60
Alignment explanation
Indices: 55952279--55952424 Score: 213
Period size: 60 Copynumber: 2.5 Consensus size: 60
55952269 AGACGCAGCA
* * **
55952279 AAAGTTTTGGGGCTAAAACATAATTTTGAGAAAG-TTAGGGGTCAAAAGGTAACTTTGAG
1 AAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAAGGTAACTTTGAG
* * *
55952338 AAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGTGGTCAAAATGTAATTTTGAG
1 AAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAAGGTAACTTTGAG
*
55952398 AAAGTTTAGGGGTCAAAATGTAATTTT
1 AAAGTTTAGGGGTTAAAATGTAATTTT
55952425 TTGATTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 30 0.38
60 48 0.62
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (60 bp):
AAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAAGGTAACTTTGAG
Found at i:55952440 original size:9 final size:8
Alignment explanation
Indices: 55952420--55952451 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
55952410 TCAAAATGTA
55952420 ATTTTTTG
1 ATTTTTTG
55952428 ATTTTTTG
1 ATTTTTTG
55952436 TATTTTTTG
1 -ATTTTTTG
55952445 ATTTTTT
1 ATTTTTT
55952452 TTAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (8 bp):
ATTTTTTG
Found at i:55955693 original size:22 final size:22
Alignment explanation
Indices: 55955633--55955690 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
55955623 AAGCTTCAAG
55955633 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
55955652 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
55955674 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
55955691 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:55959486 original size:22 final size:21
Alignment explanation
Indices: 55959455--55959501 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
55959445 TAGTAGGTAC
*
55959455 CTAAATGCAAATCACTAAGCA
1 CTAAATGCAAAACACTAAGCA
* *
55959476 CTAAAGTGCAAAACAGTAGGCA
1 CTAAA-TGCAAAACACTAAGCA
55959498 CTAA
1 CTAA
55959502 GCACTGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (21 bp):
CTAAATGCAAAACACTAAGCA
Found at i:55959511 original size:29 final size:29
Alignment explanation
Indices: 55959467--55959528 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
55959457 AAATGCAAAT
*
55959467 CACTAAGCACTAAAGTGCAAAACAGTAGG
1 CACTAAGCACTAAAGTGCAAAACAATAGG
*
55959496 CACTAAGCACTGAAGTGCAAAACAATAGG
1 CACTAAGCACTAAAGTGCAAAACAATAGG
55959525 CACT
1 CACT
55959529 GAAGTGTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.15
Consensus pattern (29 bp):
CACTAAGCACTAAAGTGCAAAACAATAGG
Found at i:55959549 original size:22 final size:22
Alignment explanation
Indices: 55959499--55959562 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
55959489 CAGTAGGCAC
55959499 TAAGCACTGAAGTGCAAAACAA
1 TAAGCACTGAAGTGCAAAACAA
* * * **
55959521 TAGGCACTGAAGTGTAGAATGA
1 TAAGCACTGAAGTGCAAAACAA
* *
55959543 TAAGCACCGAAGTGCGAAAC
1 TAAGCACTGAAGTGCAAAAC
55959563 GGTATGCGCT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.16
Consensus pattern (22 bp):
TAAGCACTGAAGTGCAAAACAA
Found at i:55964775 original size:12 final size:12
Alignment explanation
Indices: 55964758--55964782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55964748 AGTTTAGTTT
55964758 AAAATTAACACG
1 AAAATTAACACG
55964770 AAAATTAACACG
1 AAAATTAACACG
55964782 A
1 A
55964783 GTCAGGGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATTAACACG
Found at i:55968299 original size:26 final size:25
Alignment explanation
Indices: 55968270--55968318 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
55968260 ACATCAATCC
55968270 ATTCACATTAAAAGTAACA-TAATAAA
1 ATTCA-ATTAAAA-TAACATTAATAAA
*
55968296 ATTCAATTTAAATAACATTAATA
1 ATTCAATTAAAATAACATTAATA
55968319 CGATAATCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 11 0.52
26 5 0.24
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTCAATTAAAATAACATTAATAAA
Found at i:55972940 original size:25 final size:25
Alignment explanation
Indices: 55972911--55972960 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
55972901 AACAAAGGTA
55972911 AGTGCCCACAAATCCTATGGCATGC
1 AGTGCCCACAAATCCTATGGCATGC
55972936 AGTGCCCACAAATCCTATGGCATGC
1 AGTGCCCACAAATCCTATGGCATGC
55972961 CAACTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (25 bp):
AGTGCCCACAAATCCTATGGCATGC
Found at i:55975142 original size:3 final size:3
Alignment explanation
Indices: 55975134--55975198 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
55975124 GTGAGGTAAG
*
55975134 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55975182 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
55975199 AGATGAGTGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55977766 original size:36 final size:36
Alignment explanation
Indices: 55977719--55977791 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
55977709 GCTAAGCTAC
55977719 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
55977755 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
55977791 C
1 C
55977792 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:55977766 original size:43 final size:42
Alignment explanation
Indices: 55977674--55977756 Score: 112
Period size: 45 Copynumber: 1.9 Consensus size: 42
55977664 CTTACGTATG
*
55977674 ATCACTTATCATTTGTCCCTGATCAGATAAGTGTAGCTAAGCT
1 ATCACTTATCATTTGTCCCTGATCAGATAAGTATAGC-AAGCT
* *
55977717 ACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCA
1 ATCACTTATCA-TTTGTC-CCTGATCAGATAAGTATAGCA
55977757 CTTATCACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 10 0.29
44 7 0.20
45 18 0.51
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (42 bp):
ATCACTTATCATTTGTCCCTGATCAGATAAGTATAGCAAGCT
Found at i:55977823 original size:82 final size:79
Alignment explanation
Indices: 55977676--55977825 Score: 228
Period size: 82 Copynumber: 1.9 Consensus size: 79
55977666 TACGTATGAT
*
55977676 CACTTATCATTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
1 CACTTATCATTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTGA
55977741 TCAGATAAGTATAG
66 TCAGATAAGTATAG
* * **
55977755 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTTT
1 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTATCACT
55977820 TGATCA
63 TGATCA
55977826 AAAGTACTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
79 9 0.14
80 5 0.08
81 20 0.32
82 29 0.46
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (79 bp):
CACTTATCATTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTGA
TCAGATAAGTATAG
Found at i:55984631 original size:23 final size:22
Alignment explanation
Indices: 55984588--55984631 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
55984578 TTTCAAGTCA
55984588 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
55984611 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
55984632 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:55984756 original size:23 final size:23
Alignment explanation
Indices: 55984730--55984805 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
55984720 ATAAGTGCCA
