Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 160 of 182
Found at i:48918801 original size:17 final size:17
Alignment explanation
Indices: 48918746--48918811 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
48918736 TACTTAAAAC
*
48918746 TTAAATTTAAATTTGTT
1 TTAAATTTAAATTTATT
*
48918763 TTAAATTTAAATTTAGT
1 TTAAATTTAAATTTATT
* * *
48918780 ATAAATTTAAAATAATT
1 TTAAATTTAAATTTATT
* *
48918797 TTAAACTTAACTTTA
1 TTAAATTTAAATTTA
48918812 AAATTAAGGT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:48920808 original size:60 final size:59
Alignment explanation
Indices: 48920715--48920886 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 59
48920705 AAACTATCCA
* *
48920715 AAAATCATATTTTGACCCCAAACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATCATATTTTGACCCCAAACTTTTCTAAAATTACATTTTGACCCTCAAACTTTTCC
*
48920774 AAAATCATATTTTGACCCCTAAACTTTTCTAAAATTATATTTTGACCCTCAAACTTTTCC
1 AAAATCATATTTTGACCCC-AAACTTTTCTAAAATTACATTTTGACCCTCAAACTTTTCC
* *
48920834 AAAA-CTATATTTTAACCCCAAAAC--TTCTAAAAATTACATTTT-ACCCCCAAACT
1 AAAATC-ATATTTTGACCCC-AAACTTTTCT-AAAATTACATTTTGACCCTCAAACT
48920887 AACAAAAATT
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
58 14 0.14
59 32 0.31
60 57 0.55
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATCATATTTTGACCCCAAACTTTTCTAAAATTACATTTTGACCCTCAAACTTTTCC
Found at i:48920858 original size:30 final size:29
Alignment explanation
Indices: 48920715--48920886 Score: 195
Period size: 30 Copynumber: 5.8 Consensus size: 29
48920705 AAACTATCCA
*
48920715 AAAATCATATTTTGACCCCAAACTTTTCC
1 AAAATTATATTTTGACCCCAAACTTTTCC
* *
48920744 AAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTATATTTTGACCC-CAAACTTTTCC
* *
48920774 AAAATCATATTTTGACCCCTAAACTTTTCT
1 AAAATTATATTTTGACCCC-AAACTTTTCC
48920804 AAAATTATATTTTGACCCTCAAACTTTTCC
1 AAAATTATATTTTGACCC-CAAACTTTTCC
* * * *
48920834 AAAACTATATTTTAACCCCAAAACTTCT-A
1 AAAATTATATTTTGACCCC-AAACTTTTCC
*
48920863 AAAATTACATTTT-ACCCCCAAACT
1 AAAATTATATTTTGA-CCCCAAACT
48920887 AACAAAAATT
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.05
29 32 0.26
30 84 0.68
31 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCAAACTTTTCC
Found at i:48920953 original size:58 final size:58
Alignment explanation
Indices: 48920854--48921079 Score: 182
Period size: 58 Copynumber: 3.9 Consensus size: 58
48920844 TTTAACCCCA
* ** *
48920854 AAACTTCTAAAAATTAC-ATTTTACCCCCAAACTAACAAAAATTCTATTTTTATCCTCG
1 AAACTTTTAAAAATTACTATTTTACCCCTGAACTATCAAAAATTCTATTTTTAT-CTCG
* *
48920912 AAACTTTTGAAAATTACTATTTTACCCCTGAACT-TCCAAAATT-TCATTTTTGATCTCG
1 AAACTTTTAAAAATTACTATTTTACCCCTGAACTATCAAAAATTCT-ATTTTT-ATCTCG
** *
48920970 -ATTTTTCTAAAAATTACTA-TTTACCCCTGAA-TGTCTAAAAATTCTATTTTTAATCTCG
1 AAACTTT-TAAAAATTACTATTTTACCCCTGAACTATC-AAAAATTCTATTTTT-ATCTCG
** * * * *
48921028 -ATTTTTCTAAAAATTACCATTTT-GCCCTCGAA-TATCTAAAATTCCATTTTTA
1 AAACTTT-TAAAAATTACTATTTTACCCCT-GAACTATCAAAAATTCTATTTTTA
48921080 ACCCCAAATT
Statistics
Matches: 143, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
56 1 0.01
57 20 0.14
58 96 0.67
59 26 0.18
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.41
Consensus pattern (58 bp):
AAACTTTTAAAAATTACTATTTTACCCCTGAACTATCAAAAATTCTATTTTTATCTCG
Found at i:48920983 original size:30 final size:29
Alignment explanation
Indices: 48920949--48921042 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
48920939 CTGAACTTCC
48920949 AAAATTTCATTTTTGATCTCGATTTTTCTA
1 AAAATTTCATTTTT-ATCTCGATTTTTCTA
* * * * * *
48920979 AAAATTAC-TATTTACCCCTGA-ATGTCTA
1 AAAATTTCATTTTTATCTC-GATTTTTCTA
48921007 AAAA-TTCTATTTTTAATCTCGATTTTTCTA
1 AAAATTTC-ATTTTT-ATCTCGATTTTTCTA
48921037 AAAATT
1 AAAATT
48921043 ACCATTTTGC
Statistics
Matches: 46, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
27 2 0.04
28 12 0.26
29 12 0.26
30 19 0.41
31 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (29 bp):
AAAATTTCATTTTTATCTCGATTTTTCTA
Found at i:48921058 original size:30 final size:30
Alignment explanation
Indices: 48920966--48921115 Score: 86
Period size: 30 Copynumber: 5.2 Consensus size: 30
48920956 CATTTTTGAT
*
48920966 CTCGATTTTTCTAAAAATTACTA-TTTACC
1 CTCGATTTTTCTAAAAATTACCATTTTACC
* * * **
48920995 C-CTGA-ATGTCTAAAAATT-CTATTTTTAAT
1 CTC-GATTTTTCTAAAAATTACCA-TTTTACC
*
48921024 CTCGATTTTTCTAAAAATTACCATTTTGCC
1 CTCGATTTTTCTAAAAATTACCATTTTACC
* *
48921054 CTCGA-ATATCT-AAAATT-CCATTTTTAACC
1 CTCGATTTTTCTAAAAATTACCA-TTTT-ACC
* *
48921083 C-CAAATTTTCCT-AAAATTACCATTTT-CC
1 CTC-GATTTTTCTAAAAATTACCATTTTACC
48921111 CTCGA
1 CTCGA
48921116 GAGACTAAAA
Statistics
Matches: 91, Mismatches: 18, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
27 6 0.07
28 27 0.30
29 19 0.21
30 34 0.37
31 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
CTCGATTTTTCTAAAAATTACCATTTTACC
Found at i:48921080 original size:58 final size:58
Alignment explanation
Indices: 48920949--48921115 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 58
48920939 CTGAACTTCC
* * * * *
48920949 AAAATTTCATTTTTGATCTCGATTTTTCTAAAAATTACTATTTACCC-CTGAATGTCTA
1 AAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTACCATTTTCCCTC-GAATATCTA
*
48921007 AAAATTCTATTTTTAATCTCGATTTTTCTAAAAATTACCATTTTGCCCTCGAATATCT-
1 AAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTACCATTTT-CCCTCGAATATCTA
* * * *
48921065 AAAATTCCATTTTTAACCCCAAATTTTCCT-AAAATTACCATTTTCCCTCGA
1 AAAATTCCATTTTTAATCTC-GATTTTTCTAAAAATTACCATTTTCCCTCGA
48921116 GAGACTAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
57 7 0.07
58 70 0.74
59 17 0.18
60 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (58 bp):
AAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTACCATTTTCCCTCGAATATCTA
Found at i:48921092 original size:116 final size:115
Alignment explanation
Indices: 48920843--48921107 Score: 245
Period size: 116 Copynumber: 2.3 Consensus size: 115
48920833 CAAAACTATA
**
48920843 TTTTAACCCCAAAACTTCTAAAAATTACATTTTACCCCCAAACTAACAAAAATTCTATTTTTATC
1 TTTTAACCCCAAATTTTCTAAAAATTACA-TTTACCCCCAAACTAACAAAAATTCTATTTTTATC
* * *
48920908 CTCGAAACTTTTGAAAATTACTATTTTACCCCTGAACTTCCAAAATTTCAT
65 CTCGAAACTTTTAAAAATTACCATTTTACCCCTGAACTTCCAAAATTCCAT
* * * * * ** **
48920959 TTTTGATCTCGATTTTTCTAAAAATTACTATTTACCCCTGAA-TGTCTAAAAATTCTATTTTTAA
1 TTTTAACCCCAAATTTTCTAAAAATTAC-ATTTACCCCCAAACTAAC-AAAAATTCTATTTTT-A
** * *
48921023 T-CTCG-ATTTTTCTAAAAATTACCATTTT-GCCCTCGAA-TATCTAAAATTCCAT
63 TCCTCGAAACTTT-TAAAAATTACCATTTTACCCCT-GAACT-TCCAAAATTCCAT
48921075 TTTTAACCCCAAATTTTCCT-AAAATTACCATTT
1 TTTTAACCCCAAATTTT-CTAAAAATTA-CATTT
48921108 TCCCTCGAGA
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
115 11 0.09
116 101 0.86
117 6 0.05
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (115 bp):
TTTTAACCCCAAATTTTCTAAAAATTACATTTACCCCCAAACTAACAAAAATTCTATTTTTATCC
TCGAAACTTTTAAAAATTACCATTTTACCCCTGAACTTCCAAAATTCCAT
Found at i:48930989 original size:210 final size:210
Alignment explanation
Indices: 48930635--48931228 Score: 893
Period size: 210 Copynumber: 2.8 Consensus size: 210
48930625 GAAGTTGTTC
* * * *
48930635 AATGTTTGTCCCATCTAAATAGAGCTTTAGCAGGCACTCCATTTTGCCATCAATCTCCGGAAAGC
1 AATGTTTGTCCCATCTAAATAGAGCTCTAGCAAGCATTCCATTTTGCCATCAATCTCTGGAAAGC
* * * *
48930700 TTTTAAGATTGGAGCAACCTGAAAGAATT-AATTCTTTAAGAGATTCTATTCCAAATTTGATTGG
66 TTTTAAGATTGGAGCAACCTGAAAGAATTAAATT-TTCAAGAGATTCCATTCCAATTTTGGTTGG
*
48930764 AAGACTCCCAAGACTTTTGCAGCCTCTTAAATTCAAAAGTTTAAGTCTTCTGAGATTTCCGATTG
130 AAGACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAAAGTTTAAGTCTTCTGAGATTTCCGATTG
48930829 AAGAAGGTAGCTCTTT
195 AAGAAGGTAGCTCTTT
48930845 AATGTTTGTCCCATCTAAATAGAGCTCTAGCAAGCATTCCATTTTGCCATCAATCTCTGGAAAGC
1 AATGTTTGTCCCATCTAAATAGAGCTCTAGCAAGCATTCCATTTTGCCATCAATCTCTGGAAAGC
*
48930910 TTTTAAGATTGGAGCAATCTGAAAGAATTAAATTTTCAAGAGATTCCATTCCAATTTTGGTTGGA
66 TTTTAAGATTGGAGCAACCTGAAAGAATTAAATTTTCAAGAGATTCCATTCCAATTTTGGTTGGA
* * * *
48930975 AGGCTCCTAAGACTTTTGCAGTCTGTTAAATTCGAAAGTTTAAGTCTTCTGAGATTTCCGATTGA
131 AGACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAAAGTTTAAGTCTTCTGAGATTTCCGATTGA
*
48931040 AGAAGGTATCTCTTT
196 AGAAGGTAGCTCTTT
* * * * * * *
48931055 AATGTTTGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAATCTCTGGAAAGC
1 AATGTTTGTCCCATCTAAATAGAGCTCTAGCAAGCATTCCATTTTGCCATCAATCTCTGGAAAGC
* * * **
48931120 TTTGAAGTTTTGAGCAACCTGAAAGAATTAGCTTTTCAAGAGATTCCATTCCAATTTTGGTTGGA
66 TTTTAAGATTGGAGCAACCTGAAAGAATTAAATTTTCAAGAGATTCCATTCCAATTTTGGTTGGA
* * * *
48931185 AAACTCCTCAGACTTTTGCAGCCTCTTAAATTAAAAAGCTTAAG
131 AGACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAAAGTTTAAG
48931229 CCTCGTAAGA
Statistics
Matches: 347, Mismatches: 36, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
210 343 0.99
211 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (210 bp):
AATGTTTGTCCCATCTAAATAGAGCTCTAGCAAGCATTCCATTTTGCCATCAATCTCTGGAAAGC
TTTTAAGATTGGAGCAACCTGAAAGAATTAAATTTTCAAGAGATTCCATTCCAATTTTGGTTGGA
AGACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAAAGTTTAAGTCTTCTGAGATTTCCGATTGA
AGAAGGTAGCTCTTT
Found at i:48935400 original size:21 final size:21
Alignment explanation
Indices: 48935376--48935432 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
48935366 ATAATAGCAT
*
48935376 AATCTAAATATAAAGTTTAGA
1 AATCTAAATATAAAATTTAGA
* * *
48935397 AATCCAAACATAAAATTTATA
1 AATCTAAATATAAAATTTAGA
48935418 AAT-TCAAATATAAAA
1 AATCT-AAATATAAAA
48935433 CTTCAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.30
Consensus pattern (21 bp):
AATCTAAATATAAAATTTAGA
Found at i:48936158 original size:29 final size:29
Alignment explanation
Indices: 48936101--48936158 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
48936091 TGATTTAATA
* *
48936101 TGCAATTGAATACATAAACTTTGGTTTTG
1 TGCAATTGAATACATAAAATTTGGATTTG
** *
48936130 TGCAATTTTATACATAAAATTTTGATTTG
1 TGCAATTGAATACATAAAATTTGGATTTG
48936159 ATCTAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
TGCAATTGAATACATAAAATTTGGATTTG
Found at i:48936270 original size:25 final size:25
Alignment explanation
Indices: 48936223--48936270 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
48936213 TATATATTGC
* * *
48936223 ATATATAAATAATTAAATTTATTCA
1 ATATAAAAATAAATAAATGTATTCA
*
48936248 ATATAAAAATAAATAGATGTATT
1 ATATAAAAATAAATAAATGTATT
48936271 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATAAAAATAAATAAATGTATTCA
Found at i:48936829 original size:28 final size:28
Alignment explanation
Indices: 48936776--48936829 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
48936766 ATCATCCATT
*
48936776 AAATATTTATATTTATTTATTTATTTTC
1 AAATATTTATATTTATTTATTAATTTTC
48936804 AAAT-TTTACTATTTACTTT-TTAATTT
1 AAATATTTA-TATTTA-TTTATTAATTT
48936830 ATGATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 16 0.70
29 3 0.13
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (28 bp):
AAATATTTATATTTATTTATTAATTTTC
Found at i:48937495 original size:6 final size:6
Alignment explanation
Indices: 48937486--48937551 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
48937476 TTGTTTTAGG
* * * *
48937486 TTTAAA TTTAAA -TTAAT TTTAAG TTTAAA TTT-AT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
48937532 ATT--A TTTAAA CTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
48937552 TTCAAATCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
4 3 0.06
5 8 0.17
6 36 0.77
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:48937506 original size:17 final size:16
Alignment explanation
Indices: 48937486--48937549 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
48937476 TTGTTTTAGG
48937486 TTTAAATTTAAATTAAT
1 TTTAAATTTAAATT-AT
*
48937503 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAA-TTAT
*
48937520 TTTAAAATTAAAATTA-
1 TTT-AAATTTAAATTAT
*
48937536 TTTAAACTTAAATT
1 TTTAAATTTAAATT
48937550 TATTCAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 19 0.47
18 9 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:48937530 original size:23 final size:23
Alignment explanation
Indices: 48937485--48937530 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48937475 TTTGTTTTAG
**
48937485 GTTTAAATTTAAATTAATTTTAA
1 GTTTAAATTTAAATTAAAATTAA
**
48937508 GTTTAAATTTATTTTAAAATTAA
1 GTTTAAATTTAAATTAAAATTAA
48937531 AATTATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
GTTTAAATTTAAATTAAAATTAA
Found at i:48939699 original size:24 final size:24
Alignment explanation
Indices: 48939667--48939789 Score: 160
Period size: 24 Copynumber: 5.1 Consensus size: 24
48939657 ATATACTGGT
48939667 TAACCATTCTGGGCTCTTAAGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
* *
48939691 TAACCATTCTAGG-TTTGTAAGAGC
1 TAACCATTCTGGGCTCT-TAAGAGC
*
48939715 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
*
48939739 TAACCATTTTGGGCT-TGTAAGAGC
1 TAACCATTCTGGGCTCT-TAAGAGC
* *
48939763 TAACCATTCTGGGCTCGTATGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
48939787 TAA
1 TAA
48939790 ATTTCTAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
23 2 0.02
24 82 0.96
25 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
TAACCATTCTGGGCTCTTAAGAGC
Found at i:48939738 original size:48 final size:48
Alignment explanation
Indices: 48939667--48939789 Score: 192
Period size: 48 Copynumber: 2.6 Consensus size: 48
48939657 ATATACTGGT
* *
48939667 TAACCATTCTGGGCTCTTAAGAGCTAACCATTCTAGGTTTGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
* *
48939715 TAACCATTCTGGGCTCATAAGAGCTAACCATTTTGGGCTTGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
* *
48939763 TAACCATTCTGGGCTCGTATGAGCTAA
1 TAACCATTCTGGGCTCATAAGAGCTAA
48939790 ATTTCTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (48 bp):
TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
