Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 35
Found at i:4482123 original size:17 final size:17
Alignment explanation
Indices: 4482101--4482134 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4482091 TCCATAAATC
*
4482101 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
4482118 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
4482135 AAATATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:4484083 original size:21 final size:22
Alignment explanation
Indices: 4484057--4484137 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
4484047 CAGAACCCCA
*
4484057 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* * *
4484078 GGGGGGAATCGGTTCCCATTCAA
1 GGGGGGAATCGATTCCC-CTCAT
* *
4484101 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
4484122 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
4484138 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
22 3 0.06
23 14 0.29
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:4484507 original size:42 final size:42
Alignment explanation
Indices: 4484448--4484531 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
4484438 TCCAAAATCT
4484448 TTCCTTGTCTAAGGGTTTTGTAAAGATATCCGCTAATTGGTG
1 TTCCTTGTCTAAGGGTTTTGTAAAGATATCCGCTAATTGGTG
4484490 TTCCTTGTCTAAGGGTTTTGTAAAGATATCCGCTAATTGGTG
1 TTCCTTGTCTAAGGGTTTTGTAAAGATATCCGCTAATTGGTG
4484532 CAAAGTATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (42 bp):
TTCCTTGTCTAAGGGTTTTGTAAAGATATCCGCTAATTGGTG
Found at i:4490060 original size:75 final size:77
Alignment explanation
Indices: 4489951--4490160 Score: 284
Period size: 75 Copynumber: 2.8 Consensus size: 77
4489941 CCGTTGTACA
* * *
4489951 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
**
4490015 -CAAAACTGTTT
66 CCAAAACCATTT
* * *
4490026 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
4490090 CCAAAACCATTT
66 CCAAAACCATTT
* *
4490102 AGGGGGGAATCGATTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
4490161 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
74 17 0.14
75 40 0.34
76 10 0.08
77 20 0.17
78 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:4497122 original size:2 final size:2
Alignment explanation
Indices: 4497115--4497148 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4497105 ATTTATAACG
4497115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4497149 TCTTAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4497602 original size:2 final size:2
Alignment explanation
Indices: 4497595--4497648 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
4497585 ATTTATTGTA
4497595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4497637 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4497649 CAGTGGCGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4498471 original size:2 final size:2
Alignment explanation
Indices: 4498464--4498493 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4498454 GCTACTTAAT
4498464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4498494 GGGTTTTTTA
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):
TA
Found at i:4501419 original size:17 final size:18
Alignment explanation
Indices: 4501399--4501433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4501389 ATTTAAAATA
4501399 AAAATAA-AAATATATTC
1 AAAATAAGAAATATATTC
*
4501416 AAAATAAGTAATATATTC
1 AAAATAAGAAATATATTC
4501434 TCTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATAAGAAATATATTC
Found at i:4509303 original size:27 final size:28
Alignment explanation
Indices: 4509265--4509320 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
4509255 AAATAGAACT
4509265 TATGATCTCTC-TCATTTGAATTCTCAC
1 TATGATCTCTCTTCATTTGAATTCTCAC
*
4509292 TATGATCTCTCTTCATTTGTATTCTCAC
1 TATGATCTCTCTTCATTTGAATTCTCAC
4509320 T
1 T
4509321 TTCTTTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.48
Consensus pattern (28 bp):
TATGATCTCTCTTCATTTGAATTCTCAC
Found at i:4512996 original size:2 final size:2
Alignment explanation
Indices: 4512991--4513017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4512981 TCTCTCTCTC
4512991 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4513018 CATTTTTCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4533722 original size:20 final size:20
Alignment explanation
Indices: 4533699--4533759 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
4533689 AAATAACTAA
4533699 AAATAATCTTATAATAATAT
1 AAATAATCTTATAATAATAT
* *
4533719 AAATTAA-C-TA-AA-AAGAC
1 AAA-TAATCTTATAATAATAT
4533736 AAATAATCTTATAATAATAT
1 AAATAATCTTATAATAATAT
4533756 AAAT
1 AAAT
4533760 TAACTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 3 0.09
17 7 0.22
18 4 0.12
19 4 0.12
20 11 0.34
21 3 0.09
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATAATCTTATAATAATAT
Found at i:4543215 original size:100 final size:100
Alignment explanation
Indices: 4543111--4543426 Score: 254
Period size: 100 Copynumber: 3.1 Consensus size: 100
4543101 ATATTTTTAA
4543111 TTATAACAATCAAGTCATTTTTACATATATCTATAATCTATTTATTTATATAATATATAAAAACG
1 TTATAACAATCAAGTCATTTTTACATATATCTATAATCTATTTATTTATATAATATATAAAAACG
4543176 CGGATTGAAATAATATTTTAAATAAGAATATCTTT
66 CGGATTGAAATAATATTTTAAATAAGAATATCTTT
* * ** * ** *
4543211 TTATAATTAAT--TGT-ATTACTAAATAGATAT-TAGTAAAAAAATATTTTAATTTACTGCTAAA
1 TTATAA-CAATCAAGTCATTTTTACAT--ATATCTA-T---AATCTA-TTT-ATTTA----T-AT
* * * * * * * *
4543272 AATTTATATAAATCAAC-AAATG-AATAAT-TTATAAGA-CA-AATATTTTT
52 AATATATA-AAAAC-GCGGATTGAAATAATATTTTAA-ATAAGAATATCTTT
4543319 AATTATAACAATCAAGTCATTTTTACATATATCTATAATCTATTTATTTATATAATATATAAAAA
1 --TTATAACAATCAAGTCATTTTTACATATATCTATAATCTATTTATTTATATAATATATAAAAA
4543384 CGCGGATTGAAATAATATTTTAAATAAGAATATCTTT
64 CGCGGATTGAAATAATATTTTAAATAAGAATATCTTT
4543421 TTATAA
1 TTATAA
4543427 TTAATTGTAT
Statistics
Matches: 156, Mismatches: 32, Indels: 56
0.64 0.13 0.23
Matches are distributed among these distances:
98 8 0.05
99 11 0.07
100 32 0.21
101 10 0.06
102 8 0.05
103 4 0.03
104 3 0.02
105 10 0.06
106 3 0.02
107 4 0.03
108 8 0.05
109 10 0.06
110 26 0.17
111 11 0.07
112 8 0.05
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (100 bp):
TTATAACAATCAAGTCATTTTTACATATATCTATAATCTATTTATTTATATAATATATAAAAACG
CGGATTGAAATAATATTTTAAATAAGAATATCTTT
Found at i:4543312 original size:210 final size:209
Alignment explanation
Indices: 4543070--4543491 Score: 835
Period size: 210 Copynumber: 2.0 Consensus size: 209
4543060 TTAGCACTTC
4543070 TAAATCAACAAATGAATAATTTATAAGACAAATATTTTTAATTATAACAATCAAGTCATTTTTAC
1 TAAATCAACAAATGAATAATTTATAAGACAAATATTTTTAATTATAACAATCAAGTCATTTTTAC
4543135 ATATATCTATAATCTATTTATTTATATAATATATAAAAACGCGGATTGAAATAATATTTTAAATA
66 ATATATCTATAATCTATTTATTTATATAATATATAAAAACGCGGATTGAAATAATATTTTAAATA
4543200 AGAATATCTTTTTATAATTAATTGTATTACTAAATAGATATTAGTAAAAAAATATTTTAATTTAC
131 AGAATATCTTTTTATAATTAATTGTATTACTAAATAGATATTAGTAAAAAAATATTTTAATTTAC
4543265 TGCTAAAAATTTATA
196 TGCT-AAAATTTATA
4543280 TAAATCAACAAATGAATAATTTATAAGACAAATATTTTTAATTATAACAATCAAGTCATTTTTAC
1 TAAATCAACAAATGAATAATTTATAAGACAAATATTTTTAATTATAACAATCAAGTCATTTTTAC
4543345 ATATATCTATAATCTATTTATTTATATAATATATAAAAACGCGGATTGAAATAATATTTTAAATA
66 ATATATCTATAATCTATTTATTTATATAATATATAAAAACGCGGATTGAAATAATATTTTAAATA
4543410 AGAATATCTTTTTATAATTAATTGTATTACTAAATAGATATTAGTAAAAAAATATTTTAATTTAC
131 AGAATATCTTTTTATAATTAATTGTATTACTAAATAGATATTAGTAAAAAAATATTTTAATTTAC
4543475 TGCTAAAATTTATA
196 TGCTAAAATTTATA
4543489 TAA
1 TAA
4543492 TAATAAAAAT
Statistics
Matches: 212, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
209 13 0.06
210 199 0.94
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (209 bp):
TAAATCAACAAATGAATAATTTATAAGACAAATATTTTTAATTATAACAATCAAGTCATTTTTAC
ATATATCTATAATCTATTTATTTATATAATATATAAAAACGCGGATTGAAATAATATTTTAAATA
AGAATATCTTTTTATAATTAATTGTATTACTAAATAGATATTAGTAAAAAAATATTTTAATTTAC
TGCTAAAATTTATA
Found at i:4543482 original size:100 final size:100
Alignment explanation
Indices: 4543168--4543482 Score: 232
Period size: 100 Copynumber: 3.0 Consensus size: 100
4543158 ATATAATATA
4543168 TAAAAACGCGGATTGAAATAATATTTTAAATAAGAATATCTTTTTATAATTAATTGTATTACTAA
1 TAAAAACGCGGATTGAAATAATATTTTAAATAAGAATATCTTTTTATAATTAATTGTATTACTAA
4543233 ATAGATATTAGTAAAAAAATATTTTAATTTACTGC
66 ATAGATATTAGTAAAAAAATATTTTAATTTACTGC
***** * * * * *
4543268 TAAAAATTTATATAAATCAACAAATGAATAATTTATAAGACA-AATATTTTTAATTATAA-CAAT
1 TAAAAACGCGGAT---T---GAAAT-AATATTTTA-AATA-AGAATATCTTT--TTATAATTAAT
* ** * *** * * *
4543331 CAAGTCATTTTTACAT--ATATCTA-T-AATCTATTTATTTATATAATA-T-A
55 --TGT-ATTACTAAATAGATAT-TAGTAAAAAAATAT-TTTA-AT-TTACTGC
4543378 TAAAAACGCGGATTGAAATAATATTTTAAATAAGAATATCTTTTTATAATTAATTGTATTACTAA
1 TAAAAACGCGGATTGAAATAATATTTTAAATAAGAATATCTTTTTATAATTAATTGTATTACTAA
