Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2168636 original size:60 final size:60
Alignment explanation
Indices: 2168572--2168885 Score: 510
Period size: 60 Copynumber: 5.2 Consensus size: 60
2168562 ATCATCATCA
2168572 AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
* *
2168632 AATCATTACT--ATCAAATTACTATTAAATCATTAAAT-ATTAATAATAATTTCATTATTACTAT
1 AATCATTACTAAATC--ATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTAC--T
*
2168694 CAAATCATTACTAAATCATTACTATCAAATCATACATAACTAATAATAATTTCATTATTACT
1 --AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
2168756 AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
2168816 AATCATTACTAAATCATTACTATC-AATCATACATAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
2168875 AATCATTACTA
1 AATCATTACTA
2168886 TCAAATTACT
Statistics
Matches: 238, Mismatches: 6, Indels: 21
0.90 0.02 0.08
Matches are distributed among these distances:
58 3 0.01
59 46 0.19
60 130 0.55
61 4 0.02
62 2 0.01
63 4 0.02
64 46 0.19
66 3 0.01
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (60 bp):
AATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
Found at i:2168705 original size:14 final size:14
Alignment explanation
Indices: 2168686--2168726 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2168676 TAATTTCATT
2168686 ATTACTATCAAATC
1 ATTACTATCAAATC
2168700 ATTAC--T-AAATC
1 ATTACTATCAAATC
2168711 ATTACTATCAAATC
1 ATTACTATCAAATC
2168725 AT
1 AT
2168727 ACATAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 10 0.42
12 1 0.04
13 1 0.04
14 12 0.50
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTACTATCAAATC
Found at i:2168706 original size:124 final size:123
Alignment explanation
Indices: 2168567--2168913 Score: 582
Period size: 124 Copynumber: 2.8 Consensus size: 123
2168557 TTTAAATCAT
2168567 CATCAAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
1 CATCAAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
2168632 AATCATTACTATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATTATTA
66 AATCATTACTATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATTATTA
*
2168690 CTATCAAATCATTACTAAATCATTACTATCAAATCATACATAACTAATAATAATTTCATTATTAC
1 C-ATCAAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTAC
* *
2168755 TAATCATTACTA--AATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTA
65 TAATCATTACTATCAA--ATTACTATTAAATCATTAAAT-ATTAATAATAATTTCATTATTA
2168814 C-T--AATCATTACTAAATCATTACTATC-AATCATACATAATTAATAATAATTTCATTATTACT
1 CATCAAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
2168875 AATCATTACTATCAAATTACTATTAAATCATTAAATATT
66 AATCATTACTATCAAATTACTATTAAATCATTAAATATT
2168914 CTTGCCAATA
Statistics
Matches: 211, Mismatches: 6, Indels: 18
0.90 0.03 0.08
Matches are distributed among these distances:
119 62 0.29
120 28 0.13
121 2 0.01
122 3 0.01
123 5 0.02
124 111 0.53
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (123 bp):
CATCAAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACT
AATCATTACTATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATTATTA
Found at i:2168774 original size:21 final size:21
Alignment explanation
Indices: 2168750--2168837 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
2168740 TAATTTCATT
2168750 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
2168771 ATTACT-ATCA-AATCATACATA
1 ATTACTAATCATTA-C-TAAATC
* * * *
2168792 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
2168810 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
2168831 ATTACTA
1 ATTACTA
2168838 TCAATCATAC
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
20 6 0.12
21 24 0.49
22 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:2170994 original size:26 final size:27
Alignment explanation
Indices: 2170954--2171007 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
2170944 TTATATAATC
*
2170954 TAATATAAACTTAAACTAACAAATTAA
1 TAATATAAACTTAAACTAACAAACTAA
2170981 TAATAT-AACTTAAACTAACAAACTAA
1 TAATATAAACTTAAACTAACAAACTAA
2171007 T
1 T
2171008 TAACTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (27 bp):
TAATATAAACTTAAACTAACAAACTAA
Found at i:2171665 original size:30 final size:30
Alignment explanation
Indices: 2171625--2171731 Score: 178
Period size: 30 Copynumber: 3.6 Consensus size: 30
2171615 TTTGGCGAGC
2171625 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
2171655 TGGCCGTGCATAGAGGTCGTTGGGCGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
2171685 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
2171715 TGGGCGTGCATGGAGGT
1 TGGGCGTGCATGGAGGT
2171732 TGAGGTAGGT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.23
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:2171720 original size:10 final size:10
Alignment explanation
Indices: 2171645--2171727 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 10
2171635 TGGAGGTCGT
2171645 TGGGCGTGCA
1 TGGGCGTGCA
*
2171655 TGGCCGTGCA
1 TGGGCGTGCA
2171665 TAGAGGTCGT---
1 T-G-GG-CGTGCA
*
2171675 TGGGCGTGCC
1 TGGGCGTGCA
*
2171685 TGGGCATGCA
1 TGGGCGTGCA
*
2171695 TGGAG-GT-CGT
1 TGG-GCGTGC-A
2171705 TGGGCGTGCA
1 TGGGCGTGCA
2171715 TGGGCGTGCA
1 TGGGCGTGCA
2171725 TGG
1 TGG
2171728 AGGTTGAGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 3 0.05
10 41 0.73
11 3 0.05
12 1 0.02
13 3 0.05
ACGTcount: A:0.11, C:0.19, G:0.47, T:0.23
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:2171773 original size:29 final size:28
Alignment explanation
Indices: 2171738--2171853 Score: 160
Period size: 29 Copynumber: 4.0 Consensus size: 28
2171728 AGGTTGAGGT
*
2171738 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGC-GGGCGTGCATGGCGACCTACC
2171767 AGGTCGCTGGGCGTGCATGGCGACCTACC
1 AGGTCGC-GGGCGTGCATGGCGACCTACC
***
2171796 AGGTCGCCGGGCGTGCATGGCGACCTGGT
1 AGGTCG-CGGGCGTGCATGGCGACCTACC
2171825 AGGTCGTCGGGCGTGCATGGCGACCTACC
1 AGGTCG-CGGGCGTGCATGGCGACCTACC
2171854 CCCGGTACTG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 76 0.99
30 1 0.01
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (28 bp):
AGGTCGCGGGCGTGCATGGCGACCTACC
Found at i:2180703 original size:28 final size:28
Alignment explanation
Indices: 2180653--2180746 Score: 154
Period size: 28 Copynumber: 3.4 Consensus size: 28
2180643 TTTGTTCGGG
*
2180653 TCGGGTCGGG-TTTTTTGAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
2180680 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
2180708 TCGGGTCGGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
2180736 TCGGGTTGGGT
1 TCGGGTCGGGT
2180747 CGGGTTCGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 10 0.16
28 52 0.84
ACGTcount: A:0.12, C:0.07, G:0.37, T:0.44
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:2181376 original size:18 final size:17
Alignment explanation
Indices: 2181332--2181377 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2181322 ATGGAATTGG
* *
2181332 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAA
*
2181349 ATTGCAATTCCTTCACAA
1 ATTCCAATTCC-TCACAA
2181367 ATTCCAATTCC
1 ATTCCAATTCC
2181378 ATCATAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (17 bp):
ATTCCAATTCCTCACAA
Found at i:2183560 original size:66 final size:63
Alignment explanation
Indices: 2183453--2183575 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 63
2183443 TTTGTTGAAG
* *
2183453 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATGCCATT
2183518 A
63 A
* *
2183519 GTGCATCGATGCATAAGGAGTGCATCGATGCACATGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCAC-T-CATTAAAATAAAAACATCGAAT
2183576 AGGATTTACG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 10 0.20
66 39 0.76
67 1 0.02
68 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATGCCATTA
Found at i:2184195 original size:22 final size:22
Alignment explanation
Indices: 2184163--2184243 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 22
2184153 GGGTATATTA
2184163 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
* *
2184185 GTCCTTTGGGACGTATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
* * ** *
2184207 GTCTTTCGAGATGTATCAAGTG
1 GTCCTTCGGGACATATCCAGTG
*
2184229 GTCATTCGGGACATA
1 GTCCTTCGGGACATA
2184244 GTGGTCTTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGACATATCCAGTG
Found at i:2184248 original size:18 final size:18
Alignment explanation
Indices: 2184225--2184259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2184215 AGATGTATCA
*
2184225 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGAGACAT
*
2184243 AGTGGTCTTTCGAGACA
1 AGTGGTCATTCGAGACA
2184260 AATACTGAAC
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:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:2190915 original size:22 final size:22
Alignment explanation
Indices: 2190866--2190917 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2190856 TATATTAGTT
*
2190866 ATTCGAGACGTATCCAGTGGTC
1 ATTCGGGACGTATCCAGTGGTC
* *
2190888 CTTCGGGACGTATCTAGTGGTC
1 ATTCGGGACGTATCCAGTGGTC
2190910 ATTCGGGA
1 ATTCGGGA
2190918 AAAATACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (22 bp):
ATTCGGGACGTATCCAGTGGTC
Found at i:2202444 original size:20 final size:22
Alignment explanation
Indices: 2202410--2202450 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2202400 AGAGTTTTAG
*
2202410 GTTTTTTTAATTATAATATTAA
1 GTTTTTTTAATTATAAAATTAA
2202432 GTTTTTTT-A-TATAAAATTA
1 GTTTTTTTAATTATAAAATTA
2202451 TTTTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
GTTTTTTTAATTATAAAATTAA
Found at i:2203664 original size:20 final size:21
Alignment explanation
Indices: 2203639--2203678 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2203629 CTCTACATAG
2203639 TAGTATCTG-TACCAT-AGGCA
1 TAGTATC-GATACCATCAGGCA