Found at i:48943435 original size:18 final size:18
Alignment explanation
Indices: 48943412--48943453 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48943402 ATAATTACAC
*
48943412 TAATTAATAAAATAAATA
1 TAATTAATAAAATAAAAA
*
48943430 TAATTAATGAAATAAAAA
1 TAATTAATAAAATAAAAA
48943448 TAATTA
1 TAATTA
48943454 GATGTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATTAATAAAATAAAAA
Found at i:48947427 original size:210 final size:210
Alignment explanation
Indices: 48947043--48947455 Score: 657
Period size: 210 Copynumber: 2.0 Consensus size: 210
48947033 AAGATTGCTC
* * *
48947043 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
* *
48947108 TTCCATTTTGCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
* **
48947173 CAAGAGATTCCATTCCAATTTTCATTGGAAGACTCCTAAGACTTTTGCAGTCT-TCTAAATTCAA
131 CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTTTTGCACCCTCT-TAAATTCAA
*
48947237 AAGTTTAAGTCTTCTG
195 AAGCTTAAGTCTTCTG
* * ***
48947253 AGATTTCCGATTGAAGAAGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCACTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
48947318 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
** *
48947383 CAAGAGATTCCATTCCAATTTTGGTTGGAAAACTCCTCAGACTTTTGCACCCTCTTAAATTCAAA
131 CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTTTTGCACCCTCTTAAATTCAAA
48947448 AGCTTAAG
196 AGCTTAAG
48947456 CCTCGTAAGA
Statistics
Matches: 185, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
210 184 0.99
211 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (210 bp):
AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTTTTGCACCCTCTTAAATTCAAA
AGCTTAAGTCTTCTG
Found at i:48948740 original size:29 final size:30
Alignment explanation
Indices: 48948673--48948740 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
48948663 GTAATAAAAT
* *
48948673 AATAATATAAGTGACTAAAACGTAATATTTTA
1 AATAA-ATAAGTGACTAAAACG-AAAATTTGA
*
48948705 AAT--ATAAGTGATTAAAAC-AAAATTTGA
1 AATAAATAAGTGACTAAAACGAAAATTTGA
48948732 AATAAATAA
1 AATAAATAA
48948741 AAATGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 10 0.32
29 18 0.58
32 3 0.10
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (30 bp):
AATAAATAAGTGACTAAAACGAAAATTTGA
Found at i:48948900 original size:31 final size:32
Alignment explanation
Indices: 48948840--48948902 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 32
48948830 GCTGTGCACC
48948840 TCTTCTATTTGTTCCAAATCTCTCTCATACACTAT
1 TCTTCTATTTGTTCCAAA---CTCTCATACACTAT
48948875 TCTTCTATTTGTTCCAAA-TCTCATACAC
1 TCTTCTATTTGTTCCAAACTCTCATACAC
48948903 GAACCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 10 0.36
35 18 0.64
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (32 bp):
TCTTCTATTTGTTCCAAACTCTCATACACTAT
Found at i:48952423 original size:210 final size:210
Alignment explanation
Indices: 48952022--48952434 Score: 603
Period size: 210 Copynumber: 2.0 Consensus size: 210
48952012 AAGATTGCTC
* * * * *
48952022 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTCGGAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
* *
48952087 TTCCATTTTGCCATCAATCTCTGGAAAGCTTTTAAGACTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACTGGAGCAACCTGAAAGAATTAACTGTT
* * **
48952152 CAAGAGATTCCATTCCAATTTTCATTGGAAGACTCCTAAGACTTTTGCAGTCTTCTAAATTCAAA
131 CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTGTTGCACCCTTCTAAATTCAAA
*
48952217 AGTTTAAGTCTTCTG
196 AGCTTAAGTCTTCTG
* * ***
48952232 AGATTTCCGATTGAAGAAGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCACTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
* *
48952297 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGATTTGAGCAACCTGAAAGAATTAACTGTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACTGGAGCAACCTGAAAGAATTAACTGTT
* ** *
48952362 CAAGAGATTCCATTCCAGTTTTGGTTGGAAAACTCCTCAGACTGTTGCACCC-TCTTAAATTCAA
131 CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTGTTGCACCCTTC-TAAATTCAA
48952426 AAGCTTAAG
195 AAGCTTAAG
48952435 CCTCGTAAGA
Statistics
Matches: 179, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
209 2 0.01
210 177 0.99
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (210 bp):
AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCACTAGCAGGCA
TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACTGGAGCAACCTGAAAGAATTAACTGTT
CAAGAGATTCCATTCCAATTTTCATTGGAAAACTCCTAAGACTGTTGCACCCTTCTAAATTCAAA
AGCTTAAGTCTTCTG
Found at i:48956752 original size:3 final size:3
Alignment explanation
Indices: 48956744--48956800 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
48956734 AACATTTTGG
* *
48956744 TTA TTA TTA TTA TT- TTA -TA TTA TTA TTA CTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48956790 TTA TTA TTA TT
1 TTA TTA TTA TT
48956801 TTGGAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:48962879 original size:11 final size:11
Alignment explanation
Indices: 48962861--48962939 Score: 86
Period size: 11 Copynumber: 7.0 Consensus size: 11
48962851 ACCAAGTTAA
48962861 ACCGTTGACCG
1 ACCGTTGACCG
*
48962872 ATCGTTGACCG
1 ACCGTTGACCG
*
48962883 ACCGTTGATCG
1 ACCGTTGACCG
*
48962894 ACCGTTGATCG
1 ACCGTTGACCG
*
48962905 ACCGTTGATCG
1 ACCGTTGACCG
**
48962916 GTCGTTGACCTTG
1 ACCGTTGACC--G
48962929 ACCGTTGACCG
1 ACCGTTGACCG
48962940 TTGAATGTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
11 49 0.84
13 9 0.16
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:48962889 original size:22 final size:22
Alignment explanation
Indices: 48962861--48962939 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
48962851 ACCAAGTTAA
48962861 ACCGTTGACCGATCGTTGACCG
1 ACCGTTGACCGATCGTTGACCG
* * *
48962883 ACCGTTGATCGACCGTTGATCG
1 ACCGTTGACCGATCGTTGACCG
* *
48962905 ACCGTTGATCGGTCGTTGACCTTG
1 ACCGTTGACCGATCGTTGACC--G
48962929 ACCGTTGACCG
1 ACCGTTGACCG
48962940 TTGAATGTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 37 0.77
24 11 0.23
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (22 bp):
ACCGTTGACCGATCGTTGACCG
Found at i:48962938 original size:7 final size:7
Alignment explanation
Indices: 48962918--48962965 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
48962908 GTTGATCGGT
48962918 CGTTGAC
1 CGTTGAC
48962925 C-TTGAC
1 CGTTGAC
48962931 CGTTGAC
1 CGTTGAC
*
48962938 CGTTGAA
1 CGTTGAC
*
48962945 TGTTGAC
1 CGTTGAC
*
48962952 CTTTGAC
1 CGTTGAC
*
48962959 CATTGAC
1 CGTTGAC
48962966 TTTTTCGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (7 bp):
CGTTGAC
Found at i:48966020 original size:16 final size:16
Alignment explanation
Indices: 48965980--48966024 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
48965970 ATTTTAGGAT
*
48965980 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
48965997 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
48966011 TTAAAAATTTATTT
1 TTAAAAATTTATTT
48966025 TCATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:48966723 original size:31 final size:30
Alignment explanation
Indices: 48966666--48966723 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
48966656 TTTTAAATTA
*
48966666 ATAATTGTAAAATTTTATTTTGATCCTCTC
1 ATAATTGTAAAATTTTATTTTAATCCTCTC
48966696 ATAATTGATAAAATTTTGA-TTTAATCCT
1 ATAATTG-TAAAATTTT-ATTTTAATCCT
48966724 TTAAAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 17 0.68
32 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (30 bp):
ATAATTGTAAAATTTTATTTTAATCCTCTC
Found at i:48968510 original size:31 final size:31
Alignment explanation
Indices: 48968472--48968533 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
48968462 ATTTCGATTA
*
48968472 TTTTTAAAAGTTTAGTA-GTCAAATTTAACTC
1 TTTTTAAAAGTTTA-AAGGTCAAATTTAACTC
*
48968503 TTTTTAAAAGTTTAAAGGTCAAATTTCACTC
1 TTTTTAAAAGTTTAAAGGTCAAATTTAACTC
48968534 AAAAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTTTAAAAGTTTAAAGGTCAAATTTAACTC
Found at i:48974278 original size:18 final size:20
Alignment explanation
Indices: 48974238--48974278 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
48974228 TTGTAATTTT
*
48974238 AATAATGATATTTATAATTA
1 AATAATGATATTTATAATAA
*
48974258 AATAAT-ATA-TTGTAATAA
1 AATAATGATATTTATAATAA
48974276 AAT
1 AAT
48974279 GTCTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AATAATGATATTTATAATAA
Found at i:48974686 original size:24 final size:27
Alignment explanation
Indices: 48974659--48974714 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
48974649 TAAAACTCAA
48974659 ATTAAACAC-T-AAAAAA-TTAACTTC
1 ATTAAACACATAAAAAAAGTTAACTTC
*
48974683 ATT-ATCACATAAAAAAAAGTTAACTTC
1 ATTAAACACAT-AAAAAAAGTTAACTTC
48974710 ATTAA
1 ATTAA
48974715 TTTTGGGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 4 0.15
26 6 0.23
27 11 0.42
28 1 0.04
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTAAACACATAAAAAAAGTTAACTTC
Found at i:48974933 original size:18 final size:18
Alignment explanation
Indices: 48974910--48974951 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48974900 TTAATTACAC
*
48974910 TAATTAATAAAATAAATA
1 TAATTAATAAAATAAAAA
*
48974928 TAATTAATGAAATAAAAA
1 TAATTAATAAAATAAAAA
48974946 TAATTA
1 TAATTA
48974952 GATGTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATTAATAAAATAAAAA
Found at i:48978034 original size:29 final size:28
Alignment explanation
Indices: 48977969--48978247 Score: 192
Period size: 29 Copynumber: 9.5 Consensus size: 28
48977959 CTAAACTGTC
* *
48977969 CAAAAATTATATTTTGACCCCCG-AACTTCT
1 CAAAAATTACATTTTTA-CCCCGAAAC-T-T
* *
48977999 CCAAAATTACATTTTTACCTCGAAACTT
1 CAAAAATTACATTTTTACCCCGAAACTT
*
48978027 CAAAAAATTACA-TTTTACCCCTAAACTTT
1 C-AAAAATTACATTTTTACCCCGAAAC-TT
*
48978056 CAAAAATTACATTTTTGACCTTC-AAACTTT
1 CAAAAATTACATTTTT-ACC-CCGAAAC-TT
* * *
48978086 CCAAAATTTCATTTTTGA-CCCTAAACTT
1 CAAAAATTACATTTTT-ACCCCGAAACTT
* *
48978114 CCAAAAATTACATTTTCACCCCTAAACTTT
1 -CAAAAATTACATTTTTACCCCGAAAC-TT
* *
48978144 CAAAAATTCCATTTTTAACCCCAAAACTT
1 CAAAAATTACATTTTT-ACCCCGAAACTT
* * *
48978173 CCCAAAATTATATTTTTACCTCTG-AACTT
1 -CAAAAATTACATTTTTACC-CCGAAACTT
* *
48978202 CCAAAAATTTCATTTTTGACCCCAAAACTCT
1 -CAAAAATTACATTTTT-ACCCCGAAACT-T
48978233 C-AAAATTACCATTTT
1 CAAAAATTA-CATTTT
48978248 AACCTCGGAG
Statistics
Matches: 204, Mismatches: 28, Indels: 34
0.77 0.11 0.13
Matches are distributed among these distances:
28 28 0.14
29 92 0.45
30 82 0.40
31 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCGAAACTT
Found at i:48978072 original size:88 final size:89
Alignment explanation
Indices: 48977957--48978247 Score: 344
Period size: 88 Copynumber: 3.3 Consensus size: 89
48977947 CCATAGAGGT
* * *
48977957 CCCTAAACTGTCCAAAAATTATA-TTTTGACCCCCGAACTTCTCCAAAATTACATTTTTACCTCG
1 CCCTAAACT-TTCAAAAATTACATTTTTGACCCCCAAACTTCTCCAAAATTACATTTTTACCTCG
*
48978021 AAACTTCAAAAAATTACATTTT-AC
65 AAACTTCCAAAAATTACATTTTCAC
** * *
48978045 CCCTAAACTTTCAAAAATTACATTTTTGACCTTCAAACTT-TCCAAAATTTCATTTTTGACC-CT
1 CCCTAAACTTTCAAAAATTACATTTTTGACCCCCAAACTTCTCCAAAATTACATTTTT-ACCTCG
48978108 AAACTTCCAAAAATTACATTTTCAC
65 AAACTTCCAAAAATTACATTTTCAC
* * * *
48978133 CCCTAAACTTTCAAAAATTCCATTTTTAACCCCAAAACTTC-CCAAAATTATATTTTTACCTCTG
1 CCCTAAACTTTCAAAAATTACATTTTTGACCCCCAAACTTCTCCAAAATTACATTTTTACCTC-G
* *
48978197 -AACTTCCAAAAATTTCATTTTTGAC
65 AAACTTCCAAAAATTACA-TTTTCAC
* *
48978222 CCCAAAACTCTC-AAAATTACCATTTT
1 CCCTAAACTTTCAAAAATTA-CATTTT
48978248 AACCTCGGAG
Statistics
Matches: 174, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
87 52 0.30
88 100 0.57
89 22 0.13
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (89 bp):
CCCTAAACTTTCAAAAATTACATTTTTGACCCCCAAACTTCTCCAAAATTACATTTTTACCTCGA
AACTTCCAAAAATTACATTTTCAC
Found at i:48978122 original size:59 final size:59
Alignment explanation
Indices: 48977959--48978253 Score: 275
Period size: 59 Copynumber: 5.0 Consensus size: 59
48977949 ATAGAGGTCC
* * ** *
48977959 CTAAACTGTCCAAAAATT-ATATTTTGACCCCCGAACTTCTCCAAAATTACATTTTTACCT
1 CTAAACTTTCCAAAATTTCAT-TTTTGACCCCTAAACTTC-CAAAAATTACATTTTTACCT
* * * *
48978019 CGAAAC-TTCAAAAAATTACA-TTTT-ACCCCTAAACTTTCAAAAATTACATTTTTGACCT
1 CTAAACTTTC-CAAAATTTCATTTTTGACCCCTAAACTTCCAAAAATTACATTTTT-ACCT
* *
48978077 -TCAAACTTTCCAAAATTTCATTTTTGA-CCCTAAACTTCCAAAAATTACATTTTCACCC
1 CT-AAACTTTCCAAAATTTCATTTTTGACCCCTAAACTTCCAAAAATTACATTTTTACCT
* * * * * *
48978135 CTAAACTTTCAAAAATTCCATTTTTAACCCCAAAACTTCCCAAAATTATATTTTTACCT
1 CTAAACTTTCCAAAATTTCATTTTTGACCCCTAAACTTCCAAAAATTACATTTTTACCT
* * *
48978194 CTGAAC-TTCCAAAAATTTCATTTTTGACCCCAAAAC-TCTC-AAAATTACCATTTTAACCT
1 CTAAACTTTCC-AAAATTTCATTTTTGACCCCTAAACTTC-CAAAAATTA-CATTTTTACCT
48978253 C
1 C
48978254 GGAGGTCCAA
Statistics
Matches: 194, Mismatches: 29, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
57 15 0.08
58 63 0.32
59 104 0.54
60 11 0.06
61 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
CTAAACTTTCCAAAATTTCATTTTTGACCCCTAAACTTCCAAAAATTACATTTTTACCT
Found at i:48978405 original size:28 final size:28
Alignment explanation
Indices: 48978349--48978408 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
48978339 CAAATTTTAT
* *
48978349 AAAATTACCATTTTGCCCCCGATAGTCC
1 AAAATTACCATTTTGCCCCCGAAAATCC
*
48978377 AAAATTACCATTTTGCCCTC-AAACATCC
1 AAAATTACCATTTTGCCCCCGAAA-ATCC
48978405 AAAA
1 AAAA
48978409 AGTCCCGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.27
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAAAATCC
Found at i:48978407 original size:143 final size:144
Alignment explanation
Indices: 48978259--48978541 Score: 423
Period size: 143 Copynumber: 2.0 Consensus size: 144
48978249 ACCTCGGAGG
*
48978259 TCCAAAAA-TCCCGTTTTTGATCCCGATT-TTTCCAAAAATTACCGTTTTACCCTCAAGTGTCTA
1 TCCAAAAAGTCCCG-TTTTGATCCCGATTCTTT-CAAAAATTACCATTTTACCCTCAAGTGTCTA
* *
48978322 AAATGTCATTT-TAA-CCTCAAATTTTAT-AAAATTACCATTTTGCCCCCGATAGTCCAAAATTA
