Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 59 of 203
Found at i:18966908 original size:126 final size:125
Alignment explanation
Indices: 18966656--18967221 Score: 778
Period size: 126 Copynumber: 4.5 Consensus size: 125
18966646 CAAACATGTT
* *
18966656 ACTGTAGCAAAAGCGCGTCCACGTG-GCCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGAG-AGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* * *
18966720 AGAAGCG-ATTTTATACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
65 TGAAGCGTTTTTTAAACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
*
18966780 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCA-AATAGCATGCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCT
* *
18966844 TGCAGCGTTGTTTTATACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
65 TGAAGCGTT-TTTTAAACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
*
18966906 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTTATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* *
18966971 GAAGCGTTTTTTAAACTATTTGCTCAAAAATGTCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGCGTTTTTTAAACTATTTGCTCAAAAACGTCAAGTCGAAATTATTT-TTCCAGGACCA
* * * * * * * * *
18967032 ACTGTAGTAAAAACACGTCCACGAGGGCGCGATTTCACAAATTCTTATTACAAAACATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* * * *
18967097 GAAGCGTTTTTTAAACTATTTGCTCAAAAACGTTAAGTCAAAATTATTTTTCTAGGACCT
66 GAAGCGTTTTTTAAACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
* * * * * * * * *
18967157 ACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
18967222 TGATTTTATC
Statistics
Matches: 398, Mismatches: 38, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
123 2 0.01
124 61 0.15
125 101 0.25
126 232 0.58
127 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
GAAGCGTTTTTTAAACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
Found at i:18967147 original size:251 final size:249
Alignment explanation
Indices: 18966656--18967221 Score: 805
Period size: 251 Copynumber: 2.3 Consensus size: 249
18966646 CAAACATGTT
*
18966656 ACTGTAGCAAAAGCGCGTCCACGTGGCCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGTGG-CGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* *
18966721 GAAGCGATTTTATACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCAACTGTA
65 GAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTA
* * * *
18966786 GCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTCAAATAGCATGCTGCTTGCAGCG
130 GCAAAAACACGTCCACGAGAGAGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAGCG
* *
18966851 TTGTTTTATACTATTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
195 TTGTTTTAAACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGACCA
* * *
18966906 ACTGTAGCAAAAGCGCGTCCACGAGAGAGCGATTTCACAAATTCTTCTTATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTG-GCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* *
18966971 GAAGCGTTTTTTAAACTATTTGCTCAAAAATGTCAACTCGAAATTATTTCTTCCAGGACCAACTG
65 GAAGCG-ATTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTT-TTCCAGGACCAACTG
* * * *
18967036 TAGTAAAAACACGTCCACGAGGGCGCGATTTCACAAATTCTTATTACAAA-A-CATCCTGCTTGA
128 TAGCAAAAACACGTCCACGAGAGAGCGATTTCACAAATTCTT-CT-CAAATAGCATCCTGCTTGA
* * *
18967099 AGCGTT-TTTTAAACTATTTGCTCAAAAACGTTAAGTCAAAATTATTTTTCTAGGACCT
191 AGCGTTGTTTTAAACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGACCA
* * * * * *
18967157 ACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGT-GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
18967222 TGATTTTATC
Statistics
Matches: 281, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
250 65 0.23
251 141 0.50
252 69 0.25
253 2 0.01
254 4 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (249 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
AAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
CAAAAACACGTCCACGAGAGAGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAGCGT
TGTTTTAAACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGACCA
Found at i:18975207 original size:26 final size:26
Alignment explanation
Indices: 18975177--18975226 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18975167 TTCAAACCAA
*
18975177 ACTTTTCCATAGCACTTCTCAAAAGC
1 ACTTTTCCACAGCACTTCTCAAAAGC
* *
18975203 ACTTTTTCACAGCACTTTTCAAAA
1 ACTTTTCCACAGCACTTCTCAAAA
18975227 ATATTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (26 bp):
ACTTTTCCACAGCACTTCTCAAAAGC
Found at i:18976855 original size:24 final size:23
Alignment explanation
Indices: 18976828--18976873 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
18976818 CAAATTCTGT
18976828 AATA-TATTATACATATAATATTAG
1 AATAGTATTAT-C-TATAATATTAG
18976852 AATATGTATTATCTATAATATT
1 AATA-GTATTATCTATAATATT
18976874 TATAAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 13 0.65
25 1 0.05
26 6 0.30
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
AATAGTATTATCTATAATATTAG
Found at i:18985903 original size:86 final size:86
Alignment explanation
Indices: 18985758--18985930 Score: 310
Period size: 86 Copynumber: 2.0 Consensus size: 86
18985748 AATGTGATTG
* *
18985758 TATCCTTCTCATAAAGCAATGTGGTGGTAAGATGATCATATTCATCAGGAAGGGAATTCAACAAC
1 TATCCTTCCCATAAAGCAATGTGGTGGTAAGATGATCATATTCATCAGGAAGAGAATTCAACAAC
18985823 AGTAATGCCTTGTCTTCATCT
66 AGTAATGCCTTGTCTTCATCT
*
18985844 TATCCTTCCCATGAAGCAATGTGGTGGTAAGATGATCATATTCATCAGGAAGAGAATTCAACAAC
1 TATCCTTCCCATAAAGCAATGTGGTGGTAAGATGATCATATTCATCAGGAAGAGAATTCAACAAC
*
18985909 AGTAATGTCTTGTCTTCATCT
66 AGTAATGCCTTGTCTTCATCT
18985930 T
1 T
18985931 CAAATTTCTC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (86 bp):
TATCCTTCCCATAAAGCAATGTGGTGGTAAGATGATCATATTCATCAGGAAGAGAATTCAACAAC
AGTAATGCCTTGTCTTCATCT
Found at i:18986938 original size:14 final size:14
Alignment explanation
Indices: 18986919--18986969 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
18986909 TCTTATGCCA
18986919 ATATCTTGATACCC
1 ATATCTTGATACCC
* *
18986933 ATATCTTTGACTTTCCA
1 ATATC-TTGA--TACCC
18986950 ATAT-TTGATACCC
1 ATATCTTGATACCC
18986963 ATATCTT
1 ATATCTT
18986970 TGACTTTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 7 0.24
14 7 0.24
15 8 0.28
17 7 0.24
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (14 bp):
ATATCTTGATACCC
Found at i:18986956 original size:15 final size:16
Alignment explanation
Indices: 18986931--18986981 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
18986921 ATCTTGATAC
*
18986931 CCATATCTTTGACTTT
1 CCATATATTTGACTTT
**
18986947 CCA-ATATTTGA-TAC
1 CCATATATTTGACTTT
*
18986961 CCATATCTTTGACTTT
1 CCATATATTTGACTTT
18986977 CCATA
1 CCATA
18986982 AATATGGATG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.43
Consensus pattern (16 bp):
CCATATATTTGACTTT
Found at i:18986960 original size:30 final size:31
Alignment explanation
Indices: 18986916--18986979 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
18986906 ATTTCTTATG
18986916 CCAATATCTTGATACCCATATCTTTGACTTT
1 CCAATATCTTGATACCCATATCTTTGACTTT
18986947 CCAATAT-TTGATACCCATATCTTTGACTTT
1 CCAATATCTTGATACCCATATCTTTGACTTT
18986977 CCA
1 CCA
18986980 TAAATATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.41
Consensus pattern (31 bp):
CCAATATCTTGATACCCATATCTTTGACTTT
Found at i:18987869 original size:6 final size:6
Alignment explanation
Indices: 18987858--18987882 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18987848 TTATTATGCC
18987858 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
18987883 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:18987930 original size:22 final size:22
Alignment explanation
Indices: 18987878--18987938 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
18987868 TTTAAATTTA
* *
18987878 AATTTTTATATTTTTA-TATTTT
1 AATTTTT-TAATTTTATTATTAT
18987900 AA-TTTTTAATTTTATTATTAT
1 AATTTTTTAATTTTATTATTAT
*
18987921 AATTTTTTAATGTTATTA
1 AATTTTTTAATTTTATTA
18987939 GCCGGTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.21
21 11 0.32
22 16 0.47
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
AATTTTTTAATTTTATTATTAT
Found at i:18989017 original size:34 final size:35
Alignment explanation
Indices: 18988962--18989028 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
18988952 CAAACACCAG
*
18988962 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
18988997 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
18989029 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:18992489 original size:20 final size:21
Alignment explanation
Indices: 18992450--18992490 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18992440 AACACTCCAG
*
18992450 TTTGTGGATGAACCACCAGTA
1 TTTGTAGATGAACCACCAGTA
*
18992471 TTTGTAGAT-AACTACCAGTA
1 TTTGTAGATGAACCACCAGTA
18992491 GTACAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (21 bp):
TTTGTAGATGAACCACCAGTA
Found at i:18992823 original size:38 final size:38
Alignment explanation
Indices: 18992752--18992869 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 38
18992742 TTGTAAAAAT
* *
18992752 AGTAGACATGCTTAACATGTTTTTAGTTCAACAGTAAC
1 AGTAGACATGCTTAACATGTATTCAGTTCAACAGTAAC
* * * * *
18992790 ATTAGACATGCTTATCATGCATTCAGTTTAACAGTAAT
1 AGTAGACATGCTTAACATGTATTCAGTTCAACAGTAAC
** * *
18992828 AGTAGGTATGCTTAACATGTATTCGGTTCAACAGTAGC
1 AGTAGACATGCTTAACATGTATTCAGTTCAACAGTAAC
18992866 AGTA
1 AGTA
18992870 AGCATGTATT
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCAGTTCAACAGTAAC
Found at i:18994291 original size:10 final size:10