2203659 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
2203679 CCTAACGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 13 0.72
21 4 0.22
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:2207814 original size:19 final size:19
Alignment explanation
Indices: 2207790--2207864 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
2207780 ACCCTGTGGA
*
2207790 GGGTATCGGTACCCTTAGG
1 GGGTATCGATACCCTTAGG
* * *
2207809 GGGTATCAATACCTATTTAAAGA
1 GGGTATCGATACC--CTT--AGG
*
2207832 GGGTATCGGTACCCTTATGG
1 GGGTATCGATACCCTTA-GG
2207852 GGGTATCGATACC
1 GGGTATCGATACC
2207865 TATTCAAAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
19 12 0.29
20 13 0.31
21 4 0.10
23 13 0.31
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (19 bp):
GGGTATCGATACCCTTAGG
Found at i:2207834 original size:42 final size:43
Alignment explanation
Indices: 2207788--2207882 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
2207778 AGACCCTGTG
*
2207788 GAGGGTATCGGTACCCTTA-GGGGGTATCAATACCTATTTAAA
1 GAGGGTATCGGTACCCTTATGGGGGTATCAATACCTATTCAAA
*
2207830 GAGGGTATCGGTACCCTTATGGGGGTATCGATACCTATTCAAA
1 GAGGGTATCGGTACCCTTATGGGGGTATCAATACCTATTCAAA
*
2207873 GGGGGTATCG
1 GAGGGTATCG
2207883 ATAATCTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 19 0.39
43 30 0.61
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
GAGGGTATCGGTACCCTTATGGGGGTATCAATACCTATTCAAA
Found at i:2207844 original size:23 final size:23
Alignment explanation
Indices: 2207806--2207885 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
2207796 CGGTACCCTT
*
2207806 AGGGGGTATCAATACCTATTTAA
1 AGGGGGTATCGATACCTATTTAA
* * *
2207829 AGAGGGTATCGGTACC--CTT-A
1 AGGGGGTATCGATACCTATTTAA
* *
2207849 TGGGGGTATCGATACCTATTCAA
1 AGGGGGTATCGATACCTATTTAA
2207872 AGGGGGTATCGATA
1 AGGGGGTATCGATA
2207886 ATCTATGCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 14 0.32
21 2 0.05
22 1 0.02
23 27 0.61
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (23 bp):
AGGGGGTATCGATACCTATTTAA
Found at i:2214798 original size:21 final size:21
Alignment explanation
Indices: 2214774--2214816 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2214764 CCCAGAATAG
*
2214774 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
2214795 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
2214816 A
1 A
2214817 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:2214996 original size:34 final size:36
Alignment explanation
Indices: 2214927--2214996 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
2214917 AAACCTGCAG
* *
2214927 GGGTATCTGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
2214963 GGGTA-CTGTACCCCCT-GGGGGGGAATCTATACCC
1 GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
2214997 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 16 0.50
35 11 0.34
36 5 0.16
ACGTcount: A:0.14, C:0.29, G:0.34, T:0.23
Consensus pattern (36 bp):
GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
Found at i:2215120 original size:28 final size:30
Alignment explanation
Indices: 2215089--2215145 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
2215079 AAACTTTGAA
2215089 TAAATTC-ATTAAGTCCAAAAA-CATTTTT
1 TAAATTCAATTAAGTCCAAAAACCATTTTT
*
2215117 TAAATTCAATTCAGTCCAAAAACCATTTT
1 TAAATTCAATTAAGTCCAAAAACCATTTT
2215146 GCCTTAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
29 13 0.50
30 6 0.23
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTT
Found at i:2217306 original size:23 final size:23
Alignment explanation
Indices: 2217266--2217320 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2217256 TCGAGGGTTA
* *
2217266 TACGTAGTCCTTCGGGATAAATC
1 TACGTGGTCATTCGGGATAAATC
* *
2217289 TATGTGGTCATTCGGGATAATTC
1 TACGTGGTCATTCGGGATAAATC
2217312 TACGTGGTC
1 TACGTGGTC
2217321 CTTCATGACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (23 bp):
TACGTGGTCATTCGGGATAAATC
Found at i:2217336 original size:24 final size:24
Alignment explanation
Indices: 2217307--2217362 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2217297 CATTCGGGAT
* * * *
2217307 AATTCTACGTGGTCCTTCATGACA
1 AATTCTACGCGCTCATTCAGGACA
2217331 AATTCTACGCGCTCATTCAGGACA
1 AATTCTACGCGCTCATTCAGGACA
2217355 AATTCTAC
1 AATTCTAC
2217363 ATGACACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (24 bp):
AATTCTACGCGCTCATTCAGGACA
Found at i:2224437 original size:59 final size:59
Alignment explanation
Indices: 2224339--2224458 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 59
2224329 AGAATGGATT
* * * *
2224339 TGGATTCTGAACAGATTATTGTGGAAGAAATTTTAGAAATGAACCAATTTCAAATAAAG
1 TGGATTCTAAACAAATTATGGTGGAAGAAATTTCAGAAATGAACCAATTTCAAATAAAG
* * *
2224398 TGGATTCTAAACAAATTATGGTGGAAGAAATTTCGGAAATGAATCAATTTCAAGTAAAG
1 TGGATTCTAAACAAATTATGGTGGAAGAAATTTCAGAAATGAACCAATTTCAAATAAAG
2224457 TG
1 TG
2224459 TTTTTGATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (59 bp):
TGGATTCTAAACAAATTATGGTGGAAGAAATTTCAGAAATGAACCAATTTCAAATAAAG
Found at i:2236488 original size:16 final size:15
Alignment explanation
Indices: 2236461--2236503 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
2236451 AAAATTTATA
*
2236461 TATTTGATATAATTT
1 TATTTTATATAATTT
2236476 TATTTTAATATAATTT
1 TATTTT-ATATAATTT
*
2236492 TAGTTTATATAA
1 TATTTTATATAA
2236504 AAATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
TATTTTATATAATTT
Found at i:2243031 original size:2 final size:2
Alignment explanation
Indices: 2243011--2243062 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
2243001 CACCGTTATT
2243011 TA TA TA -A TA T- TA TA T- TA TA TA -A T- 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
2243048 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2243063 TAACACATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2243035 original size:8 final size:9
Alignment explanation
Indices: 2243007--2243064 Score: 68
Period size: 10 Copynumber: 6.6 Consensus size: 9
2242997 CGTCCACCGT
2243007 TATT-TATA
1 TATTATATA
*
2243015 TAATAT-TA
1 TATTATATA
2243023 TATTATATA
1 TATTATATA
2243032 -ATTATATA
1 TATTATATA
2243040 TATATATATA
1 TAT-TATATA
2243050 TATATATATA
1 TAT-TATATA
2243060 TATTA
1 TATTA
2243065 ACACATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 18 0.41
9 7 0.16
10 19 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TATTATATA
Found at i:2244152 original size:15 final size:17
Alignment explanation
Indices: 2244129--2244165 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2244119 TGTATGTATA
2244129 TATTATATTTT-TTT-G
1 TATTATATTTTCTTTAG
*
2244144 TATTTTATTTTCTTTAG
1 TATTATATTTTCTTTAG
2244161 TATTA
1 TATTA
2244166 ATAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (17 bp):
TATTATATTTTCTTTAG
Found at i:2246987 original size:24 final size:24
Alignment explanation
Indices: 2246960--2247008 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2246950 ATGGAAAGAC
* *
2246960 TTAGCCAAGTCTTTCTTGGAGCAA
1 TTAGCCAAGTATTTCTTAGAGCAA
2246984 TTAGCCAAGTATTTCTTAGAGCAA
1 TTAGCCAAGTATTTCTTAGAGCAA
2247008 T
1 T
2247009 ACAAGCATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (24 bp):
TTAGCCAAGTATTTCTTAGAGCAA
Found at i:2248537 original size:95 final size:96
Alignment explanation
Indices: 2248359--2248621 Score: 370
Period size: 95 Copynumber: 2.7 Consensus size: 96
2248349 AGATTATAAT
*
2248359 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
2248424 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
66 TGGATAAGATTCAACTAGCCTAATAAAGGTG
* *
2248455 ATTATA-ATGTACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* * *
2248519 TGGATAATATTCAACTAGCCTGATAGAGGTG
66 TGGATAAGATTCAACTAGCCTAATAAAGGTG
* * * *
2248550 ATTATAACATATATACAATGATA--TTAAGTTGTCCCTCTAGAGCAATTGGTTAAATGCTCCGGC
1 ATTAT---ATATATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGC
2248613 TTTATGGAT
62 TTTATGGAT
2248622 TTAGCTAGCC
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
95 87 0.58
96 6 0.04
98 46 0.31
99 8 0.05
100 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
TGGATAAGATTCAACTAGCCTAATAAAGGTG
Found at i:2250203 original size:25 final size:28
Alignment explanation
Indices: 2250148--2250203 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
2250138 TTGAGACATT
* *
2250148 TTCCTTGAAACAAAATCTTTGAATTTGTC
1 TTCCTTGAAACAAAATCTTTG-ATCTCTC
2250177 TTCCTTGAAAC-AAAT-TTTG-TCTCTC
1 TTCCTTGAAACAAAATCTTTGATCTCTC
2250202 TT
1 TT
2250204 GAGACAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 6 0.24
27 4 0.16
28 4 0.16
29 11 0.44
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (28 bp):
TTCCTTGAAACAAAATCTTTGATCTCTC
Found at i:2250250 original size:35 final size:34
Alignment explanation
Indices: 2249914--2250161 Score: 156
Period size: 36 Copynumber: 7.2 Consensus size: 34
2249904 AATTTACTCA
*
2249914 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTT
1 AAACAAA--TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
2249950 AAAACAAATTTTGTGTCTCTTGAGACATTTTCTCTT
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
2249986 AAAACAAA-TTGTCACTCTTGAGACAGTTTCCCTT
1 -AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
2250020 GAAACAAA-----ATCT-TTGA-ATCTGTTTTTCTT
1 -AAACAAATTTGTCTCTCTTGAGA-CAGTTTCTCTT
* * *
2250049 GAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTT
1 -AAACAAATTT-GTCTCTCTTGAGACAGTTTCTCTT
* * * *
2250085 AAAACAAATTTTGCCTCTCTTGAGAAATTTTTTCTT
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
2250121 AAAACAAATTT-TATCTCTTGAGACATTTTC-CTT
1 -AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
2250154 GAAACAAA
1 -AAACAAA
2250162 ATCTTTGAAT
Statistics
Matches: 170, Mismatches: 31, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
28 1 0.01
29 20 0.12
30 2 0.01
33 10 0.06
34 44 0.26
35 5 0.03
