Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_pilon, whole genome shotgun sequence
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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1494030 original size:20 final size:20
Alignment explanation
Indices: 1493969--1494175 Score: 203
Period size: 20 Copynumber: 10.5 Consensus size: 20
1493959 GATTTTCAAG
* ** *
1493969 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1493989 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1494009 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1494029 AACCGCAACGTGTATCCGGTA
1 AATCGCAACGCGTATCC-GTA
*
1494050 AAT-ACAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1494069 AATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
1494088 -ATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1494107 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
1494127 AATCGCAACGAG-ATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1494146 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1494166 AATCGCAACG
1 AATCGCAACG
1494176 AGAATCTGTA
Statistics
Matches: 157, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.11
19 24 0.15
20 109 0.69
21 7 0.04
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1494169 original size:59 final size:58
Alignment explanation
Indices: 1493988--1494186 Score: 172
Period size: 58 Copynumber: 3.4 Consensus size: 58
1493978 GCGAATATGA
* * * * **
1493988 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGAGTATCCGT--ATCGCAACGCATATCC-GT
* * * * * *
1494049 AAAT-ACAACGCGTATCCGTAAATCGCAATGCGTATCCGTATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGTATCGCAACGCATATCCGT
* *
1494106 AAATCGCAACGATAATCCGTAAATCGCAACGAG-ATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGT--ATCGCAACGCAT-ATCCGT
*
1494165 AAATCGCAACGAGAATCTGTAA
1 AAATCGCAACGAGAATCCGTAA
1494187 TCACAACTGA
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
57 11 0.09
58 37 0.32
59 35 0.30
60 29 0.25
61 5 0.04
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGTATCGCAACGCATATCCGT
Found at i:1494178 original size:39 final size:39
Alignment explanation
Indices: 1494007--1494175 Score: 204
Period size: 39 Copynumber: 4.3 Consensus size: 39
1493997 CGCGAACACA
* *
1494007 TAAATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGT-AATCC-G
*
1494048 TAAAT-ACAACGCGTATCCGTAAATCGCAATGCGT-ATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAA--CGTAATCCG
1494087 T--ATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TAATCCG
* *
1494125 TAAATCGCAACGAG-ATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TAATCCG
1494164 TAAATCGCAACG
1 TAAATCGCAACG
1494176 AGAATCTGTA
Statistics
Matches: 116, Mismatches: 5, Indels: 16
0.85 0.04 0.12
Matches are distributed among these distances:
36 2 0.02
37 3 0.03
38 29 0.25
39 38 0.33
40 36 0.31
41 5 0.04
42 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (39 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGTAATCCG
Found at i:1494922 original size:24 final size:24
Alignment explanation
Indices: 1494883--1494929 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1494873 AAATTTGGTC
1494883 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1494907 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1494930 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1496615 original size:19 final size:19
Alignment explanation
Indices: 1496546--1496805 Score: 285
Period size: 19 Copynumber: 14.7 Consensus size: 19
1496536 GCAACGAGAG
1496546 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1496565 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
1496579 AATCGCAATTCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1496599 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1496618 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1496637 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1496651 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1496671 AATCGCAATGC-AAATGAA
1 AATCGCAATGCGAAATGAA
*
1496689 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1496703 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1496722 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1496741 AATCGCAA--CG--A-G-A
1 AATCGCAATGCGAAATGAA
*
1496754 GATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1496774 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1496793 AATCGCATTGCGA
1 AATCGCAATGCGA
1496806 TTCTCTCGTT
Statistics
Matches: 206, Mismatches: 10, Indels: 50
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.04
14 33 0.16
15 4 0.02
16 6 0.03
17 6 0.03
18 17 0.08
19 93 0.45
20 39 0.19
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1496639 original size:72 final size:71
Alignment explanation
Indices: 1496546--1496748 Score: 270
Period size: 72 Copynumber: 2.9 Consensus size: 71
1496536 GCAACGAGAG
*
1496546 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATTCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC-
1496611 AAATGAA
65 AAATGAA
* *
1496618 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1496682 AAATGAA
65 AAATGAA
* * * * *
1496689 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA
1496749 CGAGAGATCG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
70 17 0.15
71 31 0.26
72 67 0.57
73 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCA
AATGAA
Found at i:1496686 original size:52 final size:52
Alignment explanation
Indices: 1496532--1496799 Score: 397
Period size: 52 Copynumber: 5.1 Consensus size: 52
1496522 CGGAAATTAC
*
1496532 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1496579 AATCGCAATTCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1496637 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGC-AAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1496689 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1496741 AATCGCAACGAGAG-ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1496793 AATCGCA
1 AATCGCA
1496800 TTGCGATTCT
Statistics
Matches: 204, Mismatches: 3, Indels: 23
0.89 0.01 0.10
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
51 29 0.14
52 101 0.50
53 48 0.24
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1496778 original size:33 final size:33
Alignment explanation
Indices: 1496513--1496781 Score: 212
Period size: 33 Copynumber: 7.8 Consensus size: 33
1496503 GCATTTGACT
** * *
1496513 ATCGCAACACGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGA-A
*
1496547 ATCGCAATGC-GAAATGAAAATCCCAAC-ATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAACGA-G-AA
*
1496580 ATCGCAATTCGGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-G-AA
1496619 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGA-A
*
1496652 ATCGCAATGCGGAAATGAAAATCGCAATGCAAATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--C-GA-G-AA
* * *
1496690 ATCGCAA--CGAGAGAATCG-CAATGCGAAATGA-AA
1 ATCGCAATGCG-GA-AAT-GAAAAT-CGCAACGAGAA
*
1496723 ATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAA
1496755 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
1496782 TGCGAAATGA
Statistics
Matches: 194, Mismatches: 17, Indels: 49
0.75 0.07 0.19
Matches are distributed among these distances:
31 7 0.04
32 19 0.10
33 64 0.33
34 41 0.21
35 1 0.01
36 7 0.04
37 3 0.02
38 31 0.16
39 21 0.11
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAA
Found at i:1496846 original size:21 final size:21
Alignment explanation
Indices: 1496814--1496862 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1496804 GATTCTCTCG
1496814 TTGCGA-TTTTCATTTCCGCA
1 TTGCGATTTTTCATTTCCGCA
1496834 TTGCGATTTTTCATTTCCGCA
1 TTGCGATTTTTCATTTCCGCA
1496855 TTGCGATT
1 TTGCGATT
1496863 CTCTCGTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TTGCGATTTTTCATTTCCGCA
Found at i:1497016 original size:13 final size:14
Alignment explanation
Indices: 1497000--1497035 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1496990 CATCAGTTAC
1497000 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
1497013 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1497027 ACAAATCAA
1 ACAAATCAA
1497036 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1497601 original size:15 final size:15
Alignment explanation
Indices: 1497581--1497610 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1497571 AACGAGTCCA
1497581 ATAATTGATCGCATC
1 ATAATTGATCGCATC
1497596 ATAATTGATCGCATC
1 ATAATTGATCGCATC
1497611 CAAGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAATTGATCGCATC
Found at i:1498911 original size:19 final size:19
Alignment explanation
Indices: 1498869--1498971 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
1498859 TAGTTTACTT
* *
1498869 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
1498889 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACCAAAA
*
1498908 TCGCAACGAG-AACCAAAA
1 TCGCAACGCGAAACCAAAA
1498926 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1498945 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
1498964 TCGCAACG
1 TCGCAACG
1498972 ACAGAATCGC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
18 14 0.20
19 45 0.63
20 12 0.17
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1498928 original size:37 final size:38
Alignment explanation
Indices: 1498885--1498971 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 38
1498875 CACGAAACTT
** *
1498885 AAAATCGCAACGCGAAATGAGAATCGCAACGAG-AACC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAGAAACC
* **
1498922 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAGAAACC
1498960 AAAATCGCAACG
1 AAAATCGCAACG
1498972 ACAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 29 0.67
