Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 53 of 91
Found at i:11926852 original size:22 final size:24
Alignment explanation
Indices: 11926827--11926874 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11926817 AAAAAACCAA
*
11926827 AAATAAAA-ATAAATA-AATATAT
1 AAATAAAATATAAAAATAATATAT
11926849 AAATAAAATATAAAAATAATATAT
1 AAATAAAATATAAAAATAATATAT
11926873 AA
1 AA
11926875 TGATAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAAAATATAAAAATAATATAT
Found at i:11926872 original size:13 final size:12
Alignment explanation
Indices: 11926825--11926874 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
11926815 AAAAAAAACC
11926825 AAAAATAAA-A-
1 AAAAATAAATAT
*
11926835 ATAAATAAATAT
1 AAAAATAAATAT
*
11926847 ATAAATAAAATAT
1 AAAAAT-AAATAT
11926860 AAAAATAATATAT
1 AAAAATAA-ATAT
11926873 AA
1 AA
11926875 TGATAATTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 8 0.24
13 17 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAAATAT
Found at i:11928419 original size:107 final size:107
Alignment explanation
Indices: 11928170--11928430 Score: 296
Period size: 107 Copynumber: 2.4 Consensus size: 107
11928160 ATGCAGGTCC
* * * * *
11928170 TGCTAT-TCCGAGTCCAATAT-CTTCTGTCGTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTA
1 TGCTATCT-CGAGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTA
* **
11928233 TTTTGTTGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
64 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
* * ** * * *
11928277 TGCTATCTCGAGTCTAAT-GCTCTTCAATATTAAGTTGAAATTGGCTCCGAAATTTGGGAAATT-
1 TGCTATCTCGAGTCCAATATC-CTTCGTTGTGAAGTTGAAATTGGCTCCGAAA-CTGGGAAATTA
11928340 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
64 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
* * *
11928384 TGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 TGCTATCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
11928431 TAGCTAAAAC
Statistics
Matches: 125, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
107 110 0.88
108 15 0.12
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (107 bp):
TGCTATCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTAGT
TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
Found at i:11928924 original size:67 final size:67
Alignment explanation
Indices: 11928744--11928936 Score: 233
Period size: 67 Copynumber: 2.8 Consensus size: 67
11928734 GTCTTAAAAA
* * * * * *
11928744 AGACAGAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCATCA
11928809 AGGG
64 AGGG
* * * * * *
11928813 AGACAAAATTTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTATCAA
1 AGACAGAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCATCAA
11928878 GGG
65 GGG
* *
11928881 AGACGGAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
11928937 ATTTTCAAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 44 0.42
68 28 0.27
69 10 0.10
70 23 0.22
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (67 bp):
AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCATCAAG
GG
Found at i:11928996 original size:36 final size:33
Alignment explanation
Indices: 11928891--11929005 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
11928881 AGACGGAATT
* *
11928891 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
11928922 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
11928955 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
11928991 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
11929006 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:11929151 original size:36 final size:36
Alignment explanation
Indices: 11929051--11929407 Score: 169
Period size: 36 Copynumber: 10.4 Consensus size: 36
11929041 CAAGGATTGA
*
11929051 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
11929088 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
11929125 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
11929161 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
11929190 TGTTTCAAGGGAAACTGTTTTC-A-AG-G-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
11929219 ATGTTTCAATG-GAAACTATCTCAA-AGGAGACAAAATT
1 -TGTTTCAA-GAGAAACTGTCTCAAGA-GAGACAAAATT
* *
11929256 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
11929292 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
11929320 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
11929358 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
11929394 CATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
11929408 TGTTTTCAAT
Statistics
Matches: 253, Mismatches: 34, Indels: 67
0.71 0.10 0.19
Matches are distributed among these distances:
28 3 0.01
29 34 0.13
30 26 0.10
31 2 0.01
32 2 0.01
33 3 0.01
34 2 0.01
35 6 0.02
36 92 0.36
37 64 0.25
38 19 0.08
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:11929204 original size:29 final size:29
Alignment explanation
Indices: 11929172--11929244 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 29
11929162 GTTTAATGTA
11929172 AAACATATTCAAAGATTT-TGTTTCAAGGG
1 AAAC-TATTCAAAGATTTATGTTTCAAGGG
* * *
11929201 AAACTGTTTTC-AAGGTTTATGTTTCAATGG
1 AAAC--TATTCAAAGATTTATGTTTCAAGGG
11929231 AAACTATCTCAAAG
1 AAACTAT-TCAAAG
11929245 GAGACAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.06
29 12 0.34
30 21 0.60
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (29 bp):
AAACTATTCAAAGATTTATGTTTCAAGGG
Found at i:11929379 original size:37 final size:36
Alignment explanation
Indices: 11929321--11929407 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
11929311 TCAATGTTTA
* * * *
11929321 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
11929358 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
11929394 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
11929408 TGTTTTCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 14 0.32
37 30 0.68
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:11929383 original size:102 final size:102
Alignment explanation
Indices: 11929192--11929496 Score: 479
Period size: 102 Copynumber: 3.0 Consensus size: 102
11929182 AAAGATTTTG
* * *
11929192 TTTCAAGGGAAACTGTTTTCAAGGTTTATGTTTCAATG-GAAACTATCTCAAAGGAGACAAAA-T
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATT
11929255 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
64 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
11929294 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
11929359 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
11929396 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
11929461 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
11929497 CTTGTTTTAA
Statistics
Matches: 189, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
100 1 0.01
101 43 0.23
102 110 0.58
103 3 0.02
104 32 0.17
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:11930997 original size:183 final size:183
Alignment explanation
Indices: 11930689--11931042 Score: 636
Period size: 183 Copynumber: 1.9 Consensus size: 183
11930679 ATCAGGTTTA
* *
11930689 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACTGAATT
1 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGAGGAGCAAACACCGAATT
**
11930754 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAAGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGGTTTGAACATAATCTATTCATAAAGCCAAGGCTTTCGAGTT
*
11930819 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCATCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
11930872 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGAGGAGCAAACACCGAATT
1 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGAGGAGCAAACACCGAATT
* * *
11930937 GCCAAGTGTCCGAGCAGTGTCATTGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGGTTTGAACATAATCTATTCATAAAGCCAAGGCTTTCGAGTT
11931002 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
11931043 CGGATTTAAT
Statistics
Matches: 163, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 163 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGAGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGGTTTGAACATAATCTATTCATAAAGCCAAGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:11934607 original size:72 final size:73
Alignment explanation
Indices: 11934487--11934642 Score: 278
Period size: 72 Copynumber: 2.2 Consensus size: 73
11934477 AGGTCCCCAG
*
11934487 TGGAGTCGCCAAGCTGTCGCAACCGTCTTTCGATTGGGCCCCGAAATTGGG-TTCGACTTGAAAA
1 TGGAGTCGCCAAGCTGTCGCAACCGTCTTTCGATTGGGCCCCGAAATTGGGCTTCGAATTGAAAA
11934551 ATGTGGAT
66 ATGTGGAT
* *
11934559 TGGAGTCGCCAAGCTGTCGCAACCGTCTTTCGGTTGGGCCCCGGAATTGGGCTTCGAATTGAAAA
1 TGGAGTCGCCAAGCTGTCGCAACCGTCTTTCGATTGGGCCCCGAAATTGGGCTTCGAATTGAAAA
11934624 ATGTGGAT
66 ATGTGGAT
11934632 TGGAGTCGCCA
1 TGGAGTCGCCA
11934643 CCGATCATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 49 0.61
73 31 0.39
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (73 bp):
TGGAGTCGCCAAGCTGTCGCAACCGTCTTTCGATTGGGCCCCGAAATTGGGCTTCGAATTGAAAA
ATGTGGAT
Found at i:11934956 original size:4 final size:4
Alignment explanation
Indices: 11934949--11935000 Score: 56
Period size: 4 Copynumber: 13.2 Consensus size: 4
11934939 TGAAGAGTAA
*
11934949 AAAT AAAT -AA- AAAT AAA- AGGAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
11934995 GAAAT A
1 -AAAT A
11935001 TTAAAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 5 0.12
4 31 0.76
5 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:11935013 original size:2 final size:2
Alignment explanation
Indices: 11935006--11935035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11934996 AAATATTAAA
11935006 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
11935036 CAGTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11935308 original size:2 final size:2
Alignment explanation
Indices: 11935301--11935380 Score: 80
Period size: 2 Copynumber: 42.5 Consensus size: 2
11935291 AATATTTTAA
*
11935301 AT AT AT AT AA 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 AT AT