4543443 ATAGATATTAGTAAAAAAATATTTTAATTTACTGC
66 ATAGATATTAGTAAAAAAATATTTTAATTTACTGC
4543478 TAAAA
1 TAAAA
4543483 TTTATATAAT
Statistics
Matches: 149, Mismatches: 40, Indels: 52
0.62 0.17 0.22
Matches are distributed among these distances:
98 9 0.06
99 7 0.05
100 28 0.19
101 9 0.06
102 11 0.07
103 9 0.06
104 4 0.03
106 4 0.03
107 9 0.06
108 11 0.07
109 9 0.06
110 23 0.15
111 7 0.05
112 9 0.06
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (100 bp):
TAAAAACGCGGATTGAAATAATATTTTAAATAAGAATATCTTTTTATAATTAATTGTATTACTAA
ATAGATATTAGTAAAAAAATATTTTAATTTACTGC
Found at i:4547049 original size:24 final size:25
Alignment explanation
Indices: 4547019--4547065 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
4547009 TTTTAAAATT
4547019 TTATGAATAAAT-AAA-TATATAAAA
1 TTATGAA-AAATAAAAGTATATAAAA
4547043 TTATGAAAAATAAAAGTATATAA
1 TTATGAAAAATAAAAGTATATAA
4547066 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (25 bp):
TTATGAAAAATAAAAGTATATAAAA
Found at i:4553010 original size:23 final size:22
Alignment explanation
Indices: 4552968--4553034 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
4552958 CTATACGCTG
*
4552968 GCTTACAAAAAATATGAAAAAA
1 GCTTGCAAAAAATATGAAAAAA
*
4552990 TCTTGCAAAAAATATGAAAAAA
1 GCTTGCAAAAAATATGAAAAAA
4553012 GCTTGCAAAAAAATATGAAAAAA
1 GCTTGC-AAAAAATATGAAAAAA
4553035 AATATTCAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 25 0.61
23 16 0.39
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.19
Consensus pattern (22 bp):
GCTTGCAAAAAATATGAAAAAA
Found at i:4553032 original size:11 final size:11
Alignment explanation
Indices: 4552974--4553035 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
4552964 GCTGGCTTAC
4552974 AAAAAATATG-
1 AAAAAATATGA
* *
4552984 AAAAAATCTTGC
1 AAAAAAT-ATGA
4552996 AAAAAATATGA
1 AAAAAATATGA
*
4553007 AAAAAGCT-TGCA
1 AAAAA-ATATG-A
4553019 AAAAAATATGA
1 AAAAAATATGA
4553030 AAAAAA
1 AAAAAA
4553036 ATATTCAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.17
11 19 0.45
12 16 0.38
ACGTcount: A:0.66, C:0.06, G:0.10, T:0.18
Consensus pattern (11 bp):
AAAAAATATGA
Found at i:4553033 original size:12 final size:12
Alignment explanation
Indices: 4552974--4553039 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
4552964 GCTGGCTTAC
4552974 AAAAAATATGAA
1 AAAAAATATGAA
** *
4552986 AAAATCT-TG-C
1 AAAAAATATGAA
4552996 AAAAAATATGAA
1 AAAAAATATGAA
** *
4553008 AAAAGCT-TGCA
1 AAAAAATATGAA
4553019 AAAAAATATGAA
1 AAAAAATATGAA
4553031 AAAAAATAT
1 AAAAAATAT
4553040 TCAGAGGTAA
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
10 5 0.13
11 12 0.31
12 22 0.56
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAAAATATGAA
Found at i:4555443 original size:23 final size:24
Alignment explanation
Indices: 4555413--4555459 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4555403 CTATACGTTG
4555413 GCTTGC-AAAAAATATGAAAAAAA
1 GCTTGCAAAAAAATATGAAAAAAA
4555436 GCTTGCAAAAAAATATGAAAAAAA
1 GCTTGCAAAAAAATATGAAAAAAA
4555460 ATATTCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.62, C:0.09, G:0.13, T:0.17
Consensus pattern (24 bp):
GCTTGCAAAAAAATATGAAAAAAA
Found at i:4555457 original size:12 final size:12
Alignment explanation
Indices: 4555419--4555463 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4555409 GTTGGCTTGC
4555419 AAAAAATATGAA
1 AAAAAATATGAA
* *
4555431 AAAAAGCT-TGCA
1 AAAAA-ATATGAA
4555443 AAAAAATATGAA
1 AAAAAATATGAA
4555455 AAAAAATAT
1 AAAAAATAT
4555464 TCAGATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAAAATATGAA
Found at i:4556321 original size:39 final size:40
Alignment explanation
Indices: 4556278--4556355 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
4556268 ACATGACTTA
*
4556278 CACGT-GGGTATAGCGC-GCCCCCTGATCCGCGCTATACGC
1 CACGTAGGGTATAGCGCTG-CCCCTGATCAGCGCTATACGC
*
4556317 CACGTAGGGGTATAGCGCTGCCCCTGCTCAGCGCTATAC
1 CACGTA-GGGTATAGCGCTGCCCCTGATCAGCGCTATAC
4556356 CTGGGTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 5 0.15
41 28 0.82
42 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.28, T:0.19
Consensus pattern (40 bp):
CACGTAGGGTATAGCGCTGCCCCTGATCAGCGCTATACGC
Found at i:4560007 original size:35 final size:34
Alignment explanation
Indices: 4559922--4560008 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
4559912 AATATAATTT
* *
4559922 TAAATAAAACAAACTTACAATAAGAATTAAATGG
1 TAAATGAAACAAAATTACAATAAGAATTAAATGG
*
4559956 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAATGA-AACAAAATTACAATAA--GA-ATTAAATGG
4559994 T-AAT-AAACAAAATTA
1 TAAATGAAACAAAATTA
4560009 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 6 0.13
35 23 0.51
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATGAAACAAAATTACAATAAGAATTAAATGG
Found at i:4560628 original size:18 final size:18
Alignment explanation
Indices: 4560604--4560647 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
4560594 AAAGACGGCA
4560604 GCATCATATATGGCTGC-
1 GCATCATATATGGCTGCT
*
4560621 GACATCATATATGGTTGCT
1 G-CATCATATATGGCTGCT
4560640 GCATCATA
1 GCATCATA
4560648 AATAGCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (18 bp):
GCATCATATATGGCTGCT
Found at i:4562350 original size:17 final size:18
Alignment explanation
Indices: 4562330--4562371 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4562320 AAATTATATT
4562330 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
4562347 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
4562365 ATTAAAA
1 AGTAAAA
4562372 ACATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:4562425 original size:12 final size:12
Alignment explanation
Indices: 4562410--4562441 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
4562400 ACCTTAAATA
4562410 GAGAGAATATTT
1 GAGAGAATATTT
4562422 GAGAG-A-ATTT
1 GAGAGAATATTT
4562432 GAGAGAATAT
1 GAGAGAATAT
4562442 GGTGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (12 bp):
GAGAGAATATTT
Found at i:4562837 original size:40 final size:41
Alignment explanation
Indices: 4562769--4562856 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 41
4562759 TTCGAGAAAA
*
4562769 AAAAAAGCCTTTGATTATGGGGGGAAATCAGCTAAAAGCCT
1 AAAAAAGCCTTTGATTATGGGGGAAAATCAGCTAAAAGCCT
*
4562810 AAAAAAGCCTTTGATTGT-GGGGAAAATCAGCTAAAAGCCT
1 AAAAAAGCCTTTGATTATGGGGGAAAATCAGCTAAAAGCCT
4562850 AAAAAAG
1 AAAAAAG
4562857 AGTTCGAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 28 0.62
41 17 0.38
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (41 bp):
AAAAAAGCCTTTGATTATGGGGGAAAATCAGCTAAAAGCCT
Found at i:4565382 original size:21 final size:21
Alignment explanation
Indices: 4565345--4565384 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4565335 AGTATTGAAA
*
4565345 CTCGACTCAAACTAAAAAAGG
1 CTCGACTCAAACAAAAAAAGG
4565366 CTCGAACTCAAA-AAAAAAA
1 CTCG-ACTCAAACAAAAAAA
4565385 TTTAGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.55, C:0.23, G:0.10, T:0.12
Consensus pattern (21 bp):
CTCGACTCAAACAAAAAAAGG
Found at i:4565710 original size:22 final size:22
Alignment explanation
Indices: 4565685--4565747 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 22
4565675 ACAACGCGAT
4565685 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
* *
4565707 TTTGAAAAGCGTGTTGTTGCGATAG
1 TTTGAAAA--ATG-TGTTGCGAGAG
4565732 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
4565748 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
22 8 0.23
23 6 0.17
24 2 0.06
25 10 0.29
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:4565745 original size:19 final size:19
Alignment explanation
Indices: 4565721--4565757 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4565711 AAAAGCGTGT
4565721 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
4565740 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
4565758 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:4567104 original size:28 final size:28
Alignment explanation
Indices: 4567063--4567135 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
4567053 TCACGTGAGC
*
4567063 TCACCATTTTCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
4567091 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
4567119 TCACCATTTCCAACCCG
1 TCACCATTTCCAACCCG
4567136 GGCTTACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.26
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Found at i:4576243 original size:36 final size:36
Alignment explanation
Indices: 4576087--4576276 Score: 229
Period size: 36 Copynumber: 5.2 Consensus size: 36
4576077 AAGTCAATCC
4576087 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
4576123 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
4576159 GAAGCCTTCACCGGAGAATAGTGAAGTAAACCATCA
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
