Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 173 of 433
Found at i:53888146 original size:40 final size:40
Alignment explanation
Indices: 53888005--53888225 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
53887995 AATGATGTCT
* * * *
53888005 GGGCTAAGTCCCGACGGC-TTTGTGCTAAGTGACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* * * * *
53888045 GGACTAAGAT-CCAAAGGCATTCGTGCGAGTTACTAATTTC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
53888085 GGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
53888123 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
53888163 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
* *
53888203 GGGCTATGTCCCGAAGGCGTTTG
1 GGGCTAAGTCCCGAAGGCATTTG
53888226 AACGAGTAGC
Statistics
Matches: 158, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 33 0.21
40 116 0.73
41 9 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:53888232 original size:80 final size:78
Alignment explanation
Indices: 53888070--53888248 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 78
53888060 GGCATTCGTG
* * * *
53888070 CGAGTTACTAATTTCGGGCTAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCC
1 CGAGTTACTAAATCCGGGTTAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCC
**
53888135 GAAGGCATTTGTG
66 GAAGGCATTTGAA
*
53888148 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGT
1 CGAGTTACTAAATCCGGGTTAAG--CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT
*
53888212 CCCGAAGGCGTTTGAA
63 CCCGAAGGCATTTGAA
*
53888228 CGAG-TAGCTATATCC-GGTTAA
1 CGAGTTA-CTAAATCCGGGTTAA
53888249 ACTCCGAAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
78 20 0.23
79 8 0.09
80 58 0.66
81 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (78 bp):
CGAGTTACTAAATCCGGGTTAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCC
GAAGGCATTTGAA
Found at i:53895927 original size:49 final size:49
Alignment explanation
Indices: 53895863--53896194 Score: 515
Period size: 49 Copynumber: 6.8 Consensus size: 49
53895853 ATACATATCG
* *
53895863 CATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACACTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
53895912 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
* *
53895961 CGTTCATCACATCAGCCATTAGGCCTTATCACATATATATACATTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
*
53896010 CGTTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
* *
53896059 CATTCATCACATCGGCCATTAGGCCTTATCACGTATGTATACATTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
* * * * *
53896108 CATTCATCACATTGGCCATTCGGCCTTATCAC--ACATATGCACTTTCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
* * *
53896155 CATTCATCACATTGGCCATTCGGCCTTATCACACATATAT
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
53896195 GTATATCATA
Statistics
Matches: 266, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
47 43 0.16
49 223 0.84
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (49 bp):
CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTTTCA
Found at i:53895969 original size:27 final size:27
Alignment explanation
Indices: 53895939--53896021 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
53895929 ATTAGGCCTT
53895939 ATCACATATATATACATTTTCACGTTC
1 ATCACATATATATACATTTTCACGTTC
* ** **
53895966 ATCAC--AT-CAGCCATTAGGC-C-TT-
1 ATCACATATATATACATT-TTCACGTTC
53895988 ATCACATATATATACATTTTCACGTTC
1 ATCACATATATATACATTTTCACGTTC
53896015 ATCACAT
1 ATCACAT
53896022 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
22 5 0.13
23 2 0.05
24 9 0.23
25 9 0.23
26 2 0.05
27 12 0.31
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (27 bp):
ATCACATATATATACATTTTCACGTTC
Found at i:53896133 original size:147 final size:145
Alignment explanation
Indices: 53895825--53896194 Score: 521
Period size: 147 Copynumber: 2.6 Consensus size: 145
53895815 GTTACAACAT
* * * * * *
53895825 TCACATTAGCCATTCGGCTTTA-C-CACATATACA-TATCGCATTCATCACGTCGGCCATTAGGC
1 TCACATCAGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
53895887 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
66 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
53895952 ACATTTTCACGTTCA
131 ACATTTTCACATTCA
* * *
53895967 TCACATCAGCCATTAGGCCTTATCACATATATATACATTTTCACGTTCATCACATCGGCCATTAG
1 TCACATCAGCCATTAGGCCTTATCAC--ACATATACACTTTCACATTCATCACATCGGCCATTAG
* * *
53896032 GCCTTATCACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATGT
64 GCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
53896097 ATACATTTTCACATTCA
129 ATACATTTTCACATTCA
** * * * *
53896114 TCACATTGGCCATTCGGCCTTATCACACATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 TCACATCAGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53896179 CTTATCACACATATAT