* * * *
11935342 AT AT CT A- AA AA AT AT AT GT AT AT AT A- AT A- AT A- 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
11935380 A
1 A
11935381 GTGTAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
1 5 0.08
2 61 0.92
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:11937662 original size:7 final size:6
Alignment explanation
Indices: 11937643--11937686 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
11937633 GTGCTACAAC
* * *
11937643 AAAAAG AAAAAG AAAGAAG AAAAAC AAAACG GAAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
11937687 CTCCTTCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11937678 original size:25 final size:24
Alignment explanation
Indices: 11937640--11937686 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
11937630 CAAGTGCTAC
11937640 AACAAAAAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
* *
11937665 AACAAAACGGAAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
11937687 CTCCTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:11938260 original size:24 final size:24
Alignment explanation
Indices: 11938233--11938282 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
11938223 GCATAAAATT
*
11938233 ATGAATTTTCATGAT-CCAATGGAC
1 ATGAATTTTCAT-ATGCCAAGGGAC
* *
11938257 ATGACTTTTGATATGCCAAGGGAC
1 ATGAATTTTCATATGCCAAGGGAC
11938281 AT
1 AT
11938283 TATCATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (24 bp):
ATGAATTTTCATATGCCAAGGGAC
Found at i:11944307 original size:24 final size:24
Alignment explanation
Indices: 11944280--11944330 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
11944270 CATAAAATTG
*
11944280 TGAATTTTCATGAT-CCAATGGACA
1 TGAATTTTCA-GATGCCAAGGGACA
*
11944304 TGAATTTTGAGATGCCAAGGGACA
1 TGAATTTTCAGATGCCAAGGGACA
11944328 TGA
1 TGA
11944331 TCATTCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (24 bp):
TGAATTTTCAGATGCCAAGGGACA
Found at i:11946564 original size:7 final size:6
Alignment explanation
Indices: 11946545--11946588 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
11946535 GTGCTGCAAC
* * *
11946545 AAAAAG AAAAAG AAAGAAG AAAAAC AAAACG GAAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
11946589 CTCCTACATC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11946570 original size:25 final size:24
Alignment explanation
Indices: 11946542--11946588 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
11946532 CAAGTGCTGC
11946542 AACAAAAAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
* *
11946567 AACAAAACGGAAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
11946589 CTCCTACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:11947348 original size:24 final size:24
Alignment explanation
Indices: 11947321--11947367 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11947311 AAATTGTGAA
*
11947321 TTTTCATGAT-CCAATGGACATGAC
1 TTTTCA-GATGCCAAGGGACATGAC
*
11947345 TTTTGAGATGCCAAGGGACATGA
1 TTTTCAGATGCCAAGGGACATGA
11947368 TCATTCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (24 bp):
TTTTCAGATGCCAAGGGACATGAC
Found at i:11956130 original size:33 final size:33
Alignment explanation
Indices: 11956093--11956155 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
11956083 TAGTGCTAAA
11956093 CCGTATGACACATAAGGTCGTGTCCACCATAAT
1 CCGTATGACACATAAGGTCGTGTCCACCATAAT
11956126 CCGTATGACACATAAGGTCGTGTCCACCAT
1 CCGTATGACACATAAGGTCGTGTCCACCAT
11956156 CTGTACTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (33 bp):
CCGTATGACACATAAGGTCGTGTCCACCATAAT
Found at i:11959653 original size:17 final size:17
Alignment explanation
Indices: 11959631--11959663 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11959621 ATCTTACCTT
*
11959631 TACCATATCCATTTCTA
1 TACCATAACCATTTCTA
11959648 TACCATAACCATTTCT
1 TACCATAACCATTTCT
11959664 TTTAGCCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:11974776 original size:23 final size:23
Alignment explanation
Indices: 11974750--11974797 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
11974740 TTGATGGAAG
* * *
11974750 ATGGTTGATAGTGTTAATGTTGT
1 ATGGATGATAGTGATAATGGTGT
*
11974773 ATGGATGATGGTGATAATGGTGT
1 ATGGATGATAGTGATAATGGTGT
11974796 AT
1 AT
11974798 CTCAGACACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (23 bp):
ATGGATGATAGTGATAATGGTGT
Found at i:11975187 original size:101 final size:101
Alignment explanation
Indices: 11975012--11975211 Score: 400
Period size: 101 Copynumber: 2.0 Consensus size: 101
11975002 ACTCACAAAG
11975012 GTTGTTTATATTATGAAATGAGATAAGATACAAATGAAAGCAAGCCTCTCAATTTATAGGAAATA
1 GTTGTTTATATTATGAAATGAGATAAGATACAAATGAAAGCAAGCCTCTCAATTTATAGGAAATA
11975077 AGAGGGCTTGGCCGAATAGTCACCTAGTGATTCGCC
66 AGAGGGCTTGGCCGAATAGTCACCTAGTGATTCGCC
11975113 GTTGTTTATATTATGAAATGAGATAAGATACAAATGAAAGCAAGCCTCTCAATTTATAGGAAATA
1 GTTGTTTATATTATGAAATGAGATAAGATACAAATGAAAGCAAGCCTCTCAATTTATAGGAAATA
11975178 AGAGGGCTTGGCCGAATAGTCACCTAGTGATTCG
66 AGAGGGCTTGGCCGAATAGTCACCTAGTGATTCG
11975212 GCAAGTACAT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (101 bp):
GTTGTTTATATTATGAAATGAGATAAGATACAAATGAAAGCAAGCCTCTCAATTTATAGGAAATA
AGAGGGCTTGGCCGAATAGTCACCTAGTGATTCGCC
Found at i:11976741 original size:16 final size:16
Alignment explanation
Indices: 11976722--11976755 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11976712 AAATAATAAA
11976722 AGAAAGAAATATGATT
1 AGAAAGAAATATGATT
11976738 AGAAAGAAATATGATT
1 AGAAAGAAATATGATT
11976754 AG
1 AG
11976756 TATATGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (16 bp):
AGAAAGAAATATGATT
Found at i:11976819 original size:14 final size:14
Alignment explanation
Indices: 11976800--11976826 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11976790 TGAAATAAGT
11976800 AAGGATAGAAGTAC
1 AAGGATAGAAGTAC
11976814 AAGGATAGAAGTA
1 AAGGATAGAAGTA
11976827 GATTTGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.30, T:0.15
Consensus pattern (14 bp):
AAGGATAGAAGTAC
Found at i:11981789 original size:16 final size:16
Alignment explanation
Indices: 11981770--11981805 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
11981760 TACTCTTGTG
11981770 AGTTATTTCTCTTCAA
1 AGTTATTTCTCTTCAA
11981786 AGTTATTTCTCTTCAA
1 AGTTATTTCTCTTCAA
11981802 AGTT
1 AGTT
11981806 CTTTTTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (16 bp):
AGTTATTTCTCTTCAA
Found at i:11982052 original size:22 final size:21
Alignment explanation
Indices: 11982015--11982055 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
11982005 CCATCTCCAT
*
11982015 TTCATCATCAACACCATCATC
1 TTCATCATCAAAACCATCATC
11982036 TTCATCCATCAAAACCATCA
1 TTCAT-CATCAAAACCATCA
11982056 ATTCCGCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:11982385 original size:18 final size:17
Alignment explanation
Indices: 11982362--11982413 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
11982352 AATTGGAGTG
11982362 CAAAAAGAAAAGAAAAGA
1 CAAAAA-AAAAGAAAAGA
*
11982380 CAAAAAATAAGAAAA-A
1 CAAAAAAAAAGAAAAGA
*
11982396 TTCAAAAAATAAGAAAAG
1 --CAAAAAAAAAGAAAAG
11982414 GAAAAAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.03
17 8 0.27
18 21 0.70
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.08
Consensus pattern (17 bp):
CAAAAAAAAAGAAAAGA
Found at i:11982391 original size:17 final size:18
Alignment explanation
Indices: 11982371--11982413 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
11982361 GCAAAAAGAA
11982371 AAGAAAAGA-CAAAAAAT
1 AAGAAAAGATCAAAAAAT
11982388 AAGAAAA-ATTCAAAAAAT
1 AAGAAAAGA-TCAAAAAAT
11982406 AAGAAAAG
1 AAGAAAAG
11982414 GAAAAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 15 0.65
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.09
Consensus pattern (18 bp):
AAGAAAAGATCAAAAAAT
Found at i:11987707 original size:21 final size:21
Alignment explanation
Indices: 11987668--11987711 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
11987658 GCTATCTCTA
11987668 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
11987690 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
11987711 T
1 T
11987712 AATCTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:11988455 original size:576 final size:576
Alignment explanation
Indices: 11987286--11989004 Score: 2807
Period size: 576 Copynumber: 3.0 Consensus size: 576
11987276 AAACATCATG
* * * *
11987286 TAACCATTCGACCAAGCCCTCACATTTCCTATAAATAGAGTTGCTTGCCATCATTTGTACACATC
1 TAACCATTCGGCCAAGCCCTCACATTTCCTATAAACAGAGTGGCTTGCCATCATTTGTACTCATC
* * *
11987351 TCATCTATTAAATAAAAATTACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTAATC
66 TCATCTCTTATATAAAAATTACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATC
*
11987416 GATTAAACAAGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCTTGATTCCTAAATTCCTA
131 GATTAAACAAGTATAATTCCTATACTTGTGGCATCATTCCTTCCATCTTGATTCCTAAATTCCTA
*
11987481 GATTAATATATAGTGGGTTGAAGTA-ACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGA
196 GATTAATATCTAGTGGGTTGAAG-ACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGA
* * ** *
11987545 TTGTGCTCATTAGCATTATTTCATCTTTGGCGTG-TTAAAGATACAACAACAACAGCATCTCCAT
260 TTGTGCTCCTTAGCATTATTTCATCTTTTGCGTGTTTTGAGATACAACAACAACACCATCTCCAT
* * * * * * *
11987609 TTCATCATCAATACCATAATATTTATCCATCAAAACCATCAATTCCGCAGCTATCTCTATCCTTT
325 TTCATCATCAATACCATCATCTTCATCCATCAAAACCATCAATTCCGCAACCATATCTATCATTT
11987674 CTTTATTTCATTTCATTCCTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTT
390 CTTTATTTCATTTCATTCCTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTT
*
11987739 TTTCTTATCAACGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCG
455 TTTCTTATCAATGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCG
* * * *
11987804 GGACACAATAAGGCTATCTACACTCTTCTACCAAAGTGTATAGATCACCTTACATCA
520 GGACACAATAAGGCTATCTACTCTCTTCTCCCAAAGTGTGTAGATCACCTTAAATCA
* * *
11987861 TAACCATTCGGGCAAGCCCTCCCATTTCCTATAAACAGAGTGGCTTGCCATCATTTGCACTCATC
1 TAACCATTCGGCCAAGCCCTCACATTTCCTATAAACAGAGTGGCTTGCCATCATTTGTACTCATC
*