4576195 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * * * *
4576231 TAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACCATCT
4576268 TAAGCCTTC
1 TAAGCCTTC
4576277 TCAGAAGAGT
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.02
36 117 0.88
37 14 0.11
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
Found at i:4576537 original size:51 final size:51
Alignment explanation
Indices: 4576461--4576753 Score: 351
Period size: 51 Copynumber: 5.7 Consensus size: 51
4576451 GTGAAGCAAA
* * *
4576461 TGAAGATATGCGAGTTCTATACTCCTTAGAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
4576512 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * *
4576563 TGAAGATATCCGAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCATT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * *
4576614 TGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * *
4576663 TGAAGAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGT
1 TG-A-AGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC--GT-T
4576719 TGAAGATTGTTCGAG-TCTTATACT-CTCTAAAGAAA
1 TGAAGA-TGTTCGAGTTC-TATACTCCT-TAAAGAAA
4576754 TAGGGGGGAG
Statistics
Matches: 213, Mismatches: 19, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
49 2 0.01
50 1 0.00
51 179 0.84
54 6 0.03
55 23 0.11
56 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (51 bp):
TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
Found at i:4576749 original size:55 final size:55
Alignment explanation
Indices: 4576600--4577149 Score: 427
Period size: 55 Copynumber: 10.3 Consensus size: 55
4576590 AATGAAAGAA
* * * *
4576600 GGAGCGA-ACCCA-T-TTGAAGA-TGTTCGAGT-TCCATACTCCCTAGAGAAAGAG
1 GGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTAAAGAAATAG
* * *
4576651 GGAGCGA-ACCC---G-TGAAGAGATGTTCGAGT-TCTATACTCCCTAAAGAAAGAG
1 GGAGCGAGACCCATTGTTGAAGA-TTGTTCGAGTCT-TATACTCTCTAAAGAAATAG
4576702 GGAGCGA-ACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
1 GGAGCGAGACCCA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * *
4576757 GG-GGGAGACGCGATTGATGAAGATTG-T-GGGTCTTATACTCTCTAAAGAAATAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * *
4576810 GGGGC-AGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * * * * *
4576865 GGGGC-AGACACGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAACATATAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * *
4576918 GGGGC-AGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * * * *
4576973 GGGGC-AGACGCGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAACAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * *
4577026 GGGGC-AGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG
1 GGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
* * * * *
4577081 GGGGC-AGA-CAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAG
1 GGAGCGAGACCCA--TTGTTGAAGATTG-TTCGAGTCTTATACTCTCTAAAGAAATAG
4577136 GGAGCGA-ACCCATT
1 GGAGCGAGACCCATT
4577150 TTTCTGAAGA
Statistics
Matches: 436, Mismatches: 40, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
49 6 0.01
51 51 0.12
53 142 0.33
54 14 0.03
55 211 0.48
56 12 0.03
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (55 bp):
GGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAG
Found at i:4576804 original size:53 final size:55
Alignment explanation
Indices: 4576719--4577137 Score: 573
Period size: 55 Copynumber: 7.7 Consensus size: 55
4576709 ACCCATTTGT
* *
4576719 TGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGGAGACGCGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * * * *
4576774 TGAAGATTG-T-GGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCAATCGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
4576827 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * * *
4576882 TGAAGATTG-T-GGGTCTTATACTCTCTGAACATATAGGGGGCAGACGCGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
4576935 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * * * *
4576990 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAACAGGGGGCAGACGCAATCGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
** * *
4577043 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* *
4577098 TGAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAGGG
1 TGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
4577138 AGCGAACCCA
Statistics
Matches: 323, Mismatches: 34, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
53 141 0.44
54 8 0.02
55 174 0.54
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
Found at i:4577102 original size:108 final size:108
Alignment explanation
Indices: 4576717--4577137 Score: 664
Period size: 108 Copynumber: 3.9 Consensus size: 108
4576707 GAACCCATTT
* * *
4576717 GTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGGAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
*
4576782 GTGGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
4576825 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
* * * *
4576890 GTGGGTCTTATACTCTCTGAACATATAGGGGGCAGACGCGATT
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
*
4576933 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
*
4576998 GTGGGTCTTATACTCTCTGAAGAAACAGGGGGCAGACGCAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
4577041 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGA-T
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
** *
4577105 GATTCAAGTCTTATACCCTCTGAAGAAATAGGG
66 G--T-GGGTCTTATACTCTCTGAAGAAATAGGG
4577138 AGCGAACCCA
Statistics
Matches: 288, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
107 2 0.01
108 261 0.91
109 1 0.00
110 24 0.08
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:4577989 original size:28 final size:28
Alignment explanation
Indices: 4577948--4578020 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
4577938 TCACGTGAGC
*
4577948 TCACCATTTTCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
4577976 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
4578004 TCACCATTTCCAACCCG
1 TCACCATTTCCAACCCG
4578021 GGCTTACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.26
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Found at i:4581765 original size:21 final size:21
Alignment explanation
Indices: 4581720--4581765 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
4581710 CGCGATTATC
*
4581720 ACATGTTCGCTTTCTTTTTAA
1 ACATGTTCACTTTCTTTTTAA
*
4581741 ACAT-TTCACTTTTTTTTTAA
1 ACATGTTCACTTTCTTTTTAA
4581761 TACAT
1 -ACAT
4581766 CATACGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.54
Consensus pattern (21 bp):
ACATGTTCACTTTCTTTTTAA
Found at i:4582233 original size:26 final size:25
Alignment explanation
Indices: 4582203--4582253 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
4582193 TATCGTAACA
** *
4582203 TAAAAATAGCAATATAAAGTTAAAGT
1 TAAAAATAAAAATA-AAAATTAAAGT
4582229 TAAAAATAAAAATAAAAATTAAAGT
1 TAAAAATAAAAATAAAAATTAAAGT
4582254 AGATATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (25 bp):
TAAAAATAAAAATAAAAATTAAAGT
Found at i:4584359 original size:22 final size:22
Alignment explanation
Indices: 4584333--4584379 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
4584323 ACTTTATAAG
*
4584333 TTTTTATAAATGATAATTA-ATT
1 TTTTTATAAAGGAT-ATTATATT
4584355 TTTTTATAAAGGATATTATATT
1 TTTTTATAAAGGATATTATATT
4584377 TTT
1 TTT
4584380 ATATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTATAAAGGATATTATATT
Found at i:4586956 original size:22 final size:23
Alignment explanation
Indices: 4586909--4586956 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
4586899 CATTTAGATT
*
4586909 TTTAACTAATTTATAATTATACG
1 TTTAACTAATTTATAATTATAAG
*
4586932 TTTAA-TACTTTATAATT-TAAAG
1 TTTAACTAATTTATAATTAT-AAG
4586954 TTT
1 TTT
4586957 TATAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 16 0.73
23 5 0.23
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTATAAG
Found at i:4595281 original size:13 final size:13
Alignment explanation
Indices: 4595257--4595291 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
4595247 AAAAAATCAA
4595257 ATTAAATATTAAAT
1 ATTAAAT-TTAAAT
4595271 ATTAAATTTAAAT
1 ATTAAATTTAAAT
4595284 ATTAAATT
1 ATTAAATT
4595292 GAGAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:4595281 original size:20 final size:19
Alignment explanation
Indices: 4595217--4595290 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
4595207 TTGACCACTA
*
4595217 AAATTTAAT-TTAAATATT
1 AAATTAAATATTAAATATT
* * * *
4595235 TAATTAAAAATTAAAAAATC
1 AAATTAAATATT-AAATATT
4595255 AAATTAAATATTAAATATT
1 AAATTAAATATTAAATATT
4595274 AAATTTAAATATTAAAT
1 AAA-TTAAATATTAAAT
4595291 TGAGAACAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 28 0.64