38 14 0.33
ACGTcount: A:0.47, C:0.25, G:0.20, T:0.08
Consensus pattern (38 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAGAAACC
Found at i:1498998 original size:19 final size:19
Alignment explanation
Indices: 1498976--1499041 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 19
1498966 GCAACGACAG
* *
1498976 AATCGCAATGCAAAATGAA
1 AATCGCAACGCGAAATGAA
*
1498995 AATCGCAA--CGAGA-G-A
1 AATCGCAACGCGAAATGAA
* *
1499010 ATTTGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1499029 AATCGCAATGCGA
1 AATCGCAACGCGA
1499042 TTTTGGTTTC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
15 7 0.20
16 1 0.03
17 7 0.20
18 1 0.03
19 19 0.54
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1499031 original size:34 final size:33
Alignment explanation
Indices: 1498943--1499036 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
1498933 GCGAAACCAA
1498943 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* * *
1498976 AATCGCAATGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
1499009 AATTTGCAACGCGAAATGAAAATCGCAA
1 AA-TCGCAACGCGAAATGAAAATCGCAA
1499037 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 32 0.59
34 22 0.41
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1499082 original size:33 final size:33
Alignment explanation
Indices: 1499040--1499130 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
1499030 ATCGCAATGC
1499040 GATTTTGGTTTCGCGTTGCGATTTTGTCGTTGA
1 GATTTTGGTTTCGCGTTGCGATTTTGTCGTTGA
* *
1499073 GATTTTGGTTTCGCGTTGCGATTCTGTCGTTGC
1 GATTTTGGTTTCGCGTTGCGATTTTGTCGTTGA
**
1499106 GATTTTCATTTCGCGTTGCGATTTT
1 GATTTTGGTTTCGCGTTGCGATTTT
1499131 AAGTTTCGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.09, C:0.15, G:0.27, T:0.48
Consensus pattern (33 bp):
GATTTTGGTTTCGCGTTGCGATTTTGTCGTTGA
Found at i:1499095 original size:19 final size:18
Alignment explanation
Indices: 1499037--1499146 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
1499027 AAAATCGCAA
1499037 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1499056 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1499070 TGAGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1499089 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1499103 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1499122 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
1499142 TGCGA
1 TGCGA
1499147 AGTAACTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 31 0.43
20 12 0.17
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1499487 original size:91 final size:91
Alignment explanation
Indices: 1499244--1499550 Score: 532
Period size: 91 Copynumber: 3.4 Consensus size: 91
1499234 GGGTATTAGT
1499244 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA-A
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
1499308 CTATTTCACCGTGTTAAAGAATACACAG
66 CTATTTCACAGTGTT-AA-AATACACAG
1499336 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAA-ACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1499399 CTATTTCACAGTGTTAAAATACACAG
66 CTATTTCACAGTGTTAAAATACACAG
1499425 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
1499490 CTATTTCACAGTGTTAAAGA-ATACAG
66 CTATTTCACAGTGTTAAA-ATACACAG
*
1499516 TTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1499551 AAGCAATCTA
Statistics
Matches: 208, Mismatches: 3, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
89 51 0.25
90 21 0.10
91 93 0.45
92 43 0.21
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (91 bp):
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAATACACAG
Found at i:1501044 original size:222 final size:221
Alignment explanation
Indices: 1500658--1501101 Score: 863
Period size: 222 Copynumber: 2.0 Consensus size: 221
1500648 TTTCTTCAGG
1500658 TCGTCGACGTGTAGGTTCGGCTTCTCCATTGACTCATCCGGAAAAACCCAGGATAACCATGATGG
1 TCGTCGACGTGTAGGTTCGGCTTCTCCATTGACTCATCCGGAAAAACCCAGGATAACCATGATGG
1500723 GCGGGCGATATGACGAGTGTACCGGCCTACATCATCGTGTCCGAATCGTAGACCAGTGAATTAAG
66 GCGGGCGATATGACGAGTGTACCGGCCTACATCATCGTGTCCGAATCGTAGACCAGTGAATTAAG
1500788 CAGAACTCCTTCCGCCCAAAACAAGTATACGCTGGTGGAAAATGAAACCATATCTCTTCCTCACC
131 CAGAACTCCTTCCGCCCAAAACAAGTATACGCTGGTGGAAAATGAAACCATATCTCTTCCTCA-C
1500853 CATGTTGTATACTGTCGGTAGATTTGA
195 CATGTTGTATACTGTCGGTAGATTTGA
1500880 TCGTCGACGTGTAGGTTCGGCTTCTCCATTGACTCATCCGGAAAAAACCCAGGATAACCATGATG
1 TCGTCGACGTGTAGGTTCGGCTTCTCCATTGACTCATCCGG-AAAAACCCAGGATAACCATGATG
1500945 GGCGGGCGATATGACGAGTGTACCGGCCTACATCATCGTGTCCGAATCGTAGACCAGTG-ATTAA
65 GGCGGGCGATATGACGAGTGTACCGGCCTACATCATCGTGTCCGAATCGTAGACCAGTGAATTAA
1501009 GCAGAACTCCTTCCGCCCAAAACAAGTATACGCTGGTGGAAAATGAAACCATATCTCTTCCTCAC
130 GCAGAACTCCTTCCGCCCAAAACAAGTATACGCTGGTGGAAAATGAAACCATATCTCTTCCTCAC
1501074 CATGTTGTATACTGTCGGTAGATTTGA
195 CATGTTGTATACTGTCGGTAGATTTGA
1501101 T
1 T
1501102 GTCATGGTCT
Statistics
Matches: 221, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
221 29 0.13
222 110 0.50
223 82 0.37
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (221 bp):
TCGTCGACGTGTAGGTTCGGCTTCTCCATTGACTCATCCGGAAAAACCCAGGATAACCATGATGG
GCGGGCGATATGACGAGTGTACCGGCCTACATCATCGTGTCCGAATCGTAGACCAGTGAATTAAG
CAGAACTCCTTCCGCCCAAAACAAGTATACGCTGGTGGAAAATGAAACCATATCTCTTCCTCACC
ATGTTGTATACTGTCGGTAGATTTGA
Found at i:1501439 original size:21 final size:21
Alignment explanation
Indices: 1501413--1501492 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
1501403 TCTTTTGGTT
1501413 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1501434 GAAATGAAAATCGCAAC--GA
1 GAAATGAAAATCGCAACGAGA
1501453 G--A-G--AATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
* *
1501469 AAAATGAAAATCGCAATGAGA
1 GAAATGAAAATCGCAACGAGA
1501490 GAA
1 GAA
1501493 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.18
16 3 0.06
17 1 0.02
18 1 0.02
19 4 0.08
21 31 0.63
ACGTcount: A:0.53, C:0.14, G:0.24, T:0.10
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1501460 original size:35 final size:35
Alignment explanation
Indices: 1501421--1501517 Score: 153
Period size: 35 Copynumber: 2.8 Consensus size: 35
1501411 TTGAAATGAA
1501421 AATCGCAACGAGAGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAGAAATGAAAATCGCAACGAGAG
* *
1501456 AATCGCAACGAGAAAAATGAAAATCGCAATGAGAG
1 AATCGCAACGAGAGAAATGAAAATCGCAACGAGAG
*
1501491 AATCGCAAC--GCGAAATGAAAATCGCAA
1 AATCGCAACGAGAGAAATGAAAATCGCAA
1501518 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.28
35 42 0.72
ACGTcount: A:0.49, C:0.18, G:0.23, T:0.10
Consensus pattern (35 bp):
AATCGCAACGAGAGAAATGAAAATCGCAACGAGAG
Found at i:1501461 original size:14 final size:14
Alignment explanation
Indices: 1501442--1501468 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1501432 GAGAAATGAA
1501442 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1501456 AATCGCAACGAGA
1 AATCGCAACGAGA
1501469 AAAATGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1501553 original size:14 final size:14
Alignment explanation
Indices: 1501534--1501590 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1501524 TTTGGTTTCG
1501534 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1501548 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1501567 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1501581 CGTTGCGATT
1 CGTTGCGATT
1501591 TTCATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1501566 original size:33 final size:33
Alignment explanation
Indices: 1501518--1501597 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1501508 AAAATCGCAA
**
1501518 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1501551 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1501584 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1501598 TTTCTCGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1501648 original size:21 final size:20
Alignment explanation
Indices: 1501545--1501652 Score: 95
Period size: 21 Copynumber: 5.5 Consensus size: 20
1501535 GTTGCGATTC
1501545 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
1501564 TCGCGTTGCGA--TTC----
1 TCTCGTTGCGATTTTCATTT
1501578 TCTCGTTGCGATTTTCATTTTT
1 TCTCGTTGCGATTTTCA--TTT
**
1501600 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
1501621 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
1501641 ATCTCGTTGCGA
1 -TCTCGTTGCGA
1501653 CTCTTCTGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 10 0.14
20 9 0.13
21 21 0.30
22 9 0.13
23 6 0.08
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:1501774 original size:33 final size:33
Alignment explanation
Indices: 1501732--1501802 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1501722 AATACTAACT
1501732 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1501765 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1501798 TGAAA
1 TGAAA
1501803 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1502204 original size:20 final size:20
Alignment explanation
Indices: 1502179--1502371 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
1502169 CTTTAAAAAT
1502179 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1502199 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1502219 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1502240 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1502260 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1502280 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1502300 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1502320 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1502340 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1502360 CGCGTTGCGATT
1 CGCGTTGCGATT