36 77 0.45
37 11 0.06
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (34 bp):
AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:2250321 original size:133 final size:133
Alignment explanation
Indices: 2249913--2250357 Score: 590
Period size: 133 Copynumber: 3.3 Consensus size: 133
2249903 TAATTTACTC
*
2249913 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTGTCTCTTGAGACAT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
* * * *
2249978 TTTCTCTTAAAACAAATTGTCACTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTT
65 TTTCTCTTAAAA-AATTTGTCTCTCTTGAGAAAATTTCCCTTGAAACAAAATCTTTGAATCTG-T
*
2250043 TTTCTT
128 TTCCTT
* * * * * *
2250049 GAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAAAACAAATTTTGCCTCTCTTGAGAAATT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
* * * * *
2250114 TTTTCTTAAAACAAATTT-TATCTCTTGAG-ACATTTTCCTTGAAACAAAATCTTTGAATTTGTC
66 TTCTCTT-AAA-AAATTTGTCTCTCTTGAGAAAATTTCCCTTGAAACAAAATCTTTGAATCTGT-
2250177 TTCCTT
128 TTCCTT
*
2250183 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAA-TTTGTCTCTCTTGAGACATT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
* *
2250247 TTCTCTTAAAAATTTTGTCTCTCTTGAGAAAATTTCCCTTGAAACAAAATCTTTGAATCTATTTC
66 TTCTCTTAAAAAATTTGTCTCTCTTGAGAAAATTTCCCTTGAAACAAAATCTTTGAATCTGTTT-
2250312 CCTT
130 CCTT
* * * *
2250316 AAAACAAGTTTTGTCTCTATTGAGACAGTTTCTCTTGAAACA
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACA
2250358 CAAAATCTTT
Statistics
Matches: 269, Mismatches: 34, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
131 5 0.02
132 15 0.06
133 95 0.35
134 73 0.27
135 66 0.25
136 14 0.05
137 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (133 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
TTCTCTTAAAAAATTTGTCTCTCTTGAGAAAATTTCCCTTGAAACAAAATCTTTGAATCTGTTTC
CTT
Found at i:2252375 original size:15 final size:17
Alignment explanation
Indices: 2252352--2252388 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2252342 TGTATGTATA
2252352 TATTATATTTT-TTT-G
1 TATTATATTTTCTTTAG
*
2252367 TATTTTATTTTCTTTAG
1 TATTATATTTTCTTTAG
2252384 TATTA
1 TATTA
2252389 ATAATATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (17 bp):
TATTATATTTTCTTTAG
Found at i:2257476 original size:13 final size:13
Alignment explanation
Indices: 2257458--2257483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2257448 ATCAATTAAA
2257458 TTAAAAATAATTT
1 TTAAAAATAATTT
2257471 TTAAAAATAATTT
1 TTAAAAATAATTT
2257484 CTCGAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAAATAATTT
Found at i:2265816 original size:2 final size:2
Alignment explanation
Indices: 2265809--2265851 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
2265799 TACGCACATA
2265809 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2265851 A
1 A
2265852 AAATGCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2265826 original size:15 final size:15
Alignment explanation
Indices: 2265806--2265851 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
2265796 ACATACGCAC
2265806 ATAATATATATATAT
1 ATAATATATATATAT
2265821 ATAATATATATATAT
1 ATAATATATATATAT
2265836 AT-ATATATATGATAT
1 ATAATATATAT-ATAT
2265851 A
1 A
2265852 AAATGCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATAATATATATATAT
Found at i:2265850 original size:21 final size:19
Alignment explanation
Indices: 2265809--2265851 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2265799 TACGCACATA
2265809 ATATATATATATATAATAT
1 ATATATATATATATAATAT
2265828 ATATATATATATAT-ATAT
1 ATATATATATATATAATAT
2265846 GATATA
1 -ATATA
2265852 AAATGCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATATATATATATATAATAT
Found at i:2267676 original size:36 final size:36
Alignment explanation
Indices: 2267604--2267685 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
2267594 AATTATAATC
* * *
2267604 TAATAATAAT-ACATGCAATTTTAATTATGATATAA
1 TAATAATAATAACATGCAATATTAATGATAATATAA
* * *
2267639 TAATGATAATAACATGCAATATTGATGATAATCTAA
1 TAATAATAATAACATGCAATATTAATGATAATATAA
2267675 TAATAATAATA
1 TAATAATAATA
2267686 TAAACACACA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (36 bp):
TAATAATAATAACATGCAATATTAATGATAATATAA
Found at i:2271519 original size:197 final size:198
Alignment explanation
Indices: 2271171--2271566 Score: 706
Period size: 197 Copynumber: 2.0 Consensus size: 198
2271161 CAACATTTTT
2271171 CATCTTGCCATTCTTCAATCACAATTGATGGCTCCATCATGGATTTCAAGGGATCCAACTTCGAT
1 CATCTTGCCATTCTTCAATCACAATTGATGGCTCCATCATGGATTTCAAGGGATCCAACTTCGAT
*
2271236 ATTAACCATGTAGTGTGATATAACAAATATTGCATCAACCGTTTTGTAGTCCAAACTAAAGCACA
66 ATTAACCATGTAGTATGATATAACAAATATTGCATCAACCGTTTTGTAGTCCAAACTAAAGCACA
2271301 ACACAATTTTTCAATATGAGAGTATCGAGTCTCGTAGTTAGTAAA-TTTTTACTCAAGTAAT-AA
131 ACACAATTTTTCAATATGAGAGTATCGAGTCTCGTAGTTAGTAAATTTTTTACTCAAGTAATAAA
2271364 TGG
196 TGG
* ** *
2271367 CATCTTGCCATTCTTTCAATCACAGTTGATGGCTCCATCATGTTTTTCAAGGGATCCAACTTTGA
1 CATCTTGCCATTC-TTCAATCACAATTGATGGCTCCATCATGGATTTCAAGGGATCCAACTTCGA
* *
2271432 TATTAACCATGTGGTATGATATAACAAATATTGCATCAGCCGTTTTGTAGTCCAAACTAAAGCAC
65 TATTAACCATGTAGTATGATATAACAAATATTGCATCAACCGTTTTGTAGTCCAAACTAAAGCAC
2271497 AACACAATTTTTCAATATGAGAGTATCGAGTCTCGTAGTTAGTAAATTTTTTACTCAAGTAATAA
130 AACACAATTTTTCAATATGAGAGTATCGAGTCTCGTAGTTAGTAAATTTTTTACTCAAGTAATAA
2271562 ATGG
195 ATGG
2271566 C
1 C
2271567 TCGTTCTTTT
Statistics
Matches: 190, Mismatches: 7, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
196 13 0.07
197 155 0.82
198 16 0.08
199 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (198 bp):
CATCTTGCCATTCTTCAATCACAATTGATGGCTCCATCATGGATTTCAAGGGATCCAACTTCGAT
ATTAACCATGTAGTATGATATAACAAATATTGCATCAACCGTTTTGTAGTCCAAACTAAAGCACA
ACACAATTTTTCAATATGAGAGTATCGAGTCTCGTAGTTAGTAAATTTTTTACTCAAGTAATAAA
TGG
Found at i:2273814 original size:15 final size:15
Alignment explanation
Indices: 2273796--2273838 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2273786 CGACACTTTT
*
2273796 CTTCTCCTCAGCTGG
1 CTTCTTCTCAGCTGG
* *
2273811 CTTCTTCTCCGCCGG
1 CTTCTTCTCAGCTGG
2273826 CTTCTTCTCAGCT
1 CTTCTTCTCAGCT
2273839 TTTGGTGCCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.42, G:0.16, T:0.37
Consensus pattern (15 bp):
CTTCTTCTCAGCTGG
Found at i:2286572 original size:19 final size:21
Alignment explanation
Indices: 2286531--2286573 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2286521 ATTATATAAA
*
2286531 ATATTTACTAAAAATATATTG
1 ATATTTAATAAAAATATATTG
2286552 ATATTTAAT-AAAATA-ATTG
1 ATATTTAATAAAAATATATTG
2286571 ATA
1 ATA
2286574 ATTTTCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTTAATAAAAATATATTG
Found at i:2287263 original size:20 final size:21
Alignment explanation
Indices: 2287228--2287266 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2287218 CCTTATCTAT
*
2287228 TAACTATCTATTAATTATTCA
1 TAACTATCTATGAATTATTCA
2287249 TAACTA-CTATGAATTATT
1 TAACTATCTATGAATTATT
2287267 AATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (21 bp):
TAACTATCTATGAATTATTCA
Found at i:2290036 original size:100 final size:99
Alignment explanation
Indices: 2289990--2290190 Score: 294
Period size: 100 Copynumber: 2.0 Consensus size: 99
2289980 ATATATTATT
2289990 TTTAATTAAATTCTTATTTTTTATTGAATAAATGTATGAGTAATTTTTATAAATATAATATTTAG
1 TTTAATTAAATTCTTATTTTTTATTGAATAAATGTATGAGTAA-TTTTATAAATATAATATTTAG
* * * * *
2290055 GGTTAGGTCAAATAGAGTTTAGAAAAAAATGTAAA
65 AGATAAGTCAAAAAGAATTTAGAAAAAAATGTAAA
2290090 TTTAATTAAATTCTTATTTTTTATTGAATAAATGTATGAGTAATTTTTATAAATATAATATTTAG
1 TTTAATTAAATTCTTATTTTTTATTGAATAAATGTATGAGTAA-TTTTATAAATATAATATTTAG
* * * * *
2290155 GGTTAGGTCAAATAGAGTTTAGAAAAAAATGTAAA
65 AGATAAGTCAAAAAGAATTTAGAAAAAAATGTAAA
2290190 T
1 T
2290191 AGTGTGAAGG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (99 bp):
TTTAATTAAATTCTTATTTTTTATTGAATAAATGTATGAGTAATTTTATAAATATAATATTTAGA
GATAAGTCAAAAAGAATTTAGAAAAAAATGTAAA
Found at i:2291466 original size:13 final size:13
Alignment explanation
Indices: 2291448--2291496 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
2291438 AAAGTTAGTA
2291448 AAAAATAATAAAT
1 AAAAATAATAAAT
2291461 AAAAATAATGAAAT
1 AAAAATAAT-AAAT
*
2291475 -AAAATGAATAGAGT
1 AAAAAT-AATA-AAT
2291489 AAAAATAA
1 AAAAATAA
2291497 AATAAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 15 0.48
14 11 0.35
15 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:2301878 original size:24 final size:24
Alignment explanation
Indices: 2301827--2301885 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2301817 CATCATGTTA
*
2301827 TTGATGGAATATACTTTCTCTCCT
1 TTGATGGAATTTACTTTCTCTCCT
*
2301851 TTGATAGAATTTACTTTCTCT-CT
1 TTGATGGAATTTACTTTCTCTCCT
2301874 CTTGATGGAATT
1 -TTGATGGAATT
2301886 GGATTCTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (24 bp):
TTGATGGAATTTACTTTCTCTCCT
Found at i:2302435 original size:22 final size:21
Alignment explanation
Indices: 2302387--2302515 Score: 65
Period size: 22 Copynumber: 6.2 Consensus size: 21
2302377 TAAATTATTG
**
2302387 TAAATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
*
2302408 TAAAATAAATCAAT-C-TATAC
1 T-AAATAAATCAATCCATATAA
* * *
2302428 T-AATAAAT-TAT--TTAAAA
1 TAAATAAATCAATCCATATAA
* * *
2302445 TAAATAAATCCATACAACTACAA
1 TAAATAAATCAAT-CCA-TATAA
**
2302468 T-AATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
2302488 TAAAATAAATCAATCCATACTAA
1 T-AAATAAATCAATCCATA-TAA
2302511 TAAAT
1 TAAAT
2302516 TATTTAAAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
17 6 0.07
18 14 0.17
19 2 0.02
20 7 0.09
21 4 0.05
22 42 0.51
23 7 0.09
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:2302438 original size:54 final size:53
Alignment explanation
Indices: 2302374--2302762 Score: 252
Period size: 54 Copynumber: 7.6 Consensus size: 53