66 CTTATCACATATATAT
53896195 GTATATCATA
Statistics
Matches: 201, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
142 19 0.09
143 1 0.00
144 1 0.00
145 48 0.24
146 8 0.04
147 124 0.62
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (145 bp):
TCACATCAGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
ACATTTTCACATTCA
Found at i:53896138 original size:22 final size:22
Alignment explanation
Indices: 53896113--53896187 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
53896103 TTTCACATTC
53896113 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
53896135 ATCACACATAT-GCACTTTC-ACATT
1 AT--CACAT-TGGC-CATTCGGCCTT
53896159 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
53896182 ATCACA
1 ATCACA
53896188 CATATATGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 13 0.32
23 10 0.25
24 10 0.25
25 7 0.17
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:53896142 original size:24 final size:24
Alignment explanation
Indices: 53896115--53896190 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
53896105 TCACATTCAT
53896115 CACATTGGCCATTCGGCCTTATCA
1 CACATTGGCCATTCGGCCTTATCA
* * *
53896139 CACATAT-GCACTTTC--ACAT-TCA
1 CACAT-TGGC-CATTCGGCCTTATCA
53896161 TCACATTGGCCATTCGGCCTTATCA
1 -CACATTGGCCATTCGGCCTTATCA
53896186 CACAT
1 CACAT
53896191 ATATGTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 8 0.21
23 9 0.23
24 14 0.36
25 8 0.21
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (24 bp):
CACATTGGCCATTCGGCCTTATCA
Found at i:53900445 original size:40 final size:40
Alignment explanation
Indices: 53900302--53900524 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
53900292 TCGAATGATG
* * * *
53900302 TCCGGGCTAAGTCCCGACGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
53900342 TCCGGACTAAGAT-CCAAAGGCATTCGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53900381 TTCTGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53900419 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53900459 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
53900500 -CCGGGCTATGTCCCGAAGGCGTTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53900525 AACGAGTAGC
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
37 22 0.14
38 10 0.06
39 9 0.06
40 107 0.68
41 9 0.06
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53902981 original size:17 final size:16
Alignment explanation
Indices: 53902959--53903005 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
53902949 TTTTAATAAG
53902959 ATTTAATATTAAATTAA
1 ATTTAATATTAAATT-A
*
53902976 ATTTAATATTTATATTA
1 ATTTAATA-TTAAATTA
53902993 ATTTAATATTAAA
1 ATTTAATATTAAA
53903006 GTGATTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATATTAAATTA
Found at i:53908549 original size:3 final size:3
Alignment explanation
Indices: 53908541--53908594 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
53908531 GAGTCATTAA
53908541 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
53908589 AAT AAT
1 AAT AAT
53908595 TAACAGTCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53910644 original size:40 final size:40
Alignment explanation
Indices: 53910589--53910802 Score: 349
Period size: 40 Copynumber: 5.4 Consensus size: 40
53910579 TATGTGCATA
*
53910589 GCATTCGTACGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
53910629 GCATTCGTGCGGGTTATTATAACTGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
53910669 GAATTCGTGCGGGTTATTATAACCGGGTTAAGTCCAGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* * *
53910709 GCATTCGTGCAGGTTATTATCATCGGGTTAAGTCCC-AAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
53910748 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
53910788 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
53910803 GTTACATCCG
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 36 0.23
40 123 0.77
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:53912985 original size:14 final size:14
Alignment explanation
Indices: 53912945--53912986 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
53912935 TAATTTCAAA
53912945 TTTTACTATTATGTC
1 TTTTA-TATTATGTC
*
53912960 TTTTGTATTTATGTC
1 TTTTATA-TTATGTC
53912975 TTTTATATTATG
1 TTTTATATTATG
53912987 CATGCATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.19, C:0.07, G:0.10, T:0.64
Consensus pattern (14 bp):
TTTTATATTATGTC
Found at i:53915151 original size:27 final size:26
Alignment explanation
Indices: 53915103--53915161 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
53915093 GCGAGGCTTC
*
53915103 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
53915130 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