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTAAATATTAAATATT
Found at i:4595290 original size:7 final size:7
Alignment explanation
Indices: 4595257--4595290 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
4595247 AAAAAATCAA
4595257 ATTAAAT
1 ATTAAAT
4595264 ATTAAAT
1 ATTAAAT
4595271 ATTAAAT
1 ATTAAAT
4595278 -TTAAAT
1 ATTAAAT
4595284 ATTAAAT
1 ATTAAAT
4595291 TGAGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAAAT
Found at i:4602654 original size:26 final size:27
Alignment explanation
Indices: 4602625--4602681 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
4602615 TATTTATTAT
*
4602625 ATCTTATT-AATTAAGAAATCATGTAC
1 ATCTTATTAAATTAAAAAATCATGTAC
4602651 ATCTTATTAAATTAAAAAATCATGTAC
1 ATCTTATTAAATTAAAAAATCATGTAC
4602678 ATCT
1 ATCT
4602682 GTATGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (27 bp):
ATCTTATTAAATTAAAAAATCATGTAC
Found at i:4602818 original size:31 final size:31
Alignment explanation
Indices: 4602780--4602838 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
4602770 GCAGACAAGT
*
4602780 TAAAATAATCCTTCTGCAACGAGAAAAAAAA
1 TAAAATAATCCTTCTCCAACGAGAAAAAAAA
4602811 TAAAATAATCCTTCTCCAACGAGAAAAA
1 TAAAATAATCCTTCTCCAACGAGAAAAA
4602839 GAAGAGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (31 bp):
TAAAATAATCCTTCTCCAACGAGAAAAAAAA
Found at i:4619565 original size:315 final size:314
Alignment explanation
Indices: 4618955--4619589 Score: 1236
Period size: 315 Copynumber: 2.0 Consensus size: 314
4618945 GATGGATCAA
4618955 AGAGATCAAAGTTGGTGAGGTATTGATTTTGAGAATATGTGCATATATTTATCTTTCTTCAGTTC
1 AGAG-TCAAAGTTGGTGAGGTATTGATTTTGAGAATATGTGCATATATTTATCTTTCTTCAGTTC
4619020 TCATGGATTGGAGAATCCAGTTTGACTAAATAGAGGAGATGCCATCTTGGCTTTCTATTGGTCTT
65 TCATGGATTGGAGAATCCAGTTTGACTAAATAGAGGAGATGCCATCTTGGCTTTCTATTGGTCTT
4619085 TTTGCAATACATCTGAATATTTATGCAGCTATATTTTTTTGTTTTCTTTTGTTGTTATGTAGATA
130 TTTGCAATACATCTGAATATTTATGCAGCTATATTTTTTTGTTTTCTTTTGTTGTTATGTAGATA
4619150 ATTGCCATTACTATTGAAGAGGAAGGGATATTGTGAAGTTCAGGACTTCAGTCCTGCAGACTCAG
195 ATTGCCATTACTATTGAAGAGGAAGGGATATTGTGAAGTTCAGGACTTCAGTCCTGCAGACTCAG
4619215 CTGCTCCTCCGCCACCACCAAAGAAGGAGCCCTGTTGAACATCAGTTCCTTCACC
260 CTGCTCCTCCGCCACCACCAAAGAAGGAGCCCTGTTGAACATCAGTTCCTTCACC
4619270 AGAGTCAAAGTTGGTGAGGTATTGATTTTGAGAAATATTGTGCATATATTTATCTTTCTTCAGTT
1 AGAGTCAAAGTTGGTGAGGTATTGATTTTGAG-AATA-TGTGCATATATTTATCTTTCTTCAGTT
4619335 CTCATGGATTGGAGAATCCAGTTTGACTAAATAGAGGAGATG-CATCTTGGCTTTCTATTGGTCT
64 CTCATGGATTGGAGAATCCAGTTTGACTAAATAGAGGAGATGCCATCTTGGCTTTCTATTGGTCT
4619399 TTTTGCAATACATCTGAATATTTATGCAGCTATATTTTTTTGTTTTCTTTTGTTGTTATGTAGAT
129 TTTTGCAATACATCTGAATATTTATGCAGCTATATTTTTTTGTTTTCTTTTGTTGTTATGTAGAT
4619464 AATTGCCATTACTATTGAAGAGGAAGGGATATTGTGAAGTTCAGGACTTCAGTCCTGCAGACTCA
194 AATTGCCATTACTATTGAAGAGGAAGGGATATTGTGAAGTTCAGGACTTCAGTCCTGCAGACTCA
4619529 GCTGCTCCTCCGCCACCACCAAAGAAGGAGCCCTGTTGAACATCAGTTCCTTCACC
259 GCTGCTCCTCCGCCACCACCAAAGAAGGAGCCCTGTTGAACATCAGTTCCTTCACC
4619585 AGAGT
1 AGAGT
4619590 AGATTTCCAC
Statistics
Matches: 318, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
314 28 0.09
315 221 0.69
316 69 0.22
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (314 bp):
AGAGTCAAAGTTGGTGAGGTATTGATTTTGAGAATATGTGCATATATTTATCTTTCTTCAGTTCT
CATGGATTGGAGAATCCAGTTTGACTAAATAGAGGAGATGCCATCTTGGCTTTCTATTGGTCTTT
TTGCAATACATCTGAATATTTATGCAGCTATATTTTTTTGTTTTCTTTTGTTGTTATGTAGATAA
TTGCCATTACTATTGAAGAGGAAGGGATATTGTGAAGTTCAGGACTTCAGTCCTGCAGACTCAGC
TGCTCCTCCGCCACCACCAAAGAAGGAGCCCTGTTGAACATCAGTTCCTTCACC
Found at i:4628505 original size:45 final size:45
Alignment explanation
Indices: 4628424--4628557 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
4628414 CAAGGATGAT
* *
4628424 TTCCCATGGTAACAAAGC-GTTTGTATTTTTCATCGGCATCAGAC
1 TTCCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGAC
*
4628468 TTCCCATGGGAGCAAAGCGGTCTGTATTTTTCATCGGCATCAGAC
1 TTCCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGAC
4628513 TTCCCATGGGAACAAAGCGGTC-GTATTTTTCATCGGCATCAGAC
1 TTCCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGAC
4628557 T
1 T
4628558 GCTCAGATGA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
44 39 0.46
45 46 0.54
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (45 bp):
TTCCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGAC
Found at i:4632691 original size:2 final size:2
Alignment explanation
Indices: 4632684--4632712 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4632674 ATAATCTAAA
4632684 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 A
4632713 AAACTAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4632863 original size:3 final size:3
Alignment explanation
Indices: 4632849--4632901 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
4632839 AAAATAAACA
*
4632849 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4632897 AAT AA
1 AAT AA
4632902 AGACAAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4633097 original size:24 final size:26
Alignment explanation
Indices: 4633050--4633098 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4633040 TTAAAATATC
*
4633050 ATATTAATTATTTTAATTACATAACAT
1 ATATTAA-TATTTAAATTACATAACAT
4633077 ATATTAA-ATTTAAATTA-ATAAC
1 ATATTAATATTTAAATTACATAAC
4633099 TTAACGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
27 7 0.33
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATTAATATTTAAATTACATAACAT
Found at i:4645779 original size:2 final size:2
Alignment explanation
Indices: 4645774--4645815 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4645764 GAAAAAAATA
4645774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4645816 TCCAAAGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4652913 original size:36 final size:35
Alignment explanation
Indices: 4652814--4652954 Score: 219
Period size: 36 Copynumber: 4.0 Consensus size: 35
4652804 TTCGTTCTAG
*
4652814 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGAC
1 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGAT
*
4652849 TTGAACCGGAAGTGCGATGCTTCTTTCCGTTCGAT
1 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGAT
*
4652884 TTGAATCGGAAGTGTCGATGCTTCATTCCGTTCGAT
1 TTGAATCGGAAGTG-CGATGCTTCTTTCCGTTCGAT
* *
4652920 TTAAATCGGAAGTGCAGATGCTTCCTTCCGTTCGA
1 TTGAATCGGAAGTGC-GATGCTTCTTTCCGTTCGA
4652955 CTAGAAACAC
Statistics
Matches: 98, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
35 47 0.48
36 51 0.52
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (35 bp):
TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGAT
Found at i:4652930 original size:71 final size:71
Alignment explanation
Indices: 4652814--4652954 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
4652804 TTCGTTCTAG
* * *
4652814 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGACTTGAACCGGAAGTGC-GATGCTTCTTTCCG
1 TTGAATCGGAAGTGCGATGCTTCATTCCGTTCGACTTAAACCGGAAGTGCAGATGCTTCCTTCCG
4652878 TTCGAT
66 TTCGAT
* *
4652884 TTGAATCGGAAGTGTCGATGCTTCATTCCGTTCGATTTAAATCGGAAGTGCAGATGCTTCCTTCC
1 TTGAATCGGAAGTG-CGATGCTTCATTCCGTTCGACTTAAACCGGAAGTGCAGATGCTTCCTTCC
4652949 GTTCGA
65 GTTCGA
4652955 CTAGAAACAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 14 0.22
71 32 0.50
72 18 0.28
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (71 bp):
TTGAATCGGAAGTGCGATGCTTCATTCCGTTCGACTTAAACCGGAAGTGCAGATGCTTCCTTCCG
TTCGAT
Found at i:4662772 original size:15 final size:16
Alignment explanation
Indices: 4662705--4662765 Score: 86
Period size: 16 Copynumber: 3.6 Consensus size: 16
4662695 TCACGAAATG
4662705 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
4662723 TGTAAGATTACCAGGGAA
1 --TAAGATTACCAGGGAA
4662741 TAAGATTACCAGGGAA
1 TAAGATTACCAGGGAA
4662757 TAAGATTAC
1 TAAGATTAC
4662766 TGGGAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
16 25 0.61
18 5 0.12
20 11 0.27
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:4662985 original size:37 final size:38
Alignment explanation
Indices: 4662905--4662985 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
4662895 AACAAGTTAG
* *
4662905 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
4662944 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
4662980 AAAAAT
1 AAAAAT
4662986 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:4663379 original size:96 final size:95
Alignment explanation
Indices: 4663212--4663410 Score: 353
Period size: 96 Copynumber: 2.1 Consensus size: 95
4663202 GAGGTAATGA
*
4663212 CATTCCCAGTAATATACTCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTC
1 CATTCCCAGTAATATACCCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTC
*
4663277 CTAGCTAACCAAACGGGGGAATGTAGATTC
66 CCAGCTAACCAAACGGGGGAATGTAGATTC
* *
4663307 CATTCCCGGTAATATACCCAAAAAAAATCCACTATTGGTAATCTTACATTACCGGGAATGAGATT