1502372 CTGGAACATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1508447 original size:84 final size:84
Alignment explanation
Indices: 1508326--1508549 Score: 244
Period size: 84 Copynumber: 2.7 Consensus size: 84
1508316 TGTAATGACG
* * * * * **
1508326 TTTTTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGAGTTTTTATACAAACT-CTGCAATAG
1 TTTTTCTACAAACGCCGCAACAGATTAGTACTTTAGCGGCGTTTTTATACAAAATGCCACAATAG
1508390 -GTCCAT-CTATAGTGGCATT
66 AGTCC-TCCTATAGTGGC-TT
* *
1508409 TTTTTCTGACAAACGCCGCAAAAGATTTGTACTTTAGCGGCGTTTTTATA-AAAATGCCACAATA
1 TTTTTCT-ACAAACGCCGCAACAGATTAGTACTTTAGCGGCGTTTTTATACAAAATGCCACAATA
*
1508473 GAGTTCTCCTATAGTGGCTT
65 GAGTCCTCCTATAGTGGCTT
* * * *
1508493 TTTTTCTA-ATAACGCTGCAACATATTAGAACTTTAGCGGCGTTTTTACAC-AAATGCC
1 TTTTTCTACA-AACGCCGCAACAGATTAGTACTTTAGCGGCGTTTTTATACAAAATGCC
1508550 GCAAAAATAT
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
82 1 0.01
83 51 0.43
84 54 0.45
85 13 0.11
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (84 bp):
TTTTTCTACAAACGCCGCAACAGATTAGTACTTTAGCGGCGTTTTTATACAAAATGCCACAATAG
AGTCCTCCTATAGTGGCTT
Found at i:1513167 original size:21 final size:21
Alignment explanation
Indices: 1513143--1513201 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1513133 TGATTTATTA
**
1513143 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
1513164 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
1513185 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
1513202 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:1513454 original size:43 final size:43
Alignment explanation
Indices: 1513411--1513638 Score: 350
Period size: 43 Copynumber: 5.3 Consensus size: 43
1513401 TGTTTATGGA
* *
1513411 AAAAACGCCGCTAAATCTCAAGACCTATTGCGACGTTTG-TGG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
* *
1513453 AAAAAATGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGG
1 -AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
1513497 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
* * *
1513540 AAAAACGCCACTAAATATCAACACCTATTGCGGTGTTTGTTGG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
* *
1513583 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
*
1513626 ACAAACGCCGCTA
1 AAAAACGCCGCTA
1513639 TATATCGTTA
Statistics
Matches: 172, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
43 170 0.99
44 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG
Found at i:1514159 original size:20 final size:20
Alignment explanation
Indices: 1514134--1514189 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1514124 TTATGCACAC
*
1514134 AAAGTTTCGAAACTCTGGGG
1 AAAGTTTTGAAACTCTGGGG
*
1514154 AAAGTTTTTAAACTCTGGGG
1 AAAGTTTTGAAACTCTGGGG
1514174 AAAGTTTTGAAACTCT
1 AAAGTTTTGAAACTCT
1514190 TCGAAAGAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (20 bp):
AAAGTTTTGAAACTCTGGGG
Found at i:1533180 original size:18 final size:18
Alignment explanation
Indices: 1533157--1533191 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1533147 GTTCTTAAGG
*
1533157 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
1533175 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
1533192 AATATACAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:1533609 original size:21 final size:21
Alignment explanation
Indices: 1533585--1533625 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1533575 TAATTAAAGG
1533585 AAAAGG-TATATAGATAAGTGT
1 AAAAGGATAT-TAGATAAGTGT
*
1533606 AAAAGGATATTTGATAAGTG
1 AAAAGGATATTAGATAAGTG
1533626 GTGCATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTGT
Found at i:1547684 original size:15 final size:15
Alignment explanation
Indices: 1547664--1547696 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1547654 AGAATGTTTT
1547664 GAAGGGG-AAAAGAGA
1 GAAGGGGTAAAAGA-A
1547679 GAAGGGGTAAAAGAA
1 GAAGGGGTAAAAGAA
1547694 GAA
1 GAA
1547697 ACTGAGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
GAAGGGGTAAAAGAA
Found at i:1555585 original size:25 final size:25
Alignment explanation
Indices: 1555531--1555611 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
1555521 ATATATATAT
*
1555531 TTATATATTTTTTTATTTATTTATTA
1 TTATAT-TTTTTTTATTTATCTATTA
1555557 TTATATTTTTTTTATTT-TCT-TTA
1 TTATATTTTTTTTATTTATCTATTA
* *
1555580 CGTTATATTATATTT-TTT-TCTATTA
1 --TTATATTTTTTTTATTTATCTATTA
1555605 TATATAT
1 T-TATAT
1555612 ATATATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
23 4 0.08
24 13 0.27
25 25 0.52
26 6 0.12
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (25 bp):
TTATATTTTTTTTATTTATCTATTA
Found at i:1555608 original size:2 final size:2
Alignment explanation
Indices: 1555603--1555635 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1555593 TTTTTTCTAT
1555603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1555636 TTTTTTTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1555699 original size:2 final size:2
Alignment explanation
Indices: 1555692--1555716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1555682 TTCCTAACGT
1555692 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1555717 TTTTACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1555849 original size:8 final size:8
Alignment explanation
Indices: 1555836--1555879 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
1555826 ATATACATAC
1555836 ATTTTTAT
1 ATTTTTAT
1555844 ATTTTTATAT
1 A-TTTT-TAT
1555854 ATTTTTAT
1 ATTTTTAT
1555862 ATTTTTAT
1 ATTTTTAT
*
1555870 TTTATTTAT
1 ATT-TTTAT
1555879 A
1 A
1555880 CTATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.45
9 13 0.42
10 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1555999 original size:18 final size:19
Alignment explanation
Indices: 1555978--1556024 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1555968 TTTTTATATA
*
1555978 TATTTTTTTTTCTTC-ATT
1 TATTTTTTTTTATTCAATT
*
1555996 TATTTTATTTTATTCAATT
1 TATTTTTTTTTATTCAATT
1556015 TCATTTTTTT
1 T-ATTTTTTT
1556025 ATTTGTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.54
19 4 0.17
20 7 0.29
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTTTTATTCAATT
Found at i:1556004 original size:23 final size:23
Alignment explanation
Indices: 1555956--1556006 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1555946 AATACTTTAC
*
1555956 ATTTTTTATTCTTTTTTATATAT
1 ATTTTTTATTCTTATTTATATAT
* *
1555979 ATTTTTTTTTCTTCATTTAT-TTT
1 ATTTTTTATTCTT-ATTTATATAT
1556002 ATTTT
1 ATTTT
1556007 ATTCAATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTTATTCTTATTTATATAT
Found at i:1556027 original size:18 final size:17
Alignment explanation
Indices: 1555960--1556024 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
1555950 CTTTACATTT
1555960 TTTATTCTTTTTTA-T-A
1 TTTATT-TTTTTTATTCA
* *
1555976 TATATTTTTTTTTCTTCA
1 TTTA-TTTTTTTTATTCA
1555994 TTTATTTTATTTTATTCAA
1 TTTATTTT-TTTTATTC-A
1556013 TTTCATTTTTTT
1 TTT-ATTTTTTT
1556025 ATTTGTTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 9 0.23
17 7 0.18
18 11 0.28
19 7 0.18
20 5 0.13
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTTTTATTCA
Found at i:1557132 original size:16 final size:16
Alignment explanation
Indices: 1557111--1557154 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
1557101 GAATAATAAG
1557111 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
1557127 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
1557143 CATGTGGGGTAG
1 CATGTGGGGTAG
1557155 GACTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.41, T:0.30
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:1557227 original size:18 final size:18
Alignment explanation
Indices: 1557202--1557237 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1557192 ACCTTACTAA
1557202 CTCTTTTTATTTT-TTTC
1 CTCTTTTTATTTTATTTC
1557219 CTCTCTTTTATTTTATTTC
1 CTCT-TTTTATTTTATTTC
1557238 TATCATCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.72
Consensus pattern (18 bp):
CTCTTTTTATTTTATTTC
Found at i:1560671 original size:16 final size:16
Alignment explanation
Indices: 1560652--1560712 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
1560642 AAAAGGGCAA
1560652 AAACAAAAAAGAAAAG
1 AAACAAAAAAGAAAAG
1560668 AAACAAAAAAG--AAG
1 AAACAAAAAAGAAAAG
1560682 -AACAAAAAAAGAACAA-
1 AAAC-AAAAAAGAA-AAG
1560698 AAATC-AAAAAGAAAA
1 AAA-CAAAAAAGAAAA
1560713 AGGGGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.08
14 10 0.26
15 2 0.05
16 19 0.49
17 4 0.10
18 1 0.03
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAAAAGAAAAG
Found at i:1560675 original size:14 final size:12
Alignment explanation
Indices: 1560658--1560700 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
1560648 GCAAAAACAA
1560658 AAAAGAAAAGAAAC
1 AAAA-AAAAG-AAC
1560672 AAAAAAGAAGAAC
1 AAAAAA-AAGAAC
1560685 -AAAAAAAGAAC
1 AAAAAAAAGAAC
1560696 AAAAA
1 AAAAA
1560701 TCAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
13 5 0.19
14 7 0.26
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:1560679 original size:11 final size:12
Alignment explanation
Indices: 1560663--1560700 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
1560653 AACAAAAAAG
1560663 AAAAGA-AACAA
1 AAAAGAGAACAA
1560674 AAAAGAAGAACAA
1 AAAAG-AGAACAA
1560687 AAAA-AGAACAA
1 AAAAGAGAACAA
1560698 AAA
1 AAA
1560701 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.60
12 1 0.04
13 9 0.36
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAGAGAACAA
Found at i:1562428 original size:106 final size:106
Alignment explanation
Indices: 1562299--1563571 Score: 2018
Period size: 106 Copynumber: 12.0 Consensus size: 106
1562289 ATATCGTGCC
* * *
1562299 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