Alignment explanation
Indices: 18994276--18994302 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18994266 AGGTGTCTTA
18994276 CAATTACACC
1 CAATTACACC
18994286 CAATTACACC
1 CAATTACACC
18994296 CAATTAC
1 CAATTAC
18994303 TTGCTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (10 bp):
CAATTACACC
Found at i:18999171 original size:24 final size:25
Alignment explanation
Indices: 18999139--18999188 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
18999129 ACCTCTGAAA
*
18999139 AATATATTT-ATATTATTTTTAATTT
1 AATATATTTAATA-AATTTTTAATTT
18999164 AATA-ATTTAATAAATTTTTAATTT
1 AATATATTTAATAAATTTTTAATTT
18999188 A
1 A
18999189 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATATATTTAATAAATTTTTAATTT
Found at i:18999187 original size:16 final size:16
Alignment explanation
Indices: 18999166--18999199 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18999156 TTTAATTTAA
*
18999166 TAATTTAATAAATTTT
1 TAATTTAATAAAATTT
*
18999182 TAATTTATTAAAATTT
1 TAATTTAATAAAATTT
18999198 TA
1 TA
18999200 TATATAGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTAATAAAATTT
Found at i:19000158 original size:16 final size:18
Alignment explanation
Indices: 19000134--19000170 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
19000124 ATGAAATTTA
*
19000134 TTTATTAAA-ATAATAAT
1 TTTATTAAATAAAATAAT
19000151 TTTA-TAAATAAAATAAT
1 TTTATTAAATAAAATAAT
19000168 TTT
1 TTT
19000171 CTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATTAAATAAAATAAT
Found at i:19000980 original size:17 final size:18
Alignment explanation
Indices: 19000947--19000980 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19000937 AGATAAAAAA
*
19000947 CCAAAACCAAAATCAAGC
1 CCAAAACCAAAACCAAGC
19000965 CCAAAA-CAAAACCAAG
1 CCAAAACCAAAACCAAG
19000981 ACCGAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.32, G:0.06, T:0.03
Consensus pattern (18 bp):
CCAAAACCAAAACCAAGC
Found at i:19002112 original size:29 final size:29
Alignment explanation
Indices: 19002080--19002195 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
19002070 ACACGGACTG
* * *
19002080 GCACATGGCCTACCACACGGCTGTGTGGC
1 GCACAAGGCCTAACACACGGCCGTGTGGC
*
19002109 GCACAAGGCTTAACACACGGCCGTGTGGC
1 GCACAAGGCCTAACACACGGCCGTGTGGC
* *
19002138 ACACAAGGCTTAACACACGGCCGTGTGGC
1 GCACAAGGCCTAACACACGGCCGTGTGGC
* * *
19002167 GCACATA-GTCTACCACACGGCCATGTGGC
1 GCACA-AGGCCTAACACACGGCCGTGTGGC
19002196 ACTTGACAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
29 75 0.99
30 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (29 bp):
GCACAAGGCCTAACACACGGCCGTGTGGC
Found at i:19012947 original size:26 final size:26
Alignment explanation
Indices: 19012911--19012961 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19012901 TCCTATACAT
*
19012911 ATATGCTCACACGAGTTGTAAAATGA
1 ATATGCTCACACGAGCTGTAAAATGA
*
19012937 ATATGCTCACACGAGCTGTGAAATG
1 ATATGCTCACACGAGCTGTAAAATG
19012962 GGCCTACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (26 bp):
ATATGCTCACACGAGCTGTAAAATGA
Found at i:19015147 original size:26 final size:26
Alignment explanation
Indices: 19015111--19015161 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19015101 TCCTATACAT
*
19015111 ATATGCTCACACGAGTTGTAAAATGA
1 ATATGCTCACACGAGCTGTAAAATGA
*
19015137 ATATGCTCACACGAGCTGTGAAATG
1 ATATGCTCACACGAGCTGTAAAATG
19015162 GGCCTACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (26 bp):
ATATGCTCACACGAGCTGTAAAATGA
Found at i:19019134 original size:3 final size:3
Alignment explanation
Indices: 19019126--19019269 Score: 288
Period size: 3 Copynumber: 48.0 Consensus size: 3
19019116 GATCAAGAAC
19019126 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19019174 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19019222 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19019270 GAAAAGATAA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 141 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19019388 original size:4 final size:4
Alignment explanation
Indices: 19019379--19019406 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
19019369 TGGTCATGTG
19019379 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
19019407 TCAAGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:19019496 original size:23 final size:22
Alignment explanation
Indices: 19019456--19019499 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
19019446 AAATTATAAA
*
19019456 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
19019478 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
19019500 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:19019502 original size:27 final size:25
Alignment explanation
Indices: 19019460--19019518 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
19019450 TATAAAATAT
19019460 AAAAATATATATATGT-ACA-TATAA
1 AAAAATATATATATGTGA-ATTATAA
19019484 GAAAAATATATATGTATGTGAATTATAA
1 -AAAAATATATA--TATGTGAATTATAA
19019512 AAAAATA
1 AAAAATA
19019519 AAAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 11 0.37
27 13 0.43
28 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (25 bp):
AAAAATATATATATGTGAATTATAA
Found at i:19019627 original size:42 final size:40
Alignment explanation
Indices: 19019539--19019630 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
19019529 TAAATATTTT
* *
19019539 AATATAAAATATATATAAGTATGTATATAAAATTATGAAA
1 AATAAAAAATATATAAAAGTATGTATATAAAATTATGAAA
* *
19019579 CATAAAAAATATATAAAAGTATGTATATATATATTTAT-AAA
1 AATAAAAAATATATAAAAGTATGTATATA-A-AATTATGAAA
19019620 AATTAAAAAAT
1 AA-TAAAAAAT
19019631 GTGTATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 26 0.59
41 5 0.11
42 13 0.30
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (40 bp):
AATAAAAAATATATAAAAGTATGTATATAAAATTATGAAA
Found at i:19019658 original size:30 final size:31
Alignment explanation
Indices: 19019624--19019692 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
19019614 TATAAAAATT
* * *
19019624 AAAAAATGTGTATGTAT-ATGTATATATTAC
1 AAAAAATATGTATGTATAATGCATATATAAC
*
19019654 AAAAAGTATGTATGTATACATGCATATATAAC
1 AAAAAATATGTATGTATA-ATGCATATATAAC
19019686 AAAAAAT
1 AAAAAAT
19019693 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 15 0.47
32 17 0.53
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (31 bp):
AAAAAATATGTATGTATAATGCATATATAAC
Found at i:19020253 original size:21 final size:21
Alignment explanation
Indices: 19020220--19020270 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
19020210 ACATCTTCTG
19020220 AGATTGC--ATATCATATCTA
1 AGATTGCATATATCATATCTA
19020239 AGATTGCATATATCATATCTA
1 AGATTGCATATATCATATCTA
19020260 AGATTGCATAT
1 AGATTGCATAT
19020271 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.23
21 23 0.77
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
AGATTGCATATATCATATCTA
Found at i:19020861 original size:44 final size:44
Alignment explanation
Indices: 19020812--19020922 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 44
19020802 TTCTGATCCA
* * * *
19020812 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
*
19020856 TTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
* * *
19020900 CTCTATTGCAACCTCGGGGAGAT
1 CTCCACTGCAACCTCAGGGAGAT
19020923 GAGACTGGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
Found at i:19021730 original size:45 final size:45
Alignment explanation
Indices: 19021025--19021719 Score: 933
Period size: 45 Copynumber: 15.4 Consensus size: 45
19021015 GTTACTTCTG
* * * * *
19021025 TCTTCGATCTACTTTGCTGCCAATACAGGAAAATAAGATCTGTTG
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* ** * ** * *
19021070 TTTTCGATCTACTTCGCTATCAATACAAGAAGATGAGATCCGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
19021115 TCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
19021160 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAAATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
19021205 CCTTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
19021250 CCTTCGATCTACTTCGCTGCTAATACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
19021295 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
19021340 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACCAA-ATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGA-CAAGATCTGCTA
* * *
19021385 TCTTCGATCTACTTCGTTGCCAGTACAGGAAGACGAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
19021430 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
19021475 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACGAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
19021520 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* ** *
19021565 TCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
19021610 TCTTCAATCTACTTCGCTACCAATATAGGAAGATAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * * * *
19021655 TCTTTGATCTACTTCGCTACCTATATAGGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
19021700 TCTTCGATCTACTTCGCTGC
1 TCTTCGATCTACTTCGCTGC
19021720 TAGTATAGGA
Statistics
Matches: 577, Mismatches: 71, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
44 2 0.00
45 572 0.99
46 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
Found at i:19022424 original size:16 final size:16
Alignment explanation
Indices: 19022385--19022436 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
19022375 TAAAGAAATA
19022385 TAAAGATTTATAT-TTT
1 TAAA-ATTTATATATTT
*
19022401 TATTAATTTATATATTT