55984730 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55984753 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55984776 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55984799 CACTGAT
1 CACTGAT
55984806 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55988282 original size:36 final size:36
Alignment explanation
Indices: 55988235--55988389 Score: 166
Period size: 36 Copynumber: 4.0 Consensus size: 36
55988225 GCTAAGCTAC
55988235 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
55988271 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
55988313 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
55988353 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
55988389 C
1 C
55988390 TAAAGCTACC
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 63 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 27 0.27
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:55988322 original size:46 final size:46
Alignment explanation
Indices: 55988271--55988425 Score: 195
Period size: 46 Copynumber: 3.6 Consensus size: 46
55988261 ATAAGTATAG
*
55988271 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
55988317 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
55988353 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
55988399 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
55988426 AGTACTCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
36 28 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 52 0.57
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:55988330 original size:82 final size:82
Alignment explanation
Indices: 55988192--55988425 Score: 393
Period size: 82 Copynumber: 2.9 Consensus size: 82
55988182 TACGTATGAT
* * *
55988192 CACTTATCA-TTTGTC-CCTAATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
55988254 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
55988271 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
55988336 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
* *
55988353 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
55988418 TGATCAGA
66 TGATCAGA
55988426 AGTACTCAAA
Statistics
Matches: 146, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
79 9 0.06
80 5 0.03
81 20 0.14
82 112 0.77
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTATAG
Found at i:55992252 original size:18 final size:17
Alignment explanation
Indices: 55992212--55992252 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
55992202 ACACTATCTT
*
55992212 TTTTTTCTTTTTCTTTT
1 TTTTTTCTTTTTCTTTG
55992229 TCTTTTTCTTTTTCCTTTG
1 T-TTTTTCTTTTT-CTTTG
55992248 TTTTT
1 TTTTT
55992253 GACAGAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 5 0.24
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTG
Found at i:55992253 original size:6 final size:6
Alignment explanation
Indices: 55992213--55992242 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
55992203 CACTATCTTT
55992213 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
55992243 CTTTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:55993095 original size:24 final size:24
Alignment explanation
Indices: 55993063--55993111 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
55993053 TTAATTATCC
*
55993063 TTTAATATAAAAATATTTTGATAT
1 TTTAATATAAAAATATTTTAATAT
55993087 TTTAATATAAAAATATTTTAATAT
1 TTTAATATAAAAATATTTTAATAT
55993111 T
1 T
55993112 AACTTAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTAATATAAAAATATTTTAATAT
Found at i:55993682 original size:16 final size:16
Alignment explanation
Indices: 55993648--55993685 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
55993638 AATAAAAAAT
55993648 AAAAAATATTACCCAA
1 AAAAAATATTACCCAA
55993664 AAAAACATATTACCCAA
1 AAAAA-ATATTACCCAA
55993681 AAAAA
1 AAAAA
55993686 GAGGGGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATATTACCCAA
Found at i:56005963 original size:31 final size:29
Alignment explanation
Indices: 56005928--56006004 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
56005918 CTAACGGCTC
* *
56005928 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
56005959 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
56005988 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
56006005 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:56013119 original size:7 final size:7
Alignment explanation
Indices: 56013107--56013131 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56013097 ACTGTTCAAA
56013107 ACTGGAC
1 ACTGGAC
56013114 ACTGGAC
1 ACTGGAC
56013121 ACTGGAC
1 ACTGGAC
56013128 ACTG
1 ACTG
56013132 AAACTTAGTT
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:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (7 bp):
ACTGGAC
Found at i:56017055 original size:9 final size:9
Alignment explanation
Indices: 56017041--56017083 Score: 86
Period size: 9 Copynumber: 4.8 Consensus size: 9
56017031 GGTATTTTTC
56017041 GGTAATTCG
1 GGTAATTCG
56017050 GGTAATTCG
1 GGTAATTCG
56017059 GGTAATTCG
1 GGTAATTCG
56017068 GGTAATTCG
1 GGTAATTCG
56017077 GGTAATT
1 GGTAATT
56017084 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.35
Consensus pattern (9 bp):
GGTAATTCG
Found at i:56017261 original size:12 final size:12
Alignment explanation
Indices: 56017244--56017268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56017234 AGTAATTTCG
56017244 GGTCGGTTAACC
1 GGTCGGTTAACC
56017256 GGTCGGTTAACC
1 GGTCGGTTAACC
56017268 G
1 G
56017269 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:56019442 original size:20 final size:20
Alignment explanation
Indices: 56019419--56019464 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
56019409 TATTAATATT
*
56019419 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
56019439 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
56019459 TTGTTA
1 TTGTTA
56019465 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:56024019 original size:20 final size:20
Alignment explanation
Indices: 56023996--56024041 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
56023986 TGTTAATATT
*
56023996 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
56024016 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
56024036 TTGTTA
1 TTGTTA
56024042 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:56030362 original size:12 final size:12
Alignment explanation
Indices: 56030341--56030388 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
56030331 GCTGAGGCCG
*
56030341 AGGCTGAAGCTC
1 AGGCTCAAGCTC
*
56030353 AAGCTCAAGCTC
1 AGGCTCAAGCTC
* *
56030365 AGGCACAGGCTC
1 AGGCTCAAGCTC
56030377 AGGCTCAAGCTC
1 AGGCTCAAGCTC
56030389 TGTCTCGATA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (12 bp):
AGGCTCAAGCTC
Found at i:56032900 original size:14 final size:13
Alignment explanation
Indices: 56032867--56032904 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
56032857 AAAATTCTGG
56032867 CTTACTGCTTTGC
1 CTTACTGCTTTGC
*
56032880 TTTACTGCTTGTGC
1 CTTACTGCTT-TGC
56032894 CTTACTGCTTT
1 CTTACTGCTTT
56032905 ACTTCTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.08, C:0.26, G:0.16, T:0.50