1562363 CAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1562405 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1562470 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1562511 ACTCCAGACAACGCAAGTTCAACTTCACCACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1562576 AATTTCAGAGCCAATTTCAACTTCACAGCGAA-GATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1562616 ACTCAAGACAACGCAAGTTCAACTTCATGACGAA-GGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1562680 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1562721 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1562786 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1562827 ACCCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1562892 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
1562933 ACTCGAGACAACGCAAGTTCAACTTCACGATAAAGGGACCGCTGGTTGTTAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
1562998 AATTTTGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1563039 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1563104 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1563145 ACTCCCGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1563210 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1563251 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1563316 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1563357 ACTCGAGAC-ACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1563421 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * ** *
1563462 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCTCCAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1563527 GA-TTCTAGAGCCAATTTTAACTTCAC-GACGGAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1563568 ACTC
1 ACTC
1563572 GGAATAATGC
Statistics
Matches: 1087, Mismatches: 74, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
104 61 0.06
105 182 0.17
106 842 0.77
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1565144 original size:13 final size:13
Alignment explanation
Indices: 1565126--1565166 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1565116 ATTTTTATAT
1565126 TTTTATATATTTA
1 TTTTATATATTTA
1565139 TTTTAT-TATTT-
1 TTTTATATATTTA
1565150 TATTTATACTATTTA
1 T-TTTATA-TATTTA
1565165 TT
1 TT
1565167 ATTTCATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
13 6 0.25
14 6 0.25
15 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATATATTTA
Found at i:1565151 original size:21 final size:22
Alignment explanation
Indices: 1565095--1565170 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
1565085 TACTATTTAG
* *
1565095 TATTTTATTA-TATATACATAC
1 TATTTTATTATTTTATATATAC
*
1565116 -ATTTT-TATATTTT-TATATATT
1 TATTTTAT-TATTTTATATATA-C
*
1565137 TATTTTATTATTTTATTTATAC
1 TATTTTATTATTTTATATATAC
1565159 TA-TTTATTATTT
1 TATTTTATTATTT
1565171 CATTATGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 12 0.27
21 12 0.27
22 13 0.30
23 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTTATTATTTTATATATAC
Found at i:1567662 original size:208 final size:211
Alignment explanation
Indices: 1567304--1567722 Score: 799
Period size: 208 Copynumber: 2.0 Consensus size: 211
1567294 GAAAATGCAT
1567304 TTTTCTTGGTGTTAGTGATAAGTCAAAAGCTTATAAACTATACAATCCTAGCACCATGAAAATTG
1 TTTTCTTGGTGTTAGTGATAAGTCAAAAGCTTATAAACTATACAATCCTAGCACCATGAAAATTG
1567369 TCATTAGCCGTGATGTGGTATTTGATGAAGAAGTCACTTGGTCATAGAATCAAAATGGTGTTAAA
66 TCATTAGCCGTGATGTGGTATTTGATGAAGAAGTCACTTGGTCATAGAATCAAAATGGTGTTAAA
*
1567434 GAAAGTATTCCAACAACTTTTGATGATGAAGAGAAAGGGAAACAACCTATGGAGGATGAAC-AG-
131 GAAAGTATTCCAACAACTTTTGATGATGAAGAGAAAGGGAAACAACCTATGAAGGATGAACAAGA
1567497 AGAGT-AGTCACTCAA
196 AGAGTAAGTCACTCAA
1567512 TTTTCTTGGTGTTAGTGATAAGTCAAAAGCTTATAAACTATACAATCCTAGCACCATGAAAATTG
1 TTTTCTTGGTGTTAGTGATAAGTCAAAAGCTTATAAACTATACAATCCTAGCACCATGAAAATTG
*
1567577 TCATTAGCCGTGATGTGGTATTTGATGAAGAAGTCACTTGGTCATGGAATCAAAATGGTGTTAAA
66 TCATTAGCCGTGATGTGGTATTTGATGAAGAAGTCACTTGGTCATAGAATCAAAATGGTGTTAAA
1567642 GAAAGTATTCCAACAACTTTTGATGATGAAGAGAAAGGGAAACAACCTATGAAGGATGAACAAGA
131 GAAAGTATTCCAACAACTTTTGATGATGAAGAGAAAGGGAAACAACCTATGAAGGATGAACAAGA
1567707 AGAGTAAGTCACTCAA
196 AGAGTAAGTCACTCAA
1567723 AATGTTCCAA
Statistics
Matches: 206, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
208 189 0.92
209 2 0.01
210 5 0.02
211 10 0.05
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (211 bp):
TTTTCTTGGTGTTAGTGATAAGTCAAAAGCTTATAAACTATACAATCCTAGCACCATGAAAATTG
TCATTAGCCGTGATGTGGTATTTGATGAAGAAGTCACTTGGTCATAGAATCAAAATGGTGTTAAA
GAAAGTATTCCAACAACTTTTGATGATGAAGAGAAAGGGAAACAACCTATGAAGGATGAACAAGA
AGAGTAAGTCACTCAA
Found at i:1571282 original size:17 final size:17
Alignment explanation
Indices: 1571260--1571297 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1571250 GACAAATTAC
1571260 TTGTTATGATTTTAAAA
1 TTGTTATGATTTTAAAA
1571277 TTGTTATGATTTTAAAA
1 TTGTTATGATTTTAAAA
1571294 TTGT
1 TTGT
1571298 CATAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (17 bp):
TTGTTATGATTTTAAAA
Found at i:1571391 original size:14 final size:15
Alignment explanation
Indices: 1571372--1571409 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1571362 CTTATTAATT
1571372 AATTAATTTTAT-AA
1 AATTAATTTTATAAA
1571386 AATTAATTTTTATAAA
1 AATTAA-TTTTATAAA
1571402 AATTAATT
1 AATTAATT
1571410 AAGTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTTTATAAA
Found at i:1571405 original size:16 final size:15
Alignment explanation
Indices: 1571372--1571409 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1571362 CTTATTAATT
1571372 AATTAA-TTTTATAA
1 AATTAATTTTTATAA
1571386 AATTAATTTTTATAAA
1 AATTAATTTTTAT-AA
1571402 AATTAATT
1 AATTAATT
1571410 AAGTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 6 0.27
16 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTTTTATAA
Found at i:1571812 original size:2 final size:2
Alignment explanation
Indices: 1571805--1571829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1571795 TCCCTTTTTA
1571805 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1571830 AATTTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1577278 original size:21 final size:21
Alignment explanation
Indices: 1577252--1577296 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1577242 CCGTAAATAT
** *
1577252 TAAAAACATTAATGTTTTAAA
1 TAAAAACAAAAATATTTTAAA
*
1577273 TAAAAATAAAAATATTTTAAA
1 TAAAAACAAAAATATTTTAAA
1577294 TAA
1 TAA
1577297 TTTTTTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAACAAAAATATTTTAAA
Found at i:1577902 original size:22 final size:22
Alignment explanation
Indices: 1577863--1577904 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1577853 TTGATATAAT
1577863 ATTTTTTAATAATGAAAATTGA
1 ATTTTTTAATAATGAAAATTGA
1577885 ATTTTATTAATAAT-AAAATT
1 ATTTT-TTAATAATGAAAATT
1577905 AATCAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTTTTAATAATGAAAATTGA
Found at i:1583254 original size:28 final size:28
Alignment explanation
Indices: 1583214--1583274 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
1583204 GAGTTGTAGG
*
1583214 AGTTGTATTTAAGTTTATTCTAACCTCT
1 AGTTGTATTTAAGCTTATTCTAACCTCT
1583242 AGTTGTATTTAAGCTTATTCTAACCTCT
1 AGTTGTATTTAAGCTTATTCTAACCTCT
1583270 AGTTG
1 AGTTG
1583275 AGTAGTAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (28 bp):
AGTTGTATTTAAGCTTATTCTAACCTCT
Found at i:1586032 original size:31 final size:31
Alignment explanation
Indices: 1585997--1586058 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
1585987 ATTAATTATT
1585997 TTATACATC-AAAAGTCATAATGTGATATATA
1 TTATA-ATCTAAAAGTCATAATGTGATATATA
* * * *
1586028 TTATATTCTAAAAGTGATGATGTGATGTATA
1 TTATAATCTAAAAGTCATAATGTGATATATA
1586059 CAACACGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (31 bp):
TTATAATCTAAAAGTCATAATGTGATATATA
Found at i:1589022 original size:119 final size:119
Alignment explanation
Indices: 1588811--1589051 Score: 464
Period size: 119 Copynumber: 2.0 Consensus size: 119
1588801 TTGCTGTCCC
1588811 GTACATTCAGGAAGCTTGTTCCGATGCTAGGTGTTTTGCATTACAAGGATATAAAACAGAATGTC
1 GTACATTCAGGAAGCTTGTTCCGATGCTAGGTGTTTTGCATTACAAGGATATAAAACAGAATGTC
1588876 AAAGAATTTTGAATGAATCAAAACATTAACCATTGGAATAGAGGAGATGAAGAT
66 AAAGAATTTTGAATGAATCAAAACATTAACCATTGGAATAGAGGAGATGAAGAT
*
1588930 GTACATTCAGGAAGCTTGTTCCGATGCTAGGTGTTTTGCATTACAAGGATATAAAATAGAATGTC
1 GTACATTCAGGAAGCTTGTTCCGATGCTAGGTGTTTTGCATTACAAGGATATAAAACAGAATGTC
*
1588995 AGAGAATTTTGAATGAATCAAAACATTAACCATTGGAATAGAGGAGATGAAGAT
66 AAAGAATTTTGAATGAATCAAAACATTAACCATTGGAATAGAGGAGATGAAGAT
1589049 GTA
1 GTA
1589052 ATAAACTAAT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (119 bp):
GTACATTCAGGAAGCTTGTTCCGATGCTAGGTGTTTTGCATTACAAGGATATAAAACAGAATGTC
AAAGAATTTTGAATGAATCAAAACATTAACCATTGGAATAGAGGAGATGAAGAT
Found at i:1589761 original size:12 final size:12
Alignment explanation
Indices: 1589744--1589769 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1589734 GTTTGAAACT
1589744 ATCATTTCCACC
1 ATCATTTCCACC
1589756 ATCATTTCCACC
1 ATCATTTCCACC
1589768 AT
1 AT
1589770 GACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCATTTCCACC
Found at i:1590304 original size:17 final size:18
Alignment explanation
Indices: 1590274--1590310 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1590264 GTCTACAAAA
1590274 ATATTATTTATATT-ATT
1 ATATTATTTATATTAATT
1590291 ATATTA-TTATTATTAATT
1 ATATTATTTA-TATTAATT
1590309 AT
1 AT
1590311 TTTGTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 10 0.56
18 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATTTATATTAATT
Found at i:1596712 original size:37 final size:36
Alignment explanation
Indices: 1596651--1596737 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
1596641 AGAGACATTA
* *