1 TA-AAATTTATATATTT
19022418 TAAAATTT-TATACTTT
1 TAAAATTTATATA-TTT
19022434 TAA
1 TAA
19022437 TTTCAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 4 0.13
16 21 0.68
17 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TAAAATTTATATATTT
Found at i:19029808 original size:30 final size:30
Alignment explanation
Indices: 19029774--19029838 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
19029764 ACGATTAGGG
* *
19029774 TAGTTTTGGTAATAAAGACGAAGTATAATT
1 TAGTTTTGGTAATAAAGACAAAGTAAAATT
*
19029804 TAGTTTTGGTAATGAAGACAAAGTAAAATT
1 TAGTTTTGGTAATAAAGACAAAGTAAAATT
19029834 TAGTT
1 TAGTT
19029839 ATCACTTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (30 bp):
TAGTTTTGGTAATAAAGACAAAGTAAAATT
Found at i:19045206 original size:5 final size:5
Alignment explanation
Indices: 19045196--19045224 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19045186 TAGTAACAAT
19045196 AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAAT
19045225 CGTATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:19046131 original size:18 final size:18
Alignment explanation
Indices: 19046108--19046144 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19046098 ATTAAGATCT
19046108 CTCAAAATAGAATAAGAA
1 CTCAAAATAGAATAAGAA
19046126 CTCAAAATAGAATAAGAA
1 CTCAAAATAGAATAAGAA
19046144 C
1 C
19046145 AAATGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (18 bp):
CTCAAAATAGAATAAGAA
Found at i:19053994 original size:13 final size:11
Alignment explanation
Indices: 19053958--19053988 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19053948 AGGCCCGTAT
19053958 TAATTTTTATA
1 TAATTTTTATA
*
19053969 TTATTTTTATA
1 TAATTTTTATA
19053980 TAATTTTTA
1 TAATTTTTA
19053989 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:19054312 original size:18 final size:18
Alignment explanation
Indices: 19054283--19054332 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
19054273 AATCGTGTCG
*
19054283 TTCATTTTCAAAACATTA
1 TTCAATTTCAAAACATTA
* *
19054301 TT-AATTTACAAATCGTTA
1 TTCAATTT-CAAAACATTA
19054319 TTCAATTTCAAAAC
1 TTCAATTTCAAAAC
19054333 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (18 bp):
TTCAATTTCAAAACATTA
Found at i:19060047 original size:30 final size:32
Alignment explanation
Indices: 19059981--19060051 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
19059971 AAATGTTAAC
19059981 GAGTGACTGATTTGTCACTTTTTGATAATGTT
1 GAGTGACTGATTTGTCACTTTTTGATAATGTT
* *
19060013 -AGTGACTGATTTGTTATTTTTTGA-AA-GTT
1 GAGTGACTGATTTGTCACTTTTTGATAATGTT
19060042 GAGTGACTGA
1 GAGTGACTGA
19060052 ATTGAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 3 0.08
30 11 0.31
31 22 0.61
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (32 bp):
GAGTGACTGATTTGTCACTTTTTGATAATGTT
Found at i:19060058 original size:20 final size:20
Alignment explanation
Indices: 19060042--19060090 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
19060032 TTTGAAAGTT
19060042 GAGTGACTGAATTGAAATCA
1 GAGTGACTGAATTGAAATCA
19060062 GAGTGACTGAATTGAAATCA
1 GAGTGACTGAATTGAAATCA
19060082 GAGTGACTG
1 GAGTGACTG
19060091 TTTTGTCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (20 bp):
GAGTGACTGAATTGAAATCA
Found at i:19060457 original size:37 final size:38
Alignment explanation
Indices: 19060400--19060490 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 38
19060390 ATTTCTATAT
19060400 ATTTTATGTTTCTTTA-TAAAATTT-TACAATTTT-TTGA
1 ATTTTATGTTT-TTTATTAAAATTTATA-AATTTTATTGA
* *
19060437 TTTTTATGATTTTTATTAAAATTTAATAAATTTTATTGA
1 ATTTTATGTTTTTTATTAAAATTT-ATAAATTTTATTGA
19060476 ATTTTAT-TTTTTTAT
1 ATTTTATGTTTTTTAT
19060491 CATTTTTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.09
37 17 0.37
38 13 0.28
39 12 0.26
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (38 bp):
ATTTTATGTTTTTTATTAAAATTTATAAATTTTATTGA
Found at i:19072419 original size:50 final size:51
Alignment explanation
Indices: 19072344--19072443 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 51
19072334 GCACTTTTCG
*
19072344 TCGAAAAATATCCCTTTTTGCCCCTAAATTTTGA-TTTTTCGGTTTAAAAC
1 TCGAAAAAGATCCCTTTTTGCCCCTAAATTTTGATTTTTTCGGTTTAAAAC
*
19072394 TCGAAAAAGATCCCTTTTTGCCCCTAAATTTTGATTTTTTTGGTTTAAAA
1 TCGAAAAAGATCCCTTTTTGCCCCTAAATTTTGATTTTTTCGGTTTAAAA
19072444 TTAAATTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 33 0.70
51 14 0.30
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (51 bp):
TCGAAAAAGATCCCTTTTTGCCCCTAAATTTTGATTTTTTCGGTTTAAAAC
Found at i:19083085 original size:57 final size:56
Alignment explanation
Indices: 19083019--19083128 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
19083009 ACATCAATTT
* * *
19083019 TTTTTTAAATCTAGTATTGGGGTGCCGGCCATCAGTGT-CTCAGCACCTCAAAATATA
1 TTTTTTAAATATAGTACTGAGGTGCCGGCCATCAGTGTCCT-AGCACC-CAAAATATA
* * *
19083076 TTTTTTAAATATGGTACTGATGTGCCGGCCATCATTGTCCTAGCACCCAAAAT
1 TTTTTTAAATATAGTACTGAGGTGCCGGCCATCAGTGTCCTAGCACCCAAAAT
19083129 TTTTTACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 6 0.13
57 38 0.83
58 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (56 bp):
TTTTTTAAATATAGTACTGAGGTGCCGGCCATCAGTGTCCTAGCACCCAAAATATA
Found at i:19083239 original size:54 final size:53
Alignment explanation
Indices: 19083013--19083239 Score: 140
Period size: 57 Copynumber: 4.2 Consensus size: 53
19083003 GTTCTAACAT
* * *
19083013 CAATTTTTTTTTAAATCT-AGTATTGGGGTGCCGGCCATCAGTGTCTCAGCACC
1 CAATTTTTTTTTAAATTTGA-TACTGAGGTGCCGGCCATCAGTGTCTCAGCACC
* * * * *
19083066 TCAAAATATATTTTTTAAATATGGTACTGATGTGCCGGCCATCATTGTC-CTAGCACC
1 -C--AAT-TTTTTTTTAAATTTGATACTGAGGTGCCGGCCATCAGTGTCTC-AGCACC
** * ** *** * *
19083123 CAA-AATTTTTTACAATTTTGGTACAAAGGTGCCTATCATCAATGT-TCCAGTACCC
1 CAATTTTTTTTTA-AA-TTTGATACTGAGGTGCCGGCCATCAGTGTCT-CAGCA-CC
* * *
19083178 CAA-TTTTTTTAAAATTTGATACTGGGGTGCCGGCCATCAGTGTCTTAGCACC
1 CAATTTTTTTTTAAATTTGATACTGAGGTGCCGGCCATCAGTGTCTCAGCACC
19083230 CAATTTTTTT
1 CAATTTTTTT
19083240 AATTTTAAAA
Statistics
Matches: 131, Mismatches: 30, Indels: 25
0.70 0.16 0.13
Matches are distributed among these distances:
52 13 0.10
53 32 0.24
54 30 0.23
55 12 0.09
56 5 0.04
57 39 0.30
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (53 bp):
CAATTTTTTTTTAAATTTGATACTGAGGTGCCGGCCATCAGTGTCTCAGCACC
Found at i:19084415 original size:17 final size:18
Alignment explanation
Indices: 19084378--19084423 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
19084368 CCGTTATGTC
19084378 CACGACCGCGA-C--AAA
1 CACGACCGCGACCGAAAA
*
19084393 CGCGA-CGCGACCGAAAA
1 CACGACCGCGACCGAAAA
19084410 CACGACCGCGACCG
1 CACGACCGCGACCG
19084424 CAATTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
17 7 0.28
18 8 0.32
ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00
Consensus pattern (18 bp):
CACGACCGCGACCGAAAA
Found at i:19085946 original size:40 final size:40
Alignment explanation
Indices: 19085910--19085988 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
19085900 CACTAAAGAT
*
19085910 TGAGCATTAGTGGCGTTTTT-AAAAAAATGCCGCTAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
* *
19085949 TGAGCATTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
19085989 CCTTAGCCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (40 bp):
TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
Found at i:19085964 original size:39 final size:39
Alignment explanation
Indices: 19085835--19085988 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 39
19085825 AGTGGCACTT
** * *
19085835 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATTAAGCA
1 TTAGCGGCGTTTTTA-AAAAAACGCCGCTAAAAA-TGAGCA
* ** * * *
19085876 TTAGCGGCGCTTTCT-GGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCG-TTTTTAAAAAAACGCCGCTAAA-AATGAGCA
* *
19085916 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
*
19085955 TTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTT-AAAAAAACGCCGCTAAAAA
19085989 CCTTAGCCCA
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 24 0.27
40 52 0.58
41 10 0.11
42 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
Found at i:19086089 original size:41 final size:41
Alignment explanation
Indices: 19086024--19086139 Score: 180
Period size: 41 Copynumber: 2.8 Consensus size: 41
19086014 AACATTTCGT
**
19086024 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCCT-GG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATG-CTAGG
* *
19086065 GTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGGTAGG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAGG
19086106 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
19086140 AAACATTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 68 0.99
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.28
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAGG
Found at i:19086382 original size:22 final size:22
Alignment explanation
Indices: 19086357--19086431 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
19086347 GAGTTACTGT
19086357 TTTAAGGTTTATGGAGTATGGA
1 TTTAAGGTTTATGGAGTATGGA
* * *
19086379 TTTAAGGATTATGGATTAGGGA
1 TTTAAGGTTTATGGAGTATGGA
* *
19086401 -TTATGGTTTAAGG-GT-TGAGA
1 TTTAAGGTTTATGGAGTATG-GA
19086421 TTTAAGGTTTA
1 TTTAAGGTTTA
19086432 GGGGTTAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 19 0.45
22 19 0.45
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (22 bp):
TTTAAGGTTTATGGAGTATGGA
Found at i:19086403 original size:14 final size:15
Alignment explanation