11987926 TCATCTCTTATATAAAAATTACTCTTGTGATTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATC
66 TCATCTCTTATATAAAAATTACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATC
** * * * *
11987991 GATTGCACAAGTATAATTCCTATACTTATGGCTTCGTTCCTTCCATCTTGATTTCTAAATTCCTA
131 GATTAAACAAGTATAATTCCTATACTTGTGGCATCATTCCTTCCATCTTGATTCCTAAATTCCTA
* *
11988056 TATTAATATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGAGAT
196 GATTAATATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGAT
*
11988121 TGTGTTCCTTAGCATTATTTCATCTTTTGCGTGTTTTGAGATACAACAACAACACCATCTCCATT
261 TGTGCTCCTTAGCATTATTTCATCTTTTGCGTGTTTTGAGATACAACAACAACACCATCTCCATT
* *
11988186 TCATCATCAATACCATCATCTTCATCCATCAAAACCATAAATTCCGCAACCATATCTATCATTTT
326 TCATCATCAATACCATCATCTTCATCCATCAAAACCATCAATTCCGCAACCATATCTATCATTTC
*
11988251 TTTATTTCATTTCATTACTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTTT
391 TTTATTTCATTTCATTCCTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTTT
**
11988316 TTCTTATCAATGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCAA
456 TTCTTATCAATGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGG
* * *
11988381 GACACAATAATGATATCTACTCTCTTCTCCCAAAGTGTGTAGATTACCTTAAATCA
521 GACACAATAAGGCTATCTACTCTCTTCTCCCAAAGTGTGTAGATCACCTTAAATCA
* *
11988437 TAACCATTCGGCCAAGCCCTCTCATTTCCTATAAACAGAGTGGCTTGCCATCATTTGTACTCATA
1 TAACCATTCGGCCAAGCCCTCACATTTCCTATAAACAGAGTGGCTTGCCATCATTTGTACTCATC
*
11988502 TCATCTCTTATATAAAAATTACTCTTGTGAGTTATTTATCTTCAAAGTTCTTTGTGAACTTTATC
66 TCATCTCTTATATAAAAATTACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATC
*
11988567 GATTAAACAAGTATAATTCCTATACTTGTGGCATCATTCCTTCCATATTGATTCCTAAATTCCTA
131 GATTAAACAAGTATAATTCCTATACTTGTGGCATCATTCCTTCCATCTTGATTCCTAAATTCCTA
11988632 GATTAATATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGAT
196 GATTAATATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGAT
* * **
11988697 TATGCTCCTTAGCATTATTTCATC-TTTG-GCGTTTTGAGATACAACAACAACACCATCTTTATT
261 TGTGCTCCTTAGCATTATTTCATCTTTTGCGTGTTTTGAGATACAACAACAACACCATCTCCATT
* * * *
11988760 TTATCATCAACACCATCATCTTCATCCATCAAAACCATCAATTCTGCAACCATATCTATTATTTC
326 TCATCATCAATACCATCATCTTCATCCATCAAAACCATCAATTCCGCAACCATATCTATCATTTC
* *
11988825 TTTATTTTATTTCATTCCTTATCTTTATCATTTCATTAATCTTCCTTTATTAATCATTTTCCTTT
391 TTTATTTCATTTCATTCCTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTTT
* * * *
11988890 TTCTTATCTATGTTGCAGCCAATCTTATAATTCAAGGACATCAGTATTTGTCAATCCTAGATTGG
456 TTCTTATCAATGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGG
*
11988955 GACACAATAAGGCTACCTACTCTCTTCTCCCAAAGTGTGTAGATCACCTT
521 GACACAATAAGGCTATCTACTCTCTTCTCCCAAAGTGTGTAGATCACCTT
11989005 GCATCATGAC
Statistics
Matches: 1057, Mismatches: 85, Indels: 5
0.92 0.07 0.00
Matches are distributed among these distances:
574 259 0.25
575 272 0.26
576 526 0.50
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (576 bp):
TAACCATTCGGCCAAGCCCTCACATTTCCTATAAACAGAGTGGCTTGCCATCATTTGTACTCATC
TCATCTCTTATATAAAAATTACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATC
GATTAAACAAGTATAATTCCTATACTTGTGGCATCATTCCTTCCATCTTGATTCCTAAATTCCTA
GATTAATATCTAGTGGGTTGAAGACACTATCACCACCCCTCAAACAAGTTTGTGAAGACCGGGAT
TGTGCTCCTTAGCATTATTTCATCTTTTGCGTGTTTTGAGATACAACAACAACACCATCTCCATT
TCATCATCAATACCATCATCTTCATCCATCAAAACCATCAATTCCGCAACCATATCTATCATTTC
TTTATTTCATTTCATTCCTTATCTTTATCATTTCATTAATCTTCTTTTATTAATCATTTTCCTTT
TTCTTATCAATGTTGCAGCCAAGCTTATAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGG
GACACAATAAGGCTATCTACTCTCTTCTCCCAAAGTGTGTAGATCACCTTAAATCA
Found at i:11998998 original size:25 final size:23
Alignment explanation
Indices: 11998970--11999031 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
11998960 ATTGGAGTAC
*
11998970 AAAAAGAAAGAAAAGATAAAAAAATA
1 AAAAA-AAAGAAAA-ATAAAAAAA-G
* *
11998996 AAAAAAAATAGAAAATAAGAAAAG
1 AAAAAAAAGA-AAAATAAAAAAAG
11999020 AAAAAAAAGAAA
1 AAAAAAAAGAAA
11999032 TTGGAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 2 0.06
24 9 0.29
25 12 0.39
26 8 0.26
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.06
Consensus pattern (23 bp):
AAAAAAAAGAAAAATAAAAAAAG
Found at i:11999032 original size:21 final size:21
Alignment explanation
Indices: 11998971--11999046 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
11998961 TTGGAGTACA
*
11998971 AAAAGAAAGAAAAGATAA-AA-
1 AAAAGAAAAAAAAGA-AATAAG
*
11998991 AAATAAAAAAAAATAGAAAATAAG
1 AAA-AGAAAAAAA-AG-AAATAAG
**
11999015 AAAAGAAAAAAAAGAAATTGG
1 AAAAGAAAAAAAAGAAATAAG
*
11999036 AAAAGAGAAAA
1 AAAAGAAAAAA
11999047 CAAGCCAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.07
21 22 0.49
22 6 0.13
23 11 0.24
24 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAATAAG
Found at i:12000274 original size:17 final size:18
Alignment explanation
Indices: 12000252--12000285 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12000242 TGCAGGGAAA
*
12000252 TTCAA-GAGATGTTTCAT
1 TTCAAGGAGATGATTCAT
12000269 TTCAAGGAGATGATTCA
1 TTCAAGGAGATGATTCA
12000286 AGAATCATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (18 bp):
TTCAAGGAGATGATTCAT
Found at i:12006189 original size:64 final size:64
Alignment explanation
Indices: 12006134--12006297 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
12006124 CGGTGCACAA
*
12006134 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
12006198 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCAACGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
12006263 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
12006298 CAATTAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 32 0.38
65 53 0.62
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:12006322 original size:65 final size:62
Alignment explanation
Indices: 12006138--12006344 Score: 195
Period size: 65 Copynumber: 3.2 Consensus size: 62
12006128 GCACAAAGTG
* *
12006138 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
12006202 -
62 A
* * *
12006202 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCAACGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
12006266 A
62 A
* * * * *
12006267 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
12006332 TGCATCGGTGCAT
1 TGCATCGATGCAT
12006345 CACCTCAAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
63 3 0.03
64 35 0.29
65 75 0.62
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:12006537 original size:20 final size:21
Alignment explanation
Indices: 12006514--12006553 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12006504 GAATCGAATA
12006514 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
12006534 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
12006554 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:12009371 original size:21 final size:22
Alignment explanation
Indices: 12009321--12009371 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
12009311 TGTTTCCATG
12009321 ATATGTAAATGATATGCAAAAC
1 ATATGTAAATGATATGCAAAAC
*
12009343 ATA-ATAAATGA-AT-CTAAAAC
1 ATATGTAAATGATATGC-AAAAC
12009363 ATATGTAAA
1 ATATGTAAA
12009372 CATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 11 0.44
22 3 0.12
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (22 bp):
ATATGTAAATGATATGCAAAAC
Found at i:12012586 original size:6 final size:6
Alignment explanation
Indices: 12012560--12012602 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
12012550 AAAAGCAACA
12012560 AAAAGAG AAAAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAAG
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
12012603 TCTCCTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.15
6 19 0.56
7 10 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12012589 original size:19 final size:17
Alignment explanation
Indices: 12012560--12012602 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
12012550 AAAAGCAACA
12012560 AAAAGAGAAAAAGAAAGAAG
1 AAAA-AGAAAAAG-AA-AAG
12012580 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
12012597 AAAAAG
1 AAAAAG
12012603 TCTCCTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 8 0.35
20 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:12012597 original size:11 final size:12
Alignment explanation
Indices: 12012560--12012602 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
12012550 AAAAGCAACA
12012560 AAAAGAGAAAAAG
1 AAAA-AGAAAAAG
12012573 AAAGAAGAAAAAG
1 AAA-AAGAAAAAG
12012586 AAAAAG-AAAAG
1 AAAAAGAAAAAG
12012597 AAAAAG
1 AAAAAG
12012603 TCTCCTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.38
12 3 0.10
13 14 0.48
14 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:12018768 original size:19 final size:20
Alignment explanation
Indices: 12018744--12018794 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12018734 TGGCCAAGAG
* *
12018744 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
12018763 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
12018783 CATGTATTTTCA
1 CATGTATTTTCA
12018795 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:12022824 original size:19 final size:20
Alignment explanation
Indices: 12022788--12022838 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12022778 CGGCCAAGAG
* *
12022788 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
12022807 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
12022828 -ATGTATTTTCA
1 CATGTATTTTCA
12022839 AAAGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:12022841 original size:18 final size:20
Alignment explanation
Indices: 12022802--12022841 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12022792 TATCTTCATT
12022802 AAAATCATGTATTTTCATAAA
1 AAAATCATGTATTTTCA-AAA
12022823 AAAAT-ATGTATTTTCAAAA
1 AAAATCATGTATTTTCAAAA
12022842 GGGTTTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATCATGTATTTTCAAAA
Found at i:12026505 original size:16 final size:16
Alignment explanation
Indices: 12026471--12026517 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
12026461 ATAACATCTA
*
12026471 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
