Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003125.1 Hibiscus syriacus cultivar Beakdansim tig00006542_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: 36470
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Found at i:4801 original size:20 final size:20
Alignment explanation
Indices: 4778--4852 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
4768 CTTTAGGGAA
*
4778 AGTTTCAAAACTCTTGAGAT
1 AGTTTCGAAACTCTTGAGAT
*
4798 AGTTTCGAAACTCTTTAGAT
1 AGTTTCGAAACTCTTGAGAT
4818 AGTTTCGAAACTCTTGAGAT
1 AGTTTCGAAACTCTTGAGAT
4838 AGTTTCGAAACTCTT
1 AGTTTCGAAACTCTT
4853 AAAAAGTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
AGTTTCGAAACTCTTGAGAT
Found at i:4806 original size:40 final size:38
Alignment explanation
Indices: 4762--4868 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 38
4752 AGTCAAAGTA
4762 TCGAAACTTTAGGGAAAGTTTCAAAACTCTTGAGATAGTT
1 TCGAAACTTTA--GAAAGTTTCAAAACTCTTGAGATAGTT
* *
4802 TCGAAACTCTTTAGATAGTTTCGAAACTCTTGAGATAGTT
1 TCGAAA--CTTTAGAAAGTTTCAAAACTCTTGAGATAGTT
* * *
4842 TCGAAACTCTTAAAAAGTATCGAAACT
1 TCGAAACT-TTAGAAAGTTTCAAAACT
4869 TTTTGGACTA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.03
39 15 0.25
40 37 0.63
42 5 0.08
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (38 bp):
TCGAAACTTTAGAAAGTTTCAAAACTCTTGAGATAGTT
Found at i:8584 original size:6 final size:6
Alignment explanation
Indices: 8573--8652 Score: 108
Period size: 6 Copynumber: 13.3 Consensus size: 6
8563 GCAGGTAACT
*
8573 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGGGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
* * *
8621 GGTGGA GAG-GGA GGGGGA GGAGTA GGTGGA GG
1 GGTGGA G-GTGGA GGTGGA GGTGGA GGTGGA GG
8653 GGTAGGAGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 1 0.02
6 64 0.97
7 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (6 bp):
GGTGGA
Found at i:8659 original size:18 final size:18
Alignment explanation
Indices: 8573--8661 Score: 99
Period size: 18 Copynumber: 4.9 Consensus size: 18
8563 GCAGGTAACT
* *
8573 GGTGGAGGTGGAGGTGGA
1 GGTGGAGGGGGAGGAGGA
* *
8591 GGTGGAGGTGGAGGTGGA
1 GGTGGAGGGGGAGGAGGA
*
8609 GGTGGAGGGGGAGGTGGA
1 GGTGGAGGGGGAGGAGGA
*
8627 GAG-GGAGGGGGAGGAGTA
1 G-GTGGAGGGGGAGGAGGA
*
8645 GGTGGAGGGGTAGGAGG
1 GGTGGAGGGGGAGGAGG
8662 TGTACGAGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
17 1 0.02
18 62 0.97
19 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (18 bp):
GGTGGAGGGGGAGGAGGA
Found at i:8736 original size:21 final size:21
Alignment explanation
Indices: 8710--8816 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
8700 AGGTGCGCTA
*
8710 GGAGGAGGAGTAGGTGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
8731 GTAGGAGGTGTACGAGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
8752 GGAGTAGGAGCAGGGGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
8773 GGAAGAGGTG-CGCGAGGAGGG
1 GGAGGAGGAGTAG-GAGGAGGG
* *
8794 GGAGTAGGAGCAGGAGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
8815 GG
1 GG
8817 GAAAGGTGCG
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.64, T:0.07
Consensus pattern (21 bp):
GGAGGAGGAGTAGGAGGAGGG
Found at i:8761 original size:42 final size:42
Alignment explanation
Indices: 8649--9030 Score: 289
Period size: 42 Copynumber: 9.7 Consensus size: 42
8639 GGAGTAGGTG
* *
8649 GAGGGGTAGGAGGTGTACGAGGA-GGGGAGTAGGAGCAGGGG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* ** * *
8690 GAGGGGGAAGAGGTG--CG-CTA---GGAGGAGGAGTAGGTG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* *
8726 GAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* ** *
8768 GAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* * *
8810 GAGGGGG-GAAAGGTG--CG-CGA-GGGG-G--GGAGTAGGTG
1 GAGGGGGAG-GAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
** *
8845 GAGGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* *
8887 GAGGGGGAAGAGGTG-AGCTAGGAGGGGGAGT------AGGTG
1 GAGGGGGAGGAGGTGTA-CGAGGAGGGGGAGTAGGAGCAGGTG
* * * *
8923 GAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
* **
8965 GAGGGGGAAGAGGTGCGCGAGGAGGGGGAGT------AGGTG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
*
9001 GAGGGGTAGGAGGTGTACGAGGAGGGGGAG
1 GAGGGGGAGGAGGTGTACGAGGAGGGGGAG
9031 GGGGAGGAGG
Statistics
Matches: 272, Mismatches: 46, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
35 18 0.07
36 88 0.32
37 4 0.01
38 9 0.03
39 9 0.03
40 3 0.01
41 14 0.05
42 127 0.47
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (42 bp):
GAGGGGGAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGTG
Found at i:8789 original size:119 final size:119
Alignment explanation
Indices: 8638--8920 Score: 428
Period size: 119 Copynumber: 2.4 Consensus size: 119
8628 AGGGAGGGGG
* * * * *
8638 AGGAGTAGGTGGAGGGGTAGGAGGTGTA-CGAGGA-GGGGAGTAGGAGCAGGGGGA-GGGGGAAG
1 AGGAGCAGGGGGAGGGGGAAGAGGTG-AGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-
* *
8700 AGGTGCGCTAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGT
64 AGGTGCGCGAGG-GGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
*
8757 AGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAG
1 AGGAGCAGGGGGAGGGGGAAGAGGTGAGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAG
*
8822 GTGCGCGAGGGGGGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
66 GTGCGCGAGGGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
*
8876 AGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGGGGAGTAGG
1 AGGAGCAGGGGGAGGGGGAAGAGGTGAGCGAGGAGGGGGAGTAGG
8921 TGGAGGTGGA
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
119 113 0.75
120 30 0.20
121 7 0.05
ACGTcount: A:0.25, C:0.05, G:0.61, T:0.09
Consensus pattern (119 bp):
AGGAGCAGGGGGAGGGGGAAGAGGTGAGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAG
GTGCGCGAGGGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
Found at i:8791 original size:78 final size:77
Alignment explanation
Indices: 8631--8801 Score: 306
Period size: 78 Copynumber: 2.2 Consensus size: 77
8621 GGTGGAGAGG
*
8631 GAGGGGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
1 GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
8696 GAAGAGGTGCGC
66 GAAGAGGTGCGC
*
8708 TAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
1 GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGA-GGGGAGTAGGAGCAGGGGGAGGG
8773 GGAAGAGGTGCGC
65 GGAAGAGGTGCGC
*
8786 GAGGAGGGGGAGTAGG
1 GAGGAGGAGGAGTAGG
8802 AGCAGGAGGA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 39 0.44
78 50 0.56
ACGTcount: A:0.24, C:0.05, G:0.62, T:0.09
Consensus pattern (77 bp):
GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
GAAGAGGTGCGC
Found at i:8895 original size:197 final size:197
Alignment explanation
Indices: 8631--8998 Score: 659
Period size: 197 Copynumber: 1.9 Consensus size: 197
8621 GGTGGAGAGG
*
8631 GAGGGGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
1 GAGGGGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
* *
8696 GAAGAGGTGCGCTAGGAGGAGGAGTAGGTGGAGG-GGTAGGAGGTGTACGAGGAGGGGGAGTAGG
66 GAAGAGGTGAGCTAGGAGGAGGAGTAGGTGGAGGTGG-AAGAGGTGTACGAGGAGGGGGAGTAGG
*
8760 AGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAGGTG
130 AGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAGGTG
8825 CGC
195 CGC
8828 GAGGGGG-GGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
1 GAGGGGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGA-GGGGAGTAGGAGCAGGGGGAGGG
*
8892 GGAAGAGGTGAGCTAGGAGGGGGAGTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGG
65 GGAAGAGGTGAGCTAGGAGGAGGAGTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGG
8957 AGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGG
130 AGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGG
8999 TGGAGGGGTA
Statistics
Matches: 164, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
196 32 0.20
197 130 0.79
198 2 0.01
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (197 bp):
GAGGGGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGAGTAGGAGCAGGGGGAGGGG
GAAGAGGTGAGCTAGGAGGAGGAGTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGA
GAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAGGTGC
GC
Found at i:8921 original size:21 final size:21
Alignment explanation
Indices: 8725--9000 Score: 126
Period size: 21 Copynumber: 13.8 Consensus size: 21
8715 AGGAGTAGGT
* * * *
8725 GGAGGGGTAGGAGGTGTACGA
1 GGAGGGGGAGTAGGTGCAGGA
* *
8746 GGAGGGGGAGTAGGAGCAGGG
1 GGAGGGGGAGTAGGTGCAGGA
8767 GGAGGGGGAAG-AGGTGC-GCGA
1 GGAGGGGG-AGTAGGTGCAG-GA
*
8788 GGAGGGGGAGTAGGAGCAGGA
1 GGAGGGGGAGTAGGTGCAGGA
*
8809 GGAGGGGG-GAAAGGTGC-GCGA
1 GGAGGGGGAG-TAGGTGCAG-GA
8830 GG-GGGGGAGTAGGT------
1 GGAGGGGGAGTAGGTGCAGGA
** * * *
8844 GGAGGGATAGGAGGTGTACGA
1 GGAGGGGGAGTAGGTGCAGGA
* *
8865 GGAGGGGGAGTAGGAGCAGGG
1 GGAGGGGGAGTAGGTGCAGGA
*
8886 GGAGGGGGAAG-AGGTG-AGCTA
1 GGAGGGGG-AGTAGGTGCAG-GA
8907 GGAGGGGGAGTAGGT---GGA
1 GGAGGGGGAGTAGGTGCAGGA
* * * *
8925 -G-GTGGAAG-AGGTGTACGA
1 GGAGGGGGAGTAGGTGCAGGA
* * *
8943 GGAGGGGGAGTAGGAGAAGGG
1 GGAGGGGGAGTAGGTGCAGGA
8964 GGAGGGGGAAG-AGGTGC-GCGA
1 GGAGGGGG-AGTAGGTGCAG-GA
8985 GGAGGGGGAGTAGGTG
1 GGAGGGGGAGTAGGTG
9001 GAGGGGTAGG
Statistics
Matches: 191, Mismatches: 38, Indels: 52
0.68 0.14 0.19
Matches are distributed among these distances:
14 2 0.01
15 13 0.07
16 5 0.03
17 1 0.01
18 3 0.02
19 2 0.01
20 26 0.14
21 132 0.69
22 7 0.04
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (21 bp):
GGAGGGGGAGTAGGTGCAGGA
Found at i:8950 original size:78 final size:77
Alignment explanation
Indices: 8771--9030 Score: 391
Period size: 78 Copynumber: 3.4 Consensus size: 77
8761 GCAGGGGGAG
** *
8771 GGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-AGGTGCGCGAGG-GG
1 GGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA-GGGGGAAGAGGTGCGCGAGGAGG
8834 GGGAGTAGGTGGA
65 GGGAGTAGGTGGA
* *
8847 -GGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAG
1 GGGGA-A-GAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAG
8911 GGGGAGTAGGTGGA
64 GGGGAGTAGGTGGA
*
8925 GGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGG
1 GG-GGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGG
8990 GGGAGTAGGTGGA
65 GGGAGTAGGTGGA
*
9003 GGGGTAGGAGGTGTACGAGGAGGGGGAG
1 GGGG-AAGAGGTGTACGAGGAGGGGGAG
9031 GGGGAGGAGG
Statistics
Matches: 168, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
75 4 0.02
76 8 0.05
77 44 0.26
78 107 0.64
79 2 0.01
80 3 0.02
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (77 bp):
GGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGG
GGAGTAGGTGGA
Found at i:9040 original size:36 final size:36
Alignment explanation
Indices: 8813--9040 Score: 156
Period size: 36 Copynumber: 6.1 Consensus size: 36
8803 GCAGGAGGAG
** *
8813 GGGGGAA-AGGTGCGCGAGG-GGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
** * *
8847 GGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA
1 GGGGGAAGAGGTGTACGAGGA-GGGG-G-A-G-G-AGGTGGA
* *
8889 GGGGGAAGAGGTG-AGCTAGGAGGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTA-CGAGGAGGGGGAGGAGGTGGA
* *
8925 GGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGA
1 GGGGGAAGAGGTGTACGAGGA-GGGG-G-A-G-G-AGGTGGA
** *
8967 GGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
* * * *
9003 GGGGTAGGAGGTGTACGAGGAGGGGGAGGGGGAGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
9039 GG
1 GG
9041 CGTGTTCGGA
Statistics
Matches: 149, Mismatches: 29, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
34 4 0.03
35 10 0.07
36 60 0.40
37 9 0.06
38 4 0.03
39 4 0.03
40 4 0.03
41 9 0.06
42 45 0.30
ACGTcount: A:0.24, C:0.04, G:0.63, T:0.09
Consensus pattern (36 bp):
GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
Found at i:9200 original size:26 final size:27
Alignment explanation
Indices: 9159--9214 Score: 105
Period size: 26 Copynumber: 2.1 Consensus size: 27
9149 TGGAGGAGGG
9159 GGAGGGGGAGGAGGACGACGGTTACTA
1 GGAGGGGGAGGAGGACGACGGTTACTA
9186 GGAGGGGGAGG-GGACGACGGTTACTA
1 GGAGGGGGAGGAGGACGACGGTTACTA
9212 GGA
1 GGA
9215 TTGAGAGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.25, C:0.11, G:0.54, T:0.11
Consensus pattern (27 bp):
GGAGGGGGAGGAGGACGACGGTTACTA
Found at i:10118 original size:15 final size:16
Alignment explanation
Indices: 10086--10116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10076 TCCAACGATC
10086 CTAAAAAGTTATAAAA
1 CTAAAAAGTTATAAAA
*
10102 CTAAAAAGTTTTAAA
1 CTAAAAAGTTATAAA
10117 CTGTGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
CTAAAAAGTTATAAAA
Found at i:10145 original size:2 final size:2
Alignment explanation
Indices: 10138--10181 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
10128 GATTATAGCT
10138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10180 TA
1 TA
10182 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10656 original size:2 final size:2
Alignment explanation
Indices: 10649--10729 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
10639 GATCATTCCC
10649 AT AT AT AT 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 AT AT AT AT
10691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10730 ATTTTAATAG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11657 original size:11 final size:12
Alignment explanation
Indices: 11631--11674 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
11621 GCTGCTACAA
11631 AATAATTATTTT
1 AATAATTATTTT
11643 -ATAA-TATTTT
1 AATAATTATTTT
11653 AATAA--A-TTT
1 AATAATTATTTT
11662 AATAATTATTTT
1 AATAATTATTTT
11674 A
1 A
11675 TGATTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.29
10 7 0.25
11 9 0.32
12 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATAATTATTTT
Found at i:14457 original size:19 final size:20
Alignment explanation
Indices: 14413--14459 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
14403 AGGGAAACTT
* * *
14413 TCGAAACTCTTGAGATAGTT
1 TCGAAACTCTTGAAAAAGTA
14433 TCGAAACTCTT-AAAAAGTA
1 TCGAAACTCTTGAAAAAGTA
14452 TCGAAACT
1 TCGAAACT
14460 TTTTGGACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
TCGAAACTCTTGAAAAAGTA
Found at i:18169 original size:6 final size:6
Alignment explanation
Indices: 18158--18219 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
18148 GCAGGTAACT
* *
18158 GGTGGA GGTGGA GGTGGA GGTGGA GGGGGA GGTGGA GAG-GGA GGGGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G-GTGGA GGTGGA
* *
18206 GGAGTA GGTGGA GG
1 GGTGGA GGTGGA GG
18220 GGTAGGAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 46 0.96
7 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.11
Consensus pattern (6 bp):
GGTGGA
Found at i:18181 original size:18 final size:18
Alignment explanation
Indices: 18158--18245 Score: 88
Period size: 18 Copynumber: 4.7 Consensus size: 18
18148 GCAGGTAACT
*
18158 GGTGGAGGTGGAGGTGGA
1 GGTGGAGGGGGAGGTGGA
18176 GGTGGAGGGGGAGGTGGA
1 GGTGGAGGGGGAGGTGGA
* *
18194 GAG-GGAGGGGGAGGAGTA
1 G-GTGGAGGGGGAGGTGGA
*
18212 GGTGGAGGGGTAGGAGGTGTA