64 AAATATCATTTGTAACCCT-AAATTTT-TCAAAATTACCATTTTGCCCCCGAGAGTCCAAAATTA
48978384 CCATTTTGCCCTCAAACA
127 CCATTTTGCCCTCAAACA
** *
48978402 TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTTGAAAATTACCATTTTACCCTTAAGTGTCTAAA
1 TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTCAAAAATTACCATTTTACCCTCAAGTGTCTAAA
*
48978467 ATATCATTTGTAACCCTAAATTTTTCCAAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCA
66 ATATCATTTGTAACCCTAAATTTTT-CAAAATTACCATTTTGCCCCCGAGAGTCCAAAATTACCA
48978532 TTTTGCCCTC
130 TTTTGCCCTC
48978542 GAGAGTCCAA
Statistics
Matches: 127, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
143 60 0.47
144 18 0.14
145 49 0.39
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.36
Consensus pattern (144 bp):
TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTCAAAAATTACCATTTTACCCTCAAGTGTCTAAA
ATATCATTTGTAACCCTAAATTTTTCAAAATTACCATTTTGCCCCCGAGAGTCCAAAATTACCAT
TTTGCCCTCAAACA
Found at i:48978526 original size:58 final size:57
Alignment explanation
Indices: 48978436--48978713 Score: 172
Period size: 58 Copynumber: 4.8 Consensus size: 57
48978426 GATTCTTTTG
* ** * *
48978436 AAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTGTAACCCTAAATTTTTCC
1 AAAATTACCATTTTGCCCTCGAGAGTCCAAAATATCATTT-TAACCCTAAATTTTTCC
* * ** ***
48978494 AAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTT-GCCCTCGA-GAGTCC
1 AAAATTACCATTTTGCCCTCGAGAGTCCAAAA-TATCATTTTAACCCTAAATTTTTCC
* * * ** ** *
48978550 AAAATTACCATTTTGCCCTCGA-ACATCCAAAA-AGTCCCGTTTTGA-TGTCGATTCTTCC
1 AAAATTACCATTTTGCCCTCGAGA-GTCCAAAATA-T--CATTTTAACCCTAAATTTTTCC
* * ** * * *
48978608 AAAAATTACCATTTTACTCTTAAGTGTCTAAAATATCATTTTTAACCCTAAATTTTCCC
1 -AAAATTACCATTTTGCCCTCGAGAGTCCAAAATATCA-TTTTAACCCTAAATTTTTCC
* *
48978667 AAAATTGCCATTTTGCCCTCGAGAGTCCAAAATTACCATTTT-ACCCT
1 AAAATTACCATTTTGCCCTCGAGAGTCCAAAA-TATCATTTTAACCCT
48978714 TAGGCATCCA
Statistics
Matches: 163, Mismatches: 44, Indels: 27
0.70 0.19 0.12
Matches are distributed among these distances:
54 1 0.01
55 1 0.01
56 32 0.20
57 20 0.12
58 65 0.40
59 43 0.26
60 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTGCCCTCGAGAGTCCAAAATATCATTTTAACCCTAAATTTTTCC
Found at i:48978581 original size:28 final size:28
Alignment explanation
Indices: 48978491--48978571 Score: 162
Period size: 28 Copynumber: 2.9 Consensus size: 28
48978481 CCTAAATTTT
48978491 TCCAAAATTACCATTTTGCCCTCGAGAG
1 TCCAAAATTACCATTTTGCCCTCGAGAG
48978519 TCCAAAATTACCATTTTGCCCTCGAGAG
1 TCCAAAATTACCATTTTGCCCTCGAGAG
48978547 TCCAAAATTACCATTTTGCCCTCGA
1 TCCAAAATTACCATTTTGCCCTCGA
48978572 ACATCCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCTCGAGAG
Found at i:48978638 original size:173 final size:173
Alignment explanation
Indices: 48978349--48978713 Score: 613
Period size: 173 Copynumber: 2.1 Consensus size: 173
48978339 CAAATTTTAT
* *
48978349 AAAATTACCATTTTGCCCCCGATAGTCCAAAATTACCATTTTGCCCTCAAACATCCAAAAAGTCC
1 AAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTGCCCTCAAACATCCAAAAAGTCC
***
48978414 CGTTTTGATCCCGATTCTTTTGAAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTGTA
66 CGTTTTGATCCCGATTCTTCCAAAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTGTA
*
48978479 ACCCTAAATTTTTCCAAAATTACCATTTTGCCCTCGAGAGTCC
131 ACCCTAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTCC
*
48978522 AAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAAGTCC
1 AAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTGCCCTCAAACATCCAAAAAGTCC
** * *
48978587 CGTTTTGATGTCGATTCTTCCAAAAATTACCATTTTACTCTTAAGTGTCTAAAATATCATTTTTA
66 CGTTTTGATCCCGATTCTTCCAAAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTGTA
*
48978652 ACCCTAAATTTTCCCAAAATTGCCATTTTGCCCTCGAGAGTCC
131 ACCCTAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTCC
*
48978695 AAAATTACCATTTTACCCT
1 AAAATTACCATTTTGCCCT
48978714 TAGGCATCCA
Statistics
Matches: 179, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
173 179 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (173 bp):
AAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTGCCCTCAAACATCCAAAAAGTCC
CGTTTTGATCCCGATTCTTCCAAAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTGTA
ACCCTAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTCC
Found at i:48981265 original size:25 final size:26
Alignment explanation
Indices: 48981218--48981266 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
48981208 TAAATTAATG
*
48981218 ATACTTGTCATTAATGATTATTTTTT
1 ATACTTGTCACTAATGATTATTTTTT
*
48981244 ATACTTGTC-CTAATG-TTAATTTT
1 ATACTTGTCACTAATGATTATTTTT
48981267 AAATTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (26 bp):
ATACTTGTCACTAATGATTATTTTTT
Found at i:48984268 original size:17 final size:17
Alignment explanation
Indices: 48984246--48984327 Score: 89
Period size: 17 Copynumber: 4.8 Consensus size: 17
48984236 AACTTTTAAT
48984246 TTTTAAATCTT-AATTTA
1 TTTTAAAT-TTAAATTTA
*
48984263 TTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
48984280 -TTTAGAATTTAAATTT-
1 TTTTA-AATTTAAATTTA
*
48984296 TTATTAAATTTGAATTTA
1 TT-TTAAATTTAAATTTA
*
48984314 TTTTAAATTAAAAT
1 TTTTAAATTTAAAT
48984328 AATTTAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.11
17 44 0.80
18 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:48985523 original size:29 final size:29
Alignment explanation
Indices: 48985481--48985713 Score: 182
Period size: 29 Copynumber: 8.1 Consensus size: 29
48985471 CCCTAGAGGT
48985481 CCCT-AAACTATCCAAAAATTATATTTTGA
1 CCCTGAAACT-TCCAAAAATTATATTTTGA
*
48985510 CCCTGAAACTTCCAAAAATTACATTTTGA
1 CCCTGAAACTTCCAAAAATTATATTTTGA
* * *
48985539 CCC-CAAACTTCC-AATATTACATTTTTG-
1 CCCTGAAACTTCCAAAAATTATA-TTTTGA
* **
48985566 CCCTCG-AACTTCTAAAAATTCCATTTTGA
1 CCCT-GAAACTTCCAAAAATTATATTTTGA
* * * *
48985595 CCTTGAAACTTCCCAAAATTATGTTTTTA
1 CCCTGAAACTTCCAAAAATTATATTTTGA
*
48985624 CCCTCG-AACTTCCAAAAATTCTATTTTTGA
1 CCCT-GAAACTTCCAAAAATTATA-TTTTGA
*
48985654 CCCCG-AACTTCCAAAAATTCCAT-TTTTGA
1 CCCTGAAACTTCCAAAAATT--ATATTTTGA
* *
48985683 CCC-AAAAC-TCCCAAAATTACTATTTT-A
1 CCCTGAAACTTCCAAAAATTA-TATTTTGA
48985710 CCCT
1 CCCT
48985714 CGGATGTCCA
Statistics
Matches: 166, Mismatches: 23, Indels: 31
0.75 0.10 0.14
Matches are distributed among these distances:
26 1 0.01
27 16 0.10
28 38 0.23
29 96 0.58
30 14 0.08
31 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
CCCTGAAACTTCCAAAAATTATATTTTGA
Found at i:48985635 original size:58 final size:57
Alignment explanation
Indices: 48985485--48985672 Score: 211
Period size: 58 Copynumber: 3.3 Consensus size: 57
48985475 AGAGGTCCCT
* * *
48985485 AAACTATCCAAAAATTATATTTTGACCCT-GAAACTTCCAAAAATTACATTTTGACCCC
1 AAACT-TCCAAAAATTATATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTGACCCG
* * * * *
48985543 AAACTTCC-AATATTACATTTTTGCCCTCGAACTTCTAAAAATTCCATTTTGACCTTG
1 AAACTTCCAAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACC-CG
* * *
48985600 AAACTTCCCAAAATTATGTTTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACCCCG
1 AAACTTCCAAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGA-CCCG
48985659 -AACTTCCAAAAATT
1 AAACTTCCAAAAATT
48985673 CCATTTTTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
56 38 0.35
57 12 0.11
58 50 0.46
59 7 0.06
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.35
Consensus pattern (57 bp):
AAACTTCCAAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCG
Found at i:48985697 original size:58 final size:58
Alignment explanation
Indices: 48985486--48985712 Score: 202
Period size: 58 Copynumber: 4.0 Consensus size: 58
48985476 GAGGTCCCTA
* *
48985486 AACTATCCAAAAATTATATTTTGACCCTGAAACTTCCAAAAATTAC-ATTTTGACCCCA
1 AACT-TCCAAAAATTATATTTTGACCCTCAAACTTCCAAAAATTACTATTTTGACCCCG
* * * * * **
48985544 AACTTCC-AATATTACATTTTTG-CCCTCGAACTTCTAAAAATT-CCATTTTGACCTTG
1 AACTTCCAAAAATTATA-TTTTGACCCTCAAACTTCCAAAAATTACTATTTTGACCCCG
* * * *
48985600 AAACTTCCCAAAATTATGTTTTTACCCTCGAACTTCCAAAAATT-CTATTTTTGACCCCG
1 -AACTTCCAAAAATTATATTTTGACCCTCAAACTTCCAAAAATTACTA-TTTTGACCCCG
* *
48985659 AACTTCCAAAAATTCCAT-TTTTGACCC-AAAAC-TCCCAAAATTACTATTTT-ACCC
1 AACTTCCAAAAATT--ATATTTTGACCCTCAAACTTCCAAAAATTACTATTTTGACCC
48985713 TCGGATGTCC
Statistics
Matches: 139, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
55 1 0.01
56 37 0.27
57 32 0.23
58 50 0.36
59 17 0.12
60 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATTATATTTTGACCCTCAAACTTCCAAAAATTACTATTTTGACCCCG
Found at i:48985745 original size:86 final size:87
Alignment explanation
Indices: 48985486--48985728 Score: 236
Period size: 86 Copynumber: 2.8 Consensus size: 87
48985476 GAGGTCCCTA
** * * * *
48985486 AACTATCCAAAAATTATATTTTGACC-CTGAAACTTCCAAAAATTA-CATTTTGACCC-CAAACT
1 AACT-TCCAAAAATTCCATTTTGACCTC-AAAACTTCCCAAAATTATGATTTT-ACCCTCGAACT
*
48985548 TCC-AATATTAC-ATTTTTG-CCCTCG
63 TCCAAAAATT-CTATTTTTGACCC-CG
* ** *
48985572 AACTTCTAAAAATTCCATTTTGACCTTGAAACTTCCCAAAATTATGTTTTTACCCTCGAACTTCC
1 AACTTCCAAAAATTCCATTTTGACCTCAAAACTTCCCAAAATTATGATTTTACCCTCGAACTTCC
48985637 AAAAATTCTATTTTTGACCCCG
66 AAAAATTCTATTTTTGACCCCG
*
48985659 AACTTCCAAAAATTCCATTTTTGACC-CAAAAC-TCCCAAAATTACT-ATTTTACCCTCGGA-TG
1 AACTTCCAAAAATTCCA-TTTTGACCTCAAAACTTCCCAAAATTA-TGATTTTACCCTCGAACT-
48985720 TCCAAAAAT
63 TCCAAAAAT
48985729 CTCGTTTTTT
Statistics
Matches: 134, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
85 39 0.29
86 49 0.37
87 35 0.26
88 11 0.08
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTGACCTCAAAACTTCCCAAAATTATGATTTTACCCTCGAACTTCC
AAAAATTCTATTTTTGACCCCG
Found at i:48985843 original size:118 final size:118
Alignment explanation
Indices: 48985691--48985948 Score: 295
Period size: 119 Copynumber: 2.2 Consensus size: 118
48985681 GACCCAAAAC
* * * * * * *
48985691 TCCCAAAATTACTATTTTACCCTCGGATGTCCAAAAA-TCTCGTTTTTTATCCCGATT-TCTCTA
1 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGATTCTCTC-A
** *** * * * **
48985754 AAAATTACCGTTTTACCTTCAAGTGTTTAAAATGTCATTTTTAACCTTAAATTTT
65 AAAATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAA-TTT
* *
48985809 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGATTCTTTCGA
1 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGATTCTCTCAA
*
48985874 AAATTACTGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
66 AAATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
*
48985927 TCCAAAAATTACCATTTTGCCC
1 TCCCAAAATTACCATTTTGCCC
48985949 TCGAGAGTCC
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
118 56 0.48
119 58 0.50
120 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.38
Consensus pattern (118 bp):
TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGATTCTCTCAA
AAATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
Found at i:48985888 original size:119 final size:117
Alignment explanation
Indices: 48985691--48985948 Score: 293
Period size: 118 Copynumber: 2.2 Consensus size: 117
48985681 GACCCAAAAC
* * * * * * *
48985691 TCCCAAAATTACTATTTTACCCTCGGATGTCCAAAAATCTCGTTTTTTATCCCGATTTCTCTAAA
1 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAATATCATTTTTTATCCCGATTTCTCTAAA
** *** * * * **
48985756 AATTACCGTTTTACCTTCAAGTGTTTAAAATGTCATTTTTAACCTTAAATTTT
66 AATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAA-TTT
* *
48985809 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGA-TTCTTTCG
1 TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAA-TATCATTTTTTATCCCGATTTCTCT-A
*
48985873 AAAATTACTGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
64 AAAATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
*
48985927 TCCAAAAATTACCATTTTGCCC
1 TCCCAAAATTACCATTTTGCCC
48985949 TCGAGAGTCC
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
118 61 0.52
119 56 0.48
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.38
Consensus pattern (117 bp):
TCCCAAAATTACCATTTTGCCCCCGAATATCCAAAAATATCATTTTTTATCCCGATTTCTCTAAA
AATTACCGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTT
Found at i:48985959 original size:29 final size:29
Alignment explanation
Indices: 48985927--48986001 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
48985917 CCCCAAATTT
48985927 TCCAAAAATTACCATTTTGCCCTCGAG-A
1 TCCAAAAATTACCATTTTGCCCTCGAGCA
* *
48985955 GTCC-AAAATTACCAGTTTGCCCTCGGGCA
1 -TCCAAAAATTACCATTTTGCCCTCGAGCA
* *
48985984 TCCAAAAAGTCCCATTTT
1 TCCAAAAATTACCATTTT
48986002 TTATCTTGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 24 0.62
29 15 0.38
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTGCCCTCGAGCA
Found at i:48985962 original size:146 final size:146
Alignment explanation
Indices: 48985811--48986123 Score: 405
Period size: 146 Copynumber: 2.1 Consensus size: 146
48985801 TAAATTTTTC
* * * *
48985811 CCAAAATTACCATTTTGCCCCCGAATATCCAAAAAGTATCATTTTTTATCCCGATTCTTTC-GAA
1 CCAAAATTACCATTTTGCCCCCGAACATCCAAAAAGTACCATTTTTTATCCCGATTCTTCCAAAA
48985875 AATT-ACTGTTTTACCCCCAAAAATCTAAAATGCCATTTCTAACCCCAAATTTTCCAAAAATTAC
66 AATTAAC-GTTTTACCCCCAAAAATCTAAAATGCCATTT-TAACCCCAAATTTTCCAAAAATTAC
48985939 CATTTTGCCCTCGAGAGT
129 CATTTTGCCCTCGAGAGT
* * ** * **
48985957 CCAAAATTACCAGTTTGCCCTCGGGCATCCAAAAAGTCCCATTTTTTATCTTGATTCTTCCAAAA
1 CCAAAATTACCATTTTGCCCCCGAACATCCAAAAAGTACCATTTTTTATCCCGATTCTTCCAAAA
** *** * * *
48986022 AATTAACGTTTTACCCTTAAGTGTCTAAAATGTCATTTTAACCCTAAATTTTCCCAAAATTACCA
66 AATTAACGTTTTACCCCCAAAAATCTAAAATGCCATTTTAACCCCAAATTTTCCAAAAATTACCA
48986087 TTTTGCCCTCGAGAGT
131 TTTTGCCCTCGAGAGT
**
48986103 AAAAAATTACCATTTTGCCCC
1 CCAAAATTACCATTTTGCCCC
48986124 TAAGAGTCAA
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
146 109 0.77
147 31 0.22
148 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.34
Consensus pattern (146 bp):
CCAAAATTACCATTTTGCCCCCGAACATCCAAAAAGTACCATTTTTTATCCCGATTCTTCCAAAA