Consensus pattern (13 bp):
CTTACTGCTTTGC
Found at i:56032902 original size:22 final size:22
Alignment explanation
Indices: 56032877--56032926 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
56032867 CTTACTGCTT
56032877 TGCTTTACTGCTTGTGCCTTAC
1 TGCTTTACTGCTTGTGCCTTAC
* * *
56032899 TGCTTTACTTCTTTTGCTTTAC
1 TGCTTTACTGCTTGTGCCTTAC
56032921 TGCTTT
1 TGCTTT
56032927 CGATTAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (22 bp):
TGCTTTACTGCTTGTGCCTTAC
Found at i:56032950 original size:36 final size:36
Alignment explanation
Indices: 56032910--56033001 Score: 114
Period size: 36 Copynumber: 2.4 Consensus size: 36
56032900 GCTTTACTTC
56032910 TTTTGCTTTACTGCTTTCGATTAGAA-TCAGGGAAAA
1 TTTTGC-TTACTGCTTTCGATTAGAATTCAGGGAAAA
56032946 TTTTGGCTTACTGCTTTCGATTAGAATTTTCAGGGAAAA
1 TTTT-GCTTACTGCTTTCGATTAGAA--TTCAGGGAAAA
* *
56032985 TTCTGGATTACTGCTTT
1 TT-TTGCTTACTGCTTT
56033002 GCTTTATTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
36 23 0.47
37 2 0.04
39 23 0.47
40 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (36 bp):
TTTTGCTTACTGCTTTCGATTAGAATTCAGGGAAAA
Found at i:56032996 original size:39 final size:36
Alignment explanation
Indices: 56032917--56033001 Score: 125
Period size: 39 Copynumber: 2.3 Consensus size: 36
56032907 TTCTTTTGCT
* *
56032917 TTACTGCTTTCGATTAGAATCAGGGAAAATTTTGGC
1 TTACTGCTTTCGATTAGAATCAGGGAAAATTCTGGA
56032953 TTACTGCTTTCGATTAGAATTTTCAGGGAAAATTCTGGA
1 TTACTGCTTTCGATTAGAA---TCAGGGAAAATTCTGGA
56032992 TTACTGCTTT
1 TTACTGCTTT
56033002 GCTTTATTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 19 0.43
39 25 0.57
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (36 bp):
TTACTGCTTTCGATTAGAATCAGGGAAAATTCTGGA
Found at i:56033188 original size:7 final size:7
Alignment explanation
Indices: 56033176--56033202 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
56033166 CTCTTCCCAG
56033176 ACCTCAA
1 ACCTCAA
56033183 ACCTCAA
1 ACCTCAA
56033190 ACCTCAA
1 ACCTCAA
56033197 ACCTCA
1 ACCTCA
56033203 TATTCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCTCAA
Found at i:56034305 original size:60 final size:60
Alignment explanation
Indices: 56034212--56034333 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
56034202 TCCAGGAGAG
56034212 CTTCAACTATTCCTATAAGGGCTAATGGAGCTGATTCTTGTACTATATTATCCAATTCAA
1 CTTCAACTATTCCTATAAGGGCTAATGGAGCTGATTCTTGTACTATATTATCCAATTCAA
56034272 CTTCAACTATTCCTATAAGGGCTAATGGAGCTGATTCTTGTACTATATTATCCAATTCAA
1 CTTCAACTATTCCTATAAGGGCTAATGGAGCTGATTCTTGTACTATATTATCCAATTCAA
56034332 CT
1 CT
56034334 ATCGGTCCCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (60 bp):
CTTCAACTATTCCTATAAGGGCTAATGGAGCTGATTCTTGTACTATATTATCCAATTCAA
Found at i:56036102 original size:13 final size:13
Alignment explanation
Indices: 56036084--56036112 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56036074 GGAATACTTA
56036084 TTTCTTTACTATC
1 TTTCTTTACTATC
56036097 TTTCTTTACTATC
1 TTTCTTTACTATC
56036110 TTT
1 TTT
56036113 GATAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCTTTACTATC
Found at i:56037044 original size:44 final size:45
Alignment explanation
Indices: 56036964--56037050 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 45
56036954 AAACTATAAA
* * ** *
56036964 TCTTATCTCTCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAG
*
56037009 TCTTATCTCCCTG-AGTTGTAGCGGAGCAGACTGAAGATAGCA
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCA
56037051 GATCTTGCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 24 0.67
45 12 0.33
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAG
Found at i:56037090 original size:45 final size:45
Alignment explanation
Indices: 56037028--56037172 Score: 129
Period size: 45 Copynumber: 3.2 Consensus size: 45
56037018 CCTGAGTTGT
*
56037028 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
1 AGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * * * *
56037073 AGCGAAGCAGA-TCGAAGACATCAG-CCTTGCC-TCTCTGGGT-TTG-T
1 AGCGAAGCAGACT-GAAGATAGCAGATCTTGCCTTC-CT--GTACTGAC
* * * *
56037117 AGTGGAGCAGACTAAAGATAGCAGATCTTGCCTTCATGTACTGAC
1 AGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
56037162 AGCGAAGCAGA
1 AGCGAAGCAGA
56037173 TCTTGCCTTC
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
43 4 0.05
44 28 0.38
45 38 0.51
46 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (45 bp):
AGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
Found at i:56037174 original size:31 final size:31
Alignment explanation
Indices: 56037136--56037205 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
56037126 GACTAAAGAT
* *
56037136 AGCAGATCTTGCCTTCATGTACTGACAGCGA
1 AGCAGATCTTGCCTTCATATACTAACAGCGA
56037167 AGCAGATCTTGCCTTCATATACTAACAGCGA
1 AGCAGATCTTGCCTTCATATACTAACAGCGA
56037198 AGCAGATC
1 AGCAGATC
56037206 GAAGACACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (31 bp):
AGCAGATCTTGCCTTCATATACTAACAGCGA
Found at i:56037484 original size:88 final size:88
Alignment explanation
Indices: 56037392--56037606 Score: 227
Period size: 88 Copynumber: 2.4 Consensus size: 88
56037382 AAGACGGTGA
* * * ** * *
56037392 ATCTTATCTTCC-CAAGGTAGTAGGGAAGTAGATTTAAG-CCACCAGTCTTATCTCCCTGAGTAG
1 ATCTTGTCTTCCTCAA-GTAGCAGCGAAGTAGATCGAAGACC-CCAGCCTTATCTCCCTGAGCAG
56037455 CAGTGGAATAGGTTGAAAATAGCAG
64 CAGTGGAATAGGTTGAAAATAGCAG
** * * * *
56037480 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCTTGAGCAGCA
1 ATCTTGTCTTCCTCAAGTAGCAGCGAAGTAGATCGAAGACCCCAGCCTTATCTCCCTGAGCAGCA
*
56037545 GTGGAGTAGGTTGAAAATAGCAG
66 GTGGAATAGGTTGAAAATAGCAG
** * * *
56037568 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGTTCGAAGA
1 ATCTTGTCTTCCTCAAGTAGCAGCGAAGTAGATCGAAGA
56037607 AACCAATCCT
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
88 107 0.97
89 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (88 bp):
ATCTTGTCTTCCTCAAGTAGCAGCGAAGTAGATCGAAGACCCCAGCCTTATCTCCCTGAGCAGCA
GTGGAATAGGTTGAAAATAGCAG
Found at i:56037574 original size:44 final size:43
Alignment explanation
Indices: 56037437--56037581 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 43
56037427 AAGCCACCAG
* *
56037437 TCTTATCTCCCTGAGTAGCAGTGGAATAGGTTGAAAATAGCAGA
1 TCTTGTCT-CCTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGA
* * * * * * * ***
56037481 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAG-
1 TCTTGTC-TCCTG-AGTAGCAGTGGAGTAGGTTGAAAATAGCAGA
* *
56037525 CCTTGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGA
1 TCTTGTCTCC-TGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGA
56037569 TCTTGTCTTCCTG
1 TCTTGTC-TCCTG
56037582 TATTGGCAGC
Statistics
Matches: 71, Mismatches: 25, Indels: 10
0.67 0.24 0.09
Matches are distributed among these distances:
43 22 0.31
44 26 0.37
45 23 0.32
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (43 bp):
TCTTGTCTCCTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGA
Found at i:56037622 original size:88 final size:88
Alignment explanation
Indices: 56037438--56037640 Score: 300
Period size: 88 Copynumber: 2.3 Consensus size: 88