12026487 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
12026502 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
12026515 TAT
1 TAT
12026518 TTCCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:12026519 original size:12 final size:13
Alignment explanation
Indices: 12026492--12026520 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12026482 TTTCTTATCC
12026492 TTTCATTTCTTTA
1 TTTCATTTCTTTA
12026505 TTTCATTTC-TTA
1 TTTCATTTCTTTA
12026517 TTTC
1 TTTC
12026521 CATATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:12029818 original size:24 final size:23
Alignment explanation
Indices: 12029760--12029820 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
12029750 TGGGCTGAAA
* * *
12029760 AATAAGATAAGAAAATAATGATT
1 AATAATATAAGTAAATAAGGATT
** *
12029783 AATAATGGAAGTAAATAAGGGTAT
1 AATAATATAAGTAAATAAGGAT-T
12029807 AATAATATAAGTAA
1 AATAATATAAGTAA
12029821 TTAACTGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.26
Consensus pattern (23 bp):
AATAATATAAGTAAATAAGGATT
Found at i:12047711 original size:11 final size:11
Alignment explanation
Indices: 12047695--12047730 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
12047685 GATGTAGGAG
12047695 TCTTTTTATTT
1 TCTTTTTATTT
12047706 TCTTTTTATTTT
1 TCTTTTTA-TTT
12047718 TCTTCTTTATTT
1 TCTT-TTTATTT
12047730 T
1 T
12047731 TCTCTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 11 0.48
13 4 0.17
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTATTT
Found at i:12047728 original size:13 final size:12
Alignment explanation
Indices: 12047695--12047738 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
12047685 GATGTAGGAG
12047695 TCTTTTTA-TTT
1 TCTTTTTATTTT
12047706 TCTTTTTATTTT
1 TCTTTTTATTTT
12047718 TCTTCTTTATTTT
1 TCTT-TTTATTTT
12047731 TCTCTTTT
1 TCT-TTTT
12047739 TGGTGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.27
12 7 0.23
13 14 0.47
14 1 0.03
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTATTTT
Found at i:12050935 original size:21 final size:22
Alignment explanation
Indices: 12050911--12050961 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
12050901 TTATATTATG
12050911 TTTACATATGTTTTAG-AT-TCA
1 TTTACATATGTTTT-GCATATCA
*
12050932 TTTA-TTATGTTTTGCATATCA
1 TTTACATATGTTTTGCATATCA
12050953 TTTACATAT
1 TTTACATAT
12050962 CATGGAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 11 0.44
22 3 0.12
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (22 bp):
TTTACATATGTTTTGCATATCA
Found at i:12053740 original size:29 final size:30
Alignment explanation
Indices: 12053683--12053740 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12053673 AAAAGATAAA
*
12053683 AAAAGAATAAGAAAAAATTCAGAAAAGAAT
1 AAAAGAAAAAGAAAAAATTCAGAAAAGAAT
* *
12053713 AAAAGAAAAAGAAGAATTTCA-AAAAGAA
1 AAAAGAAAAAGAAAAAATTCAGAAAAGAA
12053741 AACAAAGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.71, C:0.03, G:0.14, T:0.12
Consensus pattern (30 bp):
AAAAGAAAAAGAAAAAATTCAGAAAAGAAT
Found at i:12056302 original size:24 final size:24
Alignment explanation
Indices: 12056275--12056329 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
12056265 AAAATCAGTA
*
12056275 AAGAAAAGTCAAGCAATCCAAAAG
1 AAGAAAAGTCAAGCAATCAAAAAG
*
12056299 AAGAAAAGTCAAGCACTCAAAAAG
1 AAGAAAAGTCAAGCAATCAAAAAG
12056323 AAGAAAA
1 AAGAAAA
12056330 AGAAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.62, C:0.15, G:0.16, T:0.07
Consensus pattern (24 bp):
AAGAAAAGTCAAGCAATCAAAAAG
Found at i:12060417 original size:24 final size:24
Alignment explanation
Indices: 12060390--12060444 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
12060380 CCAATAGGTG
12060390 TGACTCTTTGTGATCCACAAGACA
1 TGACTCTTTGTGATCCACAAGACA
*
12060414 TGACTCTTTGTGATTCACAAGACA
1 TGACTCTTTGTGATCCACAAGACA
*
12060438 TGTCTCT
1 TGACTCT
12060445 CGATGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (24 bp):
TGACTCTTTGTGATCCACAAGACA
Found at i:12065298 original size:13 final size:13
Alignment explanation
Indices: 12065282--12065314 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12065272 AAGATTTATT
12065282 TTTTGAAAATCAA
1 TTTTGAAAATCAA
12065295 TTTTGAAAATCAA
1 TTTTGAAAATCAA
12065308 TTTTGAA
1 TTTTGAA
12065315 GAATTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTTGAAAATCAA
Found at i:12067099 original size:8 final size:9
Alignment explanation
Indices: 12067079--12067104 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12067069 TTTTATTTCG
12067079 AAAATTTTA
1 AAAATTTTA
12067088 AAAATTTTA
1 AAAATTTTA
12067097 AAAATTTT
1 AAAATTTT
12067105 GTGTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAATTTTA
Found at i:12073487 original size:21 final size:21
Alignment explanation
Indices: 12073438--12073487 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
12073428 GGGTGAATCA
* *
12073438 GTACATCCGAGGAGTGTATCG
1 GTACATCCGAGCAATGTATCG
* *
12073459 ATATATCCGAGCAATGTATCG
1 GTACATCCGAGCAATGTATCG
12073480 GTACATCC
1 GTACATCC
12073488 CTTTATAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (21 bp):
GTACATCCGAGCAATGTATCG
Found at i:12077814 original size:66 final size:66
Alignment explanation
Indices: 12077557--12077814 Score: 383
Period size: 66 Copynumber: 3.9 Consensus size: 66
12077547 ATATTTACGG
* * * * * *
12077557 TATTCAATTATCACTCTACTTCATGCTCCACAAAGTTACATGAGTAACATCGAGTGAACTTGTAC
1 TATTCAATTATCACTCTACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATC-TGTAC
12077622 AT
65 AT
* * *
12077624 TATTCAA-TAGCCACTCTACCTCATGCACCACAAAGGTACACAAGTCACATCGAGTGATATGTAC
1 TATTCAATTA-TCACTCTACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTGTAC
*
12077688 AA
65 AT
*
12077690 TATTCAATTATCACTCTACCTTATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTGTACA
1 TATTCAATTATCACTCTACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTGTACA
12077755 T
66 T
*
12077756 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATC
1 TATTCAATTATCACTCTACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATC
12077815 AATACAATAT
Statistics
Matches: 172, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
66 123 0.72
67 49 0.28
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (66 bp):
TATTCAATTATCACTCTACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTGTACA
T
Found at i:12077821 original size:132 final size:133
Alignment explanation
Indices: 12077533--12077825 Score: 405
Period size: 133 Copynumber: 2.2 Consensus size: 133
12077523 AAGGTAAGTG
* * * ** * * *
12077533 AGTCACACCGAATGATATTTACGGTATTCAATTATCACTCTACTTCATGCTCCACAAAGTTACAT
1 AGTCACATCGAGTGATATATACAATATTCAATTATCACTCTACTTCATGCACCACAAAGGTACAC
*
12077598 GAGTAACATCGAGTGAACTTGTACATTATTCAATAGCCACTCTACCTCATGCACCACAAAGGTAC
66 GAGTAACATCGAGTGAACTTGTACATTATTCAATAGCCACTCCACCTCATGCACCACAAAGGTAC
12077663 ACA
131 ACA
*
12077666 AGTCACATCGAGTGATATGTACAATATTCAATTATCACTCTACCTT-ATGCACCACAAAGGTACA
1 AGTCACATCGAGTGATATATACAATATTCAATTATCACTCTA-CTTCATGCACCACAAAGGTACA
* * *
12077730 CGAGTCACATCGAGTGATC-TGTACATTATTCAATTA-TCACTCCACCTCATGCACCACAAAGGT
65 CGAGTAACATCGAGTGAACTTGTACATTATTCAA-TAGCCACTCCACCTCATGCACCACAAAGGT
*
12077793 ACACG
129 ACACA
12077798 AGTCACATCGAGTGATCA-ATACAATATT
1 AGTCACATCGAGTGAT-ATATACAATATT
12077826 TAGTACCTCG
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
132 68 0.48
133 72 0.50
134 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.27
Consensus pattern (133 bp):
AGTCACATCGAGTGATATATACAATATTCAATTATCACTCTACTTCATGCACCACAAAGGTACAC
GAGTAACATCGAGTGAACTTGTACATTATTCAATAGCCACTCCACCTCATGCACCACAAAGGTAC
ACA
Found at i:12079419 original size:20 final size:20
Alignment explanation
Indices: 12079390--12079438 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
12079380 TTCCTAACAA
*
12079390 CATTTGCATGAAATTTTAAT
1 CATTTCCATGAAATTTTAAT
12079410 CATTTCCATGAAATTTTAAT
1 CATTTCCATGAAATTTTAAT
12079430 CATTTCCAT
1 CATTTCCAT
12079439 AACAAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
CATTTCCATGAAATTTTAAT
Found at i:12082298 original size:23 final size:23
Alignment explanation
Indices: 12082268--12082315 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
12082258 TGTGTTTGAA
* *
12082268 ATACAACATCATCACCATCTTTC
1 ATACAACATCAACACCATCATTC
12082291 ATACAACATCAACACCATCATTC
1 ATACAACATCAACACCATCATTC
12082314 AT
1 AT
12082316 CTTCCATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (23 bp):
ATACAACATCAACACCATCATTC
Found at i:12082680 original size:18 final size:19
Alignment explanation
Indices: 12082659--12082700 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
12082649 AAAGGAGTTC
12082659 AAAAACAAAAAGAA-AAAA
1 AAAAACAAAAAGAAGAAAA
** *
12082677 AAAAGTAAAAAGAAGAAGA
1 AAAAACAAAAAGAAGAAAA
12082696 AAAAA
1 AAAAA
12082701 TTTCAAACAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAAGAAGAAAA
Found at i:12085389 original size:15 final size:15
Alignment explanation
Indices: 12085365--12085399 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12085355 CGAGGGTCCC
*
12085365 TTCGAGAAGTACTTA
1 TTCGACAAGTACTTA
12085380 TTCGACAAGTACTTA
1 TTCGACAAGTACTTA
12085395 TTCGA
1 TTCGA
12085400 GAAGCACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (15 bp):
TTCGACAAGTACTTA
Found at i:12090217 original size:43 final size:43
Alignment explanation
Indices: 12090156--12090250 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
12090146 CCTCCAACCG
*
12090156 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
*
12090199 AACACACCATGATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
12090242 AACACACCA
1 AACACACCA
12090251 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.36, C:0.37, G:0.12, T:0.16
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:12090397 original size:24 final size:24
Alignment explanation
Indices: 12090370--12090484 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
12090360 ATAATTCATA
* * *
12090370 TCAAGTATCATATCAAAATCCAGG
1 TCAAGTATCAGATCAGAATCCATG
* * *
12090394 TCAAGTATCATATCAGCATCCAAG