AATTAACGTTTTACCCCCAAAAATCTAAAATGCCATTTTAACCCCAAATTTTCCAAAAATTACCA
TTTTGCCCTCGAGAGT
Found at i:48986110 original size:28 final size:28
Alignment explanation
Indices: 48986077--48986153 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
48986067 AAATTTTCCC
48986077 AAAATTACCATTTTGCCCTCGAGAGTAA
1 AAAATTACCATTTTGCCCTCGAGAGTAA
* *
48986105 AAAATTACCATTTTGCCC-CTAAGAGTCA
1 AAAATTACCATTTTGCCCTC-GAGAGTAA
* *
48986133 AAAATTGCCATTTTACCCTCG
1 AAAATTACCATTTTGCCCTCG
48986154 GATATCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.95
29 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCGAGAGTAA
Found at i:48986223 original size:174 final size:175
Alignment explanation
Indices: 48985930--48986297 Score: 494
Period size: 174 Copynumber: 2.1 Consensus size: 175
48985920 CAAATTTTCC
* * * *
48985930 AAAAATTACCATTTTG-CCCTCGAGAGTCCAAAATTACCAGTTTGCCCTCGGGCATCCAAAAAGT
1 AAAAATTACCATTTTGCCCCTCAAGAGTCAAAAATTACCAGTTTACCCTCGGACATCCAAAAAGT
*** * * *
48985994 CCCATTTTTTATCTTGATTCTTCCAAAAAATTAACGTTTTACCCTTAAGTGTCTAAAATGTCA-T
66 CCCATTTTTTATCCCAATTCTTCCAAAAAATTAACATTTTACCCTTAACTGTCTAAAA-ATCATT
48986058 TTTAAC-CCTAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTA
130 TTTAACTCC-AAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTA
* * *
48986104 AAAAATTACCATTTTGCCCCT-AAGAGTCAAAAATTGCCATTTTACCCTCGGATATCCAAAAAGT
1 AAAAATTACCATTTTGCCCCTCAAGAGTCAAAAATTACCAGTTTACCCTCGGACATCCAAAAAGT
* * * *
48986168 CCCATTTTTTTATCCCAATTGTTTC-AAAAATTACCATTTTGCCCTTAACTGTCTAAAAATCATT
66 CCCA-TTTTTTATCCCAATTCTTCCAAAAAATTAACATTTTACCCTTAACTGTCTAAAAATCATT
* *
48986232 TTTAACTCCAAATTTTCCCAAAATTACCATTTTGCTCTCGAGAGTC
130 TTTAACTCCAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTA
*
48986278 CAAAATTACCATTTTGCCCC
1 AAAAATTACCATTTTGCCCC
48986298 CGGGCATCCA
Statistics
Matches: 170, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
173 3 0.02
174 146 0.86
175 21 0.12
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.35
Consensus pattern (175 bp):
AAAAATTACCATTTTGCCCCTCAAGAGTCAAAAATTACCAGTTTACCCTCGGACATCCAAAAAGT
CCCATTTTTTATCCCAATTCTTCCAAAAAATTAACATTTTACCCTTAACTGTCTAAAAATCATTT
TTAACTCCAAATTTTCCCAAAATTACCATTTTGCCCTCGAGAGTA
Found at i:48988418 original size:24 final size:24
Alignment explanation
Indices: 48988379--48988430 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
48988369 TCAAATGCAT
48988379 CCTCCACCCCTAATGTATCAC-CCA
1 CCTCCACCCCTAATGTATC-CTCCA
* *
48988403 CCTCCACCGCTGATGTATCCTCCA
1 CCTCCACCCCTAATGTATCCTCCA
48988427 CCTC
1 CCTC
48988431 AAATGTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.19, C:0.50, G:0.08, T:0.23
Consensus pattern (24 bp):
CCTCCACCCCTAATGTATCCTCCA
Found at i:48988426 original size:18 final size:18
Alignment explanation
Indices: 48988403--48988444 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
48988393 GTATCACCCA
**
48988403 CCTCCACCGCTGATGTAT
1 CCTCCACCGCAAATGTAT
*
48988421 CCTCCACCTCAAATGTAT
1 CCTCCACCGCAAATGTAT
48988439 CCTCCA
1 CCTCCA
48988445 TATTAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.43, G:0.10, T:0.26
Consensus pattern (18 bp):
CCTCCACCGCAAATGTAT
Found at i:48991384 original size:210 final size:210
Alignment explanation
Indices: 48991022--48991428 Score: 645
Period size: 210 Copynumber: 1.9 Consensus size: 210
48991012 AAGACTGCTC
* * * *
48991022 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGGCCGTCCCATCTAAATAAAGCTCTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGGCCGTCCCATCAAAACAAACCACTAGCAGGCA
*
48991087 TTCCATTTTGCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
* * *
48991152 CAAGAGATTCCATTCCAATTTTGATTGGAAGACTCCTAAGACTTTTGCAG-TTTTCTAAATTCAA
131 CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCT-TAAATTCAA
48991216 AAGTTTAAGTCTTCTG
195 AAGTTTAAGTCTTCTG
* * ***
48991232 AGATTTCCGATTGAAGAAGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAACCACTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGGCCGTCCCATCAAAACAAACCACTAGCAGGCA
* *
48991297 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGATTTGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
* *
48991362 CAAGAGATTCCATTCCAATTTTGGTTGGAAAACTCCTCAGACTTTTGCAGCCTCTTAAATTCAAA
131 CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAA
48991427 AG
196 AG
48991429 CTTGAGCCTC
Statistics
Matches: 179, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
210 177 0.99
211 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (210 bp):
AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGGCCGTCCCATCAAAACAAACCACTAGCAGGCA
TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAA
AGTTTAAGTCTTCTG
Found at i:48997554 original size:31 final size:31
Alignment explanation
Indices: 48997519--48997577 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
48997509 AATTCGGCTA
48997519 TTTTTAAAAGATTT-ATAG-TCAAATTTAACTC
1 TTTTTAAAAG-TTTGA-AGATCAAATTTAACTC
48997550 TTTTTAAAAGTTTGAAGATCAAATTTAA
1 TTTTTAAAAGTTTGAAGATCAAATTTAA
48997578 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTTAAAAGTTTGAAGATCAAATTTAACTC
Found at i:49003275 original size:21 final size:21
Alignment explanation
Indices: 49003246--49003307 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
49003236 CATAATATTC
*
49003246 CAAATATAAAGTTTAGAAATT
1 CAAATATAAAATTTAGAAATT
* *
49003267 CAAACATAAAATTTATAAATT
1 CAAATATAAAATTTAGAAATT
*
49003288 CAAATATAAAACTTCAGAAA
1 CAAATATAAAA-TTTAGAAA
49003308 AATACAACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (21 bp):
CAAATATAAAATTTAGAAATT
Found at i:49006284 original size:29 final size:29
Alignment explanation
Indices: 49006227--49006284 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
49006217 TGATTTAATA
* *
49006227 TGCAATTGAATACATAAACTTTGGTTTTG
1 TGCAATTGAATACATAAAATTTGGATTTG
** *
49006256 TGCAATTTTATACATAAAATTTTGATTTG
1 TGCAATTGAATACATAAAATTTGGATTTG
49006285 ATCTAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
TGCAATTGAATACATAAAATTTGGATTTG
Found at i:49006396 original size:25 final size:25
Alignment explanation
Indices: 49006349--49006396 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
49006339 TATATATTGC
* * *
49006349 ATATATAAATAATTAAATTTATTCA
1 ATATAAAAATAAATAAATGTATTCA
*
49006374 ATATAAAAATAAATAGATGTATT
1 ATATAAAAATAAATAAATGTATT
49006397 TTTTTATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATAAAAATAAATAAATGTATTCA
Found at i:49007623 original size:6 final size:6
Alignment explanation
Indices: 49007614--49007679 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
49007604 TTGTTTTAGG
* * * *
49007614 TTTAAA TTTAAA -TTAAT TTTAAG TTTAAA TTT-AT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
49007660 ATT--A TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
49007680 TTCAAATCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 38 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:49007658 original size:23 final size:23
Alignment explanation
Indices: 49007613--49007658 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
49007603 TTTGTTTTAG
**
49007613 GTTTAAATTTAAATTAATTTTAA
1 GTTTAAATTTAAATTAAAATTAA
**
49007636 GTTTAAATTTATTTTAAAATTAA
1 GTTTAAATTTAAATTAAAATTAA
49007659 AATTATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
GTTTAAATTTAAATTAAAATTAA
Found at i:49007674 original size:33 final size:35
Alignment explanation
Indices: 49007617--49007681 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 35
49007607 TTTTAGGTTT
* *
49007617 AAATTTAAATTAATTTTAAGTTTAAATTTATTTTA
1 AAATTAAAATTAATTTTAAATTTAAATTTATTTTA
49007652 AAATTAAAATT-A-TTTAAATTTAAATTTATT
1 AAATTAAAATTAATTTTAAATTTAAATTTATT
49007682 CAAATCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.61
34 1 0.04
35 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (35 bp):
AAATTAAAATTAATTTTAAATTTAAATTTATTTTA
Found at i:49007686 original size:16 final size:17
Alignment explanation
Indices: 49007614--49007681 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 17
49007604 TTGTTTTAGG
*
49007614 TTTAAATTTAAATTAAT
1 TTTAAATTTAAATTTAT
*
49007631 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
49007648 TTTAAAATTAAAATTA-
1 TTTAAATTTAAATTTAT
49007664 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
49007681 T
1 T
49007682 CAAATCTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.33
17 29 0.67
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:49009828 original size:24 final size:24
Alignment explanation
Indices: 49009796--49009918 Score: 169
Period size: 24 Copynumber: 5.1 Consensus size: 24
49009786 ATATACTGGT
49009796 TAACCATTCTGGGCTCTTAAGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
* *
49009820 TAACCATTCTAGG-TTTGTAAGAGC
1 TAACCATTCTGGGCTCT-TAAGAGC
*
49009844 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
49009868 TAACCATTCTGGGCT-TGTAAGAGC
1 TAACCATTCTGGGCTCT-TAAGAGC
* *
49009892 TAACCATTCTGGGCTCGTATGAGC
1 TAACCATTCTGGGCTCTTAAGAGC
49009916 TAA
1 TAA
49009919 ATTTCTAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.02
24 84 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGCTCTTAAGAGC
Found at i:49009867 original size:48 final size:48
Alignment explanation
Indices: 49009796--49009918 Score: 201
Period size: 48 Copynumber: 2.6 Consensus size: 48
49009786 ATATACTGGT
* *
49009796 TAACCATTCTGGGCTCTTAAGAGCTAACCATTCTAGGTTTGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
*
49009844 TAACCATTCTGGGCTCATAAGAGCTAACCATTCTGGGCTTGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
* *
49009892 TAACCATTCTGGGCTCGTATGAGCTAA
1 TAACCATTCTGGGCTCATAAGAGCTAA
49009919 ATTTCTAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
TAACCATTCTGGGCTCATAAGAGCTAACCATTCTAGGCTTGTAAGAGC
Found at i:49016495 original size:210 final size:210
Alignment explanation
Indices: 49016133--49016545 Score: 639
Period size: 210 Copynumber: 2.0 Consensus size: 210
49016123 AAGACTGCTC
* *
49016133 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
* *
49016198 TTCCATTTTGCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
* * * *
49016263 CAAGAGATTCCATTCCAATTTTGATTGGAAGACTCCTAAGACTTTTGCAG-TTTTCTAAATTCAA
131 CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTGTTGCAGCCTCT-TAAATTCAA
*
49016327 AAGTTTAAGTCTTCTG
195 AAGCTTAAGTCTTCTG
* * ***
49016343 AGATTTCCGATTGAAGAAGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCTCTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
* * *
49016408 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGCTTTGAGCAACCTGAAAGAATTAACTGTT
66 TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
* *
49016473 CAAGAGATTCCATTCCAATTTTGGTTGGAAAACTCCTCAGACTGTTGCAGCCTCTTAAATTCAAA
131 CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTGTTGCAGCCTCTTAAATTCAAA
49016538 AGCTTAAG
196 AGCTTAAG
49016546 CCTCGTAAGA
Statistics
Matches: 183, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
210 181 0.99
211 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (210 bp):
AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
TTCCATTTTCCCACCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTGTT
CAAGAGATTCCATTCCAATTTTGATTGGAAAACTCCTAAGACTGTTGCAGCCTCTTAAATTCAAA
AGCTTAAGTCTTCTG
Found at i:49019960 original size:37 final size:37
Alignment explanation
Indices: 49019910--49019985 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
49019900 GAATGAGAAG
*
49019910 AATAGATCAAATTTGCAAGGAACGTAAACAGAGGTTT
1 AATAGATCAAATTTGCAAGGAAAGTAAACAGAGGTTT
49019947 AATAGATCAAATTTGCAAGGAAAGTAAACAGAGGTTT
1 AATAGATCAAATTTGCAAGGAAAGTAAACAGAGGTTT
49019984 AA
1 AA
49019986 GGCAATTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (37 bp):
AATAGATCAAATTTGCAAGGAAAGTAAACAGAGGTTT
Found at i:49020446 original size:29 final size:28
Alignment explanation
Indices: 49020392--49020447 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
49020382 TAATACCTTC
**
49020392 AAAGCAAGTGGAGGCTACTTTAATTATA
1 AAAGCAAGTGGAGGCTACGATAATTATA
49020420 AAAGCCAAGTGGAGGCTACAGAT-ATTAT
1 AAAG-CAAGTGGAGGCTAC-GATAATTAT
49020448 CACCTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (28 bp):
AAAGCAAGTGGAGGCTACGATAATTATA
Found at i:49020840 original size:15 final size:15
Alignment explanation
Indices: 49020819--49020858 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
49020809 AATTTTTTTA
49020819 AAAATTATAAA-GAT
1 AAAATTATAAATGAT
49020833 ATAAATTATTAAATGAT
1 A-AAATTA-TAAATGAT
49020850 AAAATTATA
1 AAAATTATA
49020859 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 10 0.43
17 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAATTATAAATGAT
Found at i:49029781 original size:41 final size:42
Alignment explanation
Indices: 49029702--49029781 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
49029692 CATAGCGAGG
** *
49029702 ATATAAAATTTTATTTTTTGTTTCATCATCTATAAAAAAATT
1 ATATAAAAACTTATTTTTCGTTTCATCATCTATAAAAAAATT
* *
49029744 ATATAAAAACTTA-TTTTCGTTTCATCATTTATTAAAAA
1 ATATAAAAACTTATTTTTCGTTTCATCATCTATAAAAAA
49029782 TTAATCATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 22 0.67
42 11 0.33
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (42 bp):
ATATAAAAACTTATTTTTCGTTTCATCATCTATAAAAAAATT
Found at i:49031967 original size:24 final size:24
Alignment explanation
Indices: 49031930--49031975 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
49031920 CCACTTAGGG
*
49031930 AATTATTGTTTAG-ATTTAATTCA
1 AATTATTCTTTAGAATTTAATTCA
49031953 AATTATCTCTTTAGAATTTAATT
1 AATTAT-TCTTTAGAATTTAATT
49031976 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (24 bp):
AATTATTCTTTAGAATTTAATTCA
Found at i:49033612 original size:14 final size:14
Alignment explanation
Indices: 49033570--49033612 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