1596651 TTTTCTTAAAAATAAATTTTGTCTCACTTAAGACAT
1 TTTTCTTCAAAACAAATTTTGTCTCACTTAAGACAT
* *
1596687 TTTTCTCTCAAAACAAATTTTGTCTCACTTGAGGCAT
1 TTTTCT-TCAAAACAAATTTTGTCTCACTTAAGACAT
*
1596724 TTTCCTTCAAAACA
1 TTTTCTTCAAAACA
1596738 CAAATTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
36 14 0.31
37 31 0.69
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (36 bp):
TTTTCTTCAAAACAAATTTTGTCTCACTTAAGACAT
Found at i:1596829 original size:102 final size:102
Alignment explanation
Indices: 1596651--1597032 Score: 493
Period size: 102 Copynumber: 3.8 Consensus size: 102
1596641 AGAGACATTA
* *
1596651 TTTTCTTAAAAATAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTTGTCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTCGTCTCACT
* **
1596716 TGAGGCATTTTCCTTCAAAACACAAATTTCAAAGTTC
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTC
* * * * *
1596753 TGTTCTTAAAAACAAATTTCGTCTCGCTTAAGACGTTTTTCTCTCAAAACAAATTTCATCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTCGTCTCACT
* *
1596818 TGAGACATTTTCTTTCGGAACACAAATTTCAAAGTTGT
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTT-C
*
1596856 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTC--AACAAATTTCGTCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTCGTCTCACT
* * *
1596919 TGAGATATTTTCCTTTGGAACACAAATTTCAAAGTTG
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTC
* * * * * * ** *
1596956 TTTTACTT-GAACCAAATTTTGTCTCGCTTGAGACA-ATTTATCTCAAAACAAACATCGTCTCGC
1 TTTT-CTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTCGTCTCAC
1597019 TTGAGACATTTTCC
65 TTGAGACATTTTCC
1597033 CAAAATTTTG
Statistics
Matches: 245, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
99 7 0.03
100 28 0.11
101 80 0.33
102 90 0.37
103 40 0.16
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (102 bp):
TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTCGTCTCACT
TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTC
Found at i:1596940 original size:101 final size:102
Alignment explanation
Indices: 1596651--1597032 Score: 477
Period size: 101 Copynumber: 3.8 Consensus size: 102
1596641 AGAGACATTA
* *
1596651 TTTTCTTAAAAATAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAAACAAATTTTGTCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTC-AAACAAATTTCGTCTCACT
* *** *
1596716 TGAGGCATTTTCCTTCAAAACACAAATTTCAAAGTT-C
65 TGAGACATTTTCCTTTGGAACACAAATTTCAAAGTTGT
* * * * *
1596753 TGTTCTTAAAAACAAATTTCGTCTCGCTTAAGACGTTTTTCTCTCAAAACAAATTTCATCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTC-AAACAAATTTCGTCTCACT
1596818 TGAGACATTTT-CTTTCGGAACACAAATTTCAAAGTTGT
65 TGAGACATTTTCCTTT-GGAACACAAATTTCAAAGTTGT
*
1596856 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTC-AACAAATTTCGTCTCACTT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAACAAATTTCGTCTCACTT
*
1596920 GAGATATTTTCCTTTGGAACACAAATTTCAAAGTTGT
66 GAGACATTTTCCTTTGGAACACAAATTTCAAAGTTGT
* * * * * * * ** *
1596957 TTTACTT-GAACCAAATTTTGTCTCGCTTGAGACAATTTATCTC-AAAACAAACATCGTCTCGCT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTAAGAC-ATTTTTCTCTCAAACAAATTTCGTCTCACT
1597020 TGAGACATTTTCC
65 TGAGACATTTTCC
1597033 CAAAATTTTG
Statistics
Matches: 246, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
100 23 0.09
101 93 0.38
102 90 0.37
103 40 0.16
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (102 bp):
TTTTCTTAAAAACAAATTTTGTCTCACTTAAGACATTTTTCTCTCAAACAAATTTCGTCTCACTT
GAGACATTTTCCTTTGGAACACAAATTTCAAAGTTGT
Found at i:1597267 original size:66 final size:67
Alignment explanation
Indices: 1597161--1597337 Score: 216
Period size: 71 Copynumber: 2.6 Consensus size: 67
1597151 ATTTTTACTC
* *
1597161 AAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACGAA-AATCT-TT-AAATATGTTTCC
1 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAACGAATAATCTATTGAAAT-TGTTTCC
1597223 TTTG
65 -TTG
** *
1597227 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAACGAATTTTGTCTCTATTGAGATTGTT
1 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAACGAA---T-AATCTATTGAAATTGTT
1597292 TCCTTG
62 TCCTTG
* *
1597298 AAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTTAAAC
1 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAAC
1597338 AATTTTTGTT
Statistics
Matches: 97, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
66 41 0.42
71 44 0.45
72 9 0.09
73 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (67 bp):
AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAACGAATAATCTATTGAAATTGTTTCCT
TG
Found at i:1597365 original size:15 final size:15
Alignment explanation
Indices: 1597345--1597388 Score: 72
Period size: 14 Copynumber: 3.0 Consensus size: 15
1597335 AACAATTTTT
*
1597345 GTTTCTCTTGAGACA
1 GTTTCTCTTGAAACA
1597360 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1597375 -TTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1597389 TAAACTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (15 bp):
GTTTCTCTTGAAACA
Found at i:1597374 original size:36 final size:35
Alignment explanation
Indices: 1597217--1597620 Score: 317
Period size: 36 Copynumber: 11.3 Consensus size: 35
1597207 CTTTAAATAT
* *
1597217 GTTTCCTTTGAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACA
* * **
1597253 GTTTCCCTTTAAACGAATTTTGTCTCTATTGAGATT
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACA
1597289 GTTT-CCTTGAAACGAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACA
* *
1597324 GTTTCCCTTTAAACAATTTTTGTTTCTCTTGAGACA
1 GTTTCCCTTGAAACAA-TTTTGTCTCTCTTGAGACA
* * *
1597360 GTTTCTCTTGAAACATTTCTCTTGAAACATAAACT-TTGAGA-A
1 GTTTCCCTTGAAACA-AT-T-TTG--TC-T---CTCTTGAGACA
*
1597402 CGTTTCCCTTGAAACGAATATTGTCTCTCTTGAGACA
1 -GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACA
*
1597439 GTTTCCCTTGAAACGTATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACA
* *
1597475 GTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAA-CAATTTTGTCTCTCTTGAGACA
* ***
1597511 GTTTCTCTTGAAAC-A---T-AAACT-TTGAGA-A
1 GTTTCCCTTGAAACAATTTTGTCTCTCTTGAGACA
* *
1597539 CGTTTCCCTTGAAATAAATTTTGTCTCTGTTGAGACA
1 -GTTTCCCTTGAAA-CAATTTTGTCTCTCTTGAGACA
* * * * *
1597576 ATTTCCCTTAAAATAA-ATTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAATTTTGTCTCTCTTGAGACA
*
1597610 TTTTCCCTTGA
1 GTTTCCCTTGA
1597621 GATAGAAGAT
Statistics
Matches: 299, Mismatches: 44, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
28 1 0.00
29 18 0.06
30 1 0.00
31 2 0.01
34 26 0.09
35 39 0.13
36 176 0.59
37 3 0.01
38 4 0.01
39 1 0.00
41 4 0.01
42 1 0.00
43 20 0.07
44 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (35 bp):
GTTTCCCTTGAAACAATTTTGTCTCTCTTGAGACA
Found at i:1597518 original size:151 final size:150
Alignment explanation
Indices: 1597245--1597526 Score: 440
Period size: 151 Copynumber: 1.9 Consensus size: 150
1597235 TTTGTCTCTC
* * **
1597245 TTGAGATAGTTTCCCTTTAAACGAATTTTGTCTCTATTGAGATTGTTTCCTTGAAACGAATTTTG
1 TTGAGATAGTTTCCCTTGAAACGAATATTGTCTCTATTGAGACAGTTTCCTTGAAACGAATTTTG
* * * *
1597310 TCTCTCTTGAGACAGTTTCCCTTTAAACAATTTTTGTTTCTCTTGAGACAGTTTCTCTTGAAACA
66 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1597375 TTTCTCTTGAAACATAAACT
131 TTTCTCTTGAAACATAAACT
* *
1597395 TTGAGA-ACGTTTCCCTTGAAACGAATATTGTCTCTCTTGAGACAGTTTCCCTTGAAACGTATTT
1 TTGAGATA-GTTTCCCTTGAAACGAATATTGTCTCTATTGAGACAGTTT-CCTTGAAACGAATTT
*
1597459 TGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
64 TGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1597524 CAT
129 CAT
1597527 AAACTTTGAG
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
149 1 0.01
150 41 0.34
151 77 0.65
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (150 bp):
TTGAGATAGTTTCCCTTGAAACGAATATTGTCTCTATTGAGACAGTTTCCTTGAAACGAATTTTG
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
TTTCTCTTGAAACATAAACT
Found at i:1597539 original size:137 final size:134
Alignment explanation
Indices: 1597366--1597620 Score: 384
Period size: 137 Copynumber: 1.9 Consensus size: 134
1597356 GACAGTTTCT
*
1597366 CTTGAAACATTTCTCTTGAAACATAAACTTTGAGAACGTTTCCCTTGAAACGAATATTGTCTCTC
1 CTTGAAACATTTCTCTTGAAACATAAACTTTGAGAACGTTTCCCTTGAAACAAATATTGTCTCTC
* * ** *
1597431 TTGAGACAGTTTCCCTTGAAACGTATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTT
66 TTGAGACAATTTCCCTT-AAA-ATAAATTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTT
1597496 GTCTCC
129 GTCTCC
* * *
1597502 CTTGAGACAGTTTCTCTTGAAACATAAACTTTGAGAACGTTTCCCTTGAAATAAATTTTGTCTCT
1 CTTGAAACA-TTTCTCTTGAAACATAAACTTTGAGAACGTTTCCCTTGAAACAAATATTGTCTCT
* *
1597567 GTTGAGACAATTTCCCTTAAAATAAATTGTCTCCCTTGAGACATTTTCCCTTGA
65 CTTGAGACAATTTCCCTTAAAATAAATTGTCTCCCTTGAGACAGTTTCCCTTGA
1597621 GATAGAAGAT
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
135 28 0.26
136 11 0.10
137 68 0.64
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (134 bp):
CTTGAAACATTTCTCTTGAAACATAAACTTTGAGAACGTTTCCCTTGAAACAAATATTGTCTCTC
TTGAGACAATTTCCCTTAAAATAAATTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGT
CTCC
Found at i:1597547 original size:101 final size:99
Alignment explanation
Indices: 1597431--1597620 Score: 274
Period size: 101 Copynumber: 1.9 Consensus size: 99
1597421 ATTGTCTCTC
** * *
1597431 TTGAGACAGTTTCCCTTGAAACGTATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTT
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAATAAA--TT
*
1597496 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACT
64 GTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACT
* *
1597532 TTGAGA-ACGTTTCCCTTGAAATAAATTTTGTCTCTGTTGAGACAATTTCCCTTAAAATAAATTG
1 TTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAATAAATTG
*
1597596 TCTCCCTTGAGACATTTTCCCTTGA
65 TCTCCCTTGAGACAGTTTCCCTTGA