1 TCAAGTATCAGATCAGAATCCATG
12090418 TCAAGTATCAGATCAGAATCCATG
1 TCAAGTATCAGATCAGAATCCATG
12090442 T-AAGATATCAGATCAGAATCCATG
1 TCAAG-TATCAGATCAGAATCCATG
12090466 TCAAGTATCAGATCAGAAT
1 TCAAGTATCAGATCAGAAT
12090485 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 3 0.04
24 77 0.93
25 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
TCAAGTATCAGATCAGAATCCATG
Found at i:12093028 original size:8 final size:8
Alignment explanation
Indices: 12093008--12093047 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
12092998 GGTAAATGTC
12093008 GGTCAAC-
1 GGTCAACG
12093015 GGTCAACG
1 GGTCAACG
12093023 GGTCAACG
1 GGTCAACG
12093031 GGT---CG
1 GGTCAACG
12093036 GGTCAACG
1 GGTCAACG
12093044 GGTC
1 GGTC
12093048 GGTTCGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.17
7 7 0.24
8 17 0.59
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:12093039 original size:13 final size:13
Alignment explanation
Indices: 12093021--12093049 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12093011 CAACGGTCAA
12093021 CGGGTCAACGGGT
1 CGGGTCAACGGGT
12093034 CGGGTCAACGGGT
1 CGGGTCAACGGGT
12093047 CGG
1 CGG
12093050 TTCGGGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.48, T:0.14
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:12095317 original size:43 final size:43
Alignment explanation
Indices: 12095247--12095341 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
12095237 CCTCCAACCG
* *
12095247 AACATACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
12095290 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
12095333 AACACACCA
1 AACACACCA
12095342 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.37, C:0.36, G:0.11, T:0.17
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:12095470 original size:24 final size:24
Alignment explanation
Indices: 12095443--12095494 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12095433 TATATCAAAA
* * *
12095443 ATCAAAACATAATTCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
12095467 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
12095491 ATCA
1 ATCA
12095495 TATCAGCATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:12095495 original size:24 final size:24
Alignment explanation
Indices: 12095457--12095571 Score: 117
Period size: 24 Copynumber: 4.8 Consensus size: 24
12095447 AAACATAATT
12095457 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAAAATC
* **
12095481 CAGGTCAAGTATCATATCAGCATC
1 CATGTCAAGTATCATATCAAAATC
* * * *
12095505 CAAGCCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAAAATC
*
12095529 CATG-CCAGATATC-TGATCAAAATC
1 CATGTCAAG-TATCAT-ATCAAAATC
*
12095553 CATGTCAAGTATCAGATCA
1 CATGTCAAGTATCATATCA
12095572 GAATTCAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.04
24 68 0.92
25 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAAAATC
Found at i:12098133 original size:18 final size:19
Alignment explanation
Indices: 12098099--12098135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12098089 GTCAAAGTTT
12098099 TGGTCAACAGTGGTCAACGC
1 TGGTCAACAG-GGTCAACGC
12098119 TGGTCAACA-GGTCAACG
1 TGGTCAACAGGGTCAACG
12098136 GGTCGAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (19 bp):
TGGTCAACAGGGTCAACGC
Found at i:12098147 original size:13 final size:13
Alignment explanation
Indices: 12098128--12098183 Score: 85
Period size: 13 Copynumber: 4.3 Consensus size: 13
12098118 CTGGTCAACA
12098128 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
12098141 AGTCAACGGGTCG
1 GGTCAACGGGTCG
12098154 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
12098167 GGTAAACGGGTTG
1 GGTCAACGGGTCG
12098180 GGTC
1 GGTC
12098184 GGGTTATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:12099125 original size:32 final size:31
Alignment explanation
Indices: 12099079--12099139 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
12099069 GTCATATTAA
12099079 TACATGTTAAATTAATCCATATTAATATGTG
1 TACATGTTAAATTAATCCATATTAATATGTG
* * *
12099110 TACATGCTTGAATTAATGCATTTTAATATG
1 TACATG-TTAAATTAATCCATATTAATATG
12099140 CTGGAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (31 bp):
TACATGTTAAATTAATCCATATTAATATGTG
Found at i:12100944 original size:18 final size:18
Alignment explanation
Indices: 12100918--12100955 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12100908 ATATTAAAAA
*
12100918 TAAATAAATAT-TAATATT
1 TAAACAAATATAT-ATATT
12100936 TAAACAAATATATATATT
1 TAAACAAATATATATATT
12100954 TA
1 TA
12100956 TATGACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAACAAATATATATATT
Found at i:12100993 original size:14 final size:11
Alignment explanation
Indices: 12100962--12100995 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12100952 TTTATATGAC
12100962 TAAAATAATAA
1 TAAAATAATAA
12100973 TAAAATAATAA
1 TAAAATAATAA
* *
12100984 TGAAGTAATAA
1 TAAAATAATAA
12100995 T
1 T
12100996 TTAAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:12102152 original size:15 final size:15
Alignment explanation
Indices: 12102127--12102162 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12102117 TTCAATGGAG
12102127 GCATC-GTGGCAGCA
1 GCATCGGTGGCAGCA
12102141 GCATCGGTGGCAGCA
1 GCATCGGTGGCAGCA
*
12102156 GAATCGG
1 GCATCGG
12102163 CGGACGCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (15 bp):
GCATCGGTGGCAGCA
Found at i:12102472 original size:3 final size:3
Alignment explanation
Indices: 12102464--12102552 Score: 85
Period size: 3 Copynumber: 30.0 Consensus size: 3
12102454 TTGTAATATG
* * *
12102464 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
12102509 TAA TAA -AA TAA TAA TAG TGA TAAA TAA -AA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
12102553 AAACAAATAG
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.08
3 61 0.86
4 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12102553 original size:17 final size:17
Alignment explanation
Indices: 12102481--12102554 Score: 85
Period size: 17 Copynumber: 4.1 Consensus size: 17
12102471 AATATTTATT
*
12102481 AATAATAATAAAAATAT
1 AATAATAATAAAAATAA
*
12102498 AATAATAATAATAATAA
1 AATAATAATAAAAATAA
12102515 AATAATAATAGTGATAAATAA
1 AATAATAATA---A-AAATAA
*
12102536 AATAATAATAACAATAA
1 AATAATAATAAAAATAA
12102553 AA
1 AA
12102555 ACAAATAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
17 32 0.65
18 1 0.02
20 1 0.02
21 15 0.31
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (17 bp):
AATAATAATAAAAATAA
Found at i:12107112 original size:16 final size:17
Alignment explanation
Indices: 12107080--12107112 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12107070 TATCAACCTC
*
12107080 AAAACCCTTTACCTTTT
1 AAAACACTTTACCTTTT
12107097 AAAACACTTT-CCTTTT
1 AAAACACTTTACCTTTT
12107113 CTTCTGAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAACACTTTACCTTTT
Found at i:12108498 original size:30 final size:31
Alignment explanation
Indices: 12108464--12108527 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
12108454 TTTTATATTT
*
12108464 AAATTTAAATAA-T-TTTTAATTTTTCTAAAA
1 AAATTTAAATAATTCTTTTAA-CTTTCTAAAA
*
12108494 AAA-TTAATTAATTCTTTTAACTTTCTAAAA
1 AAATTTAAATAATTCTTTTAACTTTCTAAAA
12108524 AAAT
1 AAAT
12108528 AATTATGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
29 7 0.24
30 16 0.55
31 6 0.21
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
AAATTTAAATAATTCTTTTAACTTTCTAAAA
Found at i:12108544 original size:29 final size:28
Alignment explanation
Indices: 12108485--12108561 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
12108475 ATTTTTAATT
* * *
12108485 TTTCTAAAAAAATTAATTAATTCTTTTAAC
1 TTTCTAAAAAAA-TAATT-ATCCCTTGAAC
12108515 TTTCTAAAAAAATAATTATGCCCTTGAAC
1 TTTCTAAAAAAATAATTAT-CCCTTGAAC
*
12108544 TTAAC-AAAAAAATAATTA
1 TT-TCTAAAAAAATAATTA
12108562 AATCCATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 26 0.63
30 13 0.32
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.38
Consensus pattern (28 bp):
TTTCTAAAAAAATAATTATCCCTTGAAC
Found at i:12117586 original size:11 final size:11
Alignment explanation
Indices: 12117562--12117595 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12117552 TTGGTGCTGG
12117562 AAACAAGATAA
1 AAACAAGATAA
* *
12117573 AAATAAGATTA
1 AAACAAGATAA
12117584 AAACAAGATAA
1 AAACAAGATAA
12117595 A
1 A
12117596 GAAAATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:12122210 original size:11 final size:11
Alignment explanation
Indices: 12122186--12122219 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12122176 TTGGTGCTGG
12122186 AAACAAGATAA
1 AAACAAGATAA
* *
12122197 AAATAAGATTA
1 AAACAAGATAA
12122208 AAACAAGATAA
1 AAACAAGATAA
12122219 A
1 A
12122220 GAAAATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:12124035 original size:44 final size:44
Alignment explanation
Indices: 12123955--12124157 Score: 334
Period size: 44 Copynumber: 4.6 Consensus size: 44
12123945 AGTCTCCGTT
12123955 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* * * * *
12123999 ATACACCATTATGCATTTCATTTATGACATCATTTCATACCTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* * *
12124043 ATGCACCATTATACATTTCATTTATGGCATCCTTTTATGCCTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
12124087 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
12124131 ATGCACCGTTATGCATTTCATTTATGG
1 ATGCACCGTTATGCATTTCATTTATGG
12124158 ATTCATTTTG
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 145 1.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.41
Consensus pattern (44 bp):
ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTA
Found at i:12124690 original size:21 final size:21
Alignment explanation
Indices: 12124666--12124716 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12124656 TACCCCATCA
12124666 GTATCGATACTACTTGCATAG
1 GTATCGATACTACTTGCATAG
**
12124687 GTATTAATACTACTTGCATAG
1 GTATCGATACTACTTGCATAG
*
12124708 GTACCGATA
1 GTATCGATA
12124717 TTGTTCGTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (21 bp):