49033560 CATCCATTTC
49033570 TTCTCTTCTTCTTT
1 TTCTCTTCTTCTTT
* *
49033584 TCCTCTCCATT-TTT
1 TTCTCTTC-TTCTTT
49033598 TTCTCTTCTTCTTT
1 TTCTCTTCTTCTTT
49033612 T
1 T
49033613 ATTGCCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTCTTCTTCTTT
Found at i:49036051 original size:210 final size:210
Alignment explanation
Indices: 49035650--49036062 Score: 605
Period size: 210 Copynumber: 2.0 Consensus size: 210
49035640 AAGATTGCTC
* * * *
49035650 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTCGGAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
* * *
49035715 TTCCATTTTGCCATCAATCTCTGGAAAGGTTTTAAGACCGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACCGGAGCAACCTGAAAGAATTAACTGTT
* * *
49035780 CAAGAGATTCCATTCCAATTTTAATTGGAAGACTCCCAAGACTTTTGCAGTCTTCTAAATTCAAA
131 CAAGAGATTCCATTCCAATTTTAATTGGAAAACTCCCAAGACTGTTGCAGCCTTCTAAATTCAAA
*
49035845 AGTTTAAGTCTTTTG
196 AGCTTAAGTCTTTTG
* * ***
49035860 AGATTTCCGATTGAAGAAGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCTCTAGCAGGCA
1 AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
***
49035925 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGATTTGAGCAACCTGAAAGAATTAACTGTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACCGGAGCAACCTGAAAGAATTAACTGTT
**
49035990 CAAGAGATTCCATTCCAATTTTGGTTGGAAAACTCCTC-AGACTGTTGCAGCC-TCTTAAATTCA
131 CAAGAGATTCCATTCCAATTTTAATTGGAAAACTCC-CAAGACTGTTGCAGCCTTC-TAAATTCA
49036053 AAAGCTTAAG
194 AAAGCTTAAG
49036063 CCTCGTAAGA
Statistics
Matches: 180, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
209 2 0.01
210 177 0.98
211 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (210 bp):
AGATTTCCAATTGAAAAAGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCTAGCAGGCA
TTCCATTTTCCCATCAATCTCTGGAAAGCTTTTAAGACCGGAGCAACCTGAAAGAATTAACTGTT
CAAGAGATTCCATTCCAATTTTAATTGGAAAACTCCCAAGACTGTTGCAGCCTTCTAAATTCAAA
AGCTTAAGTCTTTTG
Found at i:49037195 original size:29 final size:31
Alignment explanation
Indices: 49037128--49037195 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
49037118 ATAACAAAAT
49037128 AATAACATAAGTGACTAAAACGTAACATTTCA
1 AATAA-ATAAGTGACTAAAACGTAACATTTCA
* *
49037160 AAT--ATAAGTGATTAAAACG-AA-ATTTGA
1 AATAAATAAGTGACTAAAACGTAACATTTCA
49037187 AATAAATAA
1 AATAAATAA
49037196 AAATGACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 8 0.25
28 2 0.06
29 19 0.59
32 3 0.09
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.26
Consensus pattern (31 bp):
AATAAATAAGTGACTAAAACGTAACATTTCA
Found at i:49040475 original size:29 final size:29
Alignment explanation
Indices: 49040443--49040681 Score: 181
Period size: 29 Copynumber: 8.1 Consensus size: 29
49040433 TAGTGAAATC
49040443 GGGGTTAAGAATGGAA-TTTTGGAAAGTTT
1 GGGGTTAA-AATGGAATTTTTGGAAAGTTT
* *
49040472 GGGGATAAAATGGTAATTTTTGGTAAA-ATT
1 GGGGTTAAAATGG-AATTTTTGG-AAAGTTT
* *
49040502 AGGGTTAAAAATGGAA-TTTTGGAAAGTTCA
1 GGGGTT-AAAATGGAATTTTTGGAAAGTT-T
*
49040532 GGGG-TAAAATGGAAATTTTTGGTGAAA--TC
1 GGGGTTAAAATGG-AATTTTT-G-GAAAGTTT
*
49040561 GAGGTTAAAAATGGAA-TTTTGGAAAGTTT
1 GGGGTT-AAAATGGAATTTTTGGAAAGTTT
*
49040590 GGGGGTAAAATGGTAATTTTTGG-AAGTTT
1 GGGGTTAAAATGG-AATTTTTGGAAAGTTT
* *
49040619 CGGGGTTAAAATGTAATTTCTT-GAAATTTT
1 -GGGGTTAAAATGGAATTT-TTGGAAAGTTT
* * * **
49040649 AGGGTCAAAATGCAATTTTTGGACTGTTT
1 GGGGTTAAAATGGAATTTTTGGAAAGTTT
49040678 GGGG
1 GGGG
49040682 ACCTATAAAT
Statistics
Matches: 168, Mismatches: 22, Indels: 40
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.02
28 25 0.15
29 68 0.40
30 49 0.29
31 18 0.11
32 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGGTTAAAATGGAATTTTTGGAAAGTTT
Found at i:49040626 original size:59 final size:57
Alignment explanation
Indices: 49040420--49040671 Score: 267
Period size: 59 Copynumber: 4.3 Consensus size: 57
49040410 ATCAGAGGGC
* * *
49040420 AAAATGGTAATTTTAGTGAAATCGGGGTTAAGAATGGAATTTTGGAAAGTTTGGGGAT
1 AAAATGGTAATTTTTG-GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
** **
49040478 AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGG--AAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
49040537 AAAATGGAAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTT-G-GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * **
49040596 AAAATGGTAATTTTTGGAAGTTTCGGGGTT-AAAATGTAATTTCTTGAAA-TTTTAGGGT
1 AAAATGGTAATTTTTGGAA--ATCGGGGTTAAAAATGGAATTT-TGGAAAGTTTGGGGGT
*
49040654 CAAAAT-GCAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
49040672 CTGTTTGGGG
Statistics
Matches: 165, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
57 4 0.02
58 45 0.27
59 114 0.69
60 1 0.01
61 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:49040659 original size:118 final size:118
Alignment explanation
Indices: 49040415--49040670 Score: 326
Period size: 118 Copynumber: 2.2 Consensus size: 118
49040405 TGGATATCAG
* * * *
49040415 AGGG-CAAAATGGTAA-TTTTAGTGAAATCGGGGTTAAGAATGGAATTTTGGAAAGTTTGGGGAT
1 AGGGTCAAAATGGAAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGAT
49040478 AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTC
66 AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTC
*
49040531 AGGGGT-AAAATGGAAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGG
1 A-GGGTCAAAATGGAAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGA
** * * * * *
49040595 TAAAATGGTAATTTTTGG-AAGTTTCGGGGTT-AAAATGTAATTTCTTGAAATTTT
65 TAAAATGGTAATTTTTGGTAAAATT-AGGGTTAAAAATGGAATTT-TGGAAAGTTC
*
49040649 AGGGTCAAAAT-GCAATTTTTGG
1 AGGGTCAAAATGGAAATTTTTGG
49040671 ACTGTTTGGG
Statistics
Matches: 121, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
116 1 0.01
117 41 0.34
118 79 0.65
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (118 bp):
AGGGTCAAAATGGAAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGAT
AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:49042437 original size:14 final size:14
Alignment explanation
Indices: 49042418--49042445 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49042408 CCTAAATTTA
49042418 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
49042432 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
49042446 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:49042472 original size:11 final size:11
Alignment explanation
Indices: 49042410--49042463 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
49042400 TGTTTAAACC
*
49042410 TAAATTTAAAG
1 TAAATTTAAAA
49042421 TAAATTT-AAA
1 TAAATTTAAAA
* *
49042431 T-AA-GTAAATT
1 TAAATTTAAA-A
49042441 TAAATTTAAAA
1 TAAATTTAAAA
49042452 TAAATTTAAAA
1 TAAATTTAAAA
49042463 T
1 T
49042464 CCATTTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.03
9 4 0.12
10 4 0.12
11 21 0.62
12 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:49042975 original size:75 final size:75
Alignment explanation
Indices: 49042829--49043359 Score: 782
Period size: 75 Copynumber: 7.0 Consensus size: 75
49042819 GCTTTGTCCA
* * * * * * *
49042829 GCTCTTATTTCAATTTCAGAGATAAAGACTTGATGTCCAGCTTTACTTCAATTTCAAGAGGATGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-ATCTACTTCAATTTCAAGAGGATAG
49042894 GAAATGATCTT
65 GAAATGATCTT
49042905 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
49042970 AAATGA-CGTT
66 AAATGATC-TT
* *
49042980 GCTCTTACTTAAATTTCAGAGACAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
* *
49043045 AAAAGATCTC
66 AAATGATCTT
*
49043055 GCTCTTACTTCAA-TTCTAGAGATAAAGACATGTTATCCAATCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTC-AGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAG
49043119 GAAATGA-CGTT
65 GAAATGATC-TT
* *
49043130 GCTCTTACTTCAATTTCAGAGACAAAGACGTGTTATCCAATCTAATTCAATTTCAAGAGGATAGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
*
49043195 AAAAGATCTT
66 AAATGATCTT
* * * *
49043205 GCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAGCTTTACCTT-AATTCCAAGAGGATA
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-ATCTA-CTTCAATTTCAAGAGGATA
49043269 GGAAATGATCTT
64 GGAAATGATCTT
* *
49043281 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAA-TCTACTTCAATTTCAAGAGGATAG
49043346 GAAATGATCTT
65 GAAATGATCTT
49043357 GCT
1 GCT
49043360 GCGGTCTGAT
Statistics
Matches: 414, Mismatches: 31, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
74 5 0.01
75 269 0.65
76 138 0.33
77 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (75 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATAGG
AAATGATCTT
Found at i:49043032 original size:37 final size:38
Alignment explanation
Indices: 49042910--49043188 Score: 151
Period size: 37 Copynumber: 7.4 Consensus size: 38
49042900 ATCTTGCTCT
*
49042910 TACTTCAATTTC-AGAGATAAAGACGTGTTATCCAATC
1 TACTTCAATTTCAAGAGACAAAGACGTGTTATCCAATC
* **
49042947 TACTTCAATTTCAAGAGGATAGGAAATGACGT-TGCT-C--T-
1 TACTTCAATTTCAAGA-G--A-CAAA-GACGTGTTATCCAATC
*
49042985 TACTTAAATTTC-AGAGACAAAGACGTGTTATCCAATC
1 TACTTCAATTTCAAGAGACAAAGACGTGTTATCCAATC
* * *** **
49043022 TACTTCAATTTCAAGAGGA-TAGGAAAAG--ATCTCGCTC
1 TACTTCAATTTCAAGA-GACAAAGACGTGTTATC-CAATC
* * *
49043059 TTACTTCAA-TTCTAGAGATAAAGACATGTTATCCAATC
1 -TACTTCAATTTCAAGAGACAAAGACGTGTTATCCAATC
* **
49043097 TACTTCAATTTCAAGAGGATAGGAAATGACGT-TGCT-C--T-
1 TACTTCAATTTCAAGA-G--A-CAAA-GACGTGTTATCCAATC
49043135 TACTTCAATTTC-AGAGACAAAGACGTGTTATCCAATC
1 TACTTCAATTTCAAGAGACAAAGACGTGTTATCCAATC
*
49043172 TAATTCAATTTCAAGAG
1 TACTTCAATTTCAAGAG
49043189 GATAGGAAAA
Statistics
Matches: 181, Mismatches: 31, Indels: 59
0.67 0.11 0.22
Matches are distributed among these distances:
32 10 0.06
33 10 0.06
34 4 0.02
36 9 0.05
37 62 0.34
38 54 0.30
39 9 0.05
41 4 0.02
42 10 0.06
43 9 0.05
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (38 bp):
TACTTCAATTTCAAGAGACAAAGACGTGTTATCCAATC
Found at i:49052749 original size:86 final size:86
Alignment explanation
Indices: 49052642--49052815 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
49052632 GACTCCGAGT
49052642 AACGGGACCCAATCGAAATCACCACATCGGTAGAGAATCTCATCTGGGAGGAACCAAGGTGCACA
1 AACGGGACCCAATCGAAATCACCACATCGGTAGAGAATCTCATCTGGGAGGAACCAAGGTGCACA
49052707 CCATTCAATATTTTCATCCCG
66 CCATTCAATATTTTCATCCCG
49052728 AACGGGACCCAATCGAAATCACCACATCGGTAGAGAATCTCATCTGGGAGGAACCAAGGTGCACA
1 AACGGGACCCAATCGAAATCACCACATCGGTAGAGAATCTCATCTGGGAGGAACCAAGGTGCACA
49052793 CCATTCAATATTTTCATCCCG
66 CCATTCAATATTTTCATCCCG
49052814 AA
1 AA
49052816 GATTCTGGAG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (86 bp):
AACGGGACCCAATCGAAATCACCACATCGGTAGAGAATCTCATCTGGGAGGAACCAAGGTGCACA
CCATTCAATATTTTCATCCCG
Found at i:49055667 original size:59 final size:59
Alignment explanation
Indices: 49055568--49055763 Score: 315
Period size: 59 Copynumber: 3.4 Consensus size: 59
49055558 GGATACCCGA
* * * *
49055568 GGGTAAAATGGTAA-TTTTAGTGAAATCGAGGTTAAGAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
49055626 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
49055685 GGGTAAAATGGTAATTTTTGGTGAAATCGGTGTTAAAAATGGAATTTTGG-AAGTTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
49055743 GGGTAAAATGGTAATTTTTGG
1 GGGTAAAATGGTAATTTTTGG
49055764 AAGTTTCGGG
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
58 41 0.32
59 88 0.68
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:49055766 original size:29 final size:28
Alignment explanation
Indices: 49055568--49055775 Score: 137
Period size: 29 Copynumber: 7.1 Consensus size: 28
49055558 GGATACCCGA
* *
49055568 GGGTAAAATGGTAATTTTAGTGAA-ATCG
1 GGGTAAAATGGTAATTTTTG-GAAGTTCG
* *
49055596 AGGTTAAGAATGG-AA-TTTTGGAAAGTTTGG
1 -GGGTAA-AATGGTAATTTTTGG-AAG-TTCG
*
49055626 GGGTAAAATGGTAATTTTTGGTGAA-ATCG
1 GGGTAAAATGGTAATTTTT-G-GAAGTTCG
49055655 GGGTTAAAAATGG-AA-TTTTGGAAAGTTCAG
1 GGG-T-AAAATGGTAATTTTTGG-AAGTTC-G
*
49055685 GGGTAAAATGGTAATTTTTGGTGAA-ATCG
1 GGGTAAAATGGTAATTTTT-G-GAAGTTCG
*
49055714 GTGTTAAAAATGG-AA-TTTTGGAAGTTTCG
1 G-GGT-AAAATGGTAATTTTTGGAAG-TTCG
49055743 GGGTAAAATGGTAATTTTTGGAAGTTTCG
1 GGGTAAAATGGTAATTTTTGGAAG-TTCG
49055772 GGGT
1 GGGT
49055776 CAGAATGTAG
Statistics
Matches: 144, Mismatches: 12, Indels: 46
0.71 0.06 0.23
Matches are distributed among these distances:
27 12 0.08
28 26 0.18
29 56 0.39
30 28 0.19
31 20 0.14
32 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGAAGTTCG
Found at i:49055818 original size:29 final size:28
Alignment explanation
Indices: 49055720--49055822 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
49055710 ATCGGTGTTA
* *
49055720 AAAATGGAATTTTGGAAGTTTCGGGGT-
1 AAAATGTAATTTTTGAAGTTTCGGGGTC
49055747 AAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAT-GTAATTTTT-GAAGTTTCGGGGTC
* * * *
49055777 AGAATGTAGTTTCTTGAAATTTTGGGGTC
1 AAAATGTAATTT-TTGAAGTTTCGGGGTC
* *
49055806 AAAATGCAATTTCTGAA
1 AAAATGTAATTTTTGAA
49055823 CTGTTTGGGG
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
27 5 0.08
28 11 0.18
29 40 0.65
30 6 0.10
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAGTTTCGGGGTC
Found at i:49055829 original size:29 final size:30
Alignment explanation
Indices: 49055737--49055832 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 30
49055727 AATTTTGGAA
* *
49055737 GTTTCGGGGT-AAAATGGTAATTT-TTGGAA-
1 GTTT-GGGGTCAAAAT-GCAATTTCTTGAAAT
* * *
49055766 GTTTCGGGGTCAGAATGTAGTTTCTTGAAAT
1 GTTT-GGGGTCAAAATGCAATTTCTTGAAAT
*
49055797 -TTTGGGGTCAAAATGCAATTTC-TGAACT
1 GTTTGGGGTCAAAATGCAATTTCTTGAAAT
49055825 GTTTGGGG
1 GTTTGGGG
49055833 ACCTATAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
28 5 0.09
29 39 0.70
30 12 0.21
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (30 bp):
GTTTGGGGTCAAAATGCAATTTCTTGAAAT
Found at i:49057576 original size:6 final size:6
Alignment explanation
Indices: 49057567--49057635 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