2302364 ACAACTACAA
*
2302374 TAATAAATTATTGTAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATT-TAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
2302428 TAATAAATTATTTAAAATAAATAAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTT-AAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
2302485 TTTTAAAATAAATCAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* * * **
2302540 -AACTACA--A--T-AATAAATCAATCCATATTTTAAAATAAATTATTTAATA-
1 TAA-TAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * *
2302587 TAAATCAA-TATAT-ACT-AATAAAT---TA-TTTAAAATAAATCAATCCATA-
1 T-AATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
2302633 T--T---TTA---AAATAAATCAATTCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2302678 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2302732 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTT-AAATAAATCAATCCATA
2302763 CAACTACAAT
Statistics
Matches: 259, Mismatches: 43, Indels: 66
0.70 0.12 0.18
Matches are distributed among these distances:
39 2 0.01
40 6 0.02
41 2 0.01
43 3 0.01
44 20 0.08
45 1 0.00
46 18 0.07
47 3 0.01
48 24 0.09
49 5 0.02
50 14 0.05
51 4 0.02
53 2 0.01
54 112 0.43
55 6 0.02
56 5 0.02
57 12 0.05
58 20 0.08
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (53 bp):
TAATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:2302479 original size:80 final size:80
Alignment explanation
Indices: 2302389--2302842 Score: 544
Period size: 80 Copynumber: 5.9 Consensus size: 80
2302379 AATTATTGTA
* *
2302389 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
2302454 CCATACAACTACAAT
66 CCATACAACTACAAT
2302469 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
2302534 CCATACAACTACAAT
66 CCATACAACTACAAT
* * ** * * *
2302549 AATAAATCAATCCATATTTTAAAATAAATTATTTAATA-TAAATCAA-TATATACTAATAAAT--
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACT-AATAAATTATTTA-AAATAAATCA
*
2302610 -T--AT-----T-TAA-
64 ATCCATACAACTACAAT
2302617 AATAAATCAATCCATATTTTAAAATAAATCAAT---T-C--AT--A-T-TTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
2302672 TCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
2302691 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
2302756 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
2302773 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
2302838 CCATA
66 CCATA
2302843 TTTTAAAATA
Statistics
Matches: 325, Mismatches: 17, Indels: 64
0.80 0.04 0.16
Matches are distributed among these distances:
58 7 0.02
59 3 0.01
60 2 0.01
61 1 0.00
62 2 0.01
63 2 0.01
65 1 0.00
68 32 0.10
69 3 0.01
70 1 0.00
71 1 0.00
75 2 0.01
76 33 0.10
77 1 0.00
79 7 0.02
80 195 0.60
82 3 0.01
84 2 0.01
85 3 0.01
86 24 0.07
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:2302525 original size:32 final size:32
Alignment explanation
Indices: 2302486--2302941 Score: 194
Period size: 32 Copynumber: 15.4 Consensus size: 32
2302476 CAATCCATAT
2302486 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2302518 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
2302548 --T--AATAAATCAATCCATATTTTAAAATAAATTA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATTA
* **
2302580 TTTAATATAAATCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2302612 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
2302634 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* * ** * * *
2302671 TTCATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TT--TA-AAATAAATCAATCCATACT-AATAAAT---TA
2302709 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
2302742 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
2302772 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2302790 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2302822 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2302844 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2302876 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2302898 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2302930 TTTAAAATAAAT
1 TTTAAAATAAAT
2302942 TATTTTAAAA
Statistics
Matches: 327, Mismatches: 27, Indels: 140
0.66 0.05 0.28
Matches are distributed among these distances:
20 1 0.00
22 62 0.19
23 6 0.02
24 5 0.02
25 2 0.01
26 39 0.12
28 9 0.03
29 1 0.00
30 7 0.02
31 9 0.03
32 121 0.37
33 2 0.01
34 3 0.01
36 33 0.10
37 10 0.03
38 1 0.00
39 9 0.03
40 7 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:2302587 original size:22 final size:22
Alignment explanation
Indices: 2302549--2302672 Score: 92
Period size: 22 Copynumber: 5.5 Consensus size: 22
2302539 CAACTACAAT
**
2302549 AATAAATCAATCCATATTTTAA
1 AATAAATCAATTAATATTTTAA
* * *
2302571 AATAAATTATTTAATA--TAAA
1 AATAAATCAATTAATATTTTAA
* *
2302591 TCAATATATACTAATAAATTATT-TAA
1 --AATAAAT-C-AATTAAT-ATTTTAA
**
2302617 AATAAATCAATCCATATTTTAA
1 AATAAATCAATTAATATTTTAA
*
2302639 AATAAATCAATTCATATTTTAA
1 AATAAATCAATTAATATTTTAA
2302661 AATAAATCAATT
1 AATAAATCAATT
2302673 CATACTAATA
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
20 3 0.04
21 3 0.04
22 59 0.74
23 1 0.01
24 11 0.14
25 1 0.01
26 2 0.03
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATTAATATTTTAA
Found at i:2302589 original size:14 final size:14
Alignment explanation
Indices: 2302566--2302623 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
2302556 CAATCCATAT
2302566 TTTAAAATAAATTA
1 TTTAAAATAAATTA
*
2302580 TTTAATATAAATCAATA
1 TTTAAAATAAAT---TA
* *
2302597 TATACTAATAAATTA
1 TTTA-AAATAAATTA
2302612 TTTAAAATAAAT
1 TTTAAAATAAAT
2302624 CAATCCATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
14 18 0.53
15 5 0.15
17 5 0.15
18 6 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAAAATAAATTA
Found at i:2302606 original size:134 final size:137
Alignment explanation
Indices: 2302469--2302941 Score: 489
Period size: 134 Copynumber: 3.4 Consensus size: 137
2302459 CAACTACAAT
2302469 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * ** *
2302534 CCATAC-AACTACAATAATAAATCAATCCATATTTTAAAATAAATTATTTAATATAAATCAATAT
66 CCATACTAA-TA-AATATTAAATAAAT-CA-A---T-CCAT--A-T-TTTAAAATAAATCAAT-T
2302598 -ATACTAATAAATTATTTAA
118 CATACTAATAAATTATTTAA
2302617 AATAAATCAATCCATATTTTAAAATAAATCAAT---T-C--AT--A-T-TTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
2302672 TCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATA
66 CCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATA
2302737 AATTATTTAA
128 AATTATTTAA
*** * * * *
2302747 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
2302805 TCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAAT
65 TCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAAT
2302870 AAATTATTTAA
127 AAATTATTTAA
* *
2302881 AATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
2302942 TATTTTAAAA
Statistics
Matches: 285, Mismatches: 23, Indels: 42
0.81 0.07 0.12
Matches are distributed among these distances:
130 56 0.20
131 6 0.02
132 1 0.00
133 7 0.02
134 118 0.41
135 2 0.01
136 2 0.01
137 2 0.01
138 27 0.09
139 7 0.02
140 20 0.07
142 2 0.01
144 1 0.00
145 1 0.00
148 33 0.12
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (137 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACTAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAAT
TATTTAA
Found at i:2302685 original size:22 final size:22
Alignment explanation
Indices: 2302612--2302676 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
2302602 TAATAAATTA
*
2302612 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATTCATAT
2302634 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
2302656 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
2302677 CTAATAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:2302714 original size:22 final size:22
Alignment explanation
Indices: 2302688--2302730 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2302678 TAATAAATTA
2302688 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2302710 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2302731 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2302739 original size:22 final size:22
Alignment explanation
Indices: 2302690--2302738 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2302680 ATAAATTATT
**
2302690 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2302712 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2302735 TAAA
1 TAAA
2302739 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2302819 original size:22 final size:23
Alignment explanation
Indices: 2302744--2302818 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
2302734 ATAAATTATT
2302744 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
2302766 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
2302792 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
2302815 TAAA
1 TAAA
2302819 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:2302842 original size:54 final size:54
Alignment explanation
Indices: 2302580--2302941 Score: 322
Period size: 54 Copynumber: 6.8 Consensus size: 54
2302570 AAATAAATTA
* **
2302580 TTTAATATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * * * * * *
2302634 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
** * ** * ** **
2302688 TTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAAT-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
*
2302741 ATTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
2302790 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
2302844 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
2302898 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
2302942 TATTTTAAAA
Statistics