1 CATTCCCAGTAATATACCC-AAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATT
4663372 CCCAGCTAACCAAACGGGGGAATGTAGATTC
65 CCCAGCTAACCAAACGGGGGAATGTAGATTC
4663403 CATTCCCA
1 CATTCCCA
4663411 TGGGAATCAC
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 17 0.17
96 81 0.83
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (95 bp):
CATTCCCAGTAATATACCCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTC
CCAGCTAACCAAACGGGGGAATGTAGATTC
Found at i:4670551 original size:15 final size:15
Alignment explanation
Indices: 4670511--4670552 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4670501 TGGTATGGAT
*
4670511 GATGATGATCATGAC
1 GATGATGATGATGAC
*
4670526 GATGATGATGATGTC
1 GATGATGATGATGAC
*
4670541 GATGATAATGAT
1 GATGATGATGAT
4670553 AATGGTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (15 bp):
GATGATGATGATGAC
Found at i:4671226 original size:2 final size:2
Alignment explanation
Indices: 4671219--4671251 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4671209 TGGTTAGTTT
4671219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4671252 GTCAACATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4672850 original size:27 final size:27
Alignment explanation
Indices: 4672797--4672850 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
4672787 GAGAAAAGAA
*
4672797 TAATAAAAAATATTAATATAATAATAT
1 TAATAAAAAATATAAATATAATAATAT
4672824 TAAT-AAAAAT-TAAATATATATATATAT
1 TAATAAAAAATATAAATATA-ATA-ATAT
4672851 AACAATGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATAAAAAATATAAATATAATAATAT
Found at i:4673327 original size:17 final size:17
Alignment explanation
Indices: 4673305--4673347 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
4673295 TAGGGCCTGC
4673305 AAAAATAA-AATAATAAT
1 AAAAATAATAAT-ATAAT
4673322 AAAAATAATAATATAAT
1 AAAAATAATAATATAAT
*
4673339 ATAAATAAT
1 AAAAATAAT
4673348 TATAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATAATAATATAAT
Found at i:4678213 original size:8 final size:8
Alignment explanation
Indices: 4678200--4678236 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
4678190 TCTGTCTTCT
4678200 TTTATTCA
1 TTTATTCA
4678208 TTTATTCA
1 TTTATTCA
4678216 TTTATTCA
1 TTTATTCA
4678224 TTTATTCA
1 TTTATTCA
4678232 TTTAT
1 TTTAT
4678237 CTACCCTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATTCA
Found at i:4680779 original size:29 final size:29
Alignment explanation
Indices: 4680737--4680825 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
4680727 CTACAGTGGT
4680737 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4680766 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4680795 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4680824 CT
1 CT
4680826 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:4680884 original size:18 final size:18
Alignment explanation
Indices: 4680847--4680899 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
4680837 AGAATAGGGC
4680847 CATGCAATCAACAT-GGA
1 CATGCAATCAACATGGGA
4680864 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
4680882 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
4680900 GTGGGAATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:4680941 original size:62 final size:60
Alignment explanation
Indices: 4680864--4680980 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
4680854 TCAACATGGA
4680864 CATGCAATCAACATGGGACAT-GCAATCAACATGGGAGTGGGAATGCATGGGGGAGGGGATGC
1 CATGCAATCAACATGGGACATGGCAAT--ACATGGG-GTGGGAATGCATGGGGGAGGGGATGC
* ** *
4680926 CATGCAATCAACATGGGACGTGGGGATGCATGGGGTGGGAATGCATGGGGGAGGG
1 CATGCAATCAACATGGGACATGGCAATACATGGGGTGGGAATGCATGGGGGAGGG
4680981 ATCAACATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 21 0.42
61 6 0.12
62 20 0.40
63 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.42, T:0.16
Consensus pattern (60 bp):
CATGCAATCAACATGGGACATGGCAATACATGGGGTGGGAATGCATGGGGGAGGGGATGC
Found at i:4680969 original size:15 final size:15
Alignment explanation
Indices: 4680945--4681108 Score: 123
Period size: 15 Copynumber: 10.1 Consensus size: 15
4680935 AACATGGGAC
*
4680945 GTGGGGATGCATGGG
1 GTGGGAATGCATGGG
4680960 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
4680975 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
4680992 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
4681010 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
4681025 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
4681042 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
4681058 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
4681078 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
4681093 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
4681108 G
1 G
4681109 GGAGGGGATG
Statistics
Matches: 119, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.01
15 50 0.42
16 17 0.14
17 30 0.25
18 3 0.03
19 15 0.13
20 3 0.03
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:4680970 original size:39 final size:41
Alignment explanation
Indices: 4680876--4680960 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
4680866 TGCAATCAAC
4680876 ATGGGACATGCAATCAACATGGGAGTGGGAATGCATGGGGG
1 ATGGGACATGCAATCAACATGGGAGTGGGAATGCATGGGGG
* *
4680917 AGGGGATGCCATGCAATCAACATGGGACGTGGGGATGCATGGGG
1 ATGGGA---CATGCAATCAACATGGGA-GTGGGAATGCATGGGG
4680961 TGGGAATGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 5 0.13
44 18 0.47
45 15 0.39
ACGTcount: A:0.27, C:0.14, G:0.42, T:0.16
Consensus pattern (41 bp):
ATGGGACATGCAATCAACATGGGAGTGGGAATGCATGGGGG
Found at i:4681003 original size:34 final size:33
Alignment explanation
Indices: 4680947--4681042 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
4680937 CATGGGACGT
*
4680947 GGGGATGCATGGG--GTGGGAATGCATGGGGGA
1 GGGGATACATGGGACGTGGGAATGCATGGGGGA
*
4680978 -GGGATCAACATGGGATGTGGGAATGCATGGGGGA
1 GGGGAT--ACATGGGACGTGGGAATGCATGGGGGA
*
4681012 GGGGATGCATGGGACGTGGGAATGCATGGGG
1 GGGGATACATGGGACGTGGGAATGCATGGGG
4681043 TGGGAATGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
30 5 0.09
32 6 0.11
33 23 0.40
34 18 0.32
35 5 0.09
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.17
Consensus pattern (33 bp):
GGGGATACATGGGACGTGGGAATGCATGGGGGA
Found at i:4681025 original size:82 final size:83
Alignment explanation
Indices: 4680937--4681107 Score: 247
Period size: 82 Copynumber: 2.1 Consensus size: 83
4680927 ATGCAATCAA
* *
4680937 CATGGGACGTGGGGATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGATGTGGGA
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGA
*
4681000 ATGCATGGGGGAGGGGATG
66 ATGCAT-GGGGAGGGAATG
*** *
4681019 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGA
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGA
*
4681084 ATGCATGGGGTGGGAATG
66 ATGCATGGGGAGGGAATG
4681102 CATGGG
1 CATGGG
4681108 GGGAGGGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
82 40 0.51
83 21 0.27
84 18 0.23
ACGTcount: A:0.21, C:0.09, G:0.52, T:0.18
Consensus pattern (83 bp):
CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGA
ATGCATGGGGAGGGAATG
Found at i:4681031 original size:33 final size:32
Alignment explanation
Indices: 4680947--4681118 Score: 147
Period size: 32 Copynumber: 5.2 Consensus size: 32
4680937 CATGGGACGT
4680947 GGGGATGCATGGG-GTGGGAATGCATGGGGGA
1 GGGGATGCATGGGAGTGGGAATGCATGGGGGA
*
4680978 -GGGATCAACATGGGATGTGGGAATGCATGGGGGA
1 GGGGAT--GCATGGGA-GTGGGAATGCATGGGGGA
*
4681012 GGGGATGCATGGGACGTGGGAATGCAT-GGGGT
1 GGGGATGCATGGGA-GTGGGAATGCATGGGGGA
* * ** *
4681044 GGGAATGCATGGGGGAG-GGGATGGTGCATTGGACGT
1 GGGGATGCAT--GGGAGTGGGA--ATGCA-TGGGGGA
*
4681080 GGGAATGCATGGG-GTGGGAATGCATGGGGGGA
1 GGGGATGCATGGGAGTGGGAATGCAT-GGGGGA
4681112 GGGGATG
1 GGGGATG
4681119 GTGCATTGGA
Statistics
Matches: 115, Mismatches: 13, Indels: 25
0.75 0.08 0.16
Matches are distributed among these distances:
30 5 0.04
31 1 0.01
32 36 0.31
33 21 0.18
34 33 0.29
35 6 0.05
36 13 0.11
ACGTcount: A:0.21, C:0.08, G:0.54, T:0.17
Consensus pattern (32 bp):
GGGGATGCATGGGAGTGGGAATGCATGGGGGA
Found at i:4681132 original size:52 final size:51
Alignment explanation
Indices: 4680994--4681133 Score: 241
Period size: 51 Copynumber: 2.8 Consensus size: 51
4680984 AACATGGGAT
*
4680994 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
4681042 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
4681093 GTGGGAATGCATGGGGGGAGGGGATGGTGCATTGGACGTGG
1 GTGGGAATGCAT-GGGGGAGGGGATGGTGCATTGGACGTGG
4681134 AACTGGCATG
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
48 23 0.26
51 36 0.41
52 28 0.32
ACGTcount: A:0.19, C:0.08, G:0.54, T:0.19
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:4681258 original size:31 final size:32
Alignment explanation