56037428 AGCCACCAGT
* *
56037438 CTTATCTCCCTGAGTAGCAGTGGAATAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG
1 CTTATCTCCTTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG
* *
56037503 CGAAGTAGATCGAAGACCCCAGC
66 CGAAGTAGATCGAAGAACCAAGC
* *
56037526 CTTGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG
1 CTTATCTCCTTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG
* *
56037591 CGAAGTAGTTCGAAGAAACCAATC
66 CGAAGTAGATCGAAG-AACCAAGC
*
56037615 C-TATCTCCTTGAAGTTGCAGTGGAGT
1 CTTATCTCCTTG-AGTAGCAGTGGAGT
56037641 GGATTAAAAC
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 84 0.82
89 18 0.18
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (88 bp):
CTTATCTCCTTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG
CGAAGTAGATCGAAGAACCAAGC
Found at i:56041518 original size:13 final size:12
Alignment explanation
Indices: 56041478--56041510 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
56041468 TTTTTTACTG
56041478 TTTTATTTAATA
1 TTTTATTTAATA
*
56041490 TTTCATTTAATA
1 TTTTATTTAATA
56041502 TTTTATTTA
1 TTTTATTTA
56041511 TCTATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTATTTAATA
Found at i:56043436 original size:13 final size:14
Alignment explanation
Indices: 56043418--56043454 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
56043408 CTACCATATG
56043418 ATAAAAATTTCG-T
1 ATAAAAATTTCGTT
56043431 ATAAAAATTTCGTT
1 ATAAAAATTTCGTT
*
56043445 AGAAAAATTT
1 ATAAAAATTT
56043455 TACAGATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (14 bp):
ATAAAAATTTCGTT
Found at i:56044392 original size:25 final size:27
Alignment explanation
Indices: 56044364--56044427 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
56044354 GGCTCTTATG
56044364 AGCTTCCCGTTATACA-G-CTCGA-ATA
1 AGCTTCCCGTTATACATGACTC-ACATA
* *
56044389 AGCTTCTC-AT-TACATGACTCACATA
1 AGCTTCCCGTTATACATGACTCACATA
56044414 AGCTTCCCGTTATA
1 AGCTTCCCGTTATA
56044428 TGTCTCGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.13
24 3 0.10
25 20 0.67
26 1 0.03
27 2 0.07
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
AGCTTCCCGTTATACATGACTCACATA
Found at i:56044813 original size:24 final size:24
Alignment explanation
Indices: 56044781--56044828 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
56044771 GAATGGTAAG
56044781 TTAATTTCTTGTTATAAGAACTTA
1 TTAATTTCTTGTTATAAGAACTTA
56044805 TTAATTTCTTGTTATAAGAACTTA
1 TTAATTTCTTGTTATAAGAACTTA
56044829 CTAAGCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (24 bp):
TTAATTTCTTGTTATAAGAACTTA
Found at i:56047311 original size:114 final size:114
Alignment explanation
Indices: 56047107--56047312 Score: 349
Period size: 114 Copynumber: 1.8 Consensus size: 114
56047097 CCTGATAATA
* ** *
56047107 TAGTACGAGTGTGTACAAGATTCTATTGGCATGCCAATCGTATCCTAACATTTACTGAGTTCACC
1 TAGTACGAGTGTGCACAAGACCCTATTGGCATGCCAATCATATCCTAACATTTACTGAGTTCACC
* *
56047172 CAAGCATCTTTAATACACAAGAAAAAAATATCATCCAAGCTAATCAATC
66 CAAGCATCTTTAACACACAAAAAAAAAATATCATCCAAGCTAATCAATC
*
56047221 TAGTACGAGTGTGCACAAGACCCTATTGGCATGCCAATCATATCCTAACATTTACTGAGTTTACC
1 TAGTACGAGTGTGCACAAGACCCTATTGGCATGCCAATCATATCCTAACATTTACTGAGTTCACC
56047286 CAAGCATCTTTAACACACAAAAAAAAA
66 CAAGCATCTTTAACACACAAAAAAAAA
56047313 TTCTTTACTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (114 bp):
TAGTACGAGTGTGCACAAGACCCTATTGGCATGCCAATCATATCCTAACATTTACTGAGTTCACC
CAAGCATCTTTAACACACAAAAAAAAAATATCATCCAAGCTAATCAATC
Found at i:56048973 original size:5 final size:5
Alignment explanation
Indices: 56048963--56049003 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
56048953 ATTTTATATT
*
56048963 TTATA TTATA TTATA TTATA TTATA TTGTA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
56049004 AAATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:56051288 original size:5 final size:5
Alignment explanation
Indices: 56051280--56051320 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
56051270 TATTTAATTT
*
56051280 ATATA ATATA ATACA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
56051321 AACATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:56052644 original size:27 final size:26
Alignment explanation
Indices: 56052614--56052667 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
56052604 TTTTATCATA
* *
56052614 AATTATTGATATTTTTAAATATTTTAT
1 AATTATTGACATATTTAAAT-TTTTAT
* *
56052641 AATTGTTTACATATTTAAATTTTTAT
1 AATTATTGACATATTTAAATTTTTAT
56052667 A
1 A
56052668 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
AATTATTGACATATTTAAATTTTTAT
Found at i:56053624 original size:18 final size:18
Alignment explanation
Indices: 56053596--56053644 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
56053586 TCACGCTAAT
*
56053596 AAAATATTAAAAGTA-TTA
1 AAAAT-TTAAAAATATTTA
56053614 AAAATTATAAAAATATTTA
1 AAAATT-TAAAAATATTTA
*
56053633 TAAATTTAAAAA
1 AAAATTTAAAAA
56053645 AAATCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 18 0.67
19 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATTTAAAAATATTTA
Found at i:56054682 original size:9 final size:10
Alignment explanation
Indices: 56054658--56054715 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
56054648 AACTTATGAT
56054658 TATTATAAAA
1 TATTATAAAA
56054668 TATTATAAAA
1 TATTATAAAA
*
56054678 -CTTATAAAA
1 TATTATAAAA
* *
56054687 AATCAT-AAA
1 TATTATAAAA
56054696 TATTATAAGAA
1 TATTATAA-AA
56054707 T-TTATAAAA
1 TATTATAAAA
56054716 AAGACTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 17 0.43
10 20 0.50
11 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (10 bp):
TATTATAAAA
Found at i:56054682 original size:19 final size:18
Alignment explanation
Indices: 56054659--56054715 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
56054649 ACTTATGATT
56054659 ATTATAAAATATTATAAA
1 ATTATAAAATATTATAAA
* *
56054677 ACTTATAAAAAATCATAAA
1 A-TTATAAAATATTATAAA
56054696 TATTATAAGAAT-TTATAAA
1 -ATTATAA-AATATTATAAA
56054715 A
1 A
56054716 AAGACTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.06
19 27 0.84
20 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
ATTATAAAATATTATAAA
Found at i:56054983 original size:21 final size:20
Alignment explanation
Indices: 56054959--56055001 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
56054949 TAAAATATTT
*
56054959 AAAAACTTATAAATGATATAA
1 AAAAACTAATAAATGAT-TAA
* *
56054980 AAAATCTAATAAATTATTAA
1 AAAAACTAATAAATGATTAA
56055000 AA
1 AA
56055002 TTTAGAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAACTAATAAATGATTAA
Found at i:56055168 original size:222 final size:222
Alignment explanation
Indices: 56054776--56055347 Score: 680
Period size: 222 Copynumber: 2.7 Consensus size: 222
56054766 ACTGATATAA
* * *
56054776 AAAATTTAGAAATTACAATAAAAAGATATTTAAGCCCCTAAATAAAAATAAACACATGACATCTG
1 AAAATTTAGAAAGTACAATAAAAAGACATTGAAGCCCCTAAATAAAAATAAACACATGACATCTG
56054841 CCTAACAGTTAATGGGAATAATTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAAAATGTTCT
66 CCTAACAGTTAATGGGAATAATTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAAAATGTTCT
* *