GTATCGATACTACTTGCATAG
Found at i:12124783 original size:20 final size:19
Alignment explanation
Indices: 12124746--12124784 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
12124736 CTATTTACAC
* *
12124746 CTATAGTACCGGTGCTATT
1 CTATAGTACCGATACTATT
12124765 CTATCAGTACCGATACTATT
1 CTAT-AGTACCGATACTATT
12124785 ACCCCGACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (19 bp):
CTATAGTACCGATACTATT
Found at i:12130390 original size:44 final size:44
Alignment explanation
Indices: 12130300--12130708 Score: 552
Period size: 44 Copynumber: 9.3 Consensus size: 44
12130290 TACACATTAT
* *
12130300 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGGTATGCA
1 TTTCATTTATGGCATCCTTTCATGCC-TTAATGCACAGTTATGCA
*
12130345 TTTCATTTATGGCATCATTTCATGCCTTAATGCACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
*
12130389 TTTCATTTATGGAATCCTTTCATGCCTTAATGCACCA-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCA-CAGTTATGCA
*
12130433 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
* ** *
12130477 TTTCATTTATGGCATCATTTCATGCCTTAATGTTCTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
* * * *
12130521 TTTCATTTATGACATCCTTTCATGCCTAAATGCACTGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
* * *
12130565 TTTCATTTATGACATCATTTCATGCCTTAATTCACCA-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCA-CAGTTATGCA
* * * * * *
12130609 TTTCATTTATGGTATCTTTTCATGACTTAGTGCACTGTTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
* * *
12130653 TTTCATTTATGGCATCTTTTCGTGCCTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
12130697 TTTCATTTATGG
1 TTTCATTTATGG
12130709 ATTCGTTTTA
Statistics
Matches: 324, Mismatches: 36, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
43 2 0.01
44 294 0.91
45 28 0.09
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (44 bp):
TTTCATTTATGGCATCCTTTCATGCCTTAATGCACAGTTATGCA
Found at i:12130538 original size:132 final size:132
Alignment explanation
Indices: 12130300--12130708 Score: 613
Period size: 132 Copynumber: 3.1 Consensus size: 132
12130290 TACACATTAT
*
12130300 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGGTATGCATTTCATTTATGGCATCATTT
1 TTTCATTTATGGCATCCTTTCATGCC-TTAATGCACCGTTATGCATTTCATTTATGGCATCATTT
* *
12130365 CATGCCTTAATGCACAGTTATGCATTTCATTTATGGA-ATCCTTTCATGCCTTAATGCACCATTA
65 CATGCCTTAATGCACTGTTATGCATTTCATTTAT-GACATCCTTTCATGCCTTAATGCACCGTTA
12130429 TGCA
129 TGCA
12130433 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTC
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTC
** * *
12130498 ATGCCTTAATGTTCTGTTATGCATTTCATTTATGACATCCTTTCATGCCTAAATGCACTGTTATG
66 ATGCCTTAATGCACTGTTATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCACCGTTATG
*
12130563 TA
131 CA
* * * * * *
12130565 TTTCATTTATGACATCATTTCATGCCTTAATTCACCATTATGCATTTCATTTATGGTATCTTTTC
1 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTC
* * * * * *
12130630 ATGACTTAGTGCACTGTTGTGCATTTCATTTATGGCATCTTTTCGTGCCTTAATGCACCGTTATG
66 ATGCCTTAATGCACTGTTATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCACCGTTATG
12130695 CA
131 CA
12130697 TTTCATTTATGG
1 TTTCATTTATGG
12130709 ATTCGTTTTA
Statistics
Matches: 249, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 221 0.89
133 26 0.10
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (132 bp):
TTTCATTTATGGCATCCTTTCATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTC
ATGCCTTAATGCACTGTTATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCACCGTTATG
CA
Found at i:12134543 original size:88 final size:88
Alignment explanation
Indices: 12134394--12134572 Score: 340
Period size: 88 Copynumber: 2.0 Consensus size: 88
12134384 CGTAGAAAGT
12134394 TTTCCATAAACTTGTTTAATCAATTTGAGATTGAGATTGGCATTCTAAACATAGATAGGTAATAG
1 TTTCCATAAACTTGTTTAATCAATTTGAGATTGAGATTGGCATTCTAAACATAGATAGGTAATAG
12134459 ACTGGTAAACTCATGAGAATGGA
66 ACTGGTAAACTCATGAGAATGGA
* *
12134482 TTTCCATAAACTTGTTTAATCAATTTTAGATTGAGATTGGCATTCTAGACATAGATAGGTAATAG
1 TTTCCATAAACTTGTTTAATCAATTTGAGATTGAGATTGGCATTCTAAACATAGATAGGTAATAG
12134547 ACTGGTAAACTCATGAGAATGGA
66 ACTGGTAAACTCATGAGAATGGA
12134570 TTT
1 TTT
12134573 AATTAAAGTC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (88 bp):
TTTCCATAAACTTGTTTAATCAATTTGAGATTGAGATTGGCATTCTAAACATAGATAGGTAATAG
ACTGGTAAACTCATGAGAATGGA
Found at i:12142396 original size:4 final size:5
Alignment explanation
Indices: 12142364--12142415 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
12142354 CTTCTCCCAA
* *
12142364 ATTTT GTTTT GATTTT ATTTT ATTTT A-TTT ATTTT GTTTT GATTTTT
1 ATTTT ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -A-TTTT
12142411 ATTTT
1 ATTTT
12142416 TCCTTGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.10
5 26 0.67
6 5 0.13
7 4 0.10
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:12142396 original size:9 final size:10
Alignment explanation
Indices: 12142364--12142415 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
12142354 CTTCTCCCAA
*
12142364 ATTTTGTTTT
1 ATTTTATTTT
12142374 GATTTTATTTT
1 -ATTTTATTTT
12142385 ATTTTA-TTT
1 ATTTTATTTT
*
12142394 ATTTTGTTTT
1 ATTTTATTTT
12142404 GATTTTTATTTT
1 -A-TTTTATTTT
12142416 TCCTTGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.23
10 9 0.26
11 10 0.29
12 8 0.23
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:12142396 original size:14 final size:15
Alignment explanation
Indices: 12142364--12142408 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
12142354 CTTCTCCCAA
*
12142364 ATTTTGTTTTGATTTT
1 ATTTTATTTTGA-TTT
12142380 ATTTTATTTT-ATTT
1 ATTTTATTTTGATTT
*
12142394 ATTTTGTTTTGATTT
1 ATTTTATTTTGATTT
12142409 TTATTTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 12 0.46
15 5 0.19
16 9 0.35
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTGATTT
Found at i:12149922 original size:27 final size:27
Alignment explanation
Indices: 12149891--12149944 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12149881 AATGTTTTAA
12149891 TGTAATAGGGGAATTTAGGATTAAACT
1 TGTAATAGGGGAATTTAGGATTAAACT
12149918 TGTAATAGGGGAATTTAGGATTAAACT
1 TGTAATAGGGGAATTTAGGATTAAACT
12149945 CGCTTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (27 bp):
TGTAATAGGGGAATTTAGGATTAAACT
Found at i:12150200 original size:12 final size:12
Alignment explanation
Indices: 12150183--12150226 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12150173 ACAACAATGC
*
12150183 AAAAAAACAACA
1 AAAAAAACAAAA
*
12150195 AAAAAACCAAAA
1 AAAAAAACAAAA
*
12150207 AAAAAAACAAGAG
1 AAAAAAACAA-AA
12150220 AAAAAAA
1 AAAAAAA
12150227 GAAATAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:12154967 original size:26 final size:24
Alignment explanation
Indices: 12154937--12155031 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 24
12154927 CAACCCATTC
12154937 ATTTTATTTTATTTTTAGCACATTTT
1 ATTTTATTTTA-TTTTAG-ACATTTT
* **
12154963 ATTTTATTTTATTTAAGTTTATTTT
1 ATTTTATTTTATTTTAG-ACATTTT
*
12154988 ATTTTTATTTTATTTTATGAGATGCTTT
1 A-TTTTATTTTATTTTA-GACAT--TTT
12155016 ATTTTATTTTATTTTA
1 ATTTTATTTTATTTTA
12155032 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
25 11 0.19
26 27 0.47
27 16 0.28
28 4 0.07
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.68
Consensus pattern (24 bp):
ATTTTATTTTATTTTAGACATTTT
Found at i:12154993 original size:6 final size:5
Alignment explanation
Indices: 12154958--12155040 Score: 94
Period size: 5 Copynumber: 16.0 Consensus size: 5
12154948 TTTTTAGCAC
* * ***
12154958 ATTTT ATTTT ATTTT ATTTA AGTTT ATTTT ATTTTT ATTTT ATTTT ATGAG
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT
12155009 ATGCTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 AT--TTT ATTTT ATTTT ATTTT ATTTT ATTTT
12155041 TCTTCGAACA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
5 58 0.89
6 5 0.08
7 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.05, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:12157650 original size:21 final size:21
Alignment explanation
Indices: 12157626--12157665 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12157616 TTTCTTATGG
12157626 TTTTATAAAAG-TTTTCTTTTC
1 TTTT-TAAAAGTTTTTCTTTTC
*
12157647 TTTTTCAAAGTTTTTCTTT
1 TTTTTAAAAGTTTTTCTTT
12157666 GTATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTAAAAGTTTTTCTTTTC
Found at i:12159737 original size:11 final size:11
Alignment explanation
Indices: 12159723--12159747 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12159713 AATATAATAA
12159723 TTAAAAATCAT
1 TTAAAAATCAT
12159734 TTAAAAATCAT
1 TTAAAAATCAT
12159745 TTA
1 TTA
12159748 CCATACAAAG
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAAATCAT
Found at i:12165258 original size:18 final size:17
Alignment explanation
Indices: 12165237--12165279 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
12165227 GATCCTTGAA
*
12165237 TATTTTAATTTCCTTTAT
1 TATTTTAATTTCATTT-T
*
12165255 TATTTGTAATTTTATTTT
1 TATTT-TAATTTCATTTT
12165273 TATTTTA
1 TATTTTA
12165280 TTATGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTAATTTCATTTT
Found at i:12165758 original size:12 final size:12
Alignment explanation
Indices: 12165735--12165769 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12165725 TTCATATTAT
*
12165735 AGCTCTAAACCCG
1 AGCTC-AAACCCA
12165748 AGCTCAAACCCA
1 AGCTCAAACCCA
12165760 AGCTCAAACC
1 AGCTCAAACC
12165770 TGGTTTACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.37, C:0.40, G:0.11, T:0.11
Consensus pattern (12 bp):
AGCTCAAACCCA
Found at i:12179617 original size:36 final size:36
Alignment explanation
Indices: 12179577--12179699 Score: 86
Period size: 36 Copynumber: 3.3 Consensus size: 36
12179567 TAATGCAGAG
*
12179577 GATTTATCTCACTTTAGATTGTTTTTTTTAAAACAA
1 GATTTATCTCACTTAAGATTGTTTTTTTTAAAACAA
* * * * *
12179613 GATTTGTCTCGCTTGAGACCTT-TTTTTTCTCGAAACAAGAA
1 GATTTATCTCACTTAAGA--TTGTTTTTT-T--TAA-AACAA
* * **
12179654 GATTTATTTCACTCAAGATTGTTTTTCCTAAAACAA
1 GATTTATCTCACTTAAGATTGTTTTTTTTAAAACAA
*
12179690 GATTTGTCTC