Indices: 19086373--19086413 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
19086363 GTTTATGGAG
19086373 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
19086388 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
19086402 TATGG-TTTAAGG
1 TATGGATTTAAGG
19086414 GTTGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:19086452 original size:22 final size:22
Alignment explanation
Indices: 19086426--19086488 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
19086416 TGAGATTTAA
*
19086426 GGTTTAGGGGTT-AGTGGTTAGG
1 GGTTTAGGGGTTAAG-AGTTAGG
19086448 GGTTTAGGGGTTAAGAGTTAGG
1 GGTTTAGGGGTTAAGAGTTAGG
* * *
19086470 GATTTAGGGTTTATGAGTT
1 GGTTTAGGGGTTAAGAGTT
19086489 CATGGGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGTTAGG
Found at i:19086540 original size:12 final size:12
Alignment explanation
Indices: 19086519--19086561 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
19086509 TGGGTTTAGA
19086519 TTAA-TTATTTT
1 TTAATTTATTTT
19086530 TTAATTTATTTT
1 TTAATTTATTTT
* *
19086542 TAAATAT-TTTT
1 TTAATTTATTTT
19086553 TTAATTTAT
1 TTAATTTAT
19086562 ATATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:19086556 original size:23 final size:24
Alignment explanation
Indices: 19086518--19086571 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
19086508 TTGGGTTTAG
*
19086518 ATTAATTA-TTTTTTAATTTAT-T
1 ATTAAATATTTTTTTAATTTATAT
*
19086540 TTTAAATATTTTTTTAATTTATAT
1 ATTAAATATTTTTTTAATTTATAT
19086564 ATTAAATA
1 ATTAAATA
19086572 ATTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 13 0.48
24 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATATTTTTTTAATTTATAT
Found at i:19086793 original size:21 final size:21
Alignment explanation
Indices: 19086769--19086809 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19086759 GATTTAAGGT
19086769 TTAGGGATTAAGAGTTAGGGG
1 TTAGGGATTAAGAGTTAGGGG
*
19086790 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGATTAAGAGTTAGGG
19086810 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.44, T:0.29
Consensus pattern (21 bp):
TTAGGGATTAAGAGTTAGGGG
Found at i:19086818 original size:21 final size:20
Alignment explanation
Indices: 19086766--19086819 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
19086756 TAGGATTTAA
19086766 GGTTTAGGGATTAAGAGTTAG
1 GGTTTAGGG-TTAAGAGTTAG
*
19086787 GGGTTAGGGGTTAAGAGTTAG
1 GGTTTA-GGGTTAAGAGTTAG
19086808 GGATTTAGGGTT
1 GG-TTTAGGGTT
19086820 TCAAGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAGTTAG
Found at i:19091420 original size:43 final size:43
Alignment explanation
Indices: 19091369--19091614 Score: 280
Period size: 43 Copynumber: 5.7 Consensus size: 43
19091359 ATAGCACTTT
** * * *
19091369 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCTGATCTA
* * ** *
19091412 TAGTGGCGTTTAT-AAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAA-CGCCGCTAAAGGTCCTGATCTA
* **
19091455 TAGCGGCGTTTGT-GTAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCTGATCTA
* ** * *
19091497 TAGCAGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCTGATCTA
* * *
19091540 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCTGATCTA
19091583 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAG
1 TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAG
19091615 TTAGCGACGC
Statistics
Matches: 178, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 39 0.22
43 139 0.78
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCCTGATCTA
Found at i:19091602 original size:86 final size:85
Alignment explanation
Indices: 19091369--19091602 Score: 272
Period size: 85 Copynumber: 2.7 Consensus size: 85
19091359 ATAGCACTTT
* * * * * ** * *** *
19091369 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAAGTCATGATCTATAGTGGCGTTTATAAAAAAAGC
1 TAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGTGGGAAAAGT
*
19091434 GCCGCTAAAGGTCTTGATCTA
65 GTCGCTAAAGGTCTTGATCTA
* *
19091455 TAGCGGCGTTTGTGTAAAAGTGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGTGGGAAAAGTG
1 TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGTGGGAAAAGTG
19091520 TCGCTAAAGGT-TCTGATCTA
66 TCGCTAAAGGTCT-TGATCTA
* * *
19091540 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGTGGGAAAA
19091603 ACGCCGCTAA
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
84 1 0.01
85 68 0.54
86 58 0.46
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (85 bp):
TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGTGGGAAAAGTG
TCGCTAAAGGTCTTGATCTA
Found at i:19091714 original size:22 final size:22
Alignment explanation
Indices: 19091686--19091728 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19091676 CAGCGGCGCT
*
19091686 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
19091708 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
19091729 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:19096070 original size:14 final size:14
Alignment explanation
Indices: 19096028--19096071 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
19096018 CATAGAGAGG
19096028 ATTGAGGAG-GAAT
1 ATTGAGGAGAGAAT
*
19096041 ATT-TGGAGAG-AT
1 ATTGAGGAGAGAAT
19096053 -TTGAGGAGAGAAT
1 ATTGAGGAGAGAAT
19096066 ATTGAG
1 ATTGAG
19096072 ATTTGGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
11 2 0.08
12 12 0.48
13 6 0.24
14 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (14 bp):
ATTGAGGAGAGAAT
Found at i:19096790 original size:27 final size:27
Alignment explanation
Indices: 19096751--19096937 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
19096741 ACCTGCACCA
* * *
19096751 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCTCATAGGGTAGAATGACCG
19096778 AAATACCCTCATAGGGTAGAATGACCG
1 AAATACCCTCATAGGGTAGAATGACCG
* * *
19096805 AAATACCCCCATAGGGTAGAATAACCA
1 AAATACCCTCATAGGGTAGAATGACCG
* * **
19096832 AAATACCCTCATAAGGTAAAATGGTCG
1 AAATACCCTCATAGGGTAGAATGACCG
19096859 AAATACCCTCATAGGGTAGAATGACCG
1 AAATACCCTCATAGGGTAGAATGACCG
* * * * *
19096886 GAATACCCTCATAAGGTAAAATAACCC
1 AAATACCCTCATAGGGTAGAATGACCG
*
19096913 AAATACCCCCATAGGGTAGAATGAC
1 AAATACCCTCATAGGGTAGAATGAC
19096938 ATAGGGTAAA
Statistics
Matches: 133, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATACCCTCATAGGGTAGAATGACCG
Found at i:19096814 original size:54 final size:54
Alignment explanation
Indices: 19096751--19096937 Score: 266
Period size: 54 Copynumber: 3.5 Consensus size: 54
19096741 ACCTGCACCA
* * * *
19096751 AAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACCG
* * **
19096805 AAATACCCCCATAGGGTAGAATAACCAAAATACCCTCATAAGGTAAAATGGTCG
1 AAATACCCCCATAGGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACCG
* * * *
19096859 AAATACCCTCATAGGGTAGAATGACCGGAATACCCTCATAAGGTAAAATAACCC
1 AAATACCCCCATAGGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACCG
19096913 AAATACCCCCATAGGGTAGAATGAC
1 AAATACCCCCATAGGGTAGAATGAC
19096938 ATAGGGTAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (54 bp):
AAATACCCCCATAGGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACCG
Found at i:19096882 original size:81 final size:82
Alignment explanation
Indices: 19096747--19096935 Score: 283
Period size: 81 Copynumber: 2.3 Consensus size: 82
19096737 CGATACCTGC
19096747 ACCAAAATACCCCCATAGGGTAAAAT-GACTGAAATACCCTCATAGGGTAGAATGACCGAAATAC
1 ACCAAAATACCCCCATAGGGTAAAATGGACTGAAATACCCTCATAGGGTAGAATGACCGAAATAC
* *
19096811 CCCCATAGGGTAGAATA
66 CCCCATAAGGTAAAATA
* * * *
19096828 ACCAAAATACCCTCATAAGGTAAAATGGTC-GAAATACCCTCATAGGGTAGAATGACCGGAATAC
1 ACCAAAATACCCCCATAGGGTAAAATGGACTGAAATACCCTCATAGGGTAGAATGACCGAAATAC
*
19096892 CCTCATAAGGTAAAATA
66 CCCCATAAGGTAAAATA
* *
19096909 ACCCAAATACCCCCATAGGGTAGAATG
1 ACCAAAATACCCCCATAGGGTAAAATG
19096936 ACATAGGGTA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 94 0.98
82 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (82 bp):
ACCAAAATACCCCCATAGGGTAAAATGGACTGAAATACCCTCATAGGGTAGAATGACCGAAATAC
CCCCATAAGGTAAAATA
Found at i:19096951 original size:14 final size:15
Alignment explanation
Indices: 19096922--19096951 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19096912 CAAATACCCC
19096922 CATAGGGTAGAATGA
1 CATAGGGTAGAATGA
19096937 CATAGGGTA-AATGA
1 CATAGGGTAGAATGA
19096951 C
1 C
19096952 CAAAATACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (15 bp):
CATAGGGTAGAATGA
Found at i:19096959 original size:41 final size:42
Alignment explanation
Indices: 19096895--19096978 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
19096885 GGAATACCCT
* * *
19096895 CATAAGGTAAAATAACCCAAATACCCCCATAGGGTAGAATGA
1 CATAAGGTAAAATAACCAAAATACCCCCATAAGGTAAAATGA
* *
19096937 CATAGGGT-AAATGACCAAAATACCCCCATAAGGTAAAATGA
1 CATAAGGTAAAATAACCAAAATACCCCCATAAGGTAAAATGA
19096978 C
1 C
19096979 CGAAATACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (42 bp):
CATAAGGTAAAATAACCAAAATACCCCCATAAGGTAAAATGA
Found at i:19096959 original size:68 final size:69
Alignment explanation
Indices: 19096868--19097005 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 69
19096858 GAAATACCCT
** * * *
19096868 CATAGGGTAGAATGACCGGAATACCCTCATAAGGTAAAATAACCCAAATACCCCCATAGGGTAGA
1 CATAGGGTAGAATGACCAAAATACCCCCATAAGGTAAAATAACCCAAATACCCCCATAAGGTAAA
19096933 ATGA
66 ATGA
* *
19096937 CATAGGGTA-AATGACCAAAATACCCCCATAAGGTAAAATGACCGAAATACCCCCATAAGGTAAA
1 CATAGGGTAGAATGACCAAAATACCCCCATAAGGTAAAATAACCCAAATACCCCCATAAGGTAAA
19097001 ATGA
66 ATGA
19097005 C
1 C
19097006 TGTTATACCC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 53 0.85