56054906 CGATCTTCCACAAATAATCTTTATATAATTAATGAAACATATTTAAAATATTTAAAAACTTATAA
131 CGATCTTCCACAAATAATCTTTATAAAATTAATAAAACATATTTAAAATATTTAAAAACTTATAA
56054971 ATGATATAAAAAATCTAATAAATTATT
196 ATGATATAAAAAATCTAATAAATTATT
* * * * * *
56054998 AAAATTTAGAAAGTACAATAAAAAGACATTGAATCCCCTAAATAATATTGAACATATGGCATCTA
1 AAAATTTAGAAAGTACAATAAAAAGACATTGAAGCCCCTAAATAAAAATAAACACATGACATCT-
* * * *
56055063 TCC-AATAGTTAATGGGAATAGTTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAATATGTTC
65 GCCTAACAGTTAATGGGAATAATTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAAAATGTTC
* * * *
56055127 TTGATCTTCTATAAATAATTTTTATAAAATTAATAAAACATATTTAAAATATTTAAAAACTTATA
130 TCGATCTTCCACAAATAATCTTTATAAAATTAATAAAACATATTTAAAATATTTAAAAACTTATA
56055192 AATGATAT--AAAA---AAT---TTA--
195 AATGATATAAAAAATCTAATAAATTATT
* * * * * **
56055210 GAAA-TT----A-T--AATAAAAAGACATTTAGGCCCCTAAATAATAATGAACACATGACATCAA
1 AAAATTTAGAAAGTACAATAAAAAGACATTGAAGCCCCTAAATAAAAATAAACACATGACATCTG
* ** * * * * *
56055267 TCTAACAGTTAATGAAAATGATTTTCAAATCATTA-GGTCATTTTCATATTGAATAAAATGTTCT
66 CCTAACAGTTAATGGGAATAATTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAAAATGTTCT
*
56055331 CAATCTTCCACAAATAA
131 CGATCTTCCACAAATAA
56055348 AGTGATAATT
Statistics
Matches: 305, Mismatches: 43, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
203 41 0.13
204 65 0.21
206 1 0.00
207 1 0.00
211 2 0.01
212 3 0.01
214 3 0.01
217 3 0.01
220 4 0.01
222 180 0.59
223 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (222 bp):
AAAATTTAGAAAGTACAATAAAAAGACATTGAAGCCCCTAAATAAAAATAAACACATGACATCTG
CCTAACAGTTAATGGGAATAATTTTTAGATCGTTAGGGTCATTTTCATGTTGAATAAAATGTTCT
CGATCTTCCACAAATAATCTTTATAAAATTAATAAAACATATTTAAAATATTTAAAAACTTATAA
ATGATATAAAAAATCTAATAAATTATT
Found at i:56055214 original size:20 final size:21
Alignment explanation
Indices: 56055181--56055225 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
56055171 TAAAATATTT
*
56055181 AAAAACTTATAAATGAT-ATA
1 AAAAACTTAGAAATGATAATA
* *
56055201 AAAAATTTAGAAATTATAATA
1 AAAAACTTAGAAATGATAATA
56055222 AAAA
1 AAAA
56055226 GACATTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAACTTAGAAATGATAATA
Found at i:56055797 original size:17 final size:18
Alignment explanation
Indices: 56055775--56055821 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
56055765 ACTAGAACTA
56055775 TTATAACTTT-TAT-ATTT
1 TTATAA-TTTATATGATTT
56055792 TTATAATTTATATGATTT
1 TTATAATTTATATGATTT
56055810 TATATATATTTA
1 T-TATA-ATTTA
56055822 ATAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 9 0.35
18 5 0.19
19 4 0.15
20 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATAATTTATATGATTT
Found at i:56055830 original size:21 final size:18
Alignment explanation
Indices: 56055776--56055833 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 18
56055766 CTAGAACTAT
56055776 TATAACTTT-TATATTTT-
1 TATAA-TTTATATATTTTA
56055793 TATAATTTATATGATTTTA
1 TATAATTTATAT-ATTTTA
56055812 TATATATTTAATAATATTTTA
1 TATA-ATTT-AT-ATATTTTA
56055833 T
1 T
56055834 GCTTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.09
17 8 0.23
18 5 0.14
19 4 0.11
20 4 0.11
21 9 0.26
22 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TATAATTTATATATTTTA
Found at i:56055839 original size:29 final size:25
Alignment explanation
Indices: 56055781--56055839 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
56055771 ACTATTATAA
56055781 CTTTTATATTTTTATAATTTATATG
1 CTTTTATATTTTTATAATTTATATG
* *
56055806 ATTTTATATATATTTAATAATATTTTATG
1 CTTTTATAT-T-TTT-ATAAT-TTATATG
56055835 CTTTT
1 CTTTT
56055840 TTAAGATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 8 0.30
26 1 0.04
27 3 0.11
28 5 0.19
29 10 0.37
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (25 bp):
CTTTTATATTTTTATAATTTATATG
Found at i:56056776 original size:23 final size:23
Alignment explanation
Indices: 56056747--56056796 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
56056737 CGAATATATT
56056747 TTTTATTTTTTAATTTTAAAATA
1 TTTTATTTTTTAATTTTAAAATA
*
56056770 TTTTATTTTTTATTTTTAAAATA
1 TTTTATTTTTTAATTTTAAAATA
56056793 TTTT
1 TTTT
56056797 TTTAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTATTTTTTAATTTTAAAATA
Found at i:56056811 original size:23 final size:23
Alignment explanation
Indices: 56056760--56056813 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
56056750 TATTTTTTAA
**
56056760 TTTTAAAATATTTTATTTTTTAT
1 TTTTAAAATATTTTATTTAATAT
*
56056783 TTTTAAAATATTTT-TTTAATGT
1 TTTTAAAATATTTTATTTAATAT
56056805 TTATTAAAA
1 TT-TTAAAA
56056814 AATGGGCCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTAAAATATTTTATTTAATAT
Found at i:56057261 original size:11 final size:11
Alignment explanation
Indices: 56057241--56057270 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
56057231 TCCTCTCTTA
56057241 AATTTCCTCTC
1 AATTTCCTCTC
*
56057252 AATTTGCTCTC
1 AATTTCCTCTC
56057263 AATTTCCT
1 AATTTCCT
56057271 TCCAAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.47
Consensus pattern (11 bp):
AATTTCCTCTC
Found at i:56057312 original size:51 final size:51
Alignment explanation
Indices: 56057248--56057347 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 51
56057238 TTAAATTTCC
56057248 TCTCAATTTGCTCTCAA-TTTC-CTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTTCTCTT--AAATTTCTCTCAAATCCATATTTAA
* *
56057299 TCTC-ATTTCGCTCTCAATTTTCTCTTAAATTTCTCTTAAATCCTTATTT
1 TCTCAATTT-GCTCTCAATTTTCTCTTAAATTTCTCTCAAATCCATATTT
56057348 TTAAATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
50 4 0.09
51 33 0.75
52 4 0.09
53 3 0.07
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTTCTCTTAAATTTCTCTCAAATCCATATTTAA
Found at i:56060530 original size:237 final size:237
Alignment explanation
Indices: 56060115--56060556 Score: 677
Period size: 237 Copynumber: 1.9 Consensus size: 237
56060105 TGTGTGGATA
* * ** *
56060115 GGGCGTGTAACTCACTAGACTCCTGTACGACACCAACAGGGATTTTTTATTTTTAGGTTTTTGAC
1 GGGCGTGTAACTCACTAGACTCATGTACGACACCAACAAGGATTTTCGATTTTTAGGTTTTCGAC
* * *
56060180 ACTTTGAGAAGGTATATATAAGGAAATAAAAAGGGAGAACAATAGTCGTCTTATTTTTGCACAAA
66 ACTTTGAGAAGGCATATATAAGGAAATAAAAAGGGAGAACAATAGTCCTCTTATTCTTGCACAAA
* * *
56060245 AATTACCCAAAAGAACACCCTTGAAGTTGATTTTGAAATAGTTCTCCATCAAGATTGAAGATTCC
131 AATTACCCAAAAGAACACCCTTGAAGTTGATTCTGAAATAGATCTCCATCAAGATTAAAGATTCC
56060310 AAGCTAATTTGGAAGCTACACACAGTCAACAGTGTTCTACAC
196 AAGCTAATTTGGAAGCTACACACAGTCAACAGTGTTCTACAC
* * ***
56060352 GGGCGTGTAACTCGCTGGACTCATGTACGACACCTGTAAGGATTTTCGATTTTTAGGTTTTCGAC
1 GGGCGTGTAACTCACTAGACTCATGTACGACACCAACAAGGATTTTCGATTTTTAGGTTTTCGAC
* * *
56060417 ACTTTGAGAAGGCATATATAAGGAAATAAAAAGGGAGAACAGTAGTCCTCTTGTTCTTGCACGAA
66 ACTTTGAGAAGGCATATATAAGGAAATAAAAAGGGAGAACAATAGTCCTCTTATTCTTGCACAAA
* **
56060482 AATTACCCAAAAGAACATCCTTGAAGTTGATTCTGAGGTAGATCTCCATCAAGATTAAAGATTCC
131 AATTACCCAAAAGAACACCCTTGAAGTTGATTCTGAAATAGATCTCCATCAAGATTAAAGATTCC
*
56060547 AAGCTGATTT
196 AAGCTAATTT
56060557 CTGAGGAGGT
Statistics
Matches: 182, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
237 182 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (237 bp):