1 GGTGGA-GGG--GGAGGTGGA
*
18233 CGTGGAGGGGGAG
1 GGTGGAGGGGGAG
18246 TAGGAGCAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.02
18 39 0.65
19 4 0.07
20 3 0.05
21 13 0.22
ACGTcount: A:0.19, C:0.01, G:0.67, T:0.12
Consensus pattern (18 bp):
GGTGGAGGGGGAGGTGGA
Found at i:18227 original size:21 final size:21
Alignment explanation
Indices: 18175--18577 Score: 104
Period size: 21 Copynumber: 20.3 Consensus size: 21
18165 GTGGAGGTGG
*
18175 AGGTGGAGGGGGAGGTGGAG-
1 AGGTGGAGGGGGAGGAGGAGT
18195 A-G-GGA--GGG-GGAGGAGT
1 AGGTGGAGGGGGAGGAGGAGT
* *
18211 AGGTGGAGGGGTAGGAGGTGT
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18232 ACGTGGAGGGGGAGTAGGAGC
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18253 AGGGGGAGGGGGAAGAGGTG-
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18273 CGCT--A---GGAGGGGGAGT
1 AGGTGGAGGGGGAGGAGGAGT
* *
18289 AGGTGGAGGGGTAGGAGGTGT
1 AGGTGGAGGGGGAGGAGGAGT
* * * *
18310 ACGAGGAGGGGGAGTAGGAGC
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18331 AGGGGGAGGGGGAAGAGGTG-
1 AGGTGGAGGGGGAGGAGGAGT
* *
18351 CGCT--A---GGAGGAGGAGT
1 AGGTGGAGGGGGAGGAGGAGT
* *
18367 AGGTGGAGGGGTAGGAGGTGT
1 AGGTGGAGGGGGAGGAGGAGT
* * * *
18388 ACGAGGAGGGGGAGTAGGAGC
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18409 AGGGGGAGGGGGAAGAGGTG-
1 AGGTGGAGGGGGAGGAGGAGT
* * * *
18429 CGCGAGGAGGGGGAGTAGGAGC
1 AG-GTGGAGGGGGAGGAGGAGT
*
18451 AGGAGGA-GGGG-GGA--A--
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18466 AGGTGCG-CGAGGAGGGGGAGT
1 AGGTG-GAGGGGGAGGAGGAGT
** *
18487 AGGTGGAGGGATAGGAGGTGT
1 AGGTGGAGGGGGAGGAGGAGT
* * * *
18508 ACGAGGAGGGGGAGTAGGAGC
1 AGGTGGAGGGGGAGGAGGAGT
* * *
18529 AGGGGGAGGGGGAAGAGGTG-
1 AGGTGGAGGGGGAGGAGGAGT
* * * *
18549 AGCTAGGAGGGGGAGTAGGTGG
1 AGGT-GGAGGGGGAGGAGGAGT
18571 AGGTGGA
1 AGGTGGA
18578 AGAGGTGTAC
Statistics
Matches: 265, Mismatches: 88, Indels: 59
0.64 0.21 0.14
Matches are distributed among these distances:
15 25 0.09
16 12 0.05
17 4 0.02
18 10 0.04
19 4 0.02
20 13 0.05
21 193 0.73
22 4 0.02
ACGTcount: A:0.24, C:0.04, G:0.62, T:0.10
Consensus pattern (21 bp):
AGGTGGAGGGGGAGGAGGAGT
Found at i:18290 original size:78 final size:78
Alignment explanation
Indices: 18206--18447 Score: 457
Period size: 78 Copynumber: 3.1 Consensus size: 78
18196 GGGAGGGGGA
*
18206 GGAGTAGGTGGAGGGGTAGGAGGTGTACGTGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
18271 TGCGCTAGGAGGG
66 TGCGCTAGGAGGG
18284 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
*
18349 TGCGCTAGGAGGA
66 TGCGCTAGGAGGG
18362 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
*
18427 TGCGCGAGGAGGG
66 TGCGCTAGGAGGG
18440 GGAGTAGG
1 GGAGTAGG
18448 AGCAGGAGGA
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 160 1.00
ACGTcount: A:0.23, C:0.05, G:0.62, T:0.10
Consensus pattern (78 bp):
GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
TGCGCTAGGAGGG
Found at i:18377 original size:120 final size:118
Alignment explanation
Indices: 18236--18677 Score: 382
Period size: 120 Copynumber: 3.7 Consensus size: 118
18226 AGGTGTACGT
* *
18236 GGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCTAGGAGGGGGAGTAGGTGGAGGGGT
1 GGAGGGGGAGTAGGAGGAGGGGGAGGGGGAAGAGGTGCG--AGGAGGGGGAGTAGGTGGAGGGGG
* *
18301 AGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCTA
64 AGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGAAGAGGTGCGCGA
* * * * * * ** * *
18356 GGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAG-GGGGAGTAGGAGCAGGGGGAGGGG
1 GGAGGGGGAGTAGGAGGAGGGGGAGG-GG-G-AAGAGGTGCGAGGAGGGGGAGTAGGTGGAGGGG
* **
18420 GAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-AGGTGCGCGA
63 GAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGAGGA-GGGGGAAGAGGTGCGCGA
* ** * * *
18476 GGAGGGGGAGTAGGTGGA--GGGA-TAGG-AG-GTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA
1 GGAGGGGGAGTAGGAGGAGGGGGAGGGGGAAGAG-GTGCGAGGAGGGGGAGTAGGTGGAGGGGGA
* ** ** * * * **
18536 GG-GG-G-AAGAGGTGAGCTAGGAGGGGGAGTAGGTGGAGGTGGAAGAGGTGTACGA
65 GGAGGTGTACGA-G-GAG-GGGGAGTAGGAGCAGGAGGAGGGGGAAGAGGTGCGCGA
* * *
18590 GGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTTGAGGGGT
1 GGAGGGGGAGTAGGAGGAGGGGGAGGGGGAAGAGGT--GCGAGGAGGGGGAGTAGGTGGAGGGGG
18655 AGGAGGTGTACGAGGAGGGGGAG
64 AGGAGGTGTACGAGGAGGGGGAG
18678 GGGGAGGAGG
Statistics
Matches: 248, Mismatches: 54, Indels: 40
0.73 0.16 0.12
Matches are distributed among these distances:
111 2 0.01
112 3 0.01
113 13 0.05
114 59 0.24
115 1 0.00
116 5 0.02
117 2 0.01
118 7 0.03
119 1 0.00
120 128 0.52
121 14 0.06
122 4 0.02
123 9 0.04
ACGTcount: A:0.24, C:0.05, G:0.62, T:0.09
Consensus pattern (118 bp):
GGAGGGGGAGTAGGAGGAGGGGGAGGGGGAAGAGGTGCGAGGAGGGGGAGTAGGTGGAGGGGGAG
GAGGTGTACGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGAAGAGGTGCGCGA
Found at i:18495 original size:78 final size:78
Alignment explanation
Indices: 18404--18677 Score: 397
Period size: 78 Copynumber: 3.5 Consensus size: 78
18394 AGGGGGAGTA