Indices: 4681207--4681269 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
4681197 AAGGTCCTGC
4681207 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
4681239 TGCATGCATGCG-TGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
4681270 CAGAGATTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.30
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:4681621 original size:21 final size:21
Alignment explanation
Indices: 4681573--4681621 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4681563 ACTAAAATCT
*
4681573 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
4681595 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
4681616 AGTTAT
1 AGTTAT
4681622 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:4681631 original size:28 final size:28
Alignment explanation
Indices: 4681598--4681651 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
4681588 TAGTATAAAT
*
4681598 TATTAGTTTGTAAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
*
4681626 TATTAGTTTATTAGTTTAAGTTATAT
1 TATTAGTTTATAAGTTTAAGTTATAT
4681652 ATTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (28 bp):
TATTAGTTTATAAGTTTAAGTTATATTA
Found at i:4681728 original size:41 final size:44
Alignment explanation
Indices: 4681620--4681728 Score: 134
Period size: 47 Copynumber: 2.5 Consensus size: 44
4681610 AGTTTAAGTT
4681620 ATATTATATTAGTTTATTAGTTTAAGTTATATATTATATATAAAAA
1 ATATTA-ATTAGTTTATTAGTTTAAGTTATATA-TATATATAAAAA
*
4681666 ATTAGTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATATAAAAA
1 A-TA-TTAATTAGTTTATTAGTTTAAGTTATATATATATATAAAAA
* *
4681709 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTATTAGT
4681729 GTCTTTAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
41 15 0.26
42 2 0.03
43 10 0.17
44 1 0.02
46 3 0.05
47 24 0.41
48 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (44 bp):
ATATTAATTAGTTTATTAGTTTAAGTTATATATATATATAAAAA
Found at i:4682478 original size:26 final size:25
Alignment explanation
Indices: 4682449--4682507 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
4682439 AAATCATATT
*
4682449 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
4682475 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
4682501 ATTATTA
1 ATTATTA
4682508 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:4686571 original size:45 final size:45
Alignment explanation
Indices: 4686476--4686576 Score: 125
Period size: 45 Copynumber: 2.2 Consensus size: 45
4686466 CAACAAACAA
* *
4686476 ATATAACTTAACTATTTAACTACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACAACACAAACTAATTAAAT-ATTTTTCT
*
4686523 ATATAACTAACTA-TTAACAATACAAACTAATTAAAT-TTTTTAACT
1 ATATAACTAACTATTTAACAACACAAACTAATTAAATATTTTT--CT
4686568 ATATAACTA
1 ATATAACTA
4686577 TCAAACATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
43 5 0.10
45 31 0.63
46 6 0.12
47 7 0.14
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (45 bp):
ATATAACTAACTATTTAACAACACAAACTAATTAAATATTTTTCT
Found at i:4686575 original size:41 final size:44
Alignment explanation
Indices: 4686475--4686607 Score: 118
Period size: 45 Copynumber: 3.1 Consensus size: 44
4686465 TCAACAAACA
*
4686475 AATATAACTTAACTATTTAACTACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAACAACACAAACTAATT-AATAATTTTTT
* *
4686522 TATATAACTAACTATTAACAATACAAACTAATT-A-AATTTTTT
1 AATATAACTAACTATTAACAACACAAACTAATTAATAATTTTTT
* * *
4686564 AACTAT-A-TAACTA-TCA-AACATATACTAATTAA-ATATTTTTT
1 AA-TATAACTAACTATTAACAACACAAACTAATTAATA-ATTTTTT
4686605 AAT
1 AAT
4686608 TTATGTATAC
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
39 11 0.15
40 5 0.07
41 15 0.20
42 10 0.13
43 4 0.05
45 17 0.23
46 6 0.08
47 7 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (44 bp):
AATATAACTAACTATTAACAACACAAACTAATTAATAATTTTTT
Found at i:4686795 original size:20 final size:20
Alignment explanation
Indices: 4686767--4686817 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
4686757 TTTCGAATTC
*
4686767 TTCTACTTTCCTTTCTCCCT
1 TTCTTCTTTCCTTTCTCCCT
4686787 TTCTTCTTTCCTTTCTCCCT
1 TTCTTCTTTCCTTTCTCCCT
4686807 TTCTTTCTTTC
1 TTC-TTCTTTC
4686818 TCGATGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (20 bp):
TTCTTCTTTCCTTTCTCCCT
Found at i:4686908 original size:25 final size:25
Alignment explanation
Indices: 4686880--4686931 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
4686870 TTTCTTTTAT
*
4686880 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
4686905 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
4686930 AA
1 AA
4686932 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:4687072 original size:23 final size:23
Alignment explanation
Indices: 4687042--4687101 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
4687032 ACACGTGAAG
4687042 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
4687065 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
4687088 GAATGGATGATGGG
1 GAATGGATGATGGG
4687102 AATGGCGCCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.07, G:0.45, T:0.25
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:4687158 original size:29 final size:29
Alignment explanation
Indices: 4687116--4687211 Score: 192
Period size: 29 Copynumber: 3.3 Consensus size: 29
4687106 GCGCCGGGAC
4687116 GGCGACCTATAAGGTCGCCGGGACTACAT
1 GGCGACCTATAAGGTCGCCGGGACTACAT
4687145 GGCGACCTATAAGGTCGCCGGGACTACAT
1 GGCGACCTATAAGGTCGCCGGGACTACAT
4687174 GGCGACCTATAAGGTCGCCGGGACTACAT
1 GGCGACCTATAAGGTCGCCGGGACTACAT
4687203 GGCGACCTA
1 GGCGACCTA
4687212 CACCCTATTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.17
Consensus pattern (29 bp):
GGCGACCTATAAGGTCGCCGGGACTACAT
Found at i:4687259 original size:15 final size:15
Alignment explanation
Indices: 4687236--4687345 Score: 69
Period size: 15 Copynumber: 7.9 Consensus size: 15
4687226 GCATGGGGAC
4687236 CTCGCATGGCTCGCA
1 CTCGCATGGCTCGCA
* *
4687251 CTCGTATGGCTCGTA
1 CTCGCATGGCTCGCA
*
4687266 -T-GCATGG---GGA
1 CTCGCATGGCTCGCA
4687276 CCTCGCATGGCTCGCA
1 -CTCGCATGGCTCGCA
* *
4687292 CTCGTATGGCTCGTA
1 CTCGCATGGCTCGCA
*
4687307 -T-GCATGG---GGA
1 CTCGCATGGCTCGCA
4687317 CCTCGCATGGCTCGCA
1 -CTCGCATGGCTCGCA
*
4687333 CTCGTATGGCTCG
1 CTCGCATGGCTCG
4687346 TATGCATGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 24
0.67 0.10 0.22
Matches are distributed among these distances:
10 4 0.06
12 2 0.03
13 22 0.31
14 2 0.03
15 38 0.53
16 4 0.06
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.25
Consensus pattern (15 bp):
CTCGCATGGCTCGCA
Found at i:4687271 original size:41 final size:41
Alignment explanation
Indices: 4687225--4687367 Score: 286
Period size: 41 Copynumber: 3.5 Consensus size: 41
4687215 CCTATTCCAC
4687225 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4687266 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4687307 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4687348 TGCATGGGGACCTCGCATGG
1 TGCATGGGGACCTCGCATGG
4687368 GGAGAACGAC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 102 1.00
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.24
Consensus pattern (41 bp):
TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:4687446 original size:55 final size:55
Alignment explanation
Indices: 4687381--4687491 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
4687371 GAACGACCTC
4687381 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
4687436 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
4687491 T
1 T
4687492 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:4687473 original size:27 final size:27
Alignment explanation
Indices: 4687388--4687473 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
4687378 CTCTCTATTC
4687388 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
4687415 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
4687443 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
4687470 CACT
1 CACT
4687474 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:4687480 original size:15 final size:15
Alignment explanation
Indices: 4687457--4687525 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
4687447 GCATGGCCAC
4687457 CTCGCATGGCTCGCA
1 CTCGCATGGCTCGCA
* *
4687472 CTCGTATGGCTCGTA
1 CTCGCATGGCTCGCA
*
4687487 -T-GCATGG---GGA
1 CTCGCATGGCTCGCA
4687497 CCTCGCATGGCTCGCA
1 -CTCGCATGGCTCGCA
*
4687513 CTCGTATGGCTCG
1 CTCGCATGGCTCG
4687526 TATGCATGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.05
12 1 0.02
13 11 0.26
14 1 0.02
15 25 0.60
16 2 0.05
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (15 bp):
CTCGCATGGCTCGCA
Found at i:4687500 original size:41 final size:41
Alignment explanation
Indices: 4687446--4687537 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
4687436 TCTATTCCAC