GGGCGTGTAACTCACTAGACTCATGTACGACACCAACAAGGATTTTCGATTTTTAGGTTTTCGAC
ACTTTGAGAAGGCATATATAAGGAAATAAAAAGGGAGAACAATAGTCCTCTTATTCTTGCACAAA
AATTACCCAAAAGAACACCCTTGAAGTTGATTCTGAAATAGATCTCCATCAAGATTAAAGATTCC
AAGCTAATTTGGAAGCTACACACAGTCAACAGTGTTCTACAC
Found at i:56065967 original size:31 final size:29
Alignment explanation
Indices: 56065929--56066005 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
56065919 CTAACGGCTC
* *
56065929 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
56065960 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
56065989 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
56066006 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:56067274 original size:5 final size:5
Alignment explanation
Indices: 56067264--56067289 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56067254 TGGATGACAC
56067264 TAGTG TAGTG TAGTG TAGTG TAGTG T
1 TAGTG TAGTG TAGTG TAGTG TAGTG T
56067290 GTTTGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.42
Consensus pattern (5 bp):
TAGTG
Found at i:56073126 original size:38 final size:37
Alignment explanation
Indices: 56073107--56073206 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 37
56073097 AAAAAATTTT
*
56073107 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAATG
1 TATTTTAAAAATATTTTAAAATCAAAAAAAA-TAAATG
* * *
56073145 TATTTTAAAAATCTTTTAAAATTAAAAAGTTTAAA-AAAAG
1 TATTTTAAAAATATTTTAAAATCAAAAA----AAATAAATG
*
56073185 TATTTTAAAAGTATTTTAAAAT
1 TATTTTAAAAATATTTTAAAAT
56073207 TTAAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
38 27 0.50
40 24 0.44
42 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (37 bp):
TATTTTAAAAATATTTTAAAATCAAAAAAAATAAATG
Found at i:56073194 original size:11 final size:11
Alignment explanation
Indices: 56073180--56073205 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56073170 AAAGTTTAAA
56073180 AAAAGTATTTT
1 AAAAGTATTTT
56073191 AAAAGTATTTT
1 AAAAGTATTTT
56073202 AAAA
1 AAAA
56073206 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:56081742 original size:3 final size:3
Alignment explanation
Indices: 56081734--56081762 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56081724 TTCCATCGCA
56081734 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56081763 GTGGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56087892 original size:30 final size:30
Alignment explanation
Indices: 56087830--56087986 Score: 103
Period size: 30 Copynumber: 5.3 Consensus size: 30
56087820 GGTCGTCACC
* * *
56087830 ATCCCGTTTCATAATTTGATAGCCGA-AGCT
1 ATCCCTTTTCATAATTCGATAGTC-ATAGCT
*
56087860 ATCCCTTTTCATAATTCGATAGTCATATCT
1 ATCCCTTTTCATAATTCGATAGTCATAGCT
** *
56087890 ATCCCTTTTCATTGTTCGATAGTCATCA-CC
1 ATCCCTTTTCATAATTCGATAGTCAT-AGCT
* * *
56087920 AT-CCTTGTTCATTATT-GATGGT-AGTCA-CC
1 ATCCCTT-TTCATAATTCGATAGTCA-T-AGCT
* *
56087949 ATCCCTTTTCATAATTTGATAGCCGA-AGCT
1 ATCCCTTTTCATAATTCGATAGTC-ATAGCT
56087979 ATCCCTTT
1 ATCCCTTT
56087987 CCATTAGTCG
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 26 0.25
30 76 0.72
31 1 0.01
32 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAGTCATAGCT
Found at i:56095731 original size:3 final size:3
Alignment explanation
Indices: 56095723--56095750 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56095713 CAATCAATGT
56095723 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56095751 CATCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56112644 original size:3 final size:3
Alignment explanation
Indices: 56112636--56112677 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
56112626 TATATAACAG
56112636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56112678 CTAAACATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:56114648 original size:21 final size:19
Alignment explanation
Indices: 56114606--56114648 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56114596 GATGAGTTCA
*
56114606 TATATGACAGTCGTATGCT
1 TATATGACAGTCATATGCT
*
56114625 TATATGGCATGTCATATGCGT
1 TATATGACA-GTCATATGC-T
56114646 TAT
1 TAT
56114649 TATGTTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (19 bp):
TATATGACAGTCATATGCT
Found at i:56117602 original size:20 final size:23
Alignment explanation
Indices: 56117562--56117602 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
56117552 ACTCTCACCT
56117562 GATAACCAATACAATATGTATGA
1 GATAACCAATACAATATGTATGA
56117585 GATAA-CAA-ACAA-ATGTAT
1 GATAACCAATACAATATGTAT
56117603 ATATCATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 3 0.17
23 5 0.28
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (23 bp):
GATAACCAATACAATATGTATGA
Found at i:56124113 original size:15 final size:15
Alignment explanation
Indices: 56124088--56124122 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56124078 AACTCTATTT
*
56124088 TAATT-ATATTATGA
1 TAATTAATATTAAGA
56124102 TAATTAATATTAAGA
1 TAATTAATATTAAGA
56124117 TAATTA
1 TAATTA
56124123 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:56125317 original size:8 final size:10
Alignment explanation
Indices: 56125285--56125316 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56125275 GAAAATAAAG
56125285 AAAATATATA
1 AAAATATATA
56125295 AAAATATATA
1 AAAATATATA
56125305 AAAAT-TATA
1 AAAATATATA
56125314 AAA
1 AAA
56125317 TATGTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATATATA
Found at i:56131317 original size:20 final size:20
Alignment explanation
Indices: 56131292--56131338 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
56131282 AAGTGCTTAG
56131292 ATGAAAGTATAATTGAGCTT
1 ATGAAAGTATAATTGAGCTT
56131312 ATGAAAGTATAATTGAGCTT
1 ATGAAAGTATAATTGAGCTT
56131332 ATGAAAG
1 ATGAAAG
56131339 AGTGGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGAAAGTATAATTGAGCTT
Found at i:56132493 original size:13 final size:14
Alignment explanation
Indices: 56132475--56132509 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
56132465 ATCTTTTATA
56132475 TAAAAATA-AATAT
1 TAAAAATATAATAT
56132488 TAAAAATATAATAT
1 TAAAAATATAATAT
*
56132502 TAGAAATA
1 TAAAAATA
56132510 CATTAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAAAATATAATAT
Found at i:56134300 original size:154 final size:152
Alignment explanation
Indices: 56134080--56134791 Score: 998
Period size: 154 Copynumber: 4.7 Consensus size: 152
56134070 AAAAACCCTT
* ** * * *
56134080 AAAAATACGAATAAATAGCTGAAATAAGGATTTTTTAAAATTTATTT-AAAAACACAGTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
* * * *
56134144 ATACATTTCAAATATAATGTACTAAAATAATTTAAAATAATAAAATCATAAAATAGTATATTTTT
66 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
*
56134209 TAAAAGTAATAAAATCCGGAGAA
131 TTAAAGTAATAAAATCCGG-GAA
*
56134232 AAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATT
1 AAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTTTAAATTTATTTAAAAAACACAGTAAATT
56134297 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTT
65 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTT
* **
56134362 TTTAAAGTAATAAACTTTGGG-A
130 TTTAAAGTAATAAAATCCGGGAA