* * ** *
18404 GGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-AG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA-GGGGGAAGAG
18468 GTGCGCGAGGAGGG
65 GTGCGCGAGGAGGG
** *
18482 GGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
* *
18547 TGAGCTAGGAGGG
66 TGCGCGAGGAGGG
* *
18560 GGAGTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
18625 TGCGCGAGGAGGG
66 TGCGCGAGGAGGG
* * *
18638 GGAGTAGGTTGAGGGGTAGGAGGTGTACGAGGAGGGGGAG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAG
18678 GGGGAGGAGG
Statistics
Matches: 174, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
77 7 0.04
78 167 0.96
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (78 bp):
GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
TGCGCGAGGAGGG
Found at i:18507 original size:198 final size:198
Alignment explanation
Indices: 18236--18645 Score: 725
Period size: 198 Copynumber: 2.1 Consensus size: 198
18226 AGGTGTACGT
* * *
18236 GGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCTAGGAGGGGGAGTAGGTGGAGGGGT
1 GGAGGGGGAGTAGGAGCAGGAGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTGGAGGGAT
*
18301 AGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCTAGGAGGAGGAG
66 AGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGAGGAG
* *
18366 TAGGTGGAGG-GGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGC
131 TAGGTGGAGGTGG-AAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGC
18430 GCGA
195 GCGA
18434 GGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-AGGTGCGCGAGGAGGGGGAGTAGGTGGAGGGA
1 GGAGGGGGAGTAGGAGCAGGAGGA-GGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTGGAGGGA
*
18498 TAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGGGGA
65 TAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGAGGA
18563 GTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGC
130 GTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGC
18628 GCGA
195 GCGA
18632 GGAGGGGGAGTAGG
1 GGAGGGGGAGTAGG
18646 TTGAGGGGTA
Statistics
Matches: 203, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
198 194 0.96
199 9 0.04
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.09
Consensus pattern (198 bp):
GGAGGGGGAGTAGGAGCAGGAGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTGGAGGGAT
AGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGAGGAG
TAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGCG
CGA
Found at i:18646 original size:21 final size:21
Alignment explanation
Indices: 18509--18646 Score: 82
Period size: 21 Copynumber: 6.9 Consensus size: 21
18499 AGGAGGTGTA
*
18509 CGAGGAGGGGGAGTAGGAGCAG
1 CGAGGAGGGGGAGTAGGTG-AG
*
18531 -GGGGAGGGGGAAG-AGGTGAG
1 CGAGGAGGGGG-AGTAGGTGAG
*
18551 CTAGGAGGGGGAGTAGGT--G
1 CGAGGAGGGGGAGTAGGTGAG
* *
18570 -GA-G-GTGGAAG-AGGTGTA-
1 CGAGGAGGGGGAGTAGGTG-AG
*
18587 CGAGGAGGGGGAGTAGGAGAAG
1 CGAGGAGGGGGAGTAGGTG-AG
* *
18609 -GGGGAGGGGGAAG-AGGTGCG
1 CGAGGAGGGGG-AGTAGGTGAG
18629 CGAGGAGGGGGAGTAGGT
1 CGAGGAGGGGGAGTAGGT
18647 TGAGGGGTAG
Statistics
Matches: 87, Mismatches: 15, Indels: 29
0.66 0.11 0.22
Matches are distributed among these distances:
15 4 0.05
16 5 0.06
17 1 0.01
18 3 0.03
19 2 0.02
20 12 0.14
21 56 0.64
22 4 0.05
ACGTcount: A:0.25, C:0.04, G:0.62, T:0.09
Consensus pattern (21 bp):
CGAGGAGGGGGAGTAGGTGAG
Found at i:18848 original size:27 final size:27
Alignment explanation
Indices: 18808--18862 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
18798 GAGGAGGGGA
18808 AGGGGGAGGAGGACGACGGTTACTAGG
1 AGGGGGAGGAGGACGACGGTTACTAGG
*
18835 AGGGGGAGGGGGACGACGGTTACTAGG
1 AGGGGGAGGAGGACGACGGTTACTAGG
18862 A
1 A
18863 TTGAGAGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.53, T:0.11
Consensus pattern (27 bp):
AGGGGGAGGAGGACGACGGTTACTAGG
Found at i:19788 original size:2 final size:2
Alignment explanation
Indices: 19781--19822 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19771 GATTATAGCT
19781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19823 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21245 original size:11 final size:12
Alignment explanation
Indices: 21219--21262 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
21209 GCTGCTACAA
21219 AATAATTATTTT
1 AATAATTATTTT
21231 -ATAA-TATTTT
1 AATAATTATTTT
21241 AATAA--A-TTT
1 AATAATTATTTT
21250 AATAATTATTTT
1 AATAATTATTTT
21262 A
1 A
21263 TGATTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.29
10 7 0.25
11 9 0.32
12 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATAATTATTTT
Found at i:21936 original size:21 final size:20
Alignment explanation
Indices: 21912--21951 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21902 ATCAAAACGG
21912 ACTAAAAATGATAATTTAACT
1 ACTAAAAATG-TAATTTAACT
**
21933 ACTAAACTTGTAATTTAAC
1 ACTAAAAATGTAATTTAAC
21952 CTAATTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (20 bp):
ACTAAAAATGTAATTTAACT
Found at i:26031 original size:20 final size:20
Alignment explanation