1597621 GATAGAAGAT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 26 0.32
100 1 0.01
101 53 0.66
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (99 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAATAAATTGT
CTCCCTTGAGACAGTTTCCCTTGAAACATAAACT
Found at i:1597572 original size:65 final size:63
Alignment explanation
Indices: 1597467--1597592 Score: 182
Period size: 65 Copynumber: 2.0 Consensus size: 63
1597457 TTTGTCTCTC
* *
1597467 TTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACT
1 TTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAATTTCCCTT-AAA-ATAAACT
**
1597532 TTGAGA-ACGTTTCCCTTGAAATAAATTTTGTCTCTGTTGAGACAATTTCCCTTAAAATAAA
1 TTGAGACA-GTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAATTTCCCTTAAAATAAA
1597593 TTGTCTCCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 5 0.09
64 4 0.07
65 47 0.84
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (63 bp):
TTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAATTTCCCTTAAAATAAACT
Found at i:1597692 original size:39 final size:39
Alignment explanation
Indices: 1597626--1597710 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
1597616 CTTGAGATAG
* * * *
1597626 AAGATTTTATCTCGCATGAGGTTGTTTCACTCGAAACAT
1 AAGATTTTATCTCACATGAGATAGTTTCACTCGAAACAA
* * *
1597665 AAGATTTTATCTTACTTGAGATAGTTTCGCTCGAAACAA
1 AAGATTTTATCTCACATGAGATAGTTTCACTCGAAACAA
1597704 AAGATTT
1 AAGATTT
1597711 AAAGAAACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCACATGAGATAGTTTCACTCGAAACAA
Found at i:1598359 original size:86 final size:86
Alignment explanation
Indices: 1598214--1598410 Score: 324
Period size: 86 Copynumber: 2.3 Consensus size: 86
1598204 CAGAGGGGTT
* * * * *
1598214 AACATTTCTTATTGCTCGATTCACAACACTTCGAATCAGCTTAAGTCCTTTGGGCCATCCATAAG
1 AACATTTCCTATTGCTTGATTCACAAAACTTCGAATCAGCATAAGTCCTTCGGGCCATCCATAAG
*
1598279 ACCTTTGGGCAGGATGTTTTC
66 ACCTTCGGGCAGGATGTTTTC
*
1598300 AACATTTCCTATTGCTTGATTCATAAAACTTCGAATCAGCATAAGTCCTTCGGGCCATCCATAAG
1 AACATTTCCTATTGCTTGATTCACAAAACTTCGAATCAGCATAAGTCCTTCGGGCCATCCATAAG
1598365 ACCTTCGGGCAGGATGTTTTC
66 ACCTTCGGGCAGGATGTTTTC
1598386 AACATTTCCT-TTGCTTGATTCACAA
1 AACATTTCCTATTGCTTGATTCACAA
1598411 CATTTCAATT
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 14 0.14
86 89 0.86
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (86 bp):
AACATTTCCTATTGCTTGATTCACAAAACTTCGAATCAGCATAAGTCCTTCGGGCCATCCATAAG
ACCTTCGGGCAGGATGTTTTC
Found at i:1598525 original size:48 final size:48
Alignment explanation
Indices: 1598448--1598541 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
1598438 AGGGATTTTC
* * * *
1598448 GTCTCGCTTGAGATAATTTTACTCAAAACAAAATTTTATCTCACTCTT
1 GTCTCACTTGAGACAATTTCACTCAAAACAAAATGTTATCTCACTCTT
* *
1598496 GTCTCACTTGAGACAGTTTCACTCGAAACAAAATGTTATCTCACTC
1 GTCTCACTTGAGACAATTTCACTCAAAACAAAATGTTATCTCACTC
1598542 GATATTGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (48 bp):
GTCTCACTTGAGACAATTTCACTCAAAACAAAATGTTATCTCACTCTT
Found at i:1603751 original size:18 final size:18
Alignment explanation
Indices: 1603728--1603767 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1603718 ATTGAATCCT
1603728 CAACTTGAAA-AAGATAAA
1 CAACTT-AAATAAGATAAA
*
1603746 CAACTTAAATAAGATTAA
1 CAACTTAAATAAGATAAA
1603764 CAAC
1 CAAC
1603768 CAAACATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (18 bp):
CAACTTAAATAAGATAAA
Found at i:1603893 original size:17 final size:17
Alignment explanation
Indices: 1603834--1603894 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1603824 GATTTTCATT
1603834 TATTTAAAAATAAAATAA
1 TATTTAAAAAT-AAATAA
* *
1603852 TAATATAACAATAAATAA
1 T-ATTTAAAAATAAATAA
*
1603870 T-TATTAATAATAAATAA
1 TAT-TTAAAAATAAATAA
1603887 TATTTAAA
1 TATTTAAA
1603895 TGATTTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.03
17 17 0.49
18 9 0.26
19 8 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTTAAAAATAAATAA
Found at i:1604034 original size:2 final size:2
Alignment explanation
Indices: 1603989--1604022 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1603979 TAATAATTTA
1603989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1604023 TTTTTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604215 original size:60 final size:60
Alignment explanation
Indices: 1604151--1604263 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
1604141 CTGAGTGATC
*
1604151 ATTTTGTAATTTTTAATAGTTAAGAT-ACTCAATAAAGTAACACACTATAATTAAATAATT
1 ATTTTATAATTTTTAATAGTTAAG-TGACTCAATAAAGTAACACACTATAATTAAATAATT
* * * *
1604211 ATTTTATAATTTTTAATAGTTGAGTGACTTAATAAAGTAATACCCTATAATTA
1 ATTTTATAATTTTTAATAGTTAAGTGACTCAATAAAGTAACACACTATAATTA
1604264 GAGACCAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (60 bp):
ATTTTATAATTTTTAATAGTTAAGTGACTCAATAAAGTAACACACTATAATTAAATAATT
Found at i:1609446 original size:6 final size:5
Alignment explanation
Indices: 1609409--1609443 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1609399 AGGCAACAAA
*
1609409 TTTTC CTTTC TTTTC TTTTC TTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
1609444 TCTCTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1609548 original size:24 final size:24
Alignment explanation
Indices: 1609513--1609570 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
1609503 AAGACTTAAG
1609513 TTCTTC-ACTTCGATGATCATCATC
1 TTCTTCGA-TTCGATGATCATCATC
1609537 TTCTTCGATTCGATGATCATCATC
1 TTCTTCGATTCGATGATCATCATC
1609561 TTCTTCGATT
1 TTCTTCGATT
1609571 GTCAAGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (24 bp):
TTCTTCGATTCGATGATCATCATC
Found at i:1610584 original size:30 final size:30
Alignment explanation
Indices: 1610549--1610608 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1610539 GGACATAAAT
* *
1610549 ATATACATTCCAACTAGAATAGCAAAAACA
1 ATATACATGCCAACTAGAATAACAAAAACA
*
1610579 ATATACATGCTAACTAGAATAACAAAAACA
1 ATATACATGCCAACTAGAATAACAAAAACA
1610609 TCAAGAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20
Consensus pattern (30 bp):
ATATACATGCCAACTAGAATAACAAAAACA
Found at i:1612587 original size:6 final size:6
Alignment explanation
Indices: 1612576--1612639 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
1612566 ATGAACAGTG
* ** * **
1612576 AATGAT AATGAT AAGGAT AATGAT GTTGAT AATGAT AATAAT GTTGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
*
1612624 AATGAT AGTGAT AATG
1 AATGAT AATGAT AATG
1612640 CTGATGATAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (6 bp):
AATGAT
Found at i:1616819 original size:18 final size:18
Alignment explanation
Indices: 1616798--1616832 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1616788 TCATTATCCT
* *
1616798 TATTATTATTCTTATCAC
1 TATTAGTATTATTATCAC
1616816 TATTAGTATTATTATCA
1 TATTAGTATTATTATCA
1616833 TTCATATCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTAGTATTATTATCAC
Found at i:1617533 original size:24 final size:25
Alignment explanation
Indices: 1617480--1617535 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1617470 AACTTGTTCT
* * *
1617480 CTTATAT-TCTCATATATCATGTAG
1 CTTATATATCTCACATATCATATAA
*
1617504 CATATATAT-TCACATATCATATAA
1 CTTATATATCTCACATATCATATAA
1617528 CTTATATA
1 CTTATATA
1617536 ATCATATAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (25 bp):
CTTATATATCTCACATATCATATAA
Found at i:1620194 original size:23 final size:23
Alignment explanation
Indices: 1620126--1620194 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1620116 CAATCTTATA
*
1620126 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1620149 CGACACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
1620172 TGGCACTTCAGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1620195 AGTTGGGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1624053 original size:16 final size:16
Alignment explanation
Indices: 1624032--1624062 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1624022 TTCAACTGTC
1624032 TTTTAAAAGTAAATGA
1 TTTTAAAAGTAAATGA
1624048 TTTTAAAAGTAAATG
1 TTTTAAAAGTAAATG
1624063 TGACACCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTTAAAAGTAAATGA
Found at i:1627673 original size:65 final size:64
Alignment explanation
Indices: 1627583--1627718 Score: 202
Period size: 65 Copynumber: 2.1 Consensus size: 64
1627573 ATACTAATTA
* * *
1627583 CATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGTATGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATACATGG-ATGTGCATCGATACACAAAATG
* *
1627648 CATTTGATGTTTCAATA-AACTCAGGAGTGCATCGATACATGGATGTGCATCGATACACAAAATG
1 CATTCGATGTTTCAAAAGAAC-CAGGAGTGCATCGATACATGGATGTGCATCGATACACAAAATG
1627712 CATTCGA
1 CATTCGA
1627719 ATTAGGGTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 29 0.45
65 35 0.55
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (64 bp):
CATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATACATGGATGTGCATCGATACACAAAATG
Found at i:1629917 original size:14 final size:13
Alignment explanation
Indices: 1629874--1629917 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1629864 TCCTAATGGG
1629874 CAATGTTTGAAAA
1 CAATGTTTGAAAA
** *
1629887 TTATTTTTGAAAA
1 CAATGTTTGAAAA
1629900 CAATGTTTGAATAA
1 CAATGTTTGAA-AA
1629914 CAAT
1 CAAT
1629918 ATGTAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1630461 original size:44 final size:44
Alignment explanation
Indices: 1630390--1630492 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
1630380 AACCCGACGG
* * *
1630390 GTGTATCGATGCACATTTAAAGAATGCATCGGTGCACCTTCATA
1 GTGTATCGATGCATATTCAAAGAATGCATCGGTACACCTTCATA
* * *
1630434 GTGTATCGATGCATATTCAATGGATGCATCGGTACACTTTCATA
1 GTGTATCGATGCATATTCAAAGAATGCATCGGTACACCTTCATA
1630478 GTGTATCGATGCATA
1 GTGTATCGATGCATA
1630493 GAGCACAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (44 bp):