1 GATTTATCTC
12179700 GCTTGAGACG
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
36 27 0.42
37 8 0.12
38 3 0.05
39 2 0.03
40 7 0.11
41 17 0.27
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (36 bp):
GATTTATCTCACTTAAGATTGTTTTTTTTAAAACAA
Found at i:12179744 original size:76 final size:77
Alignment explanation
Indices: 12179578--12179755 Score: 243
Period size: 77 Copynumber: 2.3 Consensus size: 77
12179568 AATGCAGAGG
* ** ** ** *
12179578 ATTTATCTCACTTTAGATTGTTTTTTTTAAAACAAGATTTGTCTCGCTTGAGACCTTTTTTTTCT
1 ATTTATTTCACTCAAGATTGTTTTTCCTAAAACAAGATTTGTCTCGCTTGAGACCGGTTTTTACT
*
12179643 CGAAACAAGAAG
66 CGAAACAAGAAC
12179655 ATTTATTTCACTCAAGATTGTTTTTCCTAAAACAAGATTTGTCTCGCTTGAGA-CGGTTTTTACT
1 ATTTATTTCACTCAAGATTGTTTTTCCTAAAACAAGATTTGTCTCGCTTGAGACCGGTTTTTACT
*
12179719 CGAAAGAA-AAC
66 CGAAACAAGAAC
12179730 ATTTCATTTCACTCAAGATTGTTTTT
1 ATTT-ATTTCACTCAAGATTGTTTTT
12179756 AAAGAAGATT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 6 0.07
76 36 0.40
77 48 0.53
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (77 bp):
ATTTATTTCACTCAAGATTGTTTTTCCTAAAACAAGATTTGTCTCGCTTGAGACCGGTTTTTACT
CGAAACAAGAAC
Found at i:12179821 original size:39 final size:39
Alignment explanation
Indices: 12179758--12181045 Score: 1779
Period size: 39 Copynumber: 33.0 Consensus size: 39
12179748 TTGTTTTTAA
* * * *
12179758 AGAAGATTGTATCTCGTTTGAGATAGTTTACCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
12179797 AAAAGATTTTGTCTCGCATAAGATACTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12179836 AGAAGATTTTATCTCTCTTGAGATAGTTTCCATCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
12179875 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
12179914 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
12179953 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12179992 ATAATATTTTATCTCGCTTGAGATAGTTTTCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180031 AGAATATTTTATCTCACTTGAAATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180070 AGAAGATTTTATCTCACTTGAGATAGTTTCACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180109 AGAATATTTTTTCTCGATTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180148 ATAAGATTTTATCTCACTTGAGATAGTTTCCTTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180187 AGAAGATTTTGTTTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180226 AGAAGATTTTATCTCACTTGAGATAGTTTCACTCGAAAA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180265 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180304 AGAAGATTTTATCTCGCTTGAGATAGTTTCACACGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* **
12180343 AGAAGATTTTATCTCGCTTGATATAGTTTTACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
12180382 AAAAAATTTTATATCGCTTAAGATAGTTTCACTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
12180421 AGAAGATTTTATC-CTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTC-GCTTGAGATAGTTTCCCTCGAAAC
* * *
12180460 ATAAGATTTTGTCTCGCTTGAGATAGTTTCCATCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180499 AAAAGATTTTATGTCGCTTAAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
12180538 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
12180577 ATAAGATTTTGTCTCGCTTGATATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
12180616 AAAATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180655 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
12180694 AGAAGATTTTATCTCGCTTGAGATAGTTTTCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
12180733 AGAAGATTTTCTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
12180772 AGAAGACTTTGTCTTGCTTGGGATAATTTCCATCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12180811 AGAAGATTTCATCTCGCTTGAGATAATTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* **
12180850 A-AAAACTTTTATCTTTCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGA-TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* ** *
12180889 AGAAGATTTTTTCTTTCTTGGGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
12180928 AAAAGACTTTACCTCGCTTGAGATAGTTTCCCTCGAAAA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
12180967 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
12181006 AGAAGATTTTGTCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
12181045 A
1 A
12181046 TAAAATCTTC
Statistics
Matches: 1108, Mismatches: 137, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
38 4 0.00
39 1100 0.99
40 4 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:12180021 original size:20 final size:20
Alignment explanation
Indices: 12179881--12179981 Score: 50
Period size: 20 Copynumber: 5.2 Consensus size: 20
12179871 AAACAGAAGA
12179881 TTTTATCTCGCTTGAGATAG
1 TTTTATCTCGCTTGAGATAG
** ****
12179901 -TTTCCCTCGAAACAGA-AG
1 TTTTATCTCGCTTGAGATAG
12179919 ATTTTATCTCGCTTGAGATAG
1 -TTTTATCTCGCTTGAGATAG
** **
12179940 -TTTCCCTCGAAAT-AGA-AG
1 TTTTATCTCG-CTTGAGATAG
12179958 ATTTTATCTCGCTTGAGATAG
1 -TTTTATCTCGCTTGAGATAG
12179979 TTT
1 TTT
12179982 CCCTCGAAAC
Statistics
Matches: 53, Mismatches: 20, Indels: 16
0.60 0.22 0.18
Matches are distributed among these distances:
18 4 0.08
19 21 0.40
20 24 0.45
21 4 0.08
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
TTTTATCTCGCTTGAGATAG
Found at i:12181188 original size:44 final size:44
Alignment explanation
Indices: 12181125--12181587 Score: 239
Period size: 44 Copynumber: 10.6 Consensus size: 44
12181115 AGTTTTGCTT
* * *
12181125 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCGTTC
***** *
12181169 GATTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTCGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAG-CACCAACA-TTTCGTTC
* * * * *** * *
12181214 AAATCCATCGCAGAAGGAGTTGGATCAGCGTAAACTTTTAGCTT-
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCG-TTC
* * * * *
12181258 GATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCATTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCGTTC
* * **
12181302 GATTCCATCACAAAATGAGGTGGATC-G-A-CATTA-ATTTCACTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCA--ACATTTCGTTC
* * * * *** *
12181344 AAATCCATCGCAGAAGGAGTTGGATCAGTGTCAA-ATTTTAGCTT-
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACA-TTTCG-TTC
* * *
12181388 GAGTCTATCACAGAAGGAGGTAGG-TCAGCACCAACATCTCGTTC
1 GATTCCATCACAGAAGGAGGT-GGATCAGCACCAACATTTCGTTC
* * ** *
12181432 GATTCCATCACAGAAGGAGATAGATC-G-A-CATTTATTTCGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCA-ACATTTCGTTC
* * * * ** * * *
12181474 AAATCCATCACATAAGGAGTTGGATCAGCGTCAACTTTTAGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCGTTC
* * * * *
12181518 CATTCCATCACAGAATGAGGTAGATCAGCACCATCATCTCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCGTTC
*
12181562 GATTCCATCACAGAATGAGGTGGATC
1 GATTCCATCACAGAAGGAGGTGGATC
12181588 GATATTTCTA
Statistics
Matches: 304, Mismatches: 95, Indels: 40
0.69 0.22 0.09
Matches are distributed among these distances:
41 3 0.01
42 57 0.19
43 13 0.04
44 191 0.63
45 39 0.13
46 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
GATTCCATCACAGAAGGAGGTGGATCAGCACCAACATTTCGTTC
Found at i:12181425 original size:130 final size:131
Alignment explanation
Indices: 12181112--12181631 Score: 733
Period size: 130 Copynumber: 4.0 Consensus size: 131
12181102 AAGAGATTGT
*
12181112 TCAAGTTTT-GCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
1 TCAAATTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
* *
12181176 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACA--TTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCA
12181241 GCG
129 GCG
* *
12181244 T-AAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCATTCGATTCC
1 TCAAA-TTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCC
* * * *
12181308 ATCACAAAATGAGGTGGATCGACA-TTAATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
65 ATCACAGAAGGAGGTGGATCGACATTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAG
*
12181372 TG
130 CG
* *
12181374 TCAAATTTTAGCTTGAGTCTATCACAGAAGGAGGTAGGTCAGCACCAACATCTCGTTCGATTCCA
1 TCAAATTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
* * *
12181439 TCACAGAAGGAGATAGATCGACATTT-ATTTCGCTCAAATCCATCACATAAGGAGTTGGATCAGC
66 TCACAGAAGGAGGTGGATCGACATTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGC
12181503 G
131 G
* ** * * *
12181504 TCAACTTTTAGCTCCATTCCATCACAGAATGAGGTAGATCAGCACCATCATCTCGTTCGATTCCA
1 TCAAATTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
* * * * *
12181569 TCACAGAATGAGGTGGATCGATATTTCTATTTTCGCTCAAATCCATCACATACGGAGTTGGAT
66 TCACAGAAGGAGGTGGATCGACA-TT-TAATTTCGCTCAAATCCATCACAGAAGGAGTTGGAT
12181632 AAGAATCGTC
Statistics
Matches: 347, Mismatches: 34, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
130 226 0.65
131 9 0.03
132 6 0.02
133 106 0.31
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (131 bp):
TCAAATTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGC
G
Found at i:12186880 original size:18 final size:18
Alignment explanation
Indices: 12186857--12186891 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12186847 GTGTTGTATA
12186857 GAAAGAAGAACATAAAAG
1 GAAAGAAGAACATAAAAG
12186875 GAAAGAAGAACATAAAA
1 GAAAGAAGAACATAAAA
12186892 AGATGATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.20, T:0.06
Consensus pattern (18 bp):
GAAAGAAGAACATAAAAG
Found at i:12191584 original size:25 final size:24
Alignment explanation
Indices: 12191556--12191620 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
12191546 GGAAAAAATG
* * *
12191556 AATAAATGAAAAAATGAAGAATAAA
1 AATAAAT-AAAAAATCAAAAAGAAA
* *
12191581 AATAAGTAAAAAAAACAAAAAGAAA
1 AATAAAT-AAAAAATCAAAAAGAAA
12191606 AATAAATAAATAAAT
1 AATAAATAAA-AAAT
12191621 AAATGAAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
24 3 0.10
25 28 0.90
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AATAAATAAAAAATCAAAAAGAAA
Found at i:12191641 original size:2 final size:2
Alignment explanation
Indices: 12191634--12191660 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12191624 TGAAATATTA