Indices: 26008--26082 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
25998 CTTTAGGGAA
*
26008 AGTTTCAAAACTCTTGAGAT
1 AGTTTCGAAACTCTTGAGAT
*
26028 AGTTTCGAAACTCTTTAGAT
1 AGTTTCGAAACTCTTGAGAT
26048 AGTTTCGAAACTCTTGAGAT
1 AGTTTCGAAACTCTTGAGAT
26068 AGTTTCGAAACTCTT
1 AGTTTCGAAACTCTT
26083 AAAAAGTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
AGTTTCGAAACTCTTGAGAT
Found at i:26036 original size:40 final size:38
Alignment explanation
Indices: 25992--26098 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 38
25982 AGTCAAAGTA
25992 TCGAAACTTTAGGGAAAGTTTCAAAACTCTTGAGATAGTT
1 TCGAAACTTTA--GAAAGTTTCAAAACTCTTGAGATAGTT
* *
26032 TCGAAACTCTTTAGATAGTTTCGAAACTCTTGAGATAGTT
1 TCGAAA--CTTTAGAAAGTTTCAAAACTCTTGAGATAGTT
* * *
26072 TCGAAACTCTTAAAAAGTATCGAAACT
1 TCGAAACT-TTAGAAAGTTTCAAAACT
26099 TTTTGGACTA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.03
39 15 0.25
40 37 0.63
42 5 0.08
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (38 bp):
TCGAAACTTTAGAAAGTTTCAAAACTCTTGAGATAGTT
Found at i:29817 original size:6 final size:6
Alignment explanation
Indices: 29806--29884 Score: 108
Period size: 6 Copynumber: 13.3 Consensus size: 6
29796 GCAGGTAACT
29806 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GG-GGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
* * *
29853 GGTGGA GAG-GGA GGGGGA GGAGTA GGTGGA GG
1 GGTGGA G-GTGGA GGTGGA GGTGGA GGTGGA GG
29885 GGTAGGAGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
5 6 0.09
6 59 0.89
7 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.68, T:0.13
Consensus pattern (6 bp):
GGTGGA
Found at i:29891 original size:18 final size:17
Alignment explanation
Indices: 29806--29893 Score: 88
Period size: 18 Copynumber: 4.9 Consensus size: 17
29796 GCAGGTAACT
*
29806 GGTGGAGGTGGAGGTGGA
1 GGTGGAGG-GGAGGAGGA
*
29824 GGTGGAGGTGGAGGTGGA
1 GGTGGAGG-GGAGGAGGA
*
29842 GGTGGAGGGGAGGTGGA
1 GGTGGAGGGGAGGAGGA
*
29859 GAG-GGAGGGGGAGGAGTA
1 G-GTGGA-GGGGAGGAGGA
29877 GGTGGAGGGGTAGGAGG
1 GGTGGAGGGG-AGGAGG
29894 TGTACGAGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
17 18 0.29
18 45 0.71
ACGTcount: A:0.19, C:0.00, G:0.68, T:0.12
Consensus pattern (17 bp):
GGTGGAGGGGAGGAGGA
Found at i:29892 original size:21 final size:21
Alignment explanation
Indices: 29839--29935 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
29829 AGGTGGAGGT
*
29839 GGAGGTGGAGG-GGAGGT-GGA
1 GGAGGGGGAGGAGGA-GTAGGA
* *
29859 -GAGGGAGGGGGAGGAGTAGGT
1 GGAGGG-GGAGGAGGAGTAGGA
* * *
29880 GGAGGGGTAGGAGGTGTACGA
1 GGAGGGGGAGGAGGAGTAGGA
* * *
29901 GGAGGGGGAGTAGGAGCAGGG
1 GGAGGGGGAGGAGGAGTAGGA
*
29922 GGAGGGGGAAGAGG
1 GGAGGGGGAGGAGG
29936 TGCGCTAGGA
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
19 4 0.07
20 6 0.11
21 42 0.74
22 5 0.09
ACGTcount: A:0.24, C:0.02, G:0.66, T:0.08
Consensus pattern (21 bp):
GGAGGGGGAGGAGGAGTAGGA
Found at i:29936 original size:42 final size:42
Alignment explanation
Indices: 29870--30232 Score: 334
Period size: 42 Copynumber: 9.1 Consensus size: 42
29860 AGGGAGGGGG
* * * *
29870 AGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
** *
29912 AGGAGCAGGGGGAGGGGGAAGAGGTG--CG-CTA---GGAGG
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
* * * *
29948 AGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
**
29990 AGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
* **
30032 AGGAGCAGGAGGAGGGGGGAA-AGGTGCGCGAGGAGGGGGAGT
1 AGGAGCAGGGGGA-GGGGGAAGAGGTGTACGAGGAGGGGGAGT
* ** *
30074 ------AGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
*
30110 AGGAGCAGGGGGAGGGGGAAGAGGTG-AGCTAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTA-CGAGGAGGGGGAGT
* *
30152 ------AGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
* **
30188 AGGAGAAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGT
1 AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
30230 AGG
1 AGG
30233 TGGAGGGGTA
Statistics
Matches: 260, Mismatches: 39, Indels: 44
0.76 0.11 0.13
Matches are distributed among these distances:
35 4 0.02
36 82 0.32
37 1 0.00
38 2 0.01
39 2 0.01
40 2 0.01
41 1 0.00
42 159 0.61
43 7 0.03
ACGTcount: A:0.25, C:0.05, G:0.61, T:0.09
Consensus pattern (42 bp):
AGGAGCAGGGGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGT
Found at i:29952 original size:78 final size:78
Alignment explanation
Indices: 29863--30034 Score: 317
Period size: 78 Copynumber: 2.2 Consensus size: 78
29853 GGTGGAGAGG
*
29863 GAGGGGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
1 GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
29928 GGAAGAGGTGCGC
66 GGAAGAGGTGCGC
*
29941 TAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
1 GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
30006 GGAAGAGGTGCGC
66 GGAAGAGGTGCGC
*
30019 GAGGAGGGGGAGTAGG
1 GAGGAGGAGGAGTAGG
30035 AGCAGGAGGA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 90 1.00
ACGTcount: A:0.24, C:0.05, G:0.62, T:0.09
Consensus pattern (78 bp):
GAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGG
GGAAGAGGTGCGC
Found at i:29969 original size:21 final size:21
Alignment explanation
Indices: 29943--30049 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
29933 AGGTGCGCTA
*
29943 GGAGGAGGAGTAGGTGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
29964 GTAGGAGGTGTACGAGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
29985 GGAGTAGGAGCAGGGGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
* * *
30006 GGAAGAGGTG-CGCGAGGAGGG
1 GGAGGAGGAGTAG-GAGGAGGG
* *
30027 GGAGTAGGAGCAGGAGGAGGG
1 GGAGGAGGAGTAGGAGGAGGG
30048 GG
1 GG
30050 GAAAGGTGCG
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.64, T:0.07
Consensus pattern (21 bp):
GGAGGAGGAGTAGGAGGAGGG
Found at i:30014 original size:120 final size:119
Alignment explanation
Indices: 29870--30154 Score: 437
Period size: 120 Copynumber: 2.4 Consensus size: 119
29860 AGGGAGGGGG
* * * * *
29870 AGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA-GGGGGAAGA
1 AGGAGCAGGGGGAGGGGGAAGAGGTG-ACGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-A
* *
29934 GGTGCGCTAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGT
64 GGTGCGCGAGGAGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
*
29990 AGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAG
1 AGGAGCAGGGGGAGGGGGAAGAGGTG-ACGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAG
*
30055 GTGCGCGAGGAGGGGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
65 GTGCGCGAGGAGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
*
30110 AGGAGCAGGGGGAGGGGGAAGAGGTGAGCTAGGAGGGGGAGTAGG
1 AGGAGCAGGGGGAGGGGGAAGAGGTGA-CGAGGAGGGGGAGTAGG
30155 TGGAGGTGGA
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
120 144 0.95
121 7 0.05
ACGTcount: A:0.25, C:0.05, G:0.61, T:0.09
Consensus pattern (119 bp):
AGGAGCAGGGGGAGGGGGAAGAGGTGACGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAAAGG
TGCGCGAGGAGGAGGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGT
Found at i:30064 original size:21 final size:21
Alignment explanation
Indices: 30003--30070 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
29993 AGCAGGGGGA
30003 GGGGGAAGAGGTGCGCGAGGA-
1 GGGGGAA-AGGTGCGCGAGGAG
* *
30024 GGGGGAGTAGGAGCAG-GAGGAG
1 GGGGGA-AAGGTGC-GCGAGGAG
30046 GGGGGAAAGGTGCGCGAGGAG
1 GGGGGAAAGGTGCGCGAGGAG
30067 GGGG
1 GGGG
30071 AGTAGGTGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.03
21 31 0.79
22 7 0.18
ACGTcount: A:0.24, C:0.07, G:0.65, T:0.04
Consensus pattern (21 bp):
GGGGGAAAGGTGCGCGAGGAG
Found at i:30082 original size:78 final size:78
Alignment explanation
Indices: 29991--30264 Score: 406
Period size: 78 Copynumber: 3.5 Consensus size: 78
29981 AGGGGGAGTA
* * ** *
29991 GGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGGGGGAA-AG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA-GGGGGAAGAG
30055 GTGCGCGAGGAGGG
65 GTGCGCGAGGAGGG
** *
30069 GGAGTAGGTGGAGGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
* *
30134 TGAGCTAGGAGGG
66 TGCGCGAGGAGGG
* *
30147 GGAGTAGGTGGAGGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
30212 TGCGCGAGGAGGG
66 TGCGCGAGGAGGG
* *
30225 GGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAG
1 GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAG
30265 GGGGAGGAGG
Statistics
Matches: 175, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
77 7 0.04
78 168 0.96
ACGTcount: A:0.25, C:0.05, G:0.62, T:0.08
Consensus pattern (78 bp):
GGAGTAGGTGGAGGGGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGGGGGAAGAGG
TGCGCGAGGAGGG
Found at i:30265 original size:120 final size:117
Alignment explanation
Indices: 29863--30270 Score: 307
Period size: 120 Copynumber: 3.5 Consensus size: 117
29853 GGTGGAGAGG
* * *
29863 GAGG-GGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGAGG
1 GAGGAGGG-GGAGTAGGTGGAGGGGGAGGAGGTGTACGAGGAGGGGGAGGAGGAGCAGGAGGAGG
* * * * *
29927 GGGAAGAGGTGCGCTAGGAGGAGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGG-
65 GGGAAGAGGTGCGCGAGGAGGGGGAGTA-G-GGAGGGGGAGG-GG-G-AAGAGGTGGC
** * * * ** *
29984 G-GGAGTAGGAGCAGGGGGAGGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGAGCAGGAGGAGGG
1 GAGGAGGGGGAGTAGGTGGAGGGGGAGGAGGTGTACGAGGAGGGGGAGGAGGAGCAGGAGGA-GG
* ** * *
30048 GGGAA-AGGTGCGCGAGGAGGGGGAGT----AGGTGGAGGGATAGGAGGTGTAC
65 GGGAAGAGGTGCGCGAGGAGGGGGAGTAGGGAGGGGGAGGGGGAAGAGGTG-GC
* * * ** * * *
30097 GAGGAGGGGGAGTAGGAGCAGGGGGAGG-GG-G-AAGAGGTGAGCTAGGAGGGGGAGTAGGTGGA
1 GAGGAGGGGGAGTAGGTGGAGGGGGAGGAGGTGTACGA-G-GAG-GGGGAGGAGGAGCAGGAGGA
* **
30159 GGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGAGGGGGAAGAGGTGCGC
63 GGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGG-G-AGGGGGAGGGGGAAGAGGTG-GC
* *
30217 GAGGAGGGGGAGTAGGTGGAGGGGTAGGAGGTGTACGAGGAGGGGGAGGGGGAG
1 GAGGAGGGGGAGTAGGTGGAGGGGGAGGAGGTGTACGAGGAGGGGGAGGAGGAG
30271 GAGGCGTGTT
Statistics
Matches: 222, Mismatches: 47, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