69 9 0.15
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (69 bp):
CATAGGGTAGAATGACCAAAATACCCCCATAAGGTAAAATAACCCAAATACCCCCATAAGGTAAA
ATGA
Found at i:19097016 original size:27 final size:27
Alignment explanation
Indices: 19096937--19097005 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
19096927 GGTAGAATGA
* *
19096937 CATAGGGT-AAATGACCAAAATACCCC
1 CATAAGGTAAAATGACCGAAATACCCC
19096963 CATAAGGTAAAATGACCGAAATACCCC
1 CATAAGGTAAAATGACCGAAATACCCC
19096990 CATAAGGTAAAATGAC
1 CATAAGGTAAAATGAC
19097006 TGTTATACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 7 0.17
27 33 0.82
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (27 bp):
CATAAGGTAAAATGACCGAAATACCCC
Found at i:19098471 original size:56 final size:56
Alignment explanation
Indices: 19098409--19098516 Score: 216
Period size: 56 Copynumber: 1.9 Consensus size: 56
19098399 ACTATATTCC
19098409 ACTTACACATGCTATCATATTTCATTTGTTTCACAAATATCCCAATTCTCATTTCA
1 ACTTACACATGCTATCATATTTCATTTGTTTCACAAATATCCCAATTCTCATTTCA
19098465 ACTTACACATGCTATCATATTTCATTTGTTTCACAAATATCCCAATTCTCAT
1 ACTTACACATGCTATCATATTTCATTTGTTTCACAAATATCCCAATTCTCAT
19098517 ACTTGTTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.41
Consensus pattern (56 bp):
ACTTACACATGCTATCATATTTCATTTGTTTCACAAATATCCCAATTCTCATTTCA
Found at i:19099622 original size:14 final size:14
Alignment explanation
Indices: 19099603--19099631 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19099593 TCAATTTAAT
19099603 CCTTAAACCCTAAA
1 CCTTAAACCCTAAA
19099617 CCTTAAACCCTAAA
1 CCTTAAACCCTAAA
19099631 C
1 C
19099632 TCGAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:19103276 original size:40 final size:40
Alignment explanation
Indices: 19103228--19103362 Score: 207
Period size: 40 Copynumber: 3.4 Consensus size: 40
19103218 TGTTATACTC
*
19103228 TCTGTCTGGTGTGTTTCGATTGGATTAGCTCTTATGAGCT
1 TCTGTCTGGTGTGTTTCGATTGGATTACCTCTTATGAGCT
* * * *
19103268 TCTATCTGGCGTGTTTCGGTTGGATTACCTGTTATGAGCT
1 TCTGTCTGGTGTGTTTCGATTGGATTACCTCTTATGAGCT
* *
19103308 TCTGTCTAGTGTGTTTCAATTGGATTACCTCTTATGAGCT
1 TCTGTCTGGTGTGTTTCGATTGGATTACCTCTTATGAGCT
19103348 TCTGTCTGGTGTGTT
1 TCTGTCTGGTGTGTT
19103363 CGGTTGATCT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (40 bp):
TCTGTCTGGTGTGTTTCGATTGGATTACCTCTTATGAGCT
Found at i:19113441 original size:29 final size:28
Alignment explanation
Indices: 19113409--19113474 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
19113399 TCTATAGTCG
*
19113409 CATATATATTATATATAGTAAAACCCACA
1 CATATATATTATATATAGCAAAA-CCACA
* *
19113438 CATATATATTATGTATAGCAAAACCACG
1 CATATATATTATATATAGCAAAACCACA
19113466 CATATATAT
1 CATATATAT
19113475 GTACTATGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (28 bp):
CATATATATTATATATAGCAAAACCACA
Found at i:19114789 original size:27 final size:28
Alignment explanation
Indices: 19114734--19114787 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
19114724 CTATTTCTTC
*
19114734 AATTATTAATACCATTATTATTTTATTT
1 AATTATTAATAACATTATTATTTTATTT
*
19114762 AATTATTATTAAC-TTATTA-TTTATTT
1 AATTATTAATAACATTATTATTTTATTT
19114788 TATCCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 6 0.25
28 11 0.46
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (28 bp):
AATTATTAATAACATTATTATTTTATTT
Found at i:19127258 original size:16 final size:16
Alignment explanation
Indices: 19127237--19127268 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19127227 GTTTTGTTGC
*
19127237 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
19127253 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
19127269 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:19127466 original size:46 final size:43
Alignment explanation
Indices: 19127406--19127490 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
19127396 CATGGTGGAT
*
19127406 TCAGCACACAGCAACCACCCTTTGTAATCAATGATATCCGGTGGGA
1 TCAGCACACAGCAACCA-CC-TTATAATCAATGATA-CCGGTGGGA
* *
19127452 TCAGCACATAGCAACCACCTTATAATTAATGATACCGGT
1 TCAGCACACAGCAACCACCTTATAATCAATGATACCGGT
19127491 TCACATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 13 0.36
45 2 0.06
46 16 0.44
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
TCAGCACACAGCAACCACCTTATAATCAATGATACCGGTGGGA
Found at i:19127559 original size:51 final size:50
Alignment explanation
Indices: 19127496--19127682 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
19127486 CCGGTTCACA
* *
19127496 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT-ACTATTCGGTACGCG
* * * * *
19127547 TAATGGCCTGCACATAGTACTACACATGTGATCGA-AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATA-CTATTCGGTACGCG
*
19127598 TAGTAGCCTGCACATAGTACTACACATGCGACC-TA-TCATTCTGGTACGCG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACT-ATTC-GGTACGCG
* *
19127648 TAGTAGCCTACACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
19127683 CACTTTCACT
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 40 0.35
51 68 0.60
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACTATTCGGTACGCG
Found at i:19129351 original size:18 final size:18
Alignment explanation
Indices: 19129330--19129365 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19129320 CTCTCTAGAC
*
19129330 ATTTGGATTTTATTTTGG
1 ATTTGGATTTTAATTTGG
19129348 ATTTGGATTTTAATTTGG
1 ATTTGGATTTTAATTTGG
19129366 GATATCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
ATTTGGATTTTAATTTGG
Found at i:19131278 original size:3 final size:3
Alignment explanation
Indices: 19131270--19131316 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
19131260 ATCATCTAGT
19131270 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19131317 CAGCTTAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19134491 original size:22 final size:22
Alignment explanation
Indices: 19134466--19134508 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19134456 AACTTAATTC
*
19134466 ACATTTATTGATTGAATGTAAT
1 ACATTTATTAATTGAATGTAAT
*
19134488 ACATTTATTAATTTAATGTAA
1 ACATTTATTAATTGAATGTAA
19134509 AGGAGCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
ACATTTATTAATTGAATGTAAT
Found at i:19135198 original size:10 final size:10
Alignment explanation
Indices: 19135183--19135208 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19135173 GTAATGATTT
19135183 TCATCTGTCA
1 TCATCTGTCA
19135193 TCATCTGTCA
1 TCATCTGTCA
19135203 TCATCT
1 TCATCT
19135209 ACATGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.08, T:0.42
Consensus pattern (10 bp):
TCATCTGTCA
Found at i:19140184 original size:30 final size:30
Alignment explanation
Indices: 19140138--19140202 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
19140128 TACTTTACTA
19140138 TTTAA-TCCTTTCCCTCCAAAATTCCGAAT
1 TTTAAGTCCTTTCCCTCCAAAATTCCGAAT
*
19140167 TTTAAGTCCTCTT-CCTCCAAAATTCTGAAT
1 TTTAAGTCCT-TTCCCTCCAAAATTCCGAAT
19140197 TTTAAG
1 TTTAAG
19140203 GTTTACTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 5 0.15
30 26 0.79
31 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (30 bp):
TTTAAGTCCTTTCCCTCCAAAATTCCGAAT
Found at i:19148383 original size:274 final size:274
Alignment explanation
Indices: 19147893--19148447 Score: 867
Period size: 274 Copynumber: 2.0 Consensus size: 274
19147883 ATATCTCAAT
* * * *
19147893 CCCTCAAACCTCACACACTTATCGTAATCAGACGCTACTAGAGTCCATGCATACCTATTTAGTCG
1 CCCTCAAACCTCACACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
* * * *
19147958 CAAAAACTTGGCTTCATATTTGGCCACCGATCGGTCGCCCTGAACTAGGCTCATGAACTCGTATC
66 CAAAAACTCGACTTCATATTTGGCCACCGATCGATCGCCCTAAACTAGGCTCATGAACTCGTATC
* *
19148023 GGTGAGCTTCAACATAATTTGCCCTCACATACTAACCTTGGAATATGTTCTTGAAATAGTCCCAG
131 GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTGGAAGATGTTCTTGAAATAGTCCCAG
* * *
19148088 TTCACCTGTTCAGGCTGAACACTTTGCTCAACTGTCAACCACCATTGATAAGCTTCGTCCCGAAA
196 TTCACCTGTTCAAGCTGAACACCTTGCTCAACTGTCAACCACCACTGATAAGCTTCGTCCCGAAA
19148153 TAAGAAAACAACAC
261 TAAGAAAACAACAC
* * * *
19148167 CCCTCAAACTTTACACACTTTTCATAATTAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
1 CCCTCAAACCTCACACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
*
19148232 TAAAAACTCGACTTCATATTTGGCCACCGATCGATCGCCCTAAACTAGGCTCATGAACTCGTATC
66 CAAAAACTCGACTTCATATTTGGCCACCGATCGATCGCCCTAAACTAGGCTCATGAACTCGTATC
* * *
19148297 GGTGAGCCTCAACATAATTTGCCCTCACATACTTACCTTGGAAGGTGTTCTTGAAATAGTCTCAG
131 GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTGGAAGATGTTCTTGAAATAGTCCCAG
* *
19148362 TTCACCTGTTCAAGTTGAACACCTTGCTCAACTGTCAACCACCACTGATAAGCTTCGTCCCGGAA
196 TTCACCTGTTCAAGCTGAACACCTTGCTCAACTGTCAACCACCACTGATAAGCTTCGTCCCGAAA
* * * *
19148427 TAGGGACACAACAT
261 TAAGAAAACAACAC
19148441 CCCTCAA
1 CCCTCAA
19148448 TTTTTGAGTA
Statistics
Matches: 254, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
274 254 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (274 bp):
CCCTCAAACCTCACACACTTATCATAATCAGACGCTACTAGAGTCCATACATACCTACTCAGTCG
CAAAAACTCGACTTCATATTTGGCCACCGATCGATCGCCCTAAACTAGGCTCATGAACTCGTATC
GGTGAGCCTCAACATAATTTGCCCTCACATACTAACCTTGGAAGATGTTCTTGAAATAGTCCCAG
TTCACCTGTTCAAGCTGAACACCTTGCTCAACTGTCAACCACCACTGATAAGCTTCGTCCCGAAA
TAAGAAAACAACAC
Found at i:19151676 original size:22 final size:22
Alignment explanation
Indices: 19151651--19151693 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19151641 AACTTAATTC
*
19151651 ACATTTATTGATTGAATGTAAT
1 ACATTTATTAATTGAATGTAAT
19151673 ACATTTATTAATTGAATGTAA
1 ACATTTATTAATTGAATGTAA