12191634 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12191661 AATGAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12191929 original size:21 final size:20
Alignment explanation
Indices: 12191904--12191953 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
12191894 AAAATATTTT
*
12191904 TTAAAAAAAGTATATATA-TA
1 TTAAAAAAA-TAAATATAGTA
12191924 TATAAAAATAATAAATATAGTA
1 T-TAAAAA-AATAAATATAGTA
12191946 TTAAAAAA
1 TTAAAAAA
12191954 TAACCAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
TTAAAAAAATAAATATAGTA
Found at i:12191941 original size:19 final size:19
Alignment explanation
Indices: 12191905--12191956 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
12191895 AAATATTTTT
12191905 TAAAAAAAGTATATATATA-TA
1 TAAAAAAA-TA-A-ATATAGTA
12191926 TAAAAATAATAAATATAGTA
1 TAAAAA-AATAAATATAGTA
*
12191946 TTAAAAAATAA
1 TAAAAAAATAA
12191957 CCAAATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 8 0.29
22 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TAAAAAAATAAATATAGTA
Found at i:12191955 original size:22 final size:21
Alignment explanation
Indices: 12191917--12192019 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 21
12191907 AAAAAAGTAT
12191917 ATATA-TATATAAAAATAATAA
1 ATATAGTATA-AAAAATAATAA
*
12191938 ATATAGTATTAAAAAATAACCAA
1 ATATAGTA-TAAAAAATAA-TAA
*
12191961 ATGA-A-TATAAATAAATAAAAA
1 AT-ATAGTATAAA-AAATAATAA
* *
12191982 ATATATGTATAGATAATAATAA
1 ATATA-GTATAAAAAATAATAA
*
12192004 TATATAGTGTAAAAAA
1 -ATATAGTATAAAAAA
12192020 ATCAATTGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.02
21 14 0.22
22 32 0.49
23 17 0.26
24 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (21 bp):
ATATAGTATAAAAAATAATAA
Found at i:12191997 original size:23 final size:24
Alignment explanation
Indices: 12191966--12192014 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
12191956 ACCAAATGAA
12191966 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
12191989 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
12192013 TA
1 TA
12192015 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:12192514 original size:37 final size:36
Alignment explanation
Indices: 12192473--12192577 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 36
12192463 GTGCTTGTGG
* * *
12192473 ATCCTATCTTTAGAAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
12192510 ATCCTATTTTAAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAACTCT
12192547 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
12192578 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.05
37 51 0.88
38 4 0.07
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:12193626 original size:106 final size:106
Alignment explanation
Indices: 12193308--12194891 Score: 2230
Period size: 106 Copynumber: 15.0 Consensus size: 106
12193298 GCATTGTTCT
* * * ** * * *
12193308 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
12193373 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
12193414 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
12193473 TCAGCCG-CCTTTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
12193515 G-GTCCAAGATCCTTCGATGAGAAGTTGAAATTGGGTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
12193579 CAAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
12193620 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTACTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12193685 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12193726 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12193791 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12193832 GAGTCCAATATCCTTC-TCGGTGAAGTTGAAATTGGCTCTGAAATAGGGAAGTTTTTTATTGACA
1 GAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * ** *
12193896 ACCAACGATCTTTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12193938 GTGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
12194003 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12194044 GAGTCCAATATCCTTCGTTGTTAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12194109 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
12194150 GAGTCTAATATCCATCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12194215 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12194256 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTG--A-----AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12194313 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12194354 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGTAAGTTTTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
12194419 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12194460 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC-A
12194525 CCAGCCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 --A-CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12194570 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * *
12194635 CCAATGATCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12194676 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
12194741 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12194782 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
12194847 CCCGCGGTCCCGTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
12194888 GAGT
1 GAGT
12194892 GGCACGATAT
Statistics
Matches: 1326, Mismatches: 128, Indels: 48
0.88 0.09 0.03
Matches are distributed among these distances:
98 89 0.07
99 4 0.00
100 77 0.06
101 5 0.00
102 4 0.00
104 4 0.00
105 8 0.01
106 1030 0.78
107 5 0.00
109 2 0.00
110 98 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:12194560 original size:216 final size:212
Alignment explanation
Indices: 12194295--12194891 Score: 1034
Period size: 216 Copynumber: 2.8 Consensus size: 212
12194285 AATTGACTCT
*
12194295 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
12194360 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GTAAGTTTTTTATTGACAACCAGC
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAACCAGC
12194424 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGA
130 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGA
12194489 AATTGGCTCTGAAATTGG
195 AATTGGCTCTGAAATTGG
12194507 GAAATTGTTTATTGACAACCAGCCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
1 GAAATTGTTTATTGAC-A--A-CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
12194572 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
62 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
** * *
12194637 AATGATCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
127 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGT
12194702 TGAAATTGGCTCTGAAATTGG
192 TGAAATTGGCTCTGAAATTGG
*
12194723 GAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
12194788 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCCGCG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
* *
12194853 GTCCCGTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
131 GTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGT
12194892 GGCACGATAT
Statistics
Matches: 364, Mismatches: 16, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
212 159 0.44
213 2 0.01
215 2 0.01
216 200 0.55
217 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (212 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
GTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAA
ATTGGCTCTGAAATTGG
Found at i:12195723 original size:22 final size:22
Alignment explanation
Indices: 12195695--12195771 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
12195685 TTATGTTTGG
12195695 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
12195717 TGAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
12195739 TCAACGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
12195761 TCAACGGTTTG
1 TCAAAGGTTTG
12195772 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:12196461 original size:172 final size:172
Alignment explanation
Indices: 12196167--12196513 Score: 590
Period size: 172 Copynumber: 2.0 Consensus size: 172
12196157 TAAATAGGCC
*
12196167 CAAACAAGTGATTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCATG
1 CAAACAAGTGATTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATC---TCATG
12196232 CTCAAAATATCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
63 CTCAAAATATCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
12196297 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTACCATTT
128 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTACCATTT
* *
12196342 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATC-C-TGCTC
1 CAAACAAGTGATTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCATGCTC
*
12196405 AAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGA
66 AAAA--TATCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGA
*
12196470 TTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 TTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTACCATTT
12196514 TTTAGGGAAT
Statistics
Matches: 165, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 9 0.05
171 1 0.01
172 101 0.61
175 54 0.33
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (172 bp):
CAAACAAGTGATTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCATGCTC
AAAATATCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGATT
GTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTACCATTT
Found at i:12196567 original size:16 final size:16
Alignment explanation
Indices: 12196548--12196614 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
12196538 TTTGTCCCTT
12196548 TTTCTTTTTGTTC-TTG
1 TTTCTTTTT-TTCTTTG
12196564 TTTCTCTTTTTTCTTTG
1 TTTCT-TTTTTTCTTTG
12196581 TTT-TTTTGCTTT-TTTG
1 TTTCTTTT--TTTCTTTG
*
12196597 CTTCTTTTCTTT-TTTG
1 TTTCTTTT-TTTCTTTG
12196613 TT
1 TT
12196615 CTTGATTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.07
16 24 0.55
17 17 0.39
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTG
Done.