Matches: 254, Mismatches: 31, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
47 2 0.01
48 33 0.13
49 8 0.03
50 9 0.04
51 2 0.01
52 1 0.00
53 2 0.01
54 172 0.68
55 5 0.02
56 1 0.00
58 13 0.05
59 6 0.02
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:2302848 original size:22 final size:22
Alignment explanation
Indices: 2302822--2302864 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2302812 TAATAAATTA
2302822 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2302844 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
2302865 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2302873 original size:22 final size:22
Alignment explanation
Indices: 2302824--2302872 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2302814 ATAAATTATT
**
2302824 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2302846 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2302869 TAAA
1 TAAA
2302873 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2302902 original size:22 final size:22
Alignment explanation
Indices: 2302876--2302918 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2302866 TAATAAATTA
2302876 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
2302898 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
2302919 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:2302927 original size:22 final size:22
Alignment explanation
Indices: 2302878--2302926 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2302868 ATAAATTATT
**
2302878 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
2302900 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
2302923 TAAA
1 TAAA
2302927 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:2302950 original size:15 final size:15
Alignment explanation
Indices: 2302921--2303023 Score: 100
Period size: 15 Copynumber: 6.5 Consensus size: 15
2302911 AATTCATACT
2302921 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2302935 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2302950 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
2302972 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
2302987 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
2303002 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2303017 AATAAAT
1 AATAAAT
2303024 AACCTTATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.12
15 47 0.64
17 1 0.01
18 2 0.03
19 3 0.04
20 1 0.01
22 10 0.14
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2302956 original size:69 final size:67
Alignment explanation
Indices: 2302867--2303023 Score: 203
Period size: 67 Copynumber: 2.3 Consensus size: 67
2302857 AATTCATACT
*
2302867 AATAAATTA-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAA-TAAATTA
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAATT-ATA--AAGTAAATTA
2302930 -TTTAA
62 TTTTAA
* ** *
2302935 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAGTAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAGTAAATTATTTT
*
2303000 AT
66 AA
2303002 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
2303024 AACCTTATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
65 2 0.03
66 7 0.09
67 28 0.35
68 15 0.19
69 28 0.35
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAGTAAATTATTTT
AA
Found at i:2302980 original size:47 final size:49
Alignment explanation
Indices: 2302377--2303008 Score: 211
Period size: 54 Copynumber: 12.4 Consensus size: 49
2302367 ACTACAATAA
* * *
2302377 TAAATTATTGT-AAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAA-
1 TAAATTATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA--AAG
* ** *
2302431 TAAATTA-TTTAAAATAAATAAATCCATAC-AACTACAATAATAAATCAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTATAAAG
** *
2302479 TCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTA-AAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
* ** * ** ** *
2302525 TAAATCAATCCATACAACTACAAT-AATAAAT-C-AATCCAT-ATTT-TAAAA
1 TAAAT-TAT-TTTA-AAATA-AATCAATCCATACTAATAAATAATTTATAAAG
* ** *
2302573 TAAATTAT-TTAATATAAATCAATATATACTAATAAATTATTTAAAATAAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTT---ATAAAG
* * * *
2302623 TCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAA-
1 TAAAT---TATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA--AAG
* **
2302681 TAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-
1 TAAATTATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA--AAG
** *
2302735 TAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAATAATAAATCAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTATAAAG
** *
2302783 TCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTT---ATAAAG
* * *
2302833 TCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA-
1 TAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATAATTT---ATAAAG
* * *
2302887 TCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA-AAA-
1 T-AAAT--TATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
**
2302937 TAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTATTTTAAAG
1 TAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAATTTA---TAAAG
*
2302989 TAAATTATTTTATAATAAAT
1 TAAATTATTTTAAAATAAAT
2303009 TATTTTAAAA
Statistics
Matches: 469, Mismatches: 60, Indels: 100
0.75 0.10 0.16
Matches are distributed among these distances:
43 3 0.01
44 9 0.02
45 3 0.01
46 12 0.03
47 59 0.13
48 67 0.14
49 14 0.03
50 38 0.08
51 17 0.04
52 19 0.04
53 5 0.01
54 199 0.42
55 4 0.01
56 4 0.01
58 13 0.03
59 3 0.01
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (49 bp):
TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
Found at i:2325844 original size:56 final size:56
Alignment explanation
Indices: 2325758--2325868 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
2325748 GTTACTTTTT
*
2325758 AGTTGTTTTAATTTTGAATTATGATTTGCATTGCAGACCTGTATTCACTCACTTGA
1 AGTTGTTTTAATTGTGAATTATGATTTGCATTGCAGACCTGTATTCACTCACTTGA
* *
2325814 AGTTGTTTTAATTGTGAGTTATGATTTGCATTGCAGCCCTGTATTCACTCACTTG
1 AGTTGTTTTAATTGTGAATTATGATTTGCATTGCAGACCTGTATTCACTCACTTG
2325869 GCTGGGAGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (56 bp):
AGTTGTTTTAATTGTGAATTATGATTTGCATTGCAGACCTGTATTCACTCACTTGA
Found at i:2328023 original size:41 final size:41
Alignment explanation
Indices: 2327966--2328049 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
2327956 TCTTTTTCGC
2327966 TCCCCCGGAAATTGTTGACCAAGTTATTTCGACCGAGGCGA
1 TCCCCCGGAAATTGTTGACCAAGTTATTTCGACCGAGGCGA
2328007 TCCCCCGGAAATTGTTGACCAAGTTATTTCGACCGAGGCGA
1 TCCCCCGGAAATTGTTGACCAAGTTATTTCGACCGAGGCGA
2328048 TC
1 TC
2328050 TCTACTGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (41 bp):
TCCCCCGGAAATTGTTGACCAAGTTATTTCGACCGAGGCGA
Found at i:2332005 original size:37 final size:37
Alignment explanation
Indices: 2331948--2332031 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
2331938 GTGTTCAAAC
2331948 CTAAAATT-TTAAAAAATAAAAACAATCTTTTAATTA
1 CTAAAATTATTAAAAAATAAAAACAATCTTTTAATTA
2331984 CTAAAATTATTAAAAAATAAAAACAATCTTTTAATTA
1 CTAAAATTATTAAAAAATAAAAACAATCTTTTAATTA
2332021 CTAAAATTATT
1 CTAAAATTATT
2332032 TGATTCCTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 8 0.17
37 39 0.83
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (37 bp):
CTAAAATTATTAAAAAATAAAAACAATCTTTTAATTA
Found at i:2359826 original size:20 final size:20
Alignment explanation
Indices: 2359801--2359838 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2359791 TTTTCCATTA
2359801 GGGGGAATC-GATACCCCCAG
1 GGGGGAATCAG-TACCCCCAG
2359821 GGGGGAATCAGTACCCCC
1 GGGGGAATCAGTACCCCC
2359839 TGCGTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.11
Consensus pattern (20 bp):
GGGGGAATCAGTACCCCCAG
Found at i:2370721 original size:17 final size:17
Alignment explanation
Indices: 2370699--2370740 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
2370689 CGCTATGATA
2370699 TGCACAAGACCAGACAT
1 TGCACAAGACCAGACAT
2370716 TGCACAAGACCAGACAT
1 TGCACAAGACCAGACAT
2370733 TGCACAAG
1 TGCACAAG
2370741 CAGTGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (17 bp):
TGCACAAGACCAGACAT
Found at i:2376671 original size:19 final size:19
Alignment explanation
Indices: 2376647--2376698 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
2376637 GCGATTTTGA
2376647 AAAATGTATT-CTGATAATT
1 AAAATGTATTGC-GATAATT
*
2376666 AAAATGTATTGCGATAGTT
1 AAAATGTATTGCGATAATT
2376685 AAAATGTATTGCGA
1 AAAATGTATTGCGA
2376699 GAGTTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (19 bp):
AAAATGTATTGCGATAATT
Found at i:2376703 original size:19 final size:19
Alignment explanation
Indices: 2376664--2376703 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2376654 ATTCTGATAA
*
2376664 TTAAAATGTATTGCGATAG
1 TTAAAATGTATTGCGAGAG
2376683 TTAAAATGTATTGCGAGAG
1 TTAAAATGTATTGCGAGAG
2376702 TT
1 TT
2376704 TGAAAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (19 bp):
TTAAAATGTATTGCGAGAG
Found at i:2376721 original size:25 final size:22
Alignment explanation
Indices: 2376693--2376739 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
2376683 TTAAAATGTA
2376693 TTGCGAGAGTTTGAAAAACGTGTTG
1 TTGCGAGAG--TGAAAAA-GTGTTG
*
2376718 TTGCGATAGTGAAAAAGTGTTG
1 TTGCGAGAGTGAAAAAGTGTTG
2376740 CGATAGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
25 8 0.38
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (22 bp):
TTGCGAGAGTGAAAAAGTGTTG
Found at i:2376740 original size:19 final size:19
Alignment explanation
Indices: 2376716--2376752 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2376706 AAAAACGTGT
2376716 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
2376735 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