19151694 AGAAGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ACATTTATTAATTGAATGTAAT
Found at i:19155311 original size:3 final size:3
Alignment explanation
Indices: 19155303--19155343 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
19155293 ATCTAGTTTT
*
19155303 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19155344 CAATTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19158450 original size:28 final size:30
Alignment explanation
Indices: 19158408--19158464 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
19158398 ACCATAGTGC
19158408 CACTGTCAGTTGCATCAAAGTGCCACTTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTTT
* *
19158438 CACTGT-A-TTGCATTAAAGTTCCACTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTT
19158465 CCATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (30 bp):
CACTGTCAGTTGCATCAAAGTGCCACTTTT
Found at i:19175233 original size:39 final size:39
Alignment explanation
Indices: 19175185--19175327 Score: 223
Period size: 39 Copynumber: 3.7 Consensus size: 39
19175175 ATAAACATGT
* * *
19175185 TATGTGTATTGTGATATATACTTGAATGTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATGTTATGTGATTA
*
19175224 TATGAGTATTGTGATATATGCTTAAATTTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATGTTATGTGATTA
*
19175263 TATGAGTATTGTGATATTTGCTTAAATGTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATGTTATGTGATTA
* *
19175302 TATGTGTAATGTGATATATGCTTAAA
1 TATGAGTATTGTGATATATGCTTAAA
19175328 AGTGAATATG
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.48
Consensus pattern (39 bp):
TATGAGTATTGTGATATATGCTTAAATGTTATGTGATTA
Found at i:19177827 original size:51 final size:50
Alignment explanation
Indices: 19177676--19177864 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
19177666 AATGCTATTC
* * * * *
19177676 GGTACATATAGTAGCCTACACTTAGTACTACACACGTGACCAATACCATCC
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAA-ACTATCT
* *
19177727 GGTACACGTAGTAGCCTGCACATAGTACTACACACT-TGACCAAAGCTATCT
1 GGTACACATAGTAGCCTACACATAGTACTACACA-TGTGACCAAA-CTATCT
* *
19177778 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAACTATCT
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCA-AACTATCT
** * *
19177829 TATACTCATAGGAGCCTACACATAGTACTACACATG
1 GGTACACATAGTAGCCTACACATAGTACTACACATG
19177865 AGTTCTCATG
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
50 2 0.02
51 115 0.97
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAAACTATCT
Found at i:19177845 original size:102 final size:102
Alignment explanation
Indices: 19177676--19177862 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
19177666 AATGCTATTC
* * * *
19177676 GGTACATATAGTAGCCTACACTTAGTACTACACACGTGACCAATACCATCCGGTACACGTAGTAG
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCAATACCATCCGATACACATAGGAG
*
19177741 CCTGCACATAGTACTACACACTTGACCAAAGCTATCT
66 CCTACACATAGTACTACACACTTGACCAAAGCTATCT
* * * ** *
19177778 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-ATAACTATCTTATACTCATAGGA
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCAAT-ACCATCCGATACACATAGGA
19177842 GCCTACACATAGTACTACACA
65 GCCTACACATAGTACTACACA
19177863 TGAGTTCTCA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 2 0.03
102 71 0.97
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (102 bp):
GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCAATACCATCCGATACACATAGGAG
CCTACACATAGTACTACACACTTGACCAAAGCTATCT
Found at i:19186287 original size:21 final size:21
Alignment explanation
Indices: 19186241--19186288 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
19186231 ACCAATTTAA
*
19186241 AGTTTTATGGTAAGTGTTCAT
1 AGTTTTATGGTAAGTATTCAT
* *
19186262 CGTTTTATGGGTAAGTATT-TT
1 AGTTTTAT-GGTAAGTATTCAT
19186283 AGTTTT
1 AGTTTT
19186289 GAGATTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.52
Consensus pattern (21 bp):
AGTTTTATGGTAAGTATTCAT
Found at i:19187113 original size:17 final size:17
Alignment explanation
Indices: 19187091--19187132 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
19187081 ATTTCAGCTA
19187091 TGTGGGCCACACGGGCG
1 TGTGGGCCACACGGGCG
19187108 TGTGGGCCACACGGGCG
1 TGTGGGCCACACGGGCG
19187125 TGTGGGCC
1 TGTGGGCC
19187133 TACATAGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.10, C:0.29, G:0.48, T:0.14
Consensus pattern (17 bp):
TGTGGGCCACACGGGCG
Found at i:19194105 original size:18 final size:18
Alignment explanation
Indices: 19194071--19194119 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
19194061 GCAATAAAAA
19194071 AATGTTTGGAAATTGAAT
1 AATGTTTGGAAATTGAAT
*
19194089 AATGATTTGTAAA-TGAAT
1 AATG-TTTGGAAATTGAAT
19194107 AATGTTTTGGAAA
1 AATG-TTTGGAAA
19194120 CGAACGACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (18 bp):
AATGTTTGGAAATTGAAT
Found at i:19196139 original size:287 final size:286
Alignment explanation
Indices: 19195613--19196186 Score: 1015
Period size: 287 Copynumber: 2.0 Consensus size: 286
19195603 TTAGGCTCCA
* *
19195613 TTTGGTTAGCCTTTTAAAGCCAGTGAGGTGTAGTTGGGGGAAAAAGTGGTGCCAATCTCACTGCT
1 TTTGGTTAGCCTTTTAAAGCCAGTGAGGTGCAGTTGGGGGAAAAAATGGTGCCAATCTCACTGCT
* * * *
19195678 ATGTTGTTTGGTTTCGCAAGTTAGTGCAGTGAGATTGTATCTCCACCACACTGCTCAGTTGAAAA
66 ATGCTGTTTGGTTTCGCAAGTCAGTGCAGTGAGATTGCATCTCCACCACACTGCTCAGCTGAAAA
*
19195743 TTAGCTGGTGATTTCAGCAGCAATGGAGGTGCAGTGAGCTATTGGTACTTTAACTCTCCAAAAAT
131 TCAGCTGGTGATTTCAGCAGCAATGGAGGTGCAGTGAGCTATTGGTACTTTAACTCTCCAAAAAT
*
19195808 ACCCTTACTTTAACTCTCCACATCTTTCCTCCTCCTATCATGCTTCTCCTTCTTCAATTTGTGCA
196 ACCCTTACTTTAACTCTCCACATCTTTCCTCCTCCTACCATGCTTCTCCTTCTTCAATTTGTGCA
19195873 ACCAGTTCACTTCATAAAGCTCCAGG
261 ACCAGTTCACTTCATAAAGCTCCAGG
* *
19195899 TTTGGTTTGGCTTTTAAAGCCAGTGAGGTGCAGTTGGGGGGAAAAAATGGTGCCAATCTCACTGC
1 TTTGGTTAGCCTTTTAAAGCCAGTGAGGTGCAGTT-GGGGGAAAAAATGGTGCCAATCTCACTGC
19195964 TATGCTGTTTGG-TTCAGCAAGTCAGTGCAGTGAGATTGCATCTCCACCACACTGCTCAGCTGAA
65 TATGCTGTTTGGTTTC-GCAAGTCAGTGCAGTGAGATTGCATCTCCACCACACTGCTCAGCTGAA
19196028 AATCAGCTGGTGATTTCAGCAGCAATGGAGGTGCAGTGAGCTATTGGTACTTTAACTCTCCAAAA
129 AATCAGCTGGTGATTTCAGCAGCAATGGAGGTGCAGTGAGCTATTGGTACTTTAACTCTCCAAAA
* *
19196093 ATACCCTTACTTTAACTCTCCATATCTTTCCTCCTTCTACCATGCTTCTCCTTCTTCAATTTGTG
194 ATACCCTTACTTTAACTCTCCACATCTTTCCTCCTCCTACCATGCTTCTCCTTCTTCAATTTGTG
19196158 CAACCAGTTCACTTCATAAAGCTCCAGG
259 CAACCAGTTCACTTCATAAAGCTCCAGG
19196186 T
1 T
19196187 AAGTCATTCA
Statistics
Matches: 274, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
286 35 0.13
287 239 0.87
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (286 bp):
TTTGGTTAGCCTTTTAAAGCCAGTGAGGTGCAGTTGGGGGAAAAAATGGTGCCAATCTCACTGCT
ATGCTGTTTGGTTTCGCAAGTCAGTGCAGTGAGATTGCATCTCCACCACACTGCTCAGCTGAAAA
TCAGCTGGTGATTTCAGCAGCAATGGAGGTGCAGTGAGCTATTGGTACTTTAACTCTCCAAAAAT
ACCCTTACTTTAACTCTCCACATCTTTCCTCCTCCTACCATGCTTCTCCTTCTTCAATTTGTGCA
ACCAGTTCACTTCATAAAGCTCCAGG
Found at i:19197285 original size:21 final size:22
Alignment explanation
Indices: 19197261--19197316 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
19197251 CACCACTATT
19197261 TCTAATCTCACTGCTACAGT-A
1 TCTAATCTCACTGCTACAGTAA
* *
19197282 TCTAATCTCACCGTTACAGTAA
1 TCTAATCTCACTGCTACAGTAA
19197304 T-TAATCTCACTGC
1 TCTAATCTCACTGC
19197317 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (22 bp):
TCTAATCTCACTGCTACAGTAA
Found at i:19204093 original size:16 final size:17
Alignment explanation
Indices: 19204072--19204110 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
19204062 ATTATTCGCC
19204072 TATTTATAACAT-AAAA
1 TATTTATAACATGAAAA
19204088 TATTTATAACATGAAAA
1 TATTTATAACATGAAAA
19204105 TATTTA
1 TATTTA
19204111 ACATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TATTTATAACATGAAAA
Found at i:19205407 original size:22 final size:23
Alignment explanation
Indices: 19205360--19205417 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
19205350 TGGGCCCCTA
* *
19205360 TTTATTTTATTTTATTTTGGCCC
1 TTTATTTTATTTTATTTTGACAC
19205383 TTTATTTT-TTTTAATTTT-ACAC
1 TTTATTTTATTTT-ATTTTGACAC
19205405 TTTAAATTTTATT
1 TTT--ATTTTATT
19205418 AAATATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 9 0.31
23 13 0.45
24 5 0.17
25 2 0.07
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (23 bp):
TTTATTTTATTTTATTTTGACAC
Found at i:19205653 original size:13 final size:14
Alignment explanation
Indices: 19205630--19205658 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19205620 GTTGGATTTC
19205630 TTGGTTATTTTATT
1 TTGGTTATTTTATT
19205644 TTGG-TATTTTATT
1 TTGGTTATTTTATT
19205657 TT
1 TT
19205659 TAATTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TTGGTTATTTTATT
Found at i:19209881 original size:2 final size:2
Alignment explanation
Indices: 19209874--19209909 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19209864 CTGAACATCA
19209874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19209910 TCCGTATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19217651 original size:25 final size:25
Alignment explanation
Indices: 19217623--19217706 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 25
19217613 GGCTCTCACA
19217623 AGCTTTCTGATAATTGGCTCCCATG
1 AGCTTTCTGATAATTGGCTCCCATG
* * * *
19217648 AGC-TTCTTGGTTAA-TGGCTCTCTTA
1 AGCTTTC-T-GATAATTGGCTCCCATG
* * * *
19217673 AGCTTCCTGATATTTGGCTCGCAAG
1 AGCTTTCTGATAATTGGCTCCCATG
19217698 AGCTTTCTG
1 AGCTTTCTG
19217707 TTATATGGCT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
24 6 0.14
25 31 0.72
26 6 0.14
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