49057557 TGTTTAAACC
* * *
49057567 TAAATT TAAA-G TAAATT TAAATAAG TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAAT--T TAAATT TAAATT TAAATT TAAATT
*
49057615 TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
49057636 ATCCATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
5 12 0.24
6 33 0.66
8 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:49057587 original size:17 final size:17
Alignment explanation
Indices: 49057567--49057635 Score: 99
Period size: 17 Copynumber: 4.2 Consensus size: 17
49057557 TGTTTAAACC
*
49057567 TAAATTTAAAGTAAATT
1 TAAATTTAAAATAAATT
*
49057584 TAAA--T-AAGTAAATT
1 TAAATTTAAAATAAATT
49057598 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
49057615 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
49057632 TAAA
1 TAAA
49057636 ATCCATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
14 13 0.27
15 1 0.02
16 1 0.02
17 33 0.69
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:49057594 original size:14 final size:14
Alignment explanation
Indices: 49057575--49057602 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49057565 CCTAAATTTA
49057575 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
49057589 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
49057603 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:49057646 original size:11 final size:11
Alignment explanation
Indices: 49057567--49057637 Score: 54
Period size: 11 Copynumber: 6.1 Consensus size: 11
49057557 TGTTTAAACC
*
49057567 TAAATTTAAAG
1 TAAATTTAAAA
49057578 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
49057591 GTAAATTTAAATT
1 -TAAATTTAAA-A
* *
49057604 TAAA-ATAAATT
1 TAAATTTAAA-A
49057615 TAAATTTAAAA
1 TAAATTTAAAA
49057626 TAAATTTAAAA
1 TAAATTTAAAA
49057637 T
1 T
49057638 CCATTTAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 29 0.58
12 11 0.22
13 3 0.06
14 7 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:49057657 original size:28 final size:28
Alignment explanation
Indices: 49057567--49057657 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
49057557 TGTTTAAACC
*
49057567 TAAATTTAAAGTAAATTTAAA-TAAGTAAATT
1 TAAATTTAAAATAAATTTAAACT---TAAA-T
* *
49057598 TAAATTTAAAATAAATTTAAATTTAAAA
1 TAAATTTAAAATAAATTTAAACTTAAAT
** *
49057626 TAAATTTAAAATCCATTTAAACTTCAAT
1 TAAATTTAAAATAAATTTAAACTTAAAT
49057654 TAAA
1 TAAA
49057658 ACCAAAGGCC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 27 0.52
29 4 0.08
31 20 0.38
32 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAAACTTAAAT
Found at i:49059942 original size:24 final size:24
Alignment explanation
Indices: 49059910--49059957 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
49059900 ATCATCAGTA
49059910 ACACCATTAATCTTGAAAGTGTTG
1 ACACCATTAATCTTGAAAGTGTTG
49059934 ACACCATTAATCTTGAAAGTGTTG
1 ACACCATTAATCTTGAAAGTGTTG
49059958 CAAATATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (24 bp):
ACACCATTAATCTTGAAAGTGTTG
Found at i:49070171 original size:13 final size:13
Alignment explanation
Indices: 49070153--49070178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49070143 TCATGATTGT
49070153 TTTTTTTAATTAA
1 TTTTTTTAATTAA
49070166 TTTTTTTAATTAA
1 TTTTTTTAATTAA
49070179 AATTATTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTAATTAA
Found at i:49070510 original size:34 final size:34
Alignment explanation
Indices: 49070438--49070511 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
49070428 ACAATATTTC
*
49070438 AAATTTATATGATAGATATATTAAATTATTTTGA
1 AAATTTATATGATAGATATAGTAAATTATTTTGA
* *
49070472 AAATTTATATGCAT-GATA-AGTAATTTTTTTTGA
1 AAATTTATATG-ATAGATATAGTAAATTATTTTGA
49070505 TAAATTT
1 -AAATTT
49070512 TCTAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 12 0.34
34 21 0.60
35 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (34 bp):
AAATTTATATGATAGATATAGTAAATTATTTTGA
Found at i:49071298 original size:15 final size:15
Alignment explanation
Indices: 49071280--49071311 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49071270 TCAAGTGTGG
49071280 AAAAATTAAATATTA
1 AAAAATTAAATATTA
*
49071295 AAAAATTAAATGTTA
1 AAAAATTAAATATTA
49071310 AA
1 AA
49071312 TTTAAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATTAAATATTA
Found at i:49071454 original size:19 final size:17
Alignment explanation
Indices: 49071404--49071457 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
49071394 AATTACACTC
49071404 TATATTCATCTTTGAAT
1 TATATTCATCTTTGAAT
* * *
49071421 TACATTTTATATTTGTAATT
1 TATA-TTCATCTTTG-AA-T
49071441 TATATTCATCTTTGAAT
1 TATATTCATCTTTGAAT
49071458 AAATATTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 10 0.36
20 4 0.14
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.56
Consensus pattern (17 bp):
TATATTCATCTTTGAAT
Found at i:49072238 original size:18 final size:18
Alignment explanation
Indices: 49072215--49072256 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49072205 TTAATTACAG
*
49072215 TAATTAATAAAATAAATA
1 TAATTAATAAAATAAAAA
*
49072233 TAATTAATGAAATAAAAA
1 TAATTAATAAAATAAAAA
49072251 TAATTA
1 TAATTA
49072257 GATGTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATTAATAAAATAAAAA
Found at i:49076981 original size:213 final size:213
Alignment explanation
Indices: 49076614--49077050 Score: 669
Period size: 213 Copynumber: 2.1 Consensus size: 213
49076604 AGAATTAATT
** * ** *
49076614 CTTTCAGGTTGCTCAAAGCTTAAAAGCTTTCCAGAGATTGATGGCAAAATGGAATGCCTGCTAAA
1 CTTTCAGGTTGCTCAAAGAATAAAAGCTTTCCAGAGATTGATGGCAAAATGAAAAACCTGCGAAA
* *
49076679 GCTTTATTTAGATGGGACAGGCATTAAGGAGCTACCTGTTTCAATTGGAAATCTGAGCAGTCTTT
66 GCTTTATTTAGATAGGACAGGCATTAAAGAGCTACCTGTTTCAATTGGAAATCTGAGCAGTCTTT
* * *
49076744 ATAAGTTAGATTTGACATATTGCAGGAACCTTGTGAGTCTCCCAGGGGGCATAGGTGGGTGTGAA
131 ATAAGTTAGATTTGACAGATTGCAGGAACCTTGTGAGTCTCCCAGGGAGCATAGGTGGGTGTAAA
** *
49076809 TTTTTAGAATCTCTTAAG
196 AGTTTAAAATCTCTTAAG
* *
49076827 CTTTCAGGTTGCTCCAAGAATAAAAGCTTTCTAGAGATTGATGGCAAAATGAAAAACCTGCGAAA
1 CTTTCAGGTTGCTCAAAGAATAAAAGCTTTCCAGAGATTGATGGCAAAATGAAAAACCTGCGAAA
*
49076892 GCTTTATTTAGATAGGACGGGCATTAAAGAGCTACCTGTTTCAATTGGAAATCTGAGCAGTCTTT
66 GCTTTATTTAGATAGGACAGGCATTAAAGAGCTACCTGTTTCAATTGGAAATCTGAGCAGTCTTT
**
49076957 ATTCGTTA-AGTTTGACAGATTGCAGGAACCTTGTGAGTCTCCCAGGGAGCATAGGTGGGTGTAA
131 ATAAGTTAGA-TTTGACAGATTGCAGGAACCTTGTGAGTCTCCCAGGGAGCATAGGTGGGTGTAA
*
49077021 AAGTTTAAAATCTCTTAAT
195 AAGTTTAAAATCTCTTAAG
*
49077040 CTTTCTGGTTG
1 CTTTCAGGTTG
49077051 TTATAAAGTT
Statistics
Matches: 202, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
212 1 0.00
213 201 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (213 bp):
CTTTCAGGTTGCTCAAAGAATAAAAGCTTTCCAGAGATTGATGGCAAAATGAAAAACCTGCGAAA
GCTTTATTTAGATAGGACAGGCATTAAAGAGCTACCTGTTTCAATTGGAAATCTGAGCAGTCTTT
ATAAGTTAGATTTGACAGATTGCAGGAACCTTGTGAGTCTCCCAGGGAGCATAGGTGGGTGTAAA
AGTTTAAAATCTCTTAAG
Found at i:49087691 original size:210 final size:209
Alignment explanation
Indices: 49087034--49087656 Score: 1014
Period size: 210 Copynumber: 3.0 Consensus size: 209
49087024 TCTTACGAGG
* * * * *
49087034 CTTAAGCTTTTGAATTTAAGAGGCTGCAAAAGTCTGAGGAGTTTTCCAACCAAAATTGGAATGGA
1 CTTAAACTTTTGAATTTAA-AGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGA
* *
49087099 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAAACTTCAAAGCTTTCCAGAGATTGATGGCA
65 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCA
*
49087164 AAATGGAATGCCTGCTAGAGCTCTATTTAGATGGGACAAACATTAAAGAGATACCTTCTTCAATT
130 AAATGGAATGCCTGCTAGAGCTCTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATT
49087229 GGAAATCTCAGAAGA
195 GGAAATCTCAGAAGA
49087244 CTTAAACTTTTGAATTTAGAAGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGA
1 CTTAAACTTTTGAATTTA-AAGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGA
* *
49087309 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCCAATCTTAAAAGCTTTCCAGAGATTGAT-GTA
65 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCA
* * *
49087373 GAAATGGAATGCCTGCTAAAGCTCCATGTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAAT
130 -AAATGGAATGCCTGCTAGAGCTCTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAAT
49087438 TGGAAATCTCAGAAGA
194 TGGAAATCTCAGAAGA
*
49087454 CTTAAACTTTTGAATTTAAAAGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAACTGGAATGGA
1 CTTAAACTTTTGAATTT-AAAGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGA
49087519 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCA
65 ATCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCA
* * * *** *
49087584 AAATGGAATGCCTCCGAGAGCTTTATTTAGATGGGACGGGCATTAAAGAGCTACCTTTTTCAATT
130 AAATGGAATGCCTGCTAGAGCTCTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATT
49087649 GGAAATCT
195 GGAAATCT
49087657 GAGCAATCTT
Statistics
Matches: 383, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
209 2 0.01
210 377 0.98
211 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (209 bp):
CTTAAACTTTTGAATTTAAAGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGAA
TCTCTTGAAAAGTTAATTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAA
AATGGAATGCCTGCTAGAGCTCTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATTG
GAAATCTCAGAAGA
Found at i:49088813 original size:36 final size:36
Alignment explanation
Indices: 49088769--49088845 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
49088759 GAGAGATCTG
49088769 GAAGAGGTGCATAGCAGTCAGTGTTGTGCAAATTTA
1 GAAGAGGTGCATAGCAGTCAGTGTTGTGCAAATTTA
49088805 GAAGAGGTGCATAGCAGTCAGTGTTGTGCAAATTTA
1 GAAGAGGTGCATAGCAGTCAGTGTTGTGCAAATTTA
49088841 GAAGA
1 GAAGA
49088846 TATCCAGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.26
Consensus pattern (36 bp):
GAAGAGGTGCATAGCAGTCAGTGTTGTGCAAATTTA
Found at i:49096077 original size:210 final size:210
Alignment explanation
Indices: 49095715--49096746 Score: 1775
Period size: 210 Copynumber: 4.9 Consensus size: 210
49095705 AGCTTAAGCT
* ** * * *
49095715 TTTGAATTTAAAAAACTGCAAAAGTCTGAGGAGTTTTCCAACCAAAATTGGAATGGAATCTCTTG
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
* *
49095780 AAGGGTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
66 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
* *
49095845 CATCTGTTTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
131 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
49095910 CAGAAGACTTGGATA
196 CAGAAGACTTGGATA
*
49095925 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGGATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
*
49095990 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGATTGATGGTAACATGGAA
66 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
*
49096055 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGCTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
131 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
49096120 CAGAAGACTTGGATA
196 CAGAAGACTTGGATA
*
49096135 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGGATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
*
49096200 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTT-AAACCTTTCCAGAGATTGATGGTAACATGGAA
66 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
49096264 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
131 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
49096329 CAGAAGACTTGGATA
196 CAGAAGACTTGGATA
* *
49096344 TTTGAATTTAAGAGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGAAATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
*
49096409 -AAGTGTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGATTGATGGTAACATGGA
66 AAAGT-TTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGA
49096473 ACGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATC
130 ACGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATC
*
49096538 TCAGAAGACTTCGATA
195 TCAGAAGACTTGGATA
49096554 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
* *
49096619 -AAGTGTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCGGAGGTTGATGGTAACATGGA
66 AAAGT-TTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGA
* ** * *
49096683 ACGTC-GGTTAGATCTTCAGTTAGATGGGACGGGTATTGAAGGACTTCCCTCTTCAATTGGAAAT
130 ACGTCTGATT-TCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAAT
49096747 TTGAGCAGTC
Statistics
Matches: 789, Mismatches: 30, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
208 4 0.01
209 202 0.26
210 583 0.74
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (210 bp):
TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
CAGAAGACTTGGATA
Found at i:49096494 original size:419 final size:420
Alignment explanation
Indices: 49095715--49096746 Score: 1793
Period size: 419 Copynumber: 2.5 Consensus size: 420
49095705 AGCTTAAGCT
* ** * * *
49095715 TTTGAATTTAAAAAACTGCAAAAGTCTGAGGAGTTTTCCAACCAAAATTGGAATGGAATCTCTTG
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
* *
49095780 AAGGGTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
66 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
* *
49095845 CATCTGTTTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
131 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
*
49095910 CAGAAGACTTGGATATTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTG
196 CAGAAGACTTGGATATTTGAATTTAAGAGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTG
**
49095975 GGATGGAATCTCTTCAAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGATT
261 AAATGGAATCTCTTCAAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGATT
49096040 GATGGTAACATGGAACGTCTGATTTCTCTTCAGTTAGATGGGGCGGCTATTGAAGGACTTCCCTC
326 GATGGTAACATGGAACGTCTGATTTCTCTTCAGTTAGATGGGGCGGCTATTGAAGGACTTCCCTC
*
49096105 TTCAATTGCAAATCTCAGAAGACTTGGATA
391 TTCAATTGCAAATCTCAGAAGACTTCGATA
*