2376753 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:2379052 original size:87 final size:87
Alignment explanation
Indices: 2378952--2379368 Score: 618
Period size: 87 Copynumber: 4.8 Consensus size: 87
2378942 TACCAAGTAT
* * *
2378952 AATAACATATTAGGTACCGCTTATATAATGTAATAAGTATCATTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
* *
2379017 TACTAGAAACATTATTAAGCAC
66 TACTAGAAACATTATCAAACAC
* * * *
2379039 AATAATATATTAGGTATCACTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
2379104 TACTAGAAACATTATCAAACAC
66 TACTAGAAACATTATCAAACAC
* * * *
2379126 AATAACATATTAGGTAACGCTTATATAATGTAATAGGGAACGCTTATATAATAAAATAGATTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
2379191 TACTAGAAACATTATCAAACAC
66 TACTAGAAACATTATCAAACAC
* * *
2379213 AATAACATATTAGATACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
*
2379278 TACTAGAAACATTATCAAGCAC
66 TACTAGAAACATTATCAAACAC
* * * * * * *
2379300 AATCACATATTAGGTAGCGTTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
2379365 TACT
66 TACT
2379369 TAATTTGTTA
Statistics
Matches: 298, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 298 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (87 bp):
AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAAT
TACTAGAAACATTATCAAACAC
Found at i:2379066 original size:23 final size:23
Alignment explanation
Indices: 2379040--2379099 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2379030 ATTAAGCACA
*
2379040 ATAATATATTAGGTATCACTTAT
1 ATAATATAATAGGTATCACTTAT
*
2379063 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGGTATCACTTAT
*
2379086 ATAATAAAATAGGT
1 ATAATATAATAGGT
2379100 TAATTACTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTATCACTTAT
Found at i:2379153 original size:23 final size:23
Alignment explanation
Indices: 2379127--2379176 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2379117 ATCAAACACA
* *
2379127 ATAACATATTAGGTAACGCTTAT
1 ATAACATAATAGGGAACGCTTAT
**
2379150 ATAATGTAATAGGGAACGCTTAT
1 ATAACATAATAGGGAACGCTTAT
2379173 ATAA
1 ATAA
2379177 TAAAATAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGGAACGCTTAT
Found at i:2379183 original size:23 final size:23
Alignment explanation
Indices: 2379136--2379184 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2379126 AATAACATAT
* **
2379136 TAGGTAACGCTTATATAATGTAA
1 TAGGGAACGCTTATATAATAAAA
2379159 TAGGGAACGCTTATATAATAAAA
1 TAGGGAACGCTTATATAATAAAA
2379182 TAG
1 TAG
2379185 ATTAATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (23 bp):
TAGGGAACGCTTATATAATAAAA
Found at i:2379240 original size:23 final size:23
Alignment explanation
Indices: 2379214--2379263 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
2379204 ATCAAACACA
* *
2379214 ATAACATATTAGATACCACTTAT
1 ATAACATAATAGATAACACTTAT
** *
2379237 ATAATGTAATAGGTAACACTTAT
1 ATAACATAATAGATAACACTTAT
2379260 ATAA
1 ATAA
2379264 TAAAATAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGATAACACTTAT
Found at i:2379357 original size:23 final size:23
Alignment explanation
Indices: 2379310--2379358 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2379300 AATCACATAT
* **
2379310 TAGGTAGCGTTTATATAACGTAA
1 TAGGTAGCGCTTATATAACAAAA
*
2379333 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAACAAAA
2379356 TAG
1 TAG
2379359 ATTAATTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAACAAAA
Found at i:2379826 original size:21 final size:23
Alignment explanation
Indices: 2379769--2379826 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
2379759 TTATTAAGGA
2379769 TAACAATAACATAATATTATTTAT
1 TAACAATAA-ATAATATTATTTAT
*
2379793 TAACAAAATAATAATATTATTT-T
1 TAACAATA-AATAATATTATTTAT
2379816 TAA-AATAAATA
1 TAACAATAAATA
2379827 TTGCAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 4 0.13
24 19 0.61
25 1 0.03
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
TAACAATAAATAATATTATTTAT
Found at i:2380127 original size:24 final size:23
Alignment explanation
Indices: 2380100--2380155 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
2380090 TTATTAAGGA
2380100 TAACAATAAAATAATATTATTTAT
1 TAACAATAAAATAATATTATTT-T
2380124 TAACAA-AATAATAATATTATTTT
1 TAACAATAA-AATAATATTATTTT
2380147 TAA-AATAAA
1 TAACAATAAA
2380156 CATTGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.27
24 19 0.63
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAACAATAAAATAATATTATTTT
Found at i:2380265 original size:331 final size:331
Alignment explanation
Indices: 2379663--2380304 Score: 1230
Period size: 331 Copynumber: 1.9 Consensus size: 331
2379653 TAATAACCGC
*
2379663 TTATAACGTACAAGTTAAGTAATAATCGCTTATATAACACTATTTTGTTAATTATTTAATTTGTT
1 TTATAACGTACAAGTTAAGTAATAACCGCTTATATAACACTATTTTGTTAATTATTTAATTTGTT
*
2379728 ATTACAACATATTAGGTAAACACTTAAAATGTTATTAAGGATAACAATAACATAATATTATTTAT
66 ATTACAACATATTAGGTAAACACTTAAAATGTTATTAAGGATAACAATAAAATAATATTATTTAT
*
2379793 TAACAAAATAATAATATTATTTTTAAAATAAATATTGCAAATTTATCTATTACATTATAATTATC
131 TAACAAAATAATAATATTATTTTTAAAATAAACATTGCAAATTTATCTATTACATTATAATTATC
*
2379858 GGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGACATTTTATGCGTGCACCTCGTT
196 GGTTTCGATGTTTTTGGGATCGATACAAATTTAAATGTATCGACATTTTATGCGTGCACCTCGTT
2379923 GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATATGTCGATATTTATATTCATTAA
261 GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATATGTCGATATTTATATTCATTAA
2379988 TACTTT
326 TACTTT
2379994 TTATAACGTACAAGTTAAGTAATAACCGCTTATATAACACTATTTTGTTAATTATTTAATTTGTT
1 TTATAACGTACAAGTTAAGTAATAACCGCTTATATAACACTATTTTGTTAATTATTTAATTTGTT
2380059 ATTACAACATATTAGGTAAACACTTAAAATGTTATTAAGGATAACAATAAAATAATATTATTTAT
66 ATTACAACATATTAGGTAAACACTTAAAATGTTATTAAGGATAACAATAAAATAATATTATTTAT
*
2380124 TAACAAAATAATAATATTATTTTTAAAATAAACATTGTAAATTTATCTATTACATTATAATTATC
131 TAACAAAATAATAATATTATTTTTAAAATAAACATTGCAAATTTATCTATTACATTATAATTATC
*
2380189 GGTTTCGATGTTTTTGGGATCGATACAAATTTAAATGTATCGATATTTTATGCGTGCACCTCGTT
196 GGTTTCGATGTTTTTGGGATCGATACAAATTTAAATGTATCGACATTTTATGCGTGCACCTCGTT
2380254 GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATATGTCGATA
261 GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATATGTCGATA
2380305 CATTATGTAG
Statistics
Matches: 305, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
331 305 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (331 bp):
TTATAACGTACAAGTTAAGTAATAACCGCTTATATAACACTATTTTGTTAATTATTTAATTTGTT
ATTACAACATATTAGGTAAACACTTAAAATGTTATTAAGGATAACAATAAAATAATATTATTTAT
TAACAAAATAATAATATTATTTTTAAAATAAACATTGCAAATTTATCTATTACATTATAATTATC
GGTTTCGATGTTTTTGGGATCGATACAAATTTAAATGTATCGACATTTTATGCGTGCACCTCGTT
GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATATGTCGATATTTATATTCATTAA
TACTTT
Found at i:2380549 original size:200 final size:198
Alignment explanation
Indices: 2380155--2380595 Score: 620
Period size: 200 Copynumber: 2.2 Consensus size: 198
2380145 TTTAAAATAA
*
2380155 ACATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAAATT
1 ACATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACAAATT
* * *
2380220 TAAATGTATCGATATTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAC
66 TAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAC
*
2380285 AAACTTAAAATATGTCGATACATTATGTAGACCTATTTTATCATAAAATCGGTATATTTATACCG
131 AAACTTAAAATATGTCGATACATTATGTAGACCTATTCTATCATAAAATCGGTATATTTATACCG
2380350 AGT
196 AGT
* **
2380353 ACATTGTAAATTTATCTATTACATTGTAATTATCGGTTTCGATATTTTTGGGATCGATAC-TTTT
1 ACATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACAAATT
* *
2380417 AATAAATGTATCGACACTTTATGTATGCACCTCGTTTGGCATTCATTCTGGATAAAATA-TATCG
66 --TAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGA-AAAA-AGTATCG
*** * * * *
2380481 ACAC-TTTTTAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCGGTATATTTA
127 ACACAAACTTAAA-ATATGTCGATACATTATGTAGACCTATTCTATCATAAAATCGGTATATTTA
*
2380545 TACCGATT
191 TACCGAGT
* *
2380553 ATATTATAAATTTA-CTTATTACATTATAATTATCGGTTTCGAT
1 ACATTGTAAATTTATC-TATTACATTATAATTATCGGTTTCGAT
2380596 GTAACATATA
Statistics
Matches: 216, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
197 2 0.01
198 58 0.27
199 51 0.24
200 104 0.48
201 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (198 bp):
ACATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACAAATT
TAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAC
AAACTTAAAATATGTCGATACATTATGTAGACCTATTCTATCATAAAATCGGTATATTTATACCG
AGT
Found at i:2380739 original size:31 final size:30
Alignment explanation
Indices: 2380698--2380783 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
2380688 TTATAATAAA
*
2380698 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
2380728 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
*
2380758 TTATAAAATTATAGAT-ATAAT-ATTTT
1 TAATAAAA-TATA-ATAATAATAATTTT
2380784 AATAGTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 28 0.58
31 16 0.33
32 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:2381041 original size:21 final size:21
Alignment explanation
Indices: 2381002--2381042 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2380992 CAGTAAAAAT
* *
2381002 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
2381023 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
2381043 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:2387315 original size:22 final size:21
Alignment explanation
Indices: 2387280--2387321 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2387270 CATAATTATT
2387280 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
2387301 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
2387322 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:2395484 original size:20 final size:20
Alignment explanation
Indices: 2395444--2395484 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2395434 TTGACAAAAT