**
4687446 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4687487 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4687528 TGCATGGGGA
1 TGCATGGGGA
4687538 GAACCAGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (41 bp):
TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:4687676 original size:115 final size:115
Alignment explanation
Indices: 4687474--4687706 Score: 466
Period size: 115 Copynumber: 2.0 Consensus size: 115
4687464 GGCTCGCACT
4687474 CGTATGGCTCGTATGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGAG
1 CGTATGGCTCGTATGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGAG
4687539 AACCAGAACCATTGGCTCGTATGTTCCCGTATGTCGCCTGGATTGCATGG
66 AACCAGAACCATTGGCTCGTATGTTCCCGTATGTCGCCTGGATTGCATGG
4687589 CGTATGGCTCGTATGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGAG
1 CGTATGGCTCGTATGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGAG
4687654 AACCAGAACCATTGGCTCGTATGTTCCCGTATGTCGCCTGGATTGCATGG
66 AACCAGAACCATTGGCTCGTATGTTCCCGTATGTCGCCTGGATTGCATGG
4687704 CGT
1 CGT
4687707 CCTACAAGGT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 118 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.26
Consensus pattern (115 bp):
CGTATGGCTCGTATGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGAG
AACCAGAACCATTGGCTCGTATGTTCCCGTATGTCGCCTGGATTGCATGG
Found at i:4691300 original size:24 final size:24
Alignment explanation
Indices: 4691273--4691372 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
4691263 GATATCAAAA
*
4691273 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
4691297 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
4691321 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
4691345 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
4691369 ATCA
1 ATCA
4691373 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:4691372 original size:48 final size:48
Alignment explanation
Indices: 4691266--4691374 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
4691256 AAATGGAGAT
* * * * *
4691266 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
4691314 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
4691362 ATCAGAAATCAGA
1 ATCAGAAATCAGA
4691375 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:4692530 original size:18 final size:18
Alignment explanation
Indices: 4692509--4692543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4692499 TTCCATCTGG
*
4692509 TCTTATTATTTAATTTAA
1 TCTTATCATTTAATTTAA
*
4692527 TCTTATCATTTACTTTA
1 TCTTATCATTTAATTTA
4692544 GTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTATCATTTAATTTAA
Found at i:4696287 original size:26 final size:27
Alignment explanation
Indices: 4696204--4696296 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
4696194 AACAGCGCTG
4696204 AATGATTTAGCATCAAAGTATATTCTA
1 AATGATTTAGCATCAAAGTATATTCTA
*
4696231 AATGATTTAGCATCAAAGTATATTATA
1 AATGATTTAGCATCAAAGTATATTCTA
*
4696258 AATGATTTAGCATC-AAGTATATTCTG
1 AATGATTTAGCATCAAAGTATATTCTA
*
4696284 AATGATTCAGCAT
1 AATGATTTAGCAT
4696297 GTCACATTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 22 0.35
27 40 0.65
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (27 bp):
AATGATTTAGCATCAAAGTATATTCTA
Found at i:4696478 original size:15 final size:15
Alignment explanation
Indices: 4696444--4696484 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
4696434 ATTTCGATCA
*
4696444 TTAATATTTAATTTAAT
1 TTAA-ATTT-ATTAAAT
4696461 TTAAATTTATTAAAT
1 TTAAATTTATTAAAT
4696476 TTAAATTTA
1 TTAAATTTA
4696485 AATGTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.65
16 4 0.17
17 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAAATTTATTAAAT
Found at i:4703066 original size:2 final size:2
Alignment explanation
Indices: 4703059--4703100 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4703049 CAGATATGGC
4703059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4703101 TTTGGTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4708889 original size:14 final size:14
Alignment explanation
Indices: 4708845--4708889 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
4708835 GATTGTACAA
4708845 AATATAAATGAACG
1 AATATAAATGAACG
* *
4708859 AACATAAATGAATG
1 AATATAAATGAACG
*
4708873 AATATAAACGAACG
1 AATATAAATGAACG
4708887 AAT
1 AAT
4708890 TATTGAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (14 bp):
AATATAAATGAACG
Found at i:4709152 original size:31 final size:30
Alignment explanation
Indices: 4709117--4709183 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
4709107 AATTTGAAAA
*
4709117 TTTATAACAAAATTTAAAA-TATAATGTTCAT
1 TTTATAA-AAAATCTAAAACT-TAATGTTCAT
*
4709148 TTTAT-AAAAGTCTAAAACTTAATGTTCAT
1 TTTATAAAAAATCTAAAACTTAATGTTCAT
4709177 TTTATAA
1 TTTATAA
4709184 TTTCTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 24 0.75
30 3 0.09
31 5 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (30 bp):
TTTATAAAAAATCTAAAACTTAATGTTCAT
Found at i:4713600 original size:27 final size:27
Alignment explanation
Indices: 4713563--4713634 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
4713553 GGTCATTTCT
*
4713563 TGCTGTTGCTGTTGTTGTAATTGCTGC
1 TGCTGCTGCTGTTGTTGTAATTGCTGC
*
4713590 TGCTGCTGCTGTTGCTGTAATTGCTGC
1 TGCTGCTGCTGTTGTTGTAATTGCTGC
*
4713617 TGCTGCAGCTGTTGTTGT
1 TGCTGCTGCTGTTGTTGT
4713635 TGCCGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.07, C:0.18, G:0.31, T:0.44
Consensus pattern (27 bp):
TGCTGCTGCTGTTGTTGTAATTGCTGC
Found at i:4713671 original size:27 final size:27
Alignment explanation
Indices: 4713641--4713699 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
4713631 TTGTTGCCGT
4713641 TGTTGCAACTGCTGCTGCAATTGCAAC
1 TGTTGCAACTGCTGCTGCAATTGCAAC
*** * *
4713668 TGTTGTTGCTGTTGCTGCAATTGCAAT
1 TGTTGCAACTGCTGCTGCAATTGCAAC
4713695 TGTTG
1 TGTTG
4713700 TTGCTGCTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (27 bp):
TGTTGCAACTGCTGCTGCAATTGCAAC
Found at i:4713700 original size:27 final size:27
Alignment explanation
Indices: 4713649--4713712 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
4713639 GTTGTTGCAA
4713649 CTGCTGCTGCAATTGCAACTGTTGTTG
1 CTGCTGCTGCAATTGCAACTGTTGTTG
* *
4713676 CTGTTGCTGCAATTGCAATTGTTGTTG
1 CTGCTGCTGCAATTGCAACTGTTGTTG
4713703 CTGCTGCTGC
1 CTGCTGCTGC
4713713 TGCTGGTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (27 bp):
CTGCTGCTGCAATTGCAACTGTTGTTG
Found at i:4714223 original size:9 final size:9
Alignment explanation
Indices: 4714196--4714243 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
4714186 CATTTGTACC
4714196 TGCTGCTGT
1 TGCTGCTGT
*
4714205 GGCTGCTGT
1 TGCTGCTGT
4714214 TGCTGCTGT
1 TGCTGCTGT
*
4714223 TGTTGCAATTGT
1 TGCTGC---TGT
4714235 TGCTGCTGT
1 TGCTGCTGT
4714244 ATCATCTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 24 0.75
12 8 0.25
ACGTcount: A:0.04, C:0.19, G:0.33, T:0.44
Consensus pattern (9 bp):
TGCTGCTGT
Found at i:4721147 original size:20 final size:20
Alignment explanation
Indices: 4721117--4721188 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
4721107 TGCGATTTTT
4721117 TAAATTCGCAACTCGAATCTG
1 TAAA-TCGCAACTCGAATCTG
4721138 TAAATCGCAACTCGAATCTG
1 TAAATCGCAACTCGAATCTG
* * *
4721158 TAAATAGCAACGCGAATTTG
1 TAAATCGCAACTCGAATCTG
4721178 TAAATCGCAAC
1 TAAATCGCAAC
4721189 ACAGAAGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 43 0.91
21 4 0.09
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (20 bp):
TAAATCGCAACTCGAATCTG
Found at i:4721205 original size:20 final size:20
Alignment explanation
Indices: 4721182--4721288 Score: 105
Period size: 20 Copynumber: 5.4 Consensus size: 20
4721172 AATTTGTAAA
4721182 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
4721202 TCGCAAC-GAGAAAGTAAAAT
1 TCGCAACACAG-AAGTCAAAT
* *
4721222 TCGTAACGC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
* *
4721242 TCACAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
4721262 TCGCAACACA-AAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
4721281 TCGCAACA
1 TCGCAACA
4721289 AGTGTTAGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
19 19 0.26
20 55 0.74
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:4721208 original size:40 final size:40
Alignment explanation
Indices: 4721164--4721287 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
4721154 TCTGTAAATA
*
4721164 GCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTC
1 GCAACGCGAA-TAGTAAAATTCGCAACAC-GAAGTCAAATTC
* * *
4721204 GCAACGAGAA-AGTAAAATTCGTAACGCGAAAGTCAAATTC
1 GCAACGCGAATAGTAAAATTCGCAACACG-AAGTCAAATTC
* * *
4721244 ACAACGCG-ATAGTCAAATTCGCAACACAAAGTCAAATTC
1 GCAACGCGAATAGTAAAATTCGCAACACGAAGTCAAATTC
4721283 GCAAC
1 GCAAC
4721288 AAGTGTTAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.03