* *
56134384 AAAAATAGGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
**
56134449 ATACATTTCAAACATAATGTACTAAAATAATACAAAATAATAAAATTAGAAAATAGTATATTTTT
66 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
* *
56134514 TTAAAGTAATAAACTCTGGGGAA
131 TTAAAGTAATAAAATC-CGGGAA
* * *
56134537 AAAAATACGAACAAATGGCTGAAATAAGAGTTTTTTTTAAATTTATTTAAAAAATACAGTAAATT
1 AAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTTTAAATTTATTTAAAAAACACAGTAAATT
*
56134602 AATACATTTCAAACATGATGTACTAAAATAATGTAAAATAATAAAA-T----AATA-TAT-TTTT
65 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTT
* *
56134660 ATTGAAAGTAATAAAAT-CTGGAA
130 -TTTAAAGTAATAAAATCCGGGAA
* *
56134683 AAAAATACGAACAAAGGGCCGAAATAAGG-ATTTTTTAAATTTATTTAAAAAACACATTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
* * * *
56134747 ATATATTTCAAATATAATATACTAAAATAATGAAAAATAA-AAAAT
66 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
56134792 AGTATATTTT
Statistics
Matches: 509, Mismatches: 44, Indels: 22
0.89 0.08 0.04
Matches are distributed among these distances:
143 4 0.01
144 67 0.13
145 1 0.00
146 30 0.06
147 4 0.01
148 17 0.03
149 4 0.01
151 114 0.22
152 53 0.10
153 45 0.09
154 170 0.33
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (152 bp):
AAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
TTAAAGTAATAAAATCCGGGAA
Found at i:56134630 original size:305 final size:298
Alignment explanation
Indices: 56134080--56134791 Score: 1054
Period size: 305 Copynumber: 2.4 Consensus size: 298
56134070 AAAAACCCTT
* ** * * *
56134080 AAAAATACGAATAAATAGCTGAAATAAGGATTTTTTAAAATTTATTT-AAAAACACAGTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
* *
56134144 ATACATTTCAAATATAATGTACTAAAATAATTTAAAATAATAAAATCATAAAATAGTATATTTTT
66 ATACATTTCAAATATAATGTACTAAAATAA-TAAAAATAATAAAATCAGAAAATAGTATATTTTT
56134209 TAAAAGTAATAAAATCCGGAGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAT
130 TAAAAGTAATAAAATCCGGAGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAT
56134274 TTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
195 TTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* * * *
56134339 AAAATTAGAAAATAGTATATTTT-TTTAAAGTAATAAACTTTGGGA
260 AAAA-T----AATA-TAT-TTTTATTGAAAGTAATAAAATCTGGAA
*
56134384 AAAAATAGGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
* *
56134449 ATACATTTCAAACATAATGTACTAAAATAATACAAAATAATAAAATTAGAAAATAGTATATTTTT
66 ATACATTTCAAATATAATGTACTAAAATAATA-AAAATAATAAAATCAGAAAATAGTATATTTTT
* * * * * * *
56134514 TTAAAGTAATAAACTCTGGGGAAAAAAATACGAACAAATGGCTGAAATAAGAGTTTTTTTTAAAT
130 TAAAAGTAATAAAATCCGGAGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAT
* *
56134579 TTATTTAAAAAATACAGTAAATTAATACATTTCAAACATGATGTACTAAAATAATGTAAAATAAT
195 TTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
56134644 AAAATAATATATTTTTATTGAAAGTAATAAAATCTGGAA
260 AAAATAATATATTTTTATTGAAAGTAATAAAATCTGGAA
* *
56134683 AAAAATACGAACAAAGGGCCGAAATAA-GGATTTTTTAAATTTATTTAAAAAACACATTAAATTA
1 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
* *
56134747 ATATATTTCAAATATAATATACTAAAATAATGAAAAATAA-AAAAT
66 ATACATTTCAAATATAATGTACTAAAATAAT-AAAAATAATAAAAT
56134792 AGTATATTTT
Statistics
Matches: 374, Mismatches: 30, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
297 5 0.01
298 74 0.20
299 48 0.13
300 4 0.01
304 42 0.11
305 201 0.54
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (298 bp):
AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTA
ATACATTTCAAATATAATGTACTAAAATAATAAAAATAATAAAATCAGAAAATAGTATATTTTTT
AAAAGTAATAAAATCCGGAGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATT
TATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATAATATATTTTTATTGAAAGTAATAAAATCTGGAA
Found at i:56134755 original size:144 final size:143
Alignment explanation
Indices: 56134478--56134843 Score: 474
Period size: 144 Copynumber: 2.6 Consensus size: 143
56134468 TACTAAAATA
* *
56134478 ATAC-AAAATAA--TAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAACTCTGGGGAAAAA
1 ATACTAAAATAATGTAAAA-TAAAAAATAGTATATTTTTTTAAAGTAATAAAATCT--GGAAAAA
* * *
56134540 AATACGAACAAATGGCTGAAATAAGAGTTTTTTTTAAATTTATTTAAAAAATACAGTAAATTAAT
63 AATACGAACAAATGGCCGAAATAAGAGTATTTTTTAAATTTATTTAAAAAACACAGTAAATTAAT
*
56134605 ACATTTCAAACATGAT
128 ACATTTCAAACATAAT
* *
56134621 GTACTAAAATAATGTAAAATAATAAAATAATATATTTTTATTGAAAGTAATAAAATCTGGAAAAA
1 ATACTAAAATAATGTAAAATAA-AAAATAGTATATTTTT-TT-AAAGTAATAAAATCTGGAAAAA
* *
56134686 AATACGAACAAAGGGCCGAAATAAG-G-ATTTTTTAAATTTATTTAAAAAACACATTAAATTAAT
63 AATACGAACAAATGGCCGAAATAAGAGTATTTTTTAAATTTATTTAAAAAACACAGTAAATTAAT
* *
56134749 ATATTTCAAATATAAT
128 ACATTTCAAACATAAT
* * * **
56134765 ATACTAAAATAATGAAAAATAAAAAATAGTATATTTTTTAAAAATAATAAAAT-TCAAGAAAAAA
1 ATACTAAAATAATGTAAAATAAAAAATAGTATATTTTTTTAAAGTAATAAAATCTGGA-AAAAAA
56134829 TACGAACAAATGGCC
65 TACGAACAAATGGCC
56134844 AAAACACGAA
Statistics
Matches: 196, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
140 2 0.01
141 32 0.16
142 1 0.01
143 18 0.09
144 74 0.38
145 3 0.02
146 50 0.26
147 2 0.01
148 14 0.07
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (143 bp):
ATACTAAAATAATGTAAAATAAAAAATAGTATATTTTTTTAAAGTAATAAAATCTGGAAAAAAAT
ACGAACAAATGGCCGAAATAAGAGTATTTTTTAAATTTATTTAAAAAACACAGTAAATTAATACA
TTTCAAACATAAT
Found at i:56155128 original size:4 final size:4
Alignment explanation
Indices: 56155121--56155150 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
56155111 CACACATATA
56155121 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
56155151 CTTAGAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:56158319 original size:18 final size:18
Alignment explanation
Indices: 56158278--56158330 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
56158268 TAAAATTATA
* *
56158278 AAAAAATATTATAAAACTC
1 AAAAAATATAAT-AAATTC
*
56158297 TAAAAATATAATAAATTC
1 AAAAAATATAATAAATTC
* *
56158315 AAAAAAAATAAAAAAT
1 AAAAAATATAATAAAT
56158331 AATTAAACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAATATAATAAATTC
Found at i:56158406 original size:22 final size:22
Alignment explanation
Indices: 56158381--56158424 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56158371 TTGAAAATCT
56158381 TAAAAAATAAAATAAATATAAA
1 TAAAAAATAAAATAAATATAAA
* * **
56158403 TAAATATTAAAATTGATATAAA
1 TAAAAAATAAAATAAATATAAA
56158425 CTTATACAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAAAATAAAATAAATATAAA
Found at i:56158904 original size:9 final size:9
Alignment explanation
Indices: 56158881--56159092 Score: 73
Period size: 9 Copynumber: 22.9 Consensus size: 9
56158871 AGTTTATACC
*
56158881 AATTTTAAT
1 AATTTTTAT
*
56158890 ACTTTTTAT
1 AATTTTTAT
56158899 AATTTTTTAT
1 AA-TTTTTAT
*
56158909 GATTTTATAT
1 AATTTT-TAT
56158919 AATTTTAATAT
1 AATTTT--TAT
** *
56158930 GCTTTTTAA
1 AATTTTTAT
**
56158939 AATTTAAAT
1 AATTTTTAT
56158948 -ATATTTTATT
1 AAT-TTTTA-T
*
56158958 AA-TTTTAC
1 AATTTTTAT
*
56158966 ATTTTTTAT
1 AATTTTTAT
56158975 AATTTATT-T
1 AATTT-TTAT
* *
56158984 GATTTTATTT
1 AATTTT-TAT
*
56158994 GATTTTTAT
1 AATTTTTAT
56159003 -A-TTTTAT
1 AATTTTTAT