*
2395444 TAATAGATATGATTATCAGA
1 TAATAGATATGATGATCAGA
2395464 TAATAGATATAGATGAT-AGA
1 TAATAGATAT-GATGATCAGA
2395484 T
1 T
2395485 CACATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (20 bp):
TAATAGATATGATGATCAGA
Found at i:2409859 original size:13 final size:13
Alignment explanation
Indices: 2409843--2409873 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2409833 TTTGGAACTC
*
2409843 TTTTTTCTTTTAT
1 TTTTTTCTTCTAT
2409856 TTTTTTCTTCTAT
1 TTTTTTCTTCTAT
2409869 TTTTT
1 TTTTT
2409874 GGGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTCTAT
Found at i:2413291 original size:24 final size:25
Alignment explanation
Indices: 2413256--2413315 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
2413246 GGTATTGTTT
* *
2413256 TAAAAAAATAATTTTAAAAGTGTTG
1 TAAAAAAGTAATTTTAAAAGTATTG
*
2413281 T-AAAAAGTAATTTTAAAAGTATTT
1 TAAAAAAGTAATTTTAAAAGTATTG
2413305 TAAAAAAGTAA
1 TAAAAAAGTAA
2413316 AATTTAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (25 bp):
TAAAAAAGTAATTTTAAAAGTATTG
Found at i:2413310 original size:12 final size:11
Alignment explanation
Indices: 2413266--2413309 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
2413256 TAAAAAAATA
2413266 ATTTTAAAAGT
1 ATTTTAAAAGT
* *
2413277 GTTGTAAAAAGT
1 ATT-TTAAAAGT
2413289 AATTTTAAAAGT
1 -ATTTTAAAAGT
2413301 ATTTTAAAA
1 ATTTTAAAA
2413310 AAGTAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 11 0.41
12 14 0.52
13 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (11 bp):
ATTTTAAAAGT
Found at i:2428129 original size:6 final size:6
Alignment explanation
Indices: 2428118--2428143 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2428108 GGAGCGAAAG
2428118 AGAGGA AGAGGA AGAGGA AGAGGA AG
1 AGAGGA AGAGGA AGAGGA AGAGGA AG
2428144 CAGAAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:2430449 original size:17 final size:19
Alignment explanation
Indices: 2430413--2430451 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2430403 CTGTTGTATC
2430413 AATAAATGTATACAAATTT
1 AATAAATGTATACAAATTT
*
2430432 AATAAA-GTA-ACAAGTTT
1 AATAAATGTATACAAATTT
2430449 AAT
1 AAT
2430452 TTATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (19 bp):
AATAAATGTATACAAATTT
Found at i:2433967 original size:44 final size:44
Alignment explanation
Indices: 2433904--2433994 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
2433894 CGAATTAATA
2433904 TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
1 TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
2433948 TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
1 TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
2433992 TAA
1 TAA
2433995 GACGTAGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.32
Consensus pattern (44 bp):
TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
Found at i:2436282 original size:11 final size:11
Alignment explanation
Indices: 2436266--2436291 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2436256 TAATGAGACA
2436266 AATTGCAATTT
1 AATTGCAATTT
2436277 AATTGCAATTT
1 AATTGCAATTT
2436288 AATT
1 AATT
2436292 ATTGAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTGCAATTT
Found at i:2436651 original size:22 final size:22
Alignment explanation
Indices: 2436605--2436647 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2436595 TTAATTTATA
2436605 AAACGTTAAATTATAAAATAGT
1 AAACGTTAAATTATAAAATAGT
* *
2436627 AAACG-TATATTATAAATTAGT
1 AAACGTTAAATTATAAAATAGT
2436648 TAAAAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (22 bp):
AAACGTTAAATTATAAAATAGT
Found at i:2437092 original size:15 final size:15
Alignment explanation
Indices: 2437066--2437108 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2437056 TAATTTATAA
2437066 TTATACAATTAATAGT
1 TTATA-AATTAATAGT
* *
2437082 TTATAATTTAATATT
1 TTATAAATTAATAGT
2437097 TTATAAATTAAT
1 TTATAAATTAAT
2437109 TTAATGATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTATAAATTAATAGT
Found at i:2443411 original size:27 final size:28
Alignment explanation
Indices: 2443380--2443433 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2443370 ATAATAAAAA
* *
2443380 AAAAAGGTTAAATTAAAAA-AAAATATTT
1 AAAAA-GTAAAATAAAAAATAAAATATTT
2443408 AAAAAGTAAAATAAAAAATAAAATAT
1 AAAAAGTAAAATAAAAAATAAAATAT
2443434 AAATAGGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (28 bp):
AAAAAGTAAAATAAAAAATAAAATATTT
Found at i:2443654 original size:13 final size:13
Alignment explanation
Indices: 2443636--2443667 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2443626 TCTCATTTGG
2443636 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
2443649 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
2443662 TCTCTC
1 TCTCTC
2443668 GTCTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (13 bp):
TCTCTCTGCGCTC
Found at i:2444629 original size:3 final size:3
Alignment explanation
Indices: 2444621--2444646 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2444611 AAAAATGAAA
2444621 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2444647 CATATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2444792 original size:35 final size:34
Alignment explanation
Indices: 2444720--2444880 Score: 160
Period size: 34 Copynumber: 4.9 Consensus size: 34
2444710 ATAATATACG
* *
2444720 AATGTTTTCAACATGTTTCAAAA--ATAT-ATAT
1 AATGTTTTCAAAATGTTTAAAAACTATATAATAT
*
2444751 AA-GTTTTCAAAACGTTTAAAAACTATATAATAT
1 AATGTTTTCAAAATGTTTAAAAACTATATAATAT
*
2444784 AAATGTTTTCAAAATGTTTCAAAAC--TATAATAT
1 -AATGTTTTCAAAATGTTTAAAAACTATATAATAT
*
2444817 -ATGTTTTCAAAATGTTTTCAAAAATTATAT-ATAT
1 AATGTTTTCAAAATG-TTT-AAAAACTATATAATAT
*
2444851 AAT-TTTTCAAAATGATTTTAAAAATTATAT
1 AATGTTTTCAAAATG--TTTAAAAACTATAT
2444881 TTATATATAT
Statistics
Matches: 112, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
30 17 0.15
31 16 0.14
32 7 0.06
33 16 0.14
34 28 0.25
35 28 0.25
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTAAAAACTATATAATAT
Found at i:2444801 original size:65 final size:67
Alignment explanation
Indices: 2444708--2444880 Score: 214
Period size: 65 Copynumber: 2.6 Consensus size: 67
2444698 TTTTTCTTAA
*
2444708 ATATAATATACGAATGTTTTCAACATGTTTCAAAAATATATATAAGTTTTCAAAACG-TTT-AAA
1 ATATAATATA--AATGTTTTCAAAATGTTTCAAAAATATATATAAGTTTTCAAAACGTTTTCAAA
2444771 AACT
64 AACT
* * *
2444775 ATATAATATAAATGTTTTCAAAATGTTTCAAAACTATAATATATGTTTTCAAAATGTTTTCAAAA
1 ATATAATATAAATGTTTTCAAAATGTTTCAAAAATAT-ATATAAGTTTTCAAAACGTTTTCAAAA
*
2444840 ATT
65 ACT
*
2444843 ATAT-ATAT-AAT-TTTTCAAAATGATTTTAAAAAT-TATAT
1 ATATAATATAAATGTTTTCAAAATG-TTTCAAAAATATATAT
2444881 TTATATATAT
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
64 4 0.04
65 37 0.39
66 27 0.28
67 17 0.18
68 10 0.11
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (67 bp):
ATATAATATAAATGTTTTCAAAATGTTTCAAAAATATATATAAGTTTTCAAAACGTTTTCAAAAA
CT
Found at i:2445684 original size:85 final size:83
Alignment explanation
Indices: 2445475--2446186 Score: 741
Period size: 85 Copynumber: 8.6 Consensus size: 83
2445465 TGATATGACT
* * *
2445475 TCGAAGTTGAGTGTAATCGAACTCGGGAGTCTT--TGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGCTAT
* *
2445538 ACTGCAAATGATATG-CC
66 GCTGCAAATGATGTGCCC
* * * * ** * * *
2445555 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGCCAGATAACTCTTCTTGACTTAAGTT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTGG-TGGCAGATAACCCTTCTTGACTTAAGCT
*
2445620 ATGCTGCAAATGGTGTGCCC
64 ATGCTGCAAATGATGTGCCC
*
2445640 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTGGGCAGATAACCCTTCTTGACTTAAGTT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTGGT-GGCAGATAACCCTTCTTGACTTAAGCT
*
2445705 ATGCTGCAAATGGTGTGCCC
64 ATGCTGCAAATGATGTGCCC
* *
2445725 TCGAAGCTGAGTGTAATCGAACTC-GGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGCTAT
*
2445787 TCTGCAAATGATGTG-CC
66 GCTGCAAATGATGTGCCC
* * * * *** * * * *
2445804 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTGGTCACAGATAACCCTTCTAGCCTTGAGT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGG---CAGATAACCCTTCTTGACTTAAGC
*
2445869 TATGCTGTAAATGATGTGCCC
63 TATGCTGCAAATGATGTGCCC
* *
2445890 TCGAAGCTGA-TGTAATCGAACTCGGGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGCTAT
* *
2445952 TCTGCAAATGATGTGCCT
66 GCTGCAAATGATGTGCCC
* * * ** * * * *
2445970 TAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGTCACAGATAACCCTTCTAGCCTTGAGT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGG---CAGATAACCCTTCTTGACTTAAGC
*
2446034 TATGCTGTAAATGATGTGCCC
63 TATGCTGCAAATGATGTGCCC
*
2446055 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT--TGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGCTAT
* *
2446118 TCTGCAAATGATGTGCCT
66 GCTGCAAATGATGTGCCC
* * * ** *
2446136 TAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCT
2446187 GGCCTTGAGC
Statistics
Matches: 523, Mismatches: 87, Indels: 42
0.80 0.13 0.06
Matches are distributed among these distances:
79 28 0.05
80 150 0.29
81 42 0.08
82 23 0.04
83 5 0.01
84 48 0.09
85 192 0.37
86 35 0.07
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (83 bp):
TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGCTAT
GCTGCAAATGATGTGCCC
Found at i:2445794 original size:165 final size:164
Alignment explanation
Indices: 2445509--2446186 Score: 887
Period size: 165 Copynumber: 4.1 Consensus size: 164
2445499 GGGAGTCTTT
* * * * * * * * *
2445509 GGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTC
1 GGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
** * * * * * *
2445573 GAACTCGAAGGTCTTTGGTTGCCAGATAACTCTTCTTGACTTAAGTTATGCTGCAAATGGTGTGC
66 GAACTCGGGGGTCTTT-G--G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