AGCTTTCTGATAATTGGCTCCCATG
Found at i:19217715 original size:25 final size:25
Alignment explanation
Indices: 19217673--19217728 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
19217663 GGCTCTCTTA
* *
19217673 AGCTTCCTGATATTTGGCTCGCAAG
1 AGCTTCCTGATATATGGCTCGAAAG
* *
19217698 AGCTTTCTGTTATATGGCTCGAAAG
1 AGCTTCCTGATATATGGCTCGAAAG
19217723 AGCTTC
1 AGCTTC
19217729 TCGTTTACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
AGCTTCCTGATATATGGCTCGAAAG
Found at i:19227544 original size:29 final size:30
Alignment explanation
Indices: 19227491--19227570 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
19227481 ATATCAAAAT
* * *
19227491 TATATATCAATTATGATTTAATGTGTAATTG
1 TATATATAAATTTTGATTT-ATGTGTAATTC
19227522 TATATATAAATTTTGATTT-TGTGTAATTC
1 TATATATAAATTTTGATTTATGTGTAATTC
*
19227551 TATACAATAAATTTTGATTT
1 TATA-TATAAATTTTGATTT
19227571 GATCAAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.30
30 14 0.32
31 17 0.39
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (30 bp):
TATATATAAATTTTGATTTATGTGTAATTC
Found at i:19227571 original size:29 final size:29
Alignment explanation
Indices: 19227512--19227570 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
19227502 TATGATTTAA
* *
19227512 TGTGTAATTGTATATATAAATTTTGATTT
1 TGTGTAATTCTATAAATAAATTTTGATTT
19227541 TGTGTAATTCTATACAATAAATTTTGATTT
1 TGTGTAATTCTATA-AATAAATTTTGATTT
19227571 GATCAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (29 bp):
TGTGTAATTCTATAAATAAATTTTGATTT
Found at i:19227728 original size:31 final size:31
Alignment explanation
Indices: 19227693--19227753 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
19227683 CTCTTTAAAT
*
19227693 GTATATGATTAAATCAAAATTAAAATTTTAA
1 GTATAGGATTAAATCAAAATTAAAATTTTAA
* * * *
19227724 GTATAGGTTTGAATCACAATTAAAGTTTTA
1 GTATAGGATTAAATCAAAATTAAAATTTTA
19227754 CGTGCATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.39
Consensus pattern (31 bp):
GTATAGGATTAAATCAAAATTAAAATTTTAA
Found at i:19235634 original size:5 final size:5
Alignment explanation
Indices: 19235615--19235693 Score: 69
Period size: 5 Copynumber: 16.0 Consensus size: 5
19235605 TGTGACATTT
*
19235615 TTAAA TTATAA TTAAA TTAAA --ATA TTATAA TTAAA TTAAAA TATAAA
1 TTAAA TTA-AA TTAAA TTAAA TTAAA TTA-AA TTAAA TT-AAA T-TAAA
*
19235662 --AAA -CAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
19235694 AGCTTTCCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
3 5 0.08
4 3 0.05
5 38 0.60
6 16 0.25
7 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (5 bp):
TTAAA
Found at i:19235643 original size:19 final size:19
Alignment explanation
Indices: 19235619--19235694 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
19235609 ACATTTTTAA
19235619 ATTATAATTAAATTAAAAT
1 ATTATAATTAAATTAAAAT
19235638 ATTATAATTAAATTAAAAT
1 ATTATAATTAAATTAAAAT
* * ** *
19235657 ATAAAAAACAAATTAAATTAA
1 ATTATAATTAAATTAAA--AT
19235678 ATTA-AATTAAATTAAAA
1 ATTATAATTAAATTAAAA
19235695 GCTTTCCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
18 1 0.02
19 32 0.68
20 10 0.21
21 4 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTATAATTAAATTAAAAT
Found at i:19235652 original size:24 final size:22
Alignment explanation
Indices: 19235617--19235683 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 22
19235607 TGACATTTTT
**
19235617 AAATTATAATTAAATTAAAATATT
1 AAATTA-AATTAAATTAAAA-AAC
19235641 ATAATTAAATTAAAATATAAAAAAC
1 A-AATTAAATT-AAAT-TAAAAAAC
19235666 AAATTAAATTAAATTAAA
1 AAATTAAATTAAATTAAA
19235684 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 14 0.37
25 11 0.29
26 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATTAAATTAAATTAAAAAAC
Found at i:19236576 original size:20 final size:20
Alignment explanation
Indices: 19236540--19236577 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19236530 GCGCATAGGT
*
19236540 GGATGTCTTCGATGGGACGA
1 GGATGTCTTCGACGGGACGA
19236560 GGATGTCTAT-GACGGGAC
1 GGATGTCT-TCGACGGGAC
19236578 AGACCTCGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.16, G:0.39, T:0.24
Consensus pattern (20 bp):
GGATGTCTTCGACGGGACGA
Found at i:19246469 original size:82 final size:82
Alignment explanation
Indices: 19246355--19246541 Score: 286
Period size: 82 Copynumber: 2.3 Consensus size: 82
19246345 TGTTCGAGAT
* * * *
19246355 TTATGGCTGCTCCTTCCAACAATATCGTCCTCAAGGTTTGAACTTACGTCTTTGTGTCTATTTTA
1 TTATGGCTGCCCCTTCCAACAATATCATCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTTA
*
19246420 CGATCTATGTTT-GGGA
66 CGATCTATGTTTAGGAA
* *
19246436 TTCATGGTTGCCTCTTCCAACAATATCATCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTT
1 TT-ATGGCTGCCCCTTCCAACAATATCATCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTT
19246501 ACGATCTATGTTTAGGAA
65 ACGATCTATGTTTAGGAA
*
19246519 TTATGGCTGCCCCTCCCAACAAT
1 TTATGGCTGCCCCTTCCAACAAT
19246542 GTAGTCCTCA
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
81 2 0.02
82 87 0.93
83 5 0.05
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (82 bp):
TTATGGCTGCCCCTTCCAACAATATCATCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTTA
CGATCTATGTTTAGGAA
Found at i:19246550 original size:82 final size:81
Alignment explanation
Indices: 19246355--19246570 Score: 281
Period size: 82 Copynumber: 2.6 Consensus size: 81
19246345 TGTTCGAGAT
* * * *
19246355 TTATGGCTGCTCCTTCCAACAATATCGTCCTCAAGGTTTGAACTTACGTCTTTGTGTCTATTTTA
1 TTATGGCTGCCCCTTCCAACAATATAGTCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTTA
*
19246420 CGATCTATGTTTGGGA
66 CGATCTATGTTTGGAA
* *
19246436 TTCATGGTTGCCTCTTCCAACAATATCA-TCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTT
1 TT-ATGGCTGCCCCTTCCAACAATAT-AGTCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTT
19246500 TACGATCTATGTTTAGGAA
64 TACGATCTATGTTT-GGAA
* * ** * *
19246519 TTATGGCTGCCCCTCCCAACAATGTAGTCCTCAATATTTGAACCTACTTCTC
1 TTATGGCTGCCCCTTCCAACAATATAGTCCTCAAGGTTTGAACTTACGTCTC
19246571 CCTTTGAAAA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
81 3 0.03
82 108 0.93
83 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (81 bp):
TTATGGCTGCCCCTTCCAACAATATAGTCCTCAAGGTTTGAACTTACGTCTCTGTGTCCATTTTA
CGATCTATGTTTGGAA
Found at i:19247745 original size:31 final size:31
Alignment explanation
Indices: 19247652--19247747 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
19247642 GGCAAATTAC
*
19247652 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
19247683 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
19247715 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
19247746 AA
1 AA
19247748 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:19249324 original size:21 final size:19
Alignment explanation
Indices: 19249298--19249339 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
19249288 CAAGATAGAT
*
19249298 TTAATTGCCTGCATTTATATA
1 TTAATTGCATG-ATTTA-ATA
19249319 TTAATTGCATGATTTAATA
1 TTAATTGCATGATTTAATA
19249338 TT
1 TT
19249340 GAGGTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
TTAATTGCATGATTTAATA
Found at i:19249923 original size:30 final size:30
Alignment explanation
Indices: 19249877--19249952 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
19249867 TAGAAATTTC
* * *
19249877 AGCTTATGTGAACAACCTTGATATAATGTT
1 AGCTTGTGTGAGCAACCCTGATATAATGTT
* *
19249907 AGTTTGTTTGAGCAACCCTGATATAATGTT
1 AGCTTGTGTGAGCAACCCTGATATAATGTT
19249937 AGCTTGTGTGAGCAAC
1 AGCTTGTGTGAGCAAC
19249953 TTAATTCACC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (30 bp):
AGCTTGTGTGAGCAACCCTGATATAATGTT
Found at i:19258954 original size:5 final size:5
Alignment explanation
Indices: 19258944--19258974 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
19258934 GGAACTATAC
19258944 CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA C
1 CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA C
19258975 AAATGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAA
Found at i:19269261 original size:24 final size:20
Alignment explanation
Indices: 19269234--19269291 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
19269224 GCAAAGTATC
19269234 AAATAAATAAAAATATGAAAACA
1 AAATAAATAAAAA-AT-AAAA-A
* *
19269257 TAAATCAACAAAAAATAAAAA
1 -AAATAAATAAAAAATAAAAA
19269278 AAATAAATAAAAAA
1 AAATAAATAAAAAA
19269292 AGAGAGCGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 4 0.13
23 2 0.07
24 11 0.37
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (20 bp):
AAATAAATAAAAAATAAAAA
Found at i:19269664 original size:23 final size:22
Alignment explanation
Indices: 19269617--19269662 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
19269607 AAATATTAGT
19269617 TAAAAAATAAATATGTACATGTA
1 TAAAAAATAAATA-GTACATGTA
19269640 TAAAAAATAAATA-TACATGTA
1 TAAAAAATAAATAGTACATGTA
19269661 TA
1 TA
19269663 TATATAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.43
23 13 0.57
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAAAAATAAATAGTACATGTA
Found at i:19271233 original size:27 final size:27
Alignment explanation
Indices: 19271203--19271255 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
19271193 ATAGGCGGGA
*
19271203 GATCTAACGCTTTATGCGTGTTATATG
1 GATCCAACGCTTTATGCGTGTTATATG
* *
19271230 GATCCAATGCTTTATGTGTGTTATAT
1 GATCCAACGCTTTATGCGTGTTATAT
19271256 TTGATTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (27 bp):
GATCCAACGCTTTATGCGTGTTATATG
Found at i:19271275 original size:28 final size:27
Alignment explanation