49096135 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGGATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
*
49096200 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTT-AAACCTTTCCAGAGATTGATGGTAACATGGAA
66 AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
49096264 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
131 CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
49096329 CAGAAGACTTGGATATTTGAATTTAAGAGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTG
196 CAGAAGACTTGGATATTTGAATTTAAGAGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTG
49096394 AAATGGAATCTCTTC-AAGTGTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGAT
261 AAATGGAATCTCTTCAAAGT-TTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGAT
*
49096458 TGATGGTAACATGGAACGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCT
325 TGATGGTAACATGGAACGTCTGATTTCTCTTCAGTTAGATGGGGCGGCTATTGAAGGACTTCCCT
49096523 CTTCAATTGCAAATCTCAGAAGACTTCGATA
390 CTTCAATTGCAAATCTCAGAAGACTTCGATA
49096554 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
1 TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
* *
49096619 -AAGTGTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCGGAGGTTGATGGTAACATGGA
66 AAAGT-TTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGA
* ** * *
49096683 ACGTC-GGTTAGATCTTCAGTTAGATGGGACGGGTATTGAAGGACTTCCCTCTTCAATTGGAAAT
130 ACGTCTGATT-TCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAAT
49096747 TTGAGCAGTC
Statistics
Matches: 582, Mismatches: 26, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
418 8 0.01
419 403 0.69
420 171 0.29
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (420 bp):
TTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTC
AAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAA
CGTCTGATTTCTCTTCAGTTAGATGGGGCGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCT
CAGAAGACTTGGATATTTGAATTTAAGAGACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTG
AAATGGAATCTCTTCAAAGTTTAACTCTTTCAGGTTGCTCAAATCTTAAAATCTTTCCAGAGATT
GATGGTAACATGGAACGTCTGATTTCTCTTCAGTTAGATGGGGCGGCTATTGAAGGACTTCCCTC
TTCAATTGCAAATCTCAGAAGACTTCGATA
Found at i:49099367 original size:210 final size:210
Alignment explanation
Indices: 49099005--49099750 Score: 1172
Period size: 210 Copynumber: 3.6 Consensus size: 210
49098995 CTGGTCACGA
* * **
49099005 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTAAGAAGACTTAAACGTTTGAGTTTTGG
1 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACG
* * *
49099070 ATACTGCAAAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTGAACAGTTAATTC
66 AGACTGCAAAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCTTGAACAGTTAATTC
49099135 TTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACGTCTGTATAGG
131 TTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACGTCTGTATAGG
49099200 CTTTATTTAGATGGG
196 CTTTATTTAGATGGG
*
49099215 ACGGGTATTGAAGGACTTCCCTCTTCAATTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACG
1 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACG
* * * * *
49099280 AGGCTGCAAATGCCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCTTGAAAAATTAATTC
66 AGACTGCAAAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCTTGAACAGTTAATTC
* * * *
49099345 TTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGATAAGATTGAATGTCTGT-TAGA
131 TTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACGTCTGTATAG-
* * * *
49099409 TCTTGAGTTAGATGGA
195 GCTTTATTTAGATGGG
* *
49099425 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATTTCAGAAGACTTAAACGTTTGAGTTTTA-
1 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTCAGAAGACTTAAACATTTGAG-TTTAC
* *
49099489 GAGACTGCAAAAGTCTTAGGAGTCTTCCAAACGTAATTGGAATGGAATCTCTTGAACAGTTAATT
65 GAGACTGCAAAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCTTGAACAGTTAATT
* * *
49099554 CTTTCAGGTTGCTCAAATCCTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACATCTGTATGG
130 CTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACGTCTGTATAG
49099619 GCTTTATTTAGATGGG
195 GCTTTATTTAGATGGG
* * *
49099635 ACGGGTATTGAAGAACTTCCCTCTTCAATTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACA
1 ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACG
*
49099700 AGACTGCAGAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCT
66 AGACTGCAAAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCT
49099751 GCGAGAGCTT
Statistics
Matches: 482, Mismatches: 50, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
209 7 0.01
210 469 0.97
211 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (210 bp):
ACGGGTATTGAAGGACTTCCCTCTTCAAGTGCAAATCTCAGAAGACTTAAACATTTGAGTTTACG
AGACTGCAAAAGTCTTAGGAGTCTTCCAATCGAAATTGGAATGGAATCTCTTGAACAGTTAATTC
TTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGTAACATGGAACGTCTGTATAGG
CTTTATTTAGATGGG
Found at i:49103012 original size:16 final size:19
Alignment explanation
Indices: 49102974--49103013 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
49102964 ATCCAATATT
*
49102974 TATTTACATATTTAGTTTT
1 TATTTACATATTTAGTTTA
49102993 TATTTA-AT-TTTA-TTTA
1 TATTTACATATTTAGTTTA
49103009 TATTT
1 TATTT
49103014 TTATCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 2 0.10
19 6 0.30
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTACATATTTAGTTTA
Found at i:49105343 original size:54 final size:54
Alignment explanation
Indices: 49105279--49105381 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
49105269 AGTCTCTGAA
49105279 ATATTTTCAAACCATGGGATGGACGCCTCTACTCCAGCAGGAACCTCAATGGTC
1 ATATTTTCAAACCATGGGATGGACGCCTCTACTCCAGCAGGAACCTCAATGGTC
* * * *
49105333 ATATTTTCAAACCATGGGATGGATGTCTCTTCTCCAGCAGGAAGCTCAA
1 ATATTTTCAAACCATGGGATGGACGCCTCTACTCCAGCAGGAACCTCAA
49105382 CACTATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (54 bp):
ATATTTTCAAACCATGGGATGGACGCCTCTACTCCAGCAGGAACCTCAATGGTC
Found at i:49107478 original size:25 final size:24
Alignment explanation
Indices: 49107425--49107478 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
49107415 GATACTTTTT
* *
49107425 AAAAAAAAGAGGACCAAATTAAAC
1 AAAAAAAAAAGGACCAAAGTAAAC
*
49107449 TAAAAAAATAAGGACCAAAGT-AAC
1 -AAAAAAAAAAGGACCAAAGTAAAC
49107473 AAAAAA
1 AAAAAA
49107479 TGTAAACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 6 0.23
24 3 0.12
25 17 0.65
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAAAAAAGGACCAAAGTAAAC
Found at i:49112183 original size:28 final size:28
Alignment explanation
Indices: 49112129--49112184 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
49112119 ACGTGGATTG
* * *
49112129 CCACGTGGATGTCATGTCAATAGGTAAT
1 CCACATGGATGTCATGTCAACAAGTAAT
49112157 CCACATGGATGTCATGTCAACAAGTAAT
1 CCACATGGATGTCATGTCAACAAGTAAT
49112185 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (28 bp):
CCACATGGATGTCATGTCAACAAGTAAT
Found at i:49115512 original size:41 final size:41
Alignment explanation
Indices: 49115384--49115623 Score: 284
Period size: 42 Copynumber: 5.8 Consensus size: 41
49115374 AAAGGTAAAG
* *
49115384 CATTAGCGGCGC-TTAACAAAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTATCTAAAGCGCCGCTAAAGGTCGGGT
* * *
49115424 CATTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCAGGT
1 CATTAGCGGCGCTTTATCTA-AAGCGCCGCTAAAGGTCGGGT
* * *
49115466 CATTAGCGGCGCTTTCTCTAATGCGCCGCTAAAGGTAGGGT
1 CATTAGCGGCGCTTTATCTAAAGCGCCGCTAAAGGTCGGGT
* * ***
49115507 AATTAGCGGCGCTTGAGGGAAAGCGCCGCTAAAGGGTCGGGT
1 CATTAGCGGCGCTTTATCTAAAGCGCCGCTAAA-GGTCGGGT
* * * *
49115549 CATTAGCGGTGCTTTTTCTCAAGCGCCGCTAAAGTTCGGGT
1 CATTAGCGGCGCTTTATCTAAAGCGCCGCTAAAGGTCGGGT
*
49115590 CATTAGCGGCGCTTATATATAAAGCGCCGCTAAA
1 CATTAGCGGCGCTT-TATCTAAAGCGCCGCTAAA
49115624 TATCAGGTCA
Statistics
Matches: 166, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
40 12 0.07
41 69 0.42
42 85 0.51
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (41 bp):
CATTAGCGGCGCTTTATCTAAAGCGCCGCTAAAGGTCGGGT
Found at i:49115512 original size:83 final size:81
Alignment explanation
Indices: 49115361--49115636 Score: 295
Period size: 83 Copynumber: 3.4 Consensus size: 81
49115351 GTGTTTGGAA
* * * * *
49115361 ACAAAGCGCCGCAAAAGGTAAAG-CATTAGCGGCGC-TTAACAAAAGCGCCGCTAAAGGTCGGGT
1 ACAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATC-TAAGCGCCGCTAAAGGTCGGGT
49115424 CATTAGCGGCGCTTTAC
65 CATTAGCGGCGCTTTAC
* * *
49115441 CCACAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCTCTAATGCGCCGCTAAAGGTAGGG
1 ACA-AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCTAA-GCGCCGCTAAAGGTCGGG
* * *
49115506 TAATTAGCGGCGCTTGAG
64 TCATTAGCGGCGCTTTAC
** * * * *
49115524 GGAAAGCGCCGCTAAAGGGTCGGGTCATTAGCGGTGCTTTTTCTCAAGCGCCGCTAAAGTTCGGG
1 ACAAAGCGCCGCTAAA-GGTCAGGTCATTAGCGGCGCTTTATCT-AAGCGCCGCTAAAGGTCGGG
*
49115589 TCATTAGCGGCGCTTATAT
64 TCATTAGCGGCGCTT-TAC
* **
49115608 ATAAAGCGCCGCTAAATATCAGGTCATTA
1 ACAAAGCGCCGCTAAAGGTCAGGTCATTA
49115637 ACCCAAATTA
Statistics
Matches: 163, Mismatches: 26, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
80 2 0.01
81 17 0.10
82 27 0.17
83 100 0.61
84 17 0.10
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (81 bp):
ACAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCTAAGCGCCGCTAAAGGTCGGGTC
ATTAGCGGCGCTTTAC
Found at i:49115633 original size:42 final size:41
Alignment explanation
Indices: 49115363--49115636 Score: 275
Period size: 42 Copynumber: 6.7 Consensus size: 41
49115353 GTTTGGAAAC
* * * * *
49115363 AAAGCGCCGCAAAAGGTAAAG-CATTAGCGGCGC-TTAACA
1 AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCT
* * *
49115402 AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCC
1 AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCT
*
49115443 ACAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCTCT
1 A-AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCT
* * * ***
49115485 AATGCGCCGCTAAAGGT-AGGGTAATTAGCGGCGCTTGAGGG
1 AAAGCGCCGCTAAAGGTCA-GGTCATTAGCGGCGCTTTATCT
* * *
49115526 AAAGCGCCGCTAAAGGGTCGGGTCATTAGCGGTGCTTTTTCT
1 AAAGCGCCGCTAAA-GGTCAGGTCATTAGCGGCGCTTTATCT
* * * *
49115568 CAAGCGCCGCTAAAGTTCGGGTCATTAGCGGCGCTTATATAT
1 AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTT-TATCT
**
49115610 AAAGCGCCGCTAAATATCAGGTCATTA
1 AAAGCGCCGCTAAAGGTCAGGTCATTA
49115637 ACCCAAATTA
Statistics
Matches: 193, Mismatches: 35, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
39 17 0.09
40 13 0.07
41 69 0.36
42 94 0.49
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTATCT
Found at i:49118239 original size:13 final size:13
Alignment explanation
Indices: 49118221--49118245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49118211 AACAATAGGT
49118221 ATTATATTAAATA
1 ATTATATTAAATA
49118234 ATTATATTAAAT
1 ATTATATTAAAT
49118246 TAAATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATATTAAATA
Found at i:49118461 original size:18 final size:18
Alignment explanation
Indices: 49118232--49119350 Score: 291
Period size: 18 Copynumber: 65.3 Consensus size: 18
49118222 TTATATTAAA
49118232 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
49118248 -AA-TAT-TT-AATTATT
1 TAATTATATTAAATTATT
* **
49118262 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
*
49118280 TAAGTATATT-AA-T-TT
1 TAATTATATTAAATTATT
* **
49118295 AAAAGATA-T-AATTATT
1 TAATTATATTAAATTATT
* **
49118311 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
49118329 TAATTATATT-AATTATT
1 TAATTATATTAAATTATT
* *
49118346 TAATCATGTTTAATTATGTATT
1 TAATTAT-ATTAA--AT-TATT
*
49118368 TAATTATA--AACACTA-T
1 TAATTATATTAA-ATTATT
**
49118384 CGATTA-ATTAAA-TATT
1 TAATTATATTAAATTATT
* *
49118400 TAAGTTAAAAGATTTAATTATT
1 TAA-TT---ATATTAAATTATT
* **
49118422 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
49118440 TAATTATATTAAATTATT
1 TAATTATATTAAATTATT
* *
49118458 TAATCATGTTTAATTATGTATT
1 TAATTAT-ATTAA--AT-TATT
*
49118480 TAATTATA--AACACTA-T
1 TAATTATATTAA-ATTATT
**
49118496 CGATTA-ATTAAA-TATT
1 TAATTATATTAAATTATT
* *
49118512 TAAGTTAAAAGATTTAATTATT
1 TAA-TT---ATATTAAATTATT
* **
49118534 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
*
49118552 TAATTATATTAAGTTA--
1 TAATTATATTAAATTATT
* *
49118568 -AA--AGATTTAATTATT
1 TAATTATATTAAATTATT
* **
49118583 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
49118601 TAATTATA-TAAA--A-T
1 TAATTATATTAAATTATT
* *
49118615 TAA--AGATTTAATTATT
1 TAATTATATTAAATTATT
**
49118631 TAATTATATTAAATTAAA
1 TAATTATATTAAATTATT
49118649 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
49118665 -AA-TAT-TT-AATTATT
1 TAATTATATTAAATTATT
* **
49118679 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
*
49118697 TAAGTATATT-AA-T-TT
1 TAATTATATTAAATTATT
* **
49118712 AAAAGATA-T-AATTATT
1 TAATTATATTAAATTATT
* **
49118728 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
49118746 TAATTATATTAAATTATT
1 TAATTATATTAAATTATT
* *
49118764 TAATCATGTTTAATTATGTATT
1 TAATTAT-ATTAA--AT-TATT
*
49118786 TAATTATA--AACACTA-T
1 TAATTATATTAA-ATTATT
**
49118802 CGATTA-ATTAAA-TATT
1 TAATTATATTAAATTATT
* *
49118818 TAAGTTAAAAGATTTAATTATT
1 TAA-TT---ATATTAAATTATT
* **
49118840 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
*
49118858 TAATTATATTAAGTTA--
1 TAATTATATTAAATTATT
* *
49118874 -AA--AGATTTAATTATT
1 TAATTATATTAAATTATT
* **
49118889 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
49118907 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
49118923 -AA-TAT-TT-AATTATT
1 TAATTATATTAAATTATT
* **
49118937 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
49118955 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
*
49118971 -AA-GAT-TT-AATTATT
1 TAATTATATTAAATTATT
* **
49118985 TAATTATATTAAACTAAA
1 TAATTATATTAAATTATT
49119003 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
49119019 -AA-TAT-TT-AATTATT