* * * **
2445638 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTG
127 CCTAG-AGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTG
* *
2445678 GGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAATC
1 GGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
* *
2445743 GAACTC-GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTG
66 GAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCCTA
*
2445807 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTG
131 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
* * * *
2445841 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGA-TGTAA
1 G--GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
2445905 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
64 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCC
2445970 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
129 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
* * * *
2446006 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 G--GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
2446071 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCT
64 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCC
2446136 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT-
129 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
*
2446171 GGCAGATAGCCCTTCT
1 GGCAGATAACCCTTCT
2446187 GGCCTTGAGC
Statistics
Matches: 469, Mismatches: 35, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
163 20 0.04
164 35 0.07
165 240 0.51
166 105 0.22
168 1 0.00
169 46 0.10
170 22 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (164 bp):
GGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
GAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCCTA
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
Found at i:2451241 original size:30 final size:31
Alignment explanation
Indices: 2451207--2451273 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
2451197 AACAAAATGC
2451207 TAATAAAT-AAA-AAA-AATATAAAAATAATAA
1 TAATAAATGAAAGAAAGAA-ATAAAAA-AATAA
*
2451237 TAAT-AATGAAAGAAAGAAATAATAAAATAA
1 TAATAAATGAAAGAAAGAAATAAAAAAATAA
2451267 TAATAAA
1 TAATAAA
2451274 AGGTTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 3 0.09
30 16 0.50
31 11 0.34
32 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (31 bp):
TAATAAATGAAAGAAAGAAATAAAAAAATAA
Found at i:2451656 original size:13 final size:13
Alignment explanation
Indices: 2451638--2451669 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2451628 TCTCATTTGG
2451638 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
2451651 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
2451664 TCTCTC
1 TCTCTC
2451670 GTCTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (13 bp):
TCTCTCTGCGCTC
Found at i:2452640 original size:3 final size:3
Alignment explanation
Indices: 2452632--2452661 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2452622 AAAAATGAAA
2452632 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
2452662 CATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2452804 original size:71 final size:73
Alignment explanation
Indices: 2452728--2452917 Score: 218
Period size: 71 Copynumber: 2.7 Consensus size: 73
2452718 TTTTTTTCTT
* * *
2452728 AAACTATATAATATACGAATGTTTTCAACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAAC
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
2452792 GTTTT-AA
66 GTTTTCAA
* **
2452799 AAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAA
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAC-ATAATATATAAGTTTTCAAAAA
*
2452864 TGTTTTCAA
65 CGTTTTCAA
* *
2452873 AAA-T-TAT-ATATA-TAAT-TTTTCAAAATGATTTT-AAAA-ATTATATAT
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAACATAATATAT
2452918 TATATATATG
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
67 8 0.08
69 15 0.14
70 7 0.07
71 43 0.41
72 3 0.03
73 25 0.24
74 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (73 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
GTTTTCAA
Found at i:2452831 original size:11 final size:11
Alignment explanation
Indices: 2452815--2452839 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2452805 TATAATATAT
2452815 AAATGTTTTCA
1 AAATGTTTTCA
2452826 AAATGTTTTCA
1 AAATGTTTTCA
2452837 AAA
1 AAA
2452840 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2452869 original size:12 final size:12
Alignment explanation
Indices: 2452852--2452876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2452842 ATAATATATG
2452852 TGTTTTCAAAAA
1 TGTTTTCAAAAA
2452864 TGTTTTCAAAAA
1 TGTTTTCAAAAA
2452876 T
1 T
2452877 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:2452909 original size:108 final size:109
Alignment explanation
Indices: 2452677--2452942 Score: 298
Period size: 108 Copynumber: 2.4 Consensus size: 109
2452667 ATATATACAT
*
2452677 AAAT-ATTTTCAAAAAC-ATATAATATATAAA--TTTTCAAAATGTTTTTTTCTTAAACTATATA
1 AAATGATTTT-AAAAACTATATAATATATAAATGTTTTCAAAATG---TTTTCTAAAAC-ATATA
*
2452738 ATATACGAATGTTTTCAACATGTTTTCAAAAATATTATATAAGTTTTCAA
61 ATATACG-ATGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTCAA
*
2452788 AAACG-TTTTAAAAACTATATAATATATAAATGTTTTCAAAATGTTTTC-AAAAC-TATAATATA
1 AAATGATTTTAAAAACTATATAATATATAAATGTTTTCAAAATGTTTTCTAAAACATATAATATA
* *
2452850 TG-TGTTTTCAAAAATGTTTTCAAAAATTATATATATAATTTTTC-A
66 CGATGTTTTC-AAAATGTTTTCAAAAA-TAT-TATATAAGTTTTCAA
* * * * *
2452895 AAATGATTTTAAAAATTATATATTATATATATGTTTTTAAAACGTTTT
1 AAATGATTTTAAAAACTATATAATATATAAATGTTTTCAAAATGTTTT
2452943 TTTTAAAAAC
Statistics
Matches: 136, Mismatches: 11, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
105 7 0.05
106 15 0.11
107 18 0.13
108 49 0.36
109 4 0.03
110 11 0.08
111 21 0.15
113 11 0.08
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (109 bp):
AAATGATTTTAAAAACTATATAATATATAAATGTTTTCAAAATGTTTTCTAAAACATATAATATA
CGATGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTCAA
Found at i:2452915 original size:34 final size:34
Alignment explanation
Indices: 2452745--2452917 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
2452735 ATAATATACG
*
2452745 AATGTTTTCAACATGTTTTCAAAAA-TAT-TATAT
1 AATGTTTTCAAAATGTTTT-AAAAATTATATATAT
*
2452778 AA-GTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 AATGTTTTC-AAAATGTTTTAAAAA-T-TAT-ATATAT
* *
2452815 AAATGTTTTCAAAATGTTTTCAAAACTATA-ATAT
1 -AATGTTTTCAAAATGTTTTAAAAATTATATATAT
*
2452849 ATGTGTTTTCAAAAATGTTTTCAAAAATTATATATAT
1 A-ATGTTTTC-AAAATGTTTT-AAAAATTATATATAT
2452886 AAT-TTTTCAAAATGATTTTAAAAATTATATAT
1 AATGTTTTCAAAATG-TTTTAAAAATTATATAT
2452918 TATATATATG
Statistics
Matches: 118, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 11 0.09
33 11 0.09
34 30 0.25
35 23 0.19
36 12 0.10
37 10 0.08
38 15 0.13
39 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTTAAAAATTATATATAT
Found at i:2463162 original size:23 final size:23
Alignment explanation
Indices: 2463127--2463170 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2463117 TAACCTTTTA
*
2463127 AATTATTTAAAAAAAAGTATTAT
1 AATTATTTAAAAAAAAATATTAT
* *
2463150 AATTTTTTTAAAAAAAATATT
1 AATTATTTAAAAAAAAATATT
2463171 CTCAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTATTTAAAAAAAAATATTAT
Found at i:2463183 original size:24 final size:24
Alignment explanation
Indices: 2463125--2463183 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
2463115 ATTAACCTTT
*
2463125 TAAATTATTTAAAAAAAAGTATTA
1 TAAAATATTTAAAAAAAAGTATTA
** * *
2463149 TAATTTTTTTAAAAAAAA-TATTC
1 TAAAATATTTAAAAAAAAGTATTA
2463172 TCAAAATATTTA
1 T-AAAATATTTA
2463184 GAATACAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAAATATTTAAAAAAAAGTATTA
Found at i:2464160 original size:6 final size:6
Alignment explanation
Indices: 2464149--2464230 Score: 164
Period size: 6 Copynumber: 13.7 Consensus size: 6
2464139 AGACACGTAT
2464149 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
2464197 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
2464231 CGAGACGAGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:2464738 original size:6 final size:6
Alignment explanation
Indices: 2464727--2464783 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
2464717 TCTCGTCTCG
* * *
2464727 GGTCGT GGTCGT GGTCGA GGTCGA GGTCGA GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2464775 GGTCGT GGT
1 GGTCGT GGT
2464784 AATATCGCGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.05, C:0.16, G:0.51, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:2465927 original size:19 final size:18
Alignment explanation
Indices: 2465903--2465942 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2465893 TTTTTAAGTT
**
2465903 TAAATTAATTTAACATTAA
1 TAAATTAAACTAA-ATTAA
2465922 TAAATTAAACTAAATTAA
1 TAAATTAAACTAAATTAA
2465940 TAA
1 TAA
2465943 TTTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATTAAACTAAATTAA
Found at i:2470358 original size:20 final size:18
Alignment explanation
Indices: 2470333--2470379 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2470323 TATCAGTTTT
2470333 AACAATTTAAATTTATTAAA
1 AACAATTTAAA-TTA-TAAA
*
2470353 AACAA-TTACATTATAAA
1 AACAATTTAAATTATAAA
2470370 AACAATTTAA
1 AACAATTTAA
2470380 TTCAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 4 0.17
20 5 0.21
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
AACAATTTAAATTATAAA
Found at i:2472505 original size:12 final size:12
Alignment explanation
Indices: 2472490--2472516 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2472480 CCCTCATTCT
2472490 TCTCCTCCTTCA
1 TCTCCTCCTTCA
2472502 TCTCCTCCTTCA
1 TCTCCTCCTTCA
2472514 TCT
1 TCT
2472517 GGCTCTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCCTCCTTCA
Done.