GTGTATCGATGCATATTCAAAGAATGCATCGGTACACCTTCATA
Found at i:1632461 original size:15 final size:15
Alignment explanation
Indices: 1632443--1632477 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1632433 AACATCATGA
1632443 GTTTCCTCATCTTTC
1 GTTTCCTCATCTTTC
*
1632458 GTTTCCTCATTTTTC
1 GTTTCCTCATCTTTC
1632473 GTTTC
1 GTTTC
1632478 TTCCTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57
Consensus pattern (15 bp):
GTTTCCTCATCTTTC
Found at i:1634019 original size:20 final size:21
Alignment explanation
Indices: 1633994--1634039 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1633984 TCCATGCATT
*
1633994 GATG-CACTCCTTAATGTATC
1 GATGCCACCCCTTAATGTATC
1634014 GATGCACCACCCCTTAATGTATC
1 GATG--CCACCCCTTAATGTATC
1634037 GAT
1 GAT
1634040 CACCTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
23 18 0.82
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
GATGCCACCCCTTAATGTATC
Found at i:1636756 original size:65 final size:65
Alignment explanation
Indices: 1636684--1636839 Score: 212
Period size: 65 Copynumber: 2.4 Consensus size: 65
1636674 TACACTTGGG
* *
1636684 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-
1636747 AT
64 AT
* * *
1636749 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCGTCGATGCATGGAT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGAT
*
1636813 GTGCATCGGTACAC-AAAATGCATTCGA
1 GTGCATCGGTACACTAAAATACATTCGA
1636840 ATTAGGGTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
64 29 0.35
65 52 0.63
66 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGAT
Found at i:1639534 original size:51 final size:50
Alignment explanation
Indices: 1639430--1639566 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 50
1639420 AAAATATTAA
* * * * * *
1639430 GAGATATACATACTTACATAGATGTAAGTATGTGTTTATTTTTAGGTTTG
1 GAGATGTACATACTTACACAGGTGTAAGTATATGTTTATATTTAGGTTGG
*
1639480 GAGATGTACATACTTACACAGGTGTAAAGTGTATGTTTATATTTAGGTTGG
1 GAGATGTACATACTTACACAGGTGT-AAGTATATGTTTATATTTAGGTTGG
* * *
1639531 GAGATGTACAAACTTAAACCGGTGTAAGTATATGTT
1 GAGATGTACATACTTACACAGGTGTAAGTATATGTT
1639567 AATTGCTATA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
50 32 0.43
51 43 0.57
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (50 bp):
GAGATGTACATACTTACACAGGTGTAAGTATATGTTTATATTTAGGTTGG
Found at i:1640225 original size:17 final size:17
Alignment explanation
Indices: 1640187--1640229 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1640177 CTTTATCCAA
*
1640187 TAAGATTCA--TAATTT
1 TAAGATTCATTTAAGTT
*
1640202 TATGATTCATTTAAGTT
1 TAAGATTCATTTAAGTT
1640219 TAAGATTCATT
1 TAAGATTCATT
1640230 AATATATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
17 15 0.65
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (17 bp):
TAAGATTCATTTAAGTT
Found at i:1646020 original size:16 final size:16
Alignment explanation
Indices: 1645991--1646033 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1645981 ATAAATAAAT
1645991 GAACATAAACGAACAC
1 GAACATAAACGAACAC
* *
1646007 GAATATAAATGAACAC
1 GAACATAAACGAACAC
1646023 GAACATAAACG
1 GAACATAAACG
1646034 TTGGATACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.12
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1647153 original size:67 final size:67
Alignment explanation
Indices: 1647068--1647201 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
1647058 GAAGATTGGG
1647068 TTAAACATAAATGAATGAACATAAACGAACATAAACAAACGAACATAACCGAACGTTCACGAACG
1 TTAAACATAAATGAATGAACATAAACGAACATAAACAAACGAACATAACCGAACGTTCACGAACG
1647133 TA
66 TA
*
1647135 TTAAACATAAATGAATGAACATAAACGAACATAACCAAACGAACATAACCGAACGTTCACGAACG
1 TTAAACATAAATGAATGAACATAAACGAACATAAACAAACGAACATAACCGAACGTTCACGAACG
1647200 TA
66 TA
1647202 AATGAACAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.16
Consensus pattern (67 bp):
TTAAACATAAATGAATGAACATAAACGAACATAAACAAACGAACATAACCGAACGTTCACGAACG
TA
Found at i:1647174 original size:14 final size:14
Alignment explanation
Indices: 1647157--1647189 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1647147 GAATGAACAT
1647157 AAACGAACATAACC
1 AAACGAACATAACC
1647171 AAACGAACATAACC
1 AAACGAACATAACC
*
1647185 GAACG
1 AAACG
1647190 TTCACGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:1650390 original size:16 final size:16
Alignment explanation
Indices: 1650369--1650401 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1650359 CTCATCACTT
1650369 GTTTGATTAATAATAA
1 GTTTGATTAATAATAA
1650385 GTTTGATTAATAATAA
1 GTTTGATTAATAATAA
1650401 G
1 G
1650402 CTCTCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
GTTTGATTAATAATAA
Found at i:1659228 original size:60 final size:59
Alignment explanation
Indices: 1659121--1659251 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
1659111 TTTGGGGATC
* * * * * *
1659121 AATTTAGAAAGAAGTCATAATTTAGGGATGGAATTAGAATGTCCAAAAGCTTAAGGACT
1 AATTTAGAATGAAGTCATAATTTAAGGATGAAATTAGAATATCCAAAAGCTTAAAGACA
* * *
1659180 AATTTAGAATGAGAGTCATAGTTTAAGGATGAAATT-GAAATATTCAAAAGTTTAAAGACA
1 AATTTAGAATGA-AGTCATAATTTAAGGATGAAATTAG-AATATCCAAAAGCTTAAAGACA
*
1659240 AATTTAAAATGA
1 AATTTAGAATGA
1659252 TGATTATAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 12 0.20
60 48 0.80
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (59 bp):
AATTTAGAATGAAGTCATAATTTAAGGATGAAATTAGAATATCCAAAAGCTTAAAGACA
Found at i:1666603 original size:64 final size:63
Alignment explanation
Indices: 1666470--1666626 Score: 149
Period size: 64 Copynumber: 2.4 Consensus size: 63
1666460 TAATGAAGGT
* * * * *
1666470 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCAATGTTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAAAGAG
* * *
1666534 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCAATG-TTCTATTATTAAAGA
1666596 G
63 G
* *
1666597 AGTGCATCAATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1666627 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.86
65 8 0.10
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAAAGAG
Found at i:1671640 original size:64 final size:60
Alignment explanation
Indices: 1671493--1671645 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
1671483 TAATGAAGGT
* * * **
1671493 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTATTATAGGG
1 ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTTATTATAAAG
* * * *
1671553 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCATTACTAATGCATCGATGCA-TAAAATGCATTCGATG-TT-TATTAT-AAAG
*
1671616 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCATTACTAATGCATCGAT
1671646 ACACCTCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
60 41 0.53
61 3 0.04
62 5 0.06
63 3 0.04
64 25 0.32
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (60 bp):
ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTTATTATAAAG
Found at i:1678568 original size:38 final size:39
Alignment explanation
Indices: 1678506--1678629 Score: 151
Period size: 39 Copynumber: 3.2 Consensus size: 39
1678496 TCTATAACAA
* *
1678506 GTTGCAACCTAAAATTTTGGTTTCTATATGAAAAATCAT
1 GTTGCAACCTAAAAATTTGGTTTCTATATAAAAAATCAT
* * *
1678545 GTTGAAACC-AAAAATTTGGTTTCTATGTAAAAAATTAT
1 GTTGCAACCTAAAAATTTGGTTTCTATATAAAAAATCAT
* * * *
1678583 GTTGCAACCTAAAAATCTGGTTTCTATATTAAAGATCAG
1 GTTGCAACCTAAAAATTTGGTTTCTATATAAAAAATCAT
*
1678622 GTTACAAC
1 GTTGCAAC
1678630 ATAGAAACTG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 33 0.46
39 38 0.54
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (39 bp):
GTTGCAACCTAAAAATTTGGTTTCTATATAAAAAATCAT
Found at i:1685860 original size:39 final size:39
Alignment explanation
Indices: 1685816--1686013 Score: 236
Period size: 39 Copynumber: 5.1 Consensus size: 39
1685806 TTTTCAAACT
* * * *
1685816 AAAATCTAGTTTCTACATGAAAAAGCAGGTTGTAACCTA
1 AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
* *
1685855 GAAATCTGGTTTTTATATGAAAAATCAGGTTGAAACC-A
1 AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
* * *
1685893 AAAATCTGGTTTCTATGTGAAATATCAGGTTGCAACCTA
1 AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
* * *
1685932 AAAATCTGGTTTCTATATGAAAACTCAGTTTGCAACCTA
1 AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
* * * * *
1685971 AAAATTTGATTTCTATATGAAATATCAGGTTGCAACATA
1 AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
1686010 AAAA
1 AAAA
1686014 CGTTTTTCCT
Statistics
Matches: 137, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
38 33 0.24
39 104 0.76
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (39 bp):
AAAATCTGGTTTCTATATGAAAAATCAGGTTGAAACCTA
Found at i:1685897 original size:77 final size:78
Alignment explanation
Indices: 1685816--1686013 Score: 256
Period size: 77 Copynumber: 2.6 Consensus size: 78
1685806 TTTTCAAACT
* * * * * *
1685816 AAAATCTAGTTTCTACATGAAAAAGCAGGTTGTAACCTAGAAATCTGGTTTTTATATGAAAAATC
1 AAAATCTAGTTTCTATATGAAATATCAGGTTGCAACCTAAAAATCTGGTTTCTATATGAAAAATC
1685881 AGGTTGAAACC-A
66 AGGTTGAAACCTA
* * *
1685893 AAAATCTGGTTTCTATGTGAAATATCAGGTTGCAACCTAAAAATCTGGTTTCTATATGAAAACTC
1 AAAATCTAGTTTCTATATGAAATATCAGGTTGCAACCTAAAAATCTGGTTTCTATATGAAAAATC
* *
1685958 AGTTTGCAACCTA
66 AGGTTGAAACCTA
* *
1685971 AAAAT-TTGATTTCTATATGAAATATCAGGTTGCAACATAAAAA
1 AAAATCTAG-TTTCTATATGAAATATCAGGTTGCAACCTAAAAA
1686014 CGTTTTTCCT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
77 67 0.64
78 38 0.36
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (78 bp):
AAAATCTAGTTTCTATATGAAATATCAGGTTGCAACCTAAAAATCTGGTTTCTATATGAAAAATC
AGGTTGAAACCTA
Found at i:1685954 original size:19 final size:19
Alignment explanation
Indices: 1685893--1685954 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1685883 GTTGAAACCA
*
1685893 AAAATCTGGTTTCTATGTG
1 AAAATCTGGTTTCTATATG
* * * ** *