1 TAATTATATTAAATTATT
* **
49119033 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
*
49119051 TAAGTATATT-AA-T-TT
1 TAATTATATTAAATTATT
* **
49119066 AAAAGATA-T-AATTATT
1 TAATTATATTAAATTATT
* * **
49119082 TAATTATAGTAAACTAAA
1 TAATTATATTAAATTATT
*
49119100 TAATTATATTAAATTATC
1 TAATTATATTAAATTATT
* *
49119118 TAATCATGTTTAATTATGTATT
1 TAATTAT-ATTAA--AT-TATT
**
49119140 TAATTATA--AACACCA-T
1 TAATTATATTAA-ATTATT
**
49119156 CGATTA-ATTAAA-TATT
1 TAATTATATTAAATTATT
* *
49119172 TAAGTTAAAAGATTTAATTATT
1 TAA-TT---ATATTAAATTATT
* **
49119194 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
*
49119212 TAATTATATTAAGTTA--
1 TAATTATATTAAATTATT
* *
49119228 -AA--AGATTTAATTATT
1 TAATTATATTAAATTATT
* **
49119243 TAATTATATTAAAGTAAA
1 TAATTATATTAAATTATT
49119261 TAATTATATTAAATTA--
1 TAATTATATTAAATTATT
49119277 -AA-TAT-TT-AATTATT
1 TAATTATATTAAATTATT
** **
49119291 TAATTATATTAAGGTAAG
1 TAATTATATTAAATTATT
*
49119309 TAATTATATTAAATTTTT
1 TAATTATATTAAATTATT
*
49119327 TAATTATATTTAATTATT
1 TAATTATATTAAATTATT
49119345 TAATTA
1 TAATTA
49119351 ATAAAAACAG
Statistics
Matches: 796, Mismatches: 185, Indels: 242
0.65 0.15 0.20
Matches are distributed among these distances:
12 32 0.04
13 39 0.05
14 29 0.04
15 61 0.08
16 83 0.10
17 58 0.07
18 366 0.46
19 21 0.03
20 4 0.01
21 36 0.05
22 67 0.08
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
TAATTATATTAAATTATT
Found at i:49118497 original size:112 final size:112
Alignment explanation
Indices: 49118288--49118563 Score: 527
Period size: 112 Copynumber: 2.5 Consensus size: 112
49118278 AATAAGTATA
* *
49118288 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATT-AATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
49118352 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATAT
66 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATAT
49118399 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
49118464 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATAT
66 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATAT
49118511 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAA
49118564 GTTAAAAGAT
Statistics
Matches: 162, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
111 49 0.30
112 113 0.70
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (112 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATAT
Found at i:49118585 original size:8 final size:8
Alignment explanation
Indices: 49118572--49118690 Score: 59
Period size: 8 Copynumber: 14.8 Consensus size: 8
49118562 AAGTTAAAAG
49118572 ATTTAATT
1 ATTTAATT
49118580 ATTTAATT
1 ATTTAATT
*
49118588 ATATTAAAGT
1 AT-TT-AATT
**
49118598 AAATAATT
1 ATTTAATT
*
49118606 ATATAA--
1 ATTTAATT
* **
49118612 AATTAAAG
1 ATTTAATT
49118620 ATTTAATT
1 ATTTAATT
49118628 ATTTAATT
1 ATTTAATT
49118636 ATATTAAATT
1 AT-TT-AATT
**
49118646 AAATAATT
1 ATTTAATT
49118654 ATATTAA--
1 AT-TTAATT
*
49118661 A-TTAAAT
1 ATTTAATT
49118668 ATTTAATT
1 ATTTAATT
49118676 ATTTAATT
1 ATTTAATT
49118684 ATATTAA
1 AT-TTAA
49118691 AGTAAATAAG
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
5 4 0.05
6 4 0.05
7 2 0.02
8 53 0.62
9 13 0.15
10 9 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (8 bp):
ATTTAATT
Found at i:49118781 original size:306 final size:306
Alignment explanation
Indices: 49118399--49119323 Score: 1351
Period size: 306 Copynumber: 3.0 Consensus size: 306
49118389 AATTAAATAT
*
49118399 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
49118464 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
66 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
49118529 TTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
131 TTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
* *
49118594 AAGTAAATAATTATATAAAATTAAAGATTTAATTATTTAATTATATTAAATTAAATAATTATATT
196 AAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATT
*
49118659 AAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
261 AAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* *
49118705 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
49118770 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
66 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
49118835 TTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
131 TTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
*
49118900 AAGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATT
196 AAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATT
* *
49118965 AAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATA
261 AAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
49119011 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATT--A--ATTTAA--A
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* * * * * * *
49119069 AG-AT-ATAAT-TATTTAATTATAGTAA-ACTAAAT-AATTATATTAAATTATCTAA--T-CATG
66 TGTTTAATTATGTATTTAATTATA--AACACT--ATCGATTA-ATTAAA-TATTTAAGTTAAAAG
* * * * *
49119126 -TTTAATTATGTATTTAATTATAAACACCATCGATTAATTAAATATTTAAGTTAAAAGATTTAAT
125 ATTTAATTATTTAATT-A-TATTAA-A-C-T-AAATAATT--ATA-TTAAGTTAAAAGATTTAAT
*
49119190 TATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAA
181 TATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGATTTAATTATTTAATTATATTAA
* *
49119255 AGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAGGTAAGTAATTATA
245 AGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
49119317 TTAAATT
1 TTAAATT
49119324 TTTTAATTAT
Statistics
Matches: 572, Mismatches: 31, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
296 25 0.04
297 10 0.02
298 13 0.02
299 11 0.02
300 7 0.01
301 7 0.01
302 6 0.01
303 1 0.00
304 3 0.01
305 94 0.16
306 395 0.69
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (306 bp):
TTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
TTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
AAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATT
AAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:49118978 original size:354 final size:353
Alignment explanation
Indices: 49118228--49119323 Score: 1516
Period size: 354 Copynumber: 3.1 Consensus size: 353
49118218 GGTATTATAT
* * * *
49118228 TAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAT
1 TAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
* * * * * *
49118293 TTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAATTATTTAATCATGTTTA
66 TT-AAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATT-A--ATTTAA--AAG-AT-
* * * *
49118358 ATTATGTATTTAATTATA-AACACT--ATCGATTA-ATTAAA-TATTTAAGTTAAAAGATTTAAT
123 ATAAT-TATTTAATTATATAA-ACTAAAT-AATTATATTAAATTATTTAA--T-CATG-TTTAAT
* * * * *
49118418 TATTTAATT-A-TATTAAACTA-AAT-AATTATATTAAATTATTTAA--T-CATG-TTTAATTAT
181 TATGTATTTAATTA-TAAAC-ACAATCGATTA-ATTAAA-TATTTAAGTTAAAAGATTTAATTAT
* * * *
49118475 GTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTA
242 TTAATT-A-TATTAA-ACTA---AATAATT--ATA-TTAAGTTAAAAGATTTAATTATTTAATTA
* * *
49118540 TATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAG
298 TATTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAG
* *
49118597 TAAATAATTATATAAAATTAAAGATTTAATTATTTAATTATATTAAATTAAATAATTATATTAAA
1 TAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
49118662 TTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTAT
66 TTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTAT
49118727 TTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTA
131 TTAATTATA-TAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTA
*
49118792 TAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAA
195 TAAACACAATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAA
49118857 ATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
260 ATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
49118922 AAATATTTAATTATTTAATTATATTAAAG
325 AAATATTTAATTATTTAATTATATTAAAG
49118951 TAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
1 TAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
49119016 TTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTAT
66 TTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTAT
*
49119081 TTAATTATAGTAAACTAAATAATTATATTAAATTATCTAATCATGTTTAATTATGTATTTAATTA
131 TTAATTATA-TAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTA
* *
49119146 TAAACACCATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
195 TAAACACAATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAA
49119211 ATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
260 ATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
*
49119276 AAATATTTAATTATTTAATTATATTAAGG
325 AAATATTTAATTATTTAATTATATTAAAG
*
49119305 TAAGTAATTATATTAAATT
1 TAAATAATTATATTAAATT
49119324 TTTTAATTAT
Statistics
Matches: 677, Mismatches: 36, Indels: 43
0.90 0.05 0.06
Matches are distributed among these distances:
354 393 0.58
355 54 0.08
356 3 0.00
358 6 0.01
360 33 0.05
361 27 0.04
362 20 0.03
363 13 0.02
364 20 0.03
365 6 0.01
367 1 0.00
368 39 0.06
369 62 0.09
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (353 bp):
TAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
TTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTAT
TTAATTATATAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTAT
AAACACAATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAA
TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTA
AATATTTAATTATTTAATTATATTAAAG
Found at i:49119289 original size:209 final size:209
Alignment explanation
Indices: 49118560--49119352 Score: 752
Period size: 209 Copynumber: 3.9 Consensus size: 209
49118550 AATAATTATA
* *
49118560 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATAAAATTAAAGATTTA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTAAAGATTTA
* * * * *
49118625 ATTATTTAATTATATTAAATTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATATT
66 ATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATATAATTATTTAATTATAGT
* * * * * * *
49118689 AAAGTAAATAAGTATATT-AA-T-T-TAA-AAGATATAATTATTTAATT-A-TATTAAACTA-AA
131 AAACTAAATAATTATATTAAATTATCTAATCATATTTAATTATGTAATTAATTA-TAAAC-ACCA
*
49118746 T-AATTATATTAAATTAT
194 TCGATTA-ATTAAA-TAT
* * * * * * *
49118763 TTAA--T-CATG-TTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
1 TTAAGTTAAAAGATTTAATTATTTAATT-A-TATTAA-ACTA---AATAATT--ATA-TTAAATT
* * * *
49118824 AAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAGTTAAAAGATTTAATTATT
57 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATATAATTATT
* * *
49118889 TAATTATATTAAAGTAAATAATTATATT-AA--AT-TAA--ATATTTAATTATTTAATTATATTA
121 TAATTATAGTAAACTAAATAATTATATTAAATTATCTAATCATATTTAATTATGTAATTA-ATTA
** * *
49118948 -AAGTA-AAT-AATTATATT-AA-A-
185 TAAACACCATCGATTA-ATTAAATAT
*
49118968 -T----T-AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTAAATATTTA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTAAAGATTTA
*
49119027 ATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTATAGT
66 ATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATATAATTATTTAATTATAGT
* *
49119092 AAACTAAATAATTATATTAAATTATCTAATCATGTTTAATTATGTATTTAATTATAAACACCATC
131 AAACTAAATAATTATATTAAATTATCTAATCATATTTAATTATGTAATTAATTATAAACACCATC
49119157 GATTAATTAAATAT
196 GATTAATTAAATAT
* *
49119171 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATT-AAAGATTT
* * * *
49119236 AATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATAT
65 AATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATATAATTATTTAATTATAG
** * * * * *
49119300 TAAGGTAAGTAATTATATTAAATTTTTTAATTATATTTAATTATTTAATTAAT
130 TAAACTAAATAATTATATTAAATTATCTAATCATATTTAATTATGTAATTAAT
49119353 AAAAACAGCC
Statistics
Matches: 500, Mismatches: 55, Indels: 64
0.81 0.09 0.10
Matches are distributed among these distances:
193 85 0.17
194 8 0.02
195 3 0.01
196 2 0.00
197 9 0.02
198 4 0.01
199 32 0.06
200 12 0.02
201 17 0.03
202 8 0.02
203 17 0.03
204 2 0.00
205 6 0.01
206 1 0.00
207 3 0.01
208 8 0.02
209 186 0.37
210 94 0.19
211 1 0.00
212 2 0.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (209 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTAAAGATTTA
ATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATATAATTATTTAATTATAGT
AAACTAAATAATTATATTAAATTATCTAATCATATTTAATTATGTAATTAATTATAAACACCATC
GATTAATTAAATAT
Found at i:49125036 original size:66 final size:66
Alignment explanation
Indices: 49124872--49125029 Score: 196
Period size: 66 Copynumber: 2.4 Consensus size: 66
49124862 GCAAATTGCT
*
49124872 CAACTTAAAGAGGAGGCTA-CAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATAAACTCCATC
1 CAACTTAAAGAGGAGGC-AGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATAAACTCCATC
49124936 TA
65 TA
* ** * * *
49124938 AAACTTAAAGAGGAGGTTGTAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGA-AGAACTCCA-C
1 CAACTTAAAGAGGAGGCAGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATA-AACTCCATC
49125001 ATA
65 -TA
*
49125004 CAACTTAAAGTGGAGGCAGCAGCGAG
1 CAACTTAAAGAGGAGGCAGCAGCGAG
49125030 GCAAGCAAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
65 2 0.03
66 74 0.97
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (66 bp):
CAACTTAAAGAGGAGGCAGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATAAACTCCATCT
A
Found at i:49125061 original size:21 final size:21
Alignment explanation
Indices: 49125010--49125061 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
49125000 CATACAACTT
* *
49125010 AAAGTGGAGGCAGCAGCGAGG
1 AAAGTGAAGGCAACAGCGAGG
* **
49125031 CAAGCAAAGGCAACAGCGAGG
1 AAAGTGAAGGCAACAGCGAGG
49125052 AAAGTGAAGG
1 AAAGTGAAGG
49125062 AAGCAGAGGC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.40, T:0.04
Consensus pattern (21 bp):
AAAGTGAAGGCAACAGCGAGG
Done.