39 20 0.29
40 47 0.68
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.18
Consensus pattern (40 bp):
GCAACGCGAATAGTAAAATTCGCAACACGAAGTCAAATTC
Found at i:4722033 original size:12 final size:12
Alignment explanation
Indices: 4722012--4722045 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4722002 ACCACATTTC
*
4722012 CAATACCAAACA
1 CAATATCAAACA
4722024 CAATATCAAACA
1 CAATATCAAACA
*
4722036 CAATCTCAAA
1 CAATATCAAA
4722046 ACCTACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:4722224 original size:24 final size:24
Alignment explanation
Indices: 4722166--4722212 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4722156 AGTCAGTATT
*
4722166 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
4722190 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
4722213 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:4745365 original size:18 final size:18
Alignment explanation
Indices: 4745342--4745377 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4745332 AAGCAAAAGG
*
4745342 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
4745360 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
4745378 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:4745706 original size:20 final size:20
Alignment explanation
Indices: 4745680--4745724 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
4745670 CAAACCGAAA
4745680 ATCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
*
4745700 TTCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
4745720 ATCGC
1 ATCGC
4745725 AACGCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCGAATTTGACT
Found at i:4746200 original size:18 final size:18
Alignment explanation
Indices: 4746179--4746215 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4746169 ATAATTGAAG
4746179 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
4746197 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
4746215 T
1 T
4746216 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:4746222 original size:24 final size:25
Alignment explanation
Indices: 4746160--4746223 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
4746150 TTTCAAATTC
4746160 ATTTC-ATATATAA-TTGAAGTTTGA
1 ATTTCAATATA-AATTTGAAGTTTGA
* * *
4746184 ATTTAAATTTCAATTTG-AGTTTGA
1 ATTTCAATATAAATTTGAAGTTTGA
4746208 ATTTCAATATAAATTT
1 ATTTCAATATAAATTT
4746224 CGGCTCCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (25 bp):
ATTTCAATATAAATTTGAAGTTTGA
Found at i:4746569 original size:39 final size:39
Alignment explanation
Indices: 4746525--4746611 Score: 158
Period size: 39 Copynumber: 2.2 Consensus size: 39
4746515 TCTGATGCTC
4746525 ATCAAAATCCAAAGT-TCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAA-TCTCATATGGTGCCAAGCAAAAGGAA
4746564 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
4746603 ATCAAAATC
1 ATCAAAATC
4746612 TACAAGTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 1 0.02
39 46 0.98
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
Found at i:4746807 original size:20 final size:20
Alignment explanation
Indices: 4746782--4746878 Score: 73
Period size: 20 Copynumber: 5.2 Consensus size: 20
4746772 ATGTTGCGAT
4746782 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4746802 CAACGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*** * * *
4746816 CGTTGCGATAGCCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
4746836 CAACGCGATAG-CGAAATTCG
1 CAACGCGAAAGTC-AAATTCG
4746856 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4746876 CAA
1 CAA
4746879 ACCGAAAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
14 7 0.12
17 4 0.07
19 2 0.03
20 45 0.76
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:4747041 original size:66 final size:60
Alignment explanation
Indices: 4746961--4747100 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
4746951 TTTTAGAAAC
*
4746961 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAAC-----AAAAAATAAATCTTATTTACACAT-AAATT
4747026 A
60 A
* * * *
4747027 AACAAATCAACTTTTGCAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACACATAAATTA
4747087 AACAAATCAACTTT
1 AACAAATCAACTTT
4747101 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 20 0.29
61 21 0.30
66 28 0.41
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACACATAAATTA
Found at i:4750981 original size:22 final size:22
Alignment explanation
Indices: 4750931--4750975 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4750921 GATGGAGATA
* *
4750931 GACAGATTTCGTCGTAGATGTG
1 GACAGATGTCGTCGTAGAAGTG
4750953 GACAGATGTCGTCGTAGAGAGTG
1 GACAGATGTCGTCGTAGA-AGTG
4750976 AGAGATAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (22 bp):
GACAGATGTCGTCGTAGAAGTG
Found at i:4751112 original size:20 final size:20
Alignment explanation
Indices: 4751087--4751255 Score: 230
Period size: 20 Copynumber: 8.4 Consensus size: 20
4751077 GCGTAAAAAC
* *
4751087 ATTTGACTTTCGCATTGCGG
1 ATTTGACTTTCGCGTTGCGA
*
4751107 ATTTGACTTTCGCGTTGCGG
1 ATTTGACTTTCGCGTTGCGA
4751127 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
4751147 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
4751167 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * *
4751187 ATTTGACTATCGCATTACGA
1 ATTTGACTTTCGCGTTGCGA
* *
4751207 ATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
4751227 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
4751247 ATTTGACTT
1 ATTTGACTT
4751256 CTGTGTTACG
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 133 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:4751265 original size:60 final size:60
Alignment explanation
Indices: 4751087--4751291 Score: 238
Period size: 60 Copynumber: 3.4 Consensus size: 60
4751077 GCGTAAAAAC
* * * * *
4751087 ATTTGACTTTCGCATTGCGGATTTGACTTTCGCGTTGCGGATTTGACTT-TCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCT-GCGTTACGA
* * *
4751147 ATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATC-GCATTACGA
1 ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACT-TCTGCGTTACGA
* * *
4751207 ATTTGACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACG-
1 ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGCGTTACGA
*
4751266 ATTT-ACAGATTCGCGTTGCGAATTTG
1 ATTTGAC-TA-TCGCGTTGCGAATTTG
4751292 GAAATTGGAG
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
58 2 0.02
59 7 0.06
60 114 0.92
61 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (60 bp):
ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGCGTTACGA
Found at i:4760275 original size:22 final size:22
Alignment explanation
Indices: 4760230--4760276 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4760220 GTAAATTTCG
*
4760230 ATTTTTTTAAGAATTTCAATTA
1 ATTTTTTTAAGAATTTCAAATA
*
4760252 ATTTTTTTAATAATTT-AAGATA
1 ATTTTTTTAAGAATTTCAA-ATA
4760274 ATT
1 ATT
4760277 AGAAGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTTTTTAAGAATTTCAAATA
Found at i:4760730 original size:13 final size:13
Alignment explanation
Indices: 4760714--4760755 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4760704 TTAGTTAATT
4760714 ATAAACTTAAATA
1 ATAAACTTAAATA
*
4760727 ATAATA-TTTAATA
1 ATAA-ACTTAAATA
4760740 A-AAACTTAAATA
1 ATAAACTTAAATA
4760752 ATAA
1 ATAA
4760756 TAGAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAACTTAAATA
Found at i:4765109 original size:27 final size:27
Alignment explanation
Indices: 4765078--4765143 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
4765068 CAAAACAATG
4765078 CTGAATGATTCAACACAAAAATACATT
1 CTGAATGATTCAACACAAAAATACATT
* *
4765105 CTGAATGATTCAACACAAAAGTATATT
1 CTGAATGATTCAACACAAAAATACATT
*
4765132 TTGAATGATTCA
1 CTGAATGATTCA
4765144 GAGTCATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (27 bp):
CTGAATGATTCAACACAAAAATACATT
Found at i:4765234 original size:15 final size:16
Alignment explanation
Indices: 4765196--4765236 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4765186 ACAGAGCCTC
*
4765196 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
4765212 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
4765228 T-AATCATTC
1 TGAATCATTC
4765237 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:4767466 original size:21 final size:21
Alignment explanation
Indices: 4767437--4767502 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
4767427 TGGAACTTCA
*
4767437 AATTTATTATATTATTATTTT
1 AATTAATTATATTATTATTTT
*
4767458 AATTAATTATA--A--ATTTAA
1 AATTAATTATATTATTATTT-T
* *
4767476 AATTTATTATATTATTGTTTT
1 AATTAATTATATTATTATTTT
4767497 AATTAA
1 AATTAA
4767503 ATGTCATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 4 0.12
18 10 0.29
19 1 0.03
20 1 0.03
21 15 0.44
22 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AATTAATTATATTATTATTTT
Done.