1685912 AAATATCAGGTTGCAACCTA
1 AAA-ATCTGGTTTCTATATG
1685932 AAAATCTGGTTTCTATATG
1 AAAATCTGGTTTCTATATG
1685951 AAAA
1 AAAA
1685955 CTCAGTTTGC
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
AAAATCTGGTTTCTATATG
Found at i:1698334 original size:14 final size:15
Alignment explanation
Indices: 1698314--1698352 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1698304 AAAATCAACT
1698314 GGTTGACTCGAACGA
1 GGTTGACTCGAACGA
* *
1698329 -GTTGACTCAAACTA
1 GGTTGACTCGAACGA
1698343 GGTTGACTCG
1 GGTTGACTCG
1698353 GTCGGGTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (15 bp):
GGTTGACTCGAACGA
Found at i:1700396 original size:10 final size:9
Alignment explanation
Indices: 1700381--1700408 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1700371 CCATATTAAT
1700381 AAAAAAATA
1 AAAAAAATA
1700390 AAAAAAATA
1 AAAAAAATA
1700399 AAAAAAATA
1 AAAAAAATA
1700408 A
1 A
1700409 TTACTCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1703935 original size:20 final size:20
Alignment explanation
Indices: 1703841--1704209 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1703831 GATTTTCCAT
* ** *
1703841 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1703861 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1703881 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1703901 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1703921 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1703941 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1703961 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1703981 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1704001 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1704021 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1704041 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1704061 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1704081 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1704101 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1704121 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1704141 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1704161 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1704181 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1704201 AATCACAAC
1 AATCGCAAC
1704210 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1704929 original size:24 final size:24
Alignment explanation
Indices: 1704890--1704936 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1704880 AAATTTGGTC
1704890 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1704914 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1704937 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1707434 original size:19 final size:19
Alignment explanation
Indices: 1707412--1707685 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1707402 CGGAAAATAC
*
1707412 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1707431 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1707445 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1707465 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1707479 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707498 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1707517 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1707531 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1707550 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707569 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707588 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707607 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707626 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1707640 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1707678 AATCGCAA
1 AATCGCAA
1707686 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1707563 original size:71 final size:74
Alignment explanation
Indices: 1707412--1707707 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
1707402 CGGAAAATAC
* *
1707412 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
1707472 A--CG--A-GAG
63 ATGCGAAATGAA
*
1707479 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
1707541 CGAAATTAA
66 CGAAATGAA
1707550 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
1707615 TGCGAAATGAA
64 TGCGAAATGAA
1707626 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
1707686 --CG--A-GAT
64 TGCGAAATGAA
1707692 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1707708 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:1707611 original size:109 final size:104
Alignment explanation
Indices: 1707440--1707707 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
1707430 AAATCCCAAC
*
1707440 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
1707505 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1707545 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
1707610 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1707654 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
1707708 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1707673 original size:161 final size:157
Alignment explanation
Indices: 1707412--1707723 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
1707402 CGGAAAATAC
*
1707412 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
1707477 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
1707542 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
1707569 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
1707633 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
1707698 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
1707724 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:1707723 original size:52 final size:52
Alignment explanation
Indices: 1707440--1707707 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
1707430 AAATCCCAAC
1707440 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1707493 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1707545 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1707602 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1707654 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1707706 AT
1 AT
1707708 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1707823 original size:19 final size:19
Alignment explanation
Indices: 1707714--1707815 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1707704 AAATTATAAA
1707714 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1707733 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1707753 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1707769 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1707786 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1707805 CGCATTGCGAT
1 CGCATTGCGAT
1707816 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1707941 original size:14 final size:14
Alignment explanation
Indices: 1707922--1707958 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1707912 CATCAATTAC
1707922 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1707936 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1707950 ACAAATCAA
1 ACAAATCAA
1707959 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1709931 original size:14 final size:14
Alignment explanation
Indices: 1709912--1709968 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1709902 GCGAAATGAA
*
1709912 AATCGCAACGACAG
1 AATCGCAACGAAAG
1709926 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1709943 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1709959 AATCGCAACG
1 AATCGCAACG
1709969 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1709939 original size:33 final size:33
Alignment explanation
Indices: 1709893--1709985 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1709883 GCGAAACCAA
*
1709893 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1709926 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1709959 AATCGCAACGCGAAATGAAAATTGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1709986 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1709950 original size:19 final size:19
Alignment explanation
Indices: 1709856--1709990 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1709846 TAGTTTACTT
* *
1709856 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1709876 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1709895 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1709914 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1709928 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1709947 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1709961 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
1709980 TTGCAATGCGA
1 TCGCAACGCGA
1709991 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.11
17 11 0.11
19 46 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1710008 original size:19 final size:19
Alignment explanation
Indices: 1709986--1710113 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1709976 AAAATTGCAA
1709986 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1710005 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1710019 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1710038 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1710052 TGCGA-TTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1710070 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1710089 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1710109 TGCGA
1 TGCGA
1710114 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 19 0.22
15 1 0.01
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Done.