Indices: 19271212--19271292 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 27
19271202 AGATCTAACG
* * * *
19271212 CTTTATGCGTGTTATATGGATCCAATG
1 CTTTATGTGTGTTATATTGATTCAATA
*
19271239 CTTTATGTGTGTTATATTTGATTCAGTA
1 CTTTATGTGTGTTATA-TTGATTCAATA
19271267 CTTTATGTGTGTTATACTTGATTCAA
1 CTTTATGTGTGTTATA-TTGATTCAA
19271293 CTAAATTCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 15 0.33
28 31 0.67
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (27 bp):
CTTTATGTGTGTTATATTGATTCAATA
Found at i:19275606 original size:27 final size:28
Alignment explanation
Indices: 19275551--19275615 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
19275541 ATAAAAAATA
*
19275551 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
19275579 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
19275606 ACCAAAATAT
1 ACCAAAATAT
19275616 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:19276204 original size:82 final size:82
Alignment explanation
Indices: 19276105--19276269 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
19276095 TTAATTAAAA
* *
19276105 TAGTCTAACATGTTTATGTTATAAGTCTATTACGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGCTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
19276170 TTTATGTTTCCATTATT
66 TTTATGTTTCCATTATT
19276187 TAGTCTAACATGCTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGCTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
*
19276252 TTTATGTTTCCGTTATT
66 TTTATGTTTCCATTATT
19276269 T
1 T
19276270 TTTCCTTTTG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (82 bp):
TAGTCTAACATGCTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
TTTATGTTTCCATTATT
Found at i:19276371 original size:19 final size:19
Alignment explanation
Indices: 19276349--19276414 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
19276339 TTTAATTTTT
19276349 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
19276368 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
19276386 TTACATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
19276405 TTAAATTAAA
1 TTAAATTAAA
19276415 CTATTTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:19276856 original size:27 final size:28
Alignment explanation
Indices: 19276826--19276890 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
19276816 TTTTTTGGGT
*
19276826 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
19276853 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
19276881 ATATTTTGGT
1 ATATTTTGGT
19276891 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:19277197 original size:14 final size:12
Alignment explanation
Indices: 19277160--19277190 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19277150 TAGTTTTTTT
*
19277160 TAAAAAATTATA
1 TAAAAAATAATA
19277172 TAAAAAATAATA
1 TAAAAAATAATA
19277184 TAAAAAA
1 TAAAAAA
19277191 CCTAATACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:19287419 original size:17 final size:17
Alignment explanation
Indices: 19287397--19287429 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19287387 ATTAATGTCA
*
19287397 ATGTTATTGTTATAATT
1 ATGTTATTATTATAATT
19287414 ATGTTATTATTATAAT
1 ATGTTATTATTATAAT
19287430 ATTTCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
ATGTTATTATTATAATT
Found at i:19296343 original size:44 final size:44
Alignment explanation
Indices: 19296237--19297199 Score: 668
Period size: 44 Copynumber: 21.2 Consensus size: 44
19296227 TCTCCTTTAG
* *
19296237 GTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCT--CTGAA
1 GTTGCAGTGGAGCAGATTG-AAGTTACAAATCTTATCTCCCTGAA
** * * *
19296280 GTTGCAGTACAACAAATTGAAGTTACAAATCTTATCTCTCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * * * *
19296324 GTTGTAGTAGAGTAGATTGAAGATAACAAATCTTATCTCTCTGAA
1 GTTGCAGTGGAGCAGATTGAAG-TTACAAATCTTATCTCCCTGAA
* * *
19296369 GTTGCAGTAGAGCAAATTGAAGTCACTGTAGTGAATCTTATC-CACCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTAC---A---AATCTTATCTC-CCTGAA
* ** *
19296419 GTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCTTCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* *
19296463 GTTGTAGTGGAGCAAATTGAAGTTACAAATCTTATCTCCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * *
19296507 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTAAA
1 GTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCCTGAA
* * * ** * *
19296552 GTTACAGTAGAGTAGATTGAAGCGACAAATCATATAC-CTCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTAT-CTCCCTGAA
* * *
19296596 GTTGCAGTGG-GTCAGATT-AAATCTATCGTAATGAGTCTTATTTCCTTGAA
1 GTTGCAGTGGAG-CAGATTGAAGT-TA-C--AA--A-TCTTATCTCCCTGAA
* ** * *
19296646 G-TGCAGCGGAATAGATTAAAGCTACAAGTTACAAACCTTATCTCTCTGAA
1 GTTGCAGTGGAGCAGATT---G----AAGTTACAAATCTTATCTCCCTGAA
* * * * *
19296696 GTTACAATGGAGCAGATTGAA-TATGCGAATCTTATTTCCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGT-TACAAATCTTATCTCCCTGAA
* * * * * **
19296740 TTTGCAGTGGAGCAGATTGAAGATAGAAAATATTATTTCCCCAAA
1 GTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCCTGAA
* * *
19296785 GTTGTAGTGGAACAGATTAAAGCTACAAGTTACAAATCTCATCTCCCTGAA
1 GTTGCAGTGGAGCAGATT---G----AAGTTACAAATCTTATCTCCCTGAA
* * *
19296836 GTTGCAGTGGAGCAGGTT-AGAGCTACAAATCTTATCTTCCTGAA
1 GTTGCAGTGGAGCAGATTGA-AGTTACAAATCTTATCTCCCTGAA
* ** * * *
19296880 GTTGCGGTGGAATAGATTGAAGATAGCGAATCTCATCTCCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCCTGAA
* * * * *
19296925 GTTGCCGTGGAGCAGATTGAAGCTACAAATCTCATCTTCCTAAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * *
19296969 GTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * * *
19297013 GTTACAGTGGAGCAAATTGAAGATAGCAAATCTTATCTCTCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCCTGAA
* ** * * *
19297058 GCTGCAGTAAACCTGATTGAAGCTACAAATCTTATCTCCCTGAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * * * *
19297102 GTTACAGTGGAGCAGATTAAAGCTACAAATCTTATGTCCCTAAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
* * * ** * *
19297146 GTTGCAGTGGAGTAGGTTGAAATTACATTTCCTATAC-CCCTAAA
1 GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTAT-CTCCCTGAA
19297190 GTTGCAGTGG
1 GTTGCAGTGG
19297200 GTTAGAATGA
Statistics
Matches: 722, Mismatches: 151, Indels: 93
0.75 0.16 0.10
Matches are distributed among these distances:
42 16 0.02
43 20 0.03
44 374 0.52
45 180 0.25
47 4 0.01
48 2 0.00
49 14 0.02
50 59 0.08
51 40 0.06
52 5 0.01
53 2 0.00
55 1 0.00
56 2 0.00
57 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
GTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAA
Found at i:19296595 original size:89 final size:88
Alignment explanation
Indices: 19296237--19297166 Score: 642
Period size: 89 Copynumber: 10.2 Consensus size: 88
19296227 TCTCCTTTAG
* * ** * *
19296237 GTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCT--CTGAAGTTGCAGTACAACAAATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
*
19296300 AGTTACAAATCTTATCTCTCTGAA
66 AGCTACAAATCTTATC-CTCTGAA
* * * * * * *
19296324 GTTGTAGTAGAGTAGATTGAAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
*
19296389 AG-TCACTGTAGTGAATCTTATCCACCTGAA
66 AGCT-AC---A---AATCTTATCC-TCTGAA
* ** * * *
19296419 GTTGCAGTGGAGCAGATTAAAGCCA-CAAATCTTATCTTCCTGAAGTTGTAGTGGAGCAAATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* *
19296483 AGTTACAAATCTTATCTCCCTGAA
66 AGCTACAAATCTTATC-CTCTGAA
* * * * *
19296507 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTAAAGTTACAGTAGAGTAGATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* *
19296572 AGCGACAAATCATATACCTCTGAA
66 AGCTACAAATCTTAT-CCTCTGAA
* * * * * * * **
19296596 GTTGCAGTGG-GTCAGATTAAATCTATCGTAATGAGTCTTATTTCCTTGAAG-TGCAGCGGAATA
1 GTTGCAGTGGAG-CAGATTGAA--GATAGCAA--A-TCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
19296659 GATTAAAGCTACAAGTTACAAACCTTATCTCTCTGAA
60 GATT---G----AAGCTACAAATCTTATC-CTCTGAA
* * * * * *
19296696 GTTACAATGGAGCAGATTGAATAT-GCGAATCTTATTTCCCTGAATTTGCAGTGGAGCAGATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * **
19296760 AGATAGAAAATATTATTTCC-CCAAA
66 AGCTA-CAAATCTTA--TCCTCTGAA
* * * * *
19296785 GTTGTAGTGGAACAGATTAAAGCTACAAGTTACAAATCTCATCTCCCTGAAGTTGCAGTGGAGCA
1 GTTGCAGTGGAGCAGATTGAAG--A-TAG---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
19296850 GGTT-AGAGCTACAAATCTTATCTTCCTGAA
60 GATTGA-AGCTACAAATCTTATCCT-CTGAA
* ** * * *
19296880 GTTGCGGTGGAATAGATTGAAGATAGCGAATCTCATCTCCCTGAAGTTGCCGTGGAGCAGATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * *
19296945 AGCTACAAATCTCATCTTCCTAAA
66 AGCTACAAATCTTATCCT-CTGAA
* * * * *
19296969 GTTGTAGTGGAGCAGATTGAAGCTA-CAAATCTTATTTCCCTGAAGTTACAGTGGAGCAAATTGA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
*
19297033 AGATAGCAAATCTTATCTCTCTGAA
66 AGCTA-CAAATCTTATC-CTCTGAA
* ** * * * * *
19297058 GCTGCAGTAAACCTGATTGAAGCTA-CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAA
1 GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
*
19297122 AGCTACAAATCTTATGTCC-CTAAA
66 AGCTACAAATCTTA--TCCTCTGAA
* *
19297146 GTTGCAGTGGAGTAGGTTGAA
1 GTTGCAGTGGAGCAGATTGAA
19297167 ATTACATTTC
Statistics
Matches: 670, Mismatches: 125, Indels: 95
0.75 0.14 0.11
Matches are distributed among these distances:
87 34 0.05
88 106 0.16
89 271 0.40
90 6 0.01
91 9 0.01
92 4 0.01
93 17 0.03
94 67 0.10
95 77 0.11
96 37 0.06
97 2 0.00
98 3 0.00
99 1 0.00
100 35 0.05
101 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (88 bp):
GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
AGCTACAAATCTTATCCTCTGAA
Done.