111 8 0.04
112 2 0.01
113 13 0.06
114 60 0.27
120 120 0.54
121 14 0.06
122 2 0.01
123 3 0.01
ACGTcount: A:0.25, C:0.04, G:0.62, T:0.09
Consensus pattern (117 bp):
GAGGAGGGGGAGTAGGTGGAGGGGGAGGAGGTGTACGAGGAGGGGGAGGAGGAGCAGGAGGAGGG
GGAAGAGGTGCGCGAGGAGGGGGAGTAGGGAGGGGGAGGGGGAAGAGGTGGC
Found at i:30274 original size:36 final size:36
Alignment explanation
Indices: 30046--30274 Score: 165
Period size: 36 Copynumber: 6.1 Consensus size: 36
30036 GCAGGAGGAG
** *
30046 GGGGGAA-AGGTGCGCGAGGAGGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
** * *
30081 GGGATAGGAGGTGTACGAGGAGGGGGAGTAGGAGCAGGGGGA
1 GGGGGAAGAGGTGTACGAGGA-GGGG-G-A-G-G-AGGTGGA
* *
30123 GGGGGAAGAGGTG-AGCTAGGAGGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTA-CGAGGAGGGGGAGGAGGTGGA
* *
30159 GGTGGAAGAGGTGTACGAGGAGGGGGAGTAGGAGAAGGGGGA
1 GGGGGAAGAGGTGTACGAGGA-GGGG-G-A-G-G-AGGTGGA
** *
30201 GGGGGAAGAGGTGCGCGAGGAGGGGGAGTAGGTGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
* * * *
30237 GGGGTAGGAGGTGTACGAGGAGGGGGAGGGGGAGGA
1 GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
30273 GG
1 GG
30275 CGTGTTCGGA
Statistics
Matches: 150, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
35 4 0.03
36 71 0.47
37 9 0.06
38 4 0.03
39 4 0.03
40 4 0.03
41 9 0.06
42 45 0.30
ACGTcount: A:0.24, C:0.04, G:0.62, T:0.09
Consensus pattern (36 bp):
GGGGGAAGAGGTGTACGAGGAGGGGGAGGAGGTGGA
Found at i:30433 original size:27 final size:27
Alignment explanation
Indices: 30395--30447 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
30385 GAGGAGGGGA
30395 GGGGAGGAGGACGACGGTTACTAGGAG
1 GGGGAGGAGGACGACGGTTACTAGGAG
*
30422 GGGGAGGGGGACGACGGTTACTAGGA
1 GGGGAGGAGGACGACGGTTACTAGGA
30448 TTGAGAGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.53, T:0.11
Consensus pattern (27 bp):
GGGGAGGAGGACGACGGTTACTAGGAG
Found at i:31360 original size:15 final size:16
Alignment explanation
Indices: 31328--31358 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31318 TCCAACGATC
31328 CTAAAAAGTTATAAAA
1 CTAAAAAGTTATAAAA
*
31344 CTAAAAAGTTTTAAA
1 CTAAAAAGTTATAAA
31359 CTGTGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
CTAAAAAGTTATAAAA
Found at i:31387 original size:2 final size:2
Alignment explanation
Indices: 31380--31421 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31370 GATTATAGCT
31380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31422 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31896 original size:2 final size:2
Alignment explanation
Indices: 31889--31961 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
31879 GATCATTCCC
31889 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31929 AT AT AT AT AT AT AT AT AT -T 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
31962 TTTAATAGTT
Statistics
Matches: 68, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 65 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:31915 original size:21 final size:21
Alignment explanation
Indices: 31889--31961 Score: 119
Period size: 21 Copynumber: 3.4 Consensus size: 21
31879 GATCATTCCC
31889 ATATATATAATATATATATAT
1 ATATATATAATATATATATAT
*
31910 ATATATATTATATATATATAT
1 ATATATATAATATATATATAT
31931 ATATATATATATATATTATATAT
1 ATATATATA-ATATA-TATATAT
31954 ATATATAT
1 ATATATAT
31962 TTTAATAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 28 0.58
22 5 0.10
23 15 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATATAATATATATATAT
Found at i:32879 original size:11 final size:12
Alignment explanation
Indices: 32853--32896 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
32843 GCTGCTACAA
32853 AATAATTATTTT
1 AATAATTATTTT
32865 -ATAA-TATTTT
1 AATAATTATTTT
32875 AATAA--A-TTT
1 AATAATTATTTT
32884 AATAATTATTTT
1 AATAATTATTTT
32896 A
1 A
32897 TGATTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.29
10 7 0.25
11 9 0.32
12 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATAATTATTTT
Found at i:34497 original size:38 final size:39
Alignment explanation
Indices: 34455--34533 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
34445 CTTAACATTG
34455 AATTTTGAACGGAGGT-G-CTAAAATGAAACAAAAACTAA
1 AATTTTGAAC-GAGGTGGACTAAAATGAAACAAAAACTAA
* * *
34493 AATTTTTAACGATGTGGAACTAAAATGAAATAAAAACTAA
1 AATTTTGAACGAGGTGG-ACTAAAATGAAACAAAAACTAA
34533 A
1 A
34534 CTTTAGGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 4 0.11
38 10 0.29
40 21 0.60
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (39 bp):
AATTTTGAACGAGGTGGACTAAAATGAAACAAAAACTAA
Found at i:35658 original size:26 final size:26
Alignment explanation
Indices: 35629--35681 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35619 AACTTTCGAA
35629 AGATAGTTTCGAAACTCTTAAAAAGT
1 AGATAGTTTCGAAACTCTTAAAAAGT
35655 AGATAGTTTCGAAACTCTTAAAAAGT
1 AGATAGTTTCGAAACTCTTAAAAAGT
35681 A
1 A
35682 TCGAAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (26 bp):
AGATAGTTTCGAAACTCTTAAAAAGT
Done.