56159010 AATTTTTAT
1 AATTTTTAT
* *
56159019 AAGTGTATAT
1 AA-TTTTTAT
56159029 CAATTTTTAT
1 -AATTTTTAT
56159039 --TTTTTAT
1 AATTTTTAT
*
56159046 ATTTTATTA-
1 AATTT-TTAT
56159055 ATATTTTTAT
1 A-ATTTTTAT
*
56159065 -TTTTTTGAT
1 AATTTTT-AT
56159074 AATTTTTTAT
1 AA-TTTTTAT
56159084 GAATTTTTA
1 -AATTTTTA
56159093 ATCTTTTTTA
Statistics
Matches: 152, Mismatches: 28, Indels: 45
0.68 0.12 0.20
Matches are distributed among these distances:
7 13 0.09
8 11 0.07
9 60 0.39
10 50 0.33
11 18 0.12
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:56158904 original size:18 final size:17
Alignment explanation
Indices: 56158881--56158979 Score: 74
Period size: 19 Copynumber: 5.3 Consensus size: 17
56158871 AGTTTATACC
56158881 AATTTTAATACTTTTTAT
1 AATTTTAATA-TTTTTAT
*
56158899 AATTTTTTATGATTTTATAT
1 AA-TTTTAAT-ATTTT-TAT
*
56158919 AATTTTAATATGCTTTTTAA
1 AATTTTAATA---TTTTTAT
*
56158939 AATTTAAATATATTTTATT
1 AATTTTAATAT-TTTTA-T
56158958 AATTTTACAT-TTTTTAT
1 AATTTTA-ATATTTTTAT
56158975 AATTT
1 AATTT
56158980 ATTTGATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
17 7 0.11
18 13 0.20
19 23 0.35
20 19 0.29
21 4 0.06
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (17 bp):
AATTTTAATATTTTTAT
Found at i:56158919 original size:20 final size:20
Alignment explanation
Indices: 56158892--56159010 Score: 60
Period size: 19 Copynumber: 6.3 Consensus size: 20
56158882 ATTTTAATAC
56158892 TTTT-TATAATTTTTTATGA
1 TTTTATATAATTTTTTATGA
* *
56158911 TTTTATATAATTTTAATATGC
1 TTTTATATAATTTT-TTATGA
* **
56158932 TTTT-TAAAATTTAAATAT-A
1 TTTTATATAATTT-TTTATGA
*
56158951 TTTTAT-TAA--TTTTA-CA
1 TTTTATATAATTTTTTATGA
* *
56158967 TTTTTTATAATTTATT-TGA
1 TTTTATATAATTTTTTATGA
* *
56158986 TTTTATTTGA-TTTTTAT-A
1 TTTTATATAATTTTTTATGA
56159004 TTTTATA
1 TTTTATA
56159011 ATTTTTATAA
Statistics
Matches: 74, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
16 8 0.11
17 4 0.05
18 11 0.15
19 22 0.30
20 21 0.28
21 8 0.11
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTATATAATTTTTTATGA
Found at i:56158925 original size:10 final size:10
Alignment explanation
Indices: 56158862--56159047 Score: 62
Period size: 10 Copynumber: 19.8 Consensus size: 10
56158852 TTTTATGATT
*
56158862 TTTTTTATAA
1 TTTTATATAA
* *
56158872 GTTTATACCAA
1 TTTTATA-TAA
*
56158883 TTTTA-ATAC
1 TTTTATATAA
56158892 TTTT-TATAA
1 TTTTATATAA
* *
56158901 TTTTTTATGA
1 TTTTATATAA
56158911 TTTTATATAA
1 TTTTATATAA
**
56158921 TTTTAATATGC
1 TTTT-ATATAA
56158932 TTTT-TA-AA
1 TTTTATATAA
* *
56158940 ATTTAAATATA
1 TTTTATATA-A
56158951 TTTTAT-TAA
1 TTTTATATAA
*
56158960 TTTTACAT--
1 TTTTATATAA
56158968 TTTT-TATAA
1 TTTTATATAA
* *
56158977 -TTTATTTGA
1 TTTTATATAA
* *
56158986 TTTTATTTGA
1 TTTTATATAA
56158996 TTTT-TAT-A
1 TTTTATATAA
56159004 -TTT-TATAA
1 TTTTATATAA
56159012 TTTT-TATAA
1 TTTTATATAA
* *
56159021 GTGTATATCAA
1 TTTTATAT-AA
*
56159032 TTTT-TAT-T
1 TTTTATATAA
56159040 TTTTATAT
1 TTTTATAT
56159048 TTTATTAATA
Statistics
Matches: 131, Mismatches: 28, Indels: 35
0.68 0.14 0.18
Matches are distributed among these distances:
7 8 0.06
8 16 0.12
9 39 0.30
10 45 0.34
11 23 0.18
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (10 bp):
TTTTATATAA
Found at i:56159060 original size:11 final size:9
Alignment explanation
Indices: 56159032--56159103 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
56159022 TGTATATCAA
56159032 TTTT-TATT
1 TTTTATATT
56159040 TTTTATATT
1 TTTTATATT
56159049 TTATTA-ATAT
1 TT-TTATAT-T
56159059 TTTTAT-TT
1 TTTTATATT
56159067 TTTTGATAATT
1 TTTT-AT-ATT
56159078 TTTTATGAATT
1 TTTTAT--ATT
* *
56159089 TTTAATCTT
1 TTTTATATT
56159098 TTTTAT
1 TTTTAT
56159104 TGGAAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
8 9 0.17
9 21 0.40
10 8 0.15
11 15 0.28
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:56159061 original size:20 final size:19
Alignment explanation
Indices: 56159036--56159103 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
56159026 TATCAATTTT
56159036 TATTTTTTATATTTTATTAA
1 TATTTTTTATATTTT-TTAA
*
56159056 TA-TTTTTAT-TTTTTTGA
1 TATTTTTTATATTTTTTAA
*
56159073 TAATTTTTTATGAATTTTTAA
1 T-ATTTTTTAT-ATTTTTTAA
*
56159094 TCTTTTTTAT
1 TATTTTTTAT
56159104 TGGAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 4 0.10
18 5 0.12
19 14 0.35
20 10 0.25
21 7 0.17
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (19 bp):
TATTTTTTATATTTTTTAA
Found at i:56160117 original size:52 final size:52
Alignment explanation
Indices: 56160052--56160151 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
56160042 TAGGTCTAGT
* * * *
56160052 AGAGGGACTAAAAGTGATATTTTATCAATATTGTATAAAATGCAAAGAAGAG
1 AGAGGGACGAAAAGAGATATTTGACCAATATTGTATAAAATGCAAAGAAGAG
56160104 AGAGGGACGAAAAGAGATATTTGACCAATATTGTATAAAATGCAAAGA
1 AGAGGGACGAAAAGAGATATTTGACCAATATTGTATAAAATGCAAAGA
56160152 GAAAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (52 bp):
AGAGGGACGAAAAGAGATATTTGACCAATATTGTATAAAATGCAAAGAAGAG
Found at i:56162418 original size:14 final size:16
Alignment explanation
Indices: 56162394--56162425 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56162384 TGTAATTGCA
56162394 TTTTAATAAAT-AATT
1 TTTTAATAAATAAATT
56162409 TTTTAA-AAATAAATT
1 TTTTAATAAATAAATT
56162424 TT
1 TT
56162426 CATTATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAATAAATAAATT
Found at i:56162818 original size:27 final size:27
Alignment explanation
Indices: 56162788--56162842 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
56162778 TATTTAACAC
56162788 AATATT-TAGAAAAAAAATTAAAGTTAA
1 AATATTGT-GAAAAAAAATTAAAGTTAA
* *
56162815 AATATTGTGAAAGAAAATTAAGGTTAA
1 AATATTGTGAAAAAAAATTAAAGTTAA
56162842 A
1 A
56162843 TTGGCGAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (27 bp):
AATATTGTGAAAAAAAATTAAAGTTAA
Found at i:56169662 original size:19 final size:18
Alignment explanation
Indices: 56169630--56169677 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
56169620 ATATTTATAG
56169630 TATTT-ATATATCAAAAAAT
1 TATTTGATATATC--AAAAT
56169649 TATTTGATAT-TCAAAAT
1 TATTTGATATATCAAAAT
*
56169666 TATTTGAGATAT
1 TATTTGATATAT
56169678 TATTACAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 7 0.27
20 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (18 bp):
TATTTGATATATCAAAAT
Found at i:56176783 original size:69 final size:69
Alignment explanation
Indices: 56176702--56176839 Score: 172
Period size: 69 Copynumber: 2.0 Consensus size: 69
56176692 AAAATAAAAA
* * * * * * *
56176702 TAAAAGTTTCACAAAATCTCAACACA-TCATAGGTATGTTGGATCGGAAGGTA-ACCTAAATGCA
1 TAAAAATTTCACAAAATCCCAACACACT-ATAGATACGTTGGATCGAAACGCAGA-CTAAATGCA
56176765 TCAATG
64 TCAATG
*
56176771 TAAAAATTTCACAAAATCCCAACACACTATAGATACGTTGGATTGAAACGCAGACTAAATGCATC
1 TAAAAATTTCACAAAATCCCAACACACTATAGATACGTTGGATCGAAACGCAGACTAAATGCATC
56176836 AATG
66 AATG
56176840 ACAAACTCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 57 0.97
70 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (69 bp):
TAAAAATTTCACAAAATCCCAACACACTATAGATACGTTGGATCGAAACGCAGACTAAATGCATC
AATG
Done.