53915156 CAGATA
1 CAGATA
53915162 CATATATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:53915181 original size:31 final size:32
Alignment explanation
Indices: 53915124--53915185 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
53915114 ACGAAGTCAC
* *
53915124 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
*
53915156 CAGATACATATA-TGTGGCGAAGCCACCAGA
1 CAGATACAGATATTGTGGCGAAGCCACCAGA
53915186 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:53922430 original size:27 final size:26
Alignment explanation
Indices: 53922382--53922433 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53922372 GTGAAGCTGC
*
53922382 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
53922408 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
53922434 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:53923845 original size:68 final size:69
Alignment explanation
Indices: 53923768--53923901 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 69
53923758 TTTAATAGTT
* * * *
53923768 TAATATTAAATTTAATTTAATACTTATCTTAAT-AGTATTTTGTTAATTTAATATTAAAGTGATT
1 TAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATT
53923832 ATCG
66 ATCG
*
53923836 TAATATTAAATTTAATATAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATT
1 TAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATT
53923901 A
66 A
53923902 AGTTTAATCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
68 31 0.52
69 29 0.48
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (69 bp):
TAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATT
ATCG
Found at i:53923873 original size:21 final size:20
Alignment explanation
Indices: 53923849--53923889 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
53923839 TATTAAATTT
*
53923849 AATATAATATTTATCTTAATA
1 AATATAATATTAAT-TTAATA
*
53923870 AATATTATATTAATTTAATA
1 AATATAATATTAATTTAATA
53923890 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATAATATTAATTTAATA
Found at i:53924679 original size:15 final size:15
Alignment explanation
Indices: 53924659--53924701 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
53924649 TAGATCTTCA
53924659 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
53924674 TTTTTTTTTC-TTTC
1 TTTTTTTTTCTTTTC
53924688 TTTTTCTTTT-TTTT
1 TTTTT-TTTTCTTTT
53924702 TTGTTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:53924692 original size:20 final size:18
Alignment explanation
Indices: 53924659--53924703 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 18
53924649 TAGATCTTCA
53924659 TTTTTTTTTCTTTTCTTT
1 TTTTTTTTTCTTTTCTTT
53924677 TTTTTTCTTTCTTTTTCTTT
1 TTTTTT-TTTC-TTTTCTTT
53924697 TTTTTTT
1 TTTTTTT
53924704 GTTTTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 5 0.20
20 14 0.56
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTCTTTTCTTT
Found at i:53924702 original size:10 final size:10
Alignment explanation
Indices: 53924659--53924702 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
53924649 TAGATCTTCA
53924659 TTTTT-TTTT
1 TTTTTCTTTT
*
53924668 CTTTTCTTTT
1 TTTTTCTTTT
*
53924678 TTTTTCTTTC
1 TTTTTCTTTT
53924688 TTTTTCTTTT
1 TTTTTCTTTT
53924698 TTTTT
1 TTTTT
53924703 TGTTTTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 4 0.13
10 26 0.87
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:53924933 original size:55 final size:55
Alignment explanation
Indices: 53924847--53924956 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
53924837 CCTACTATGT
* *
53924847 GTTTGTTAAAATGCTTGTATGGCATTTAAGTTTAGTCATGTGCTGAATTGTTTTA
1 GTTTGTTAAAATGCTTGTATGGCATTAAAGTTTAATCATGTGCTGAATTGTTTTA
53924902 GTTTGTTAAAATGCTTGTATGGCATTAAAGTTTAATCATGTGCTGAATTGTTTTA
1 GTTTGTTAAAATGCTTGTATGGCATTAAAGTTTAATCATGTGCTGAATTGTTTTA
53924957 TTGTTTGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (55 bp):
GTTTGTTAAAATGCTTGTATGGCATTAAAGTTTAATCATGTGCTGAATTGTTTTA
Found at i:53926518 original size:27 final size:26
Alignment explanation
Indices: 53926485--53926554 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
53926475 AATACATTAG
* *
53926485 GAAAGAAAAACCTTTTTGATGTAATAT
1 GAAAG-AAAACCTTTGTGATGGAATAT
* *
53926512 GAAAGAAAGCCTTTGTGGTGGAATAT
1 GAAAGAAAACCTTTGTGATGGAATAT
53926538 GAAAGAAAACCTTTGTG
1 GAAAGAAAACCTTTGTG
53926555 GCAGAATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
26 33 0.87
27 5 0.13
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (26 bp):
GAAAGAAAACCTTTGTGATGGAATAT
Found at i:53926536 original size:26 final size:25
Alignment explanation
Indices: 53926507--53926586 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 25
53926497 TTTTTGATGT
53926507 AATATGAAAGAAAGCCTTTGTGGTGG
1 AATATGAAAGAAAGCCTTTGTGG-GG
* *
53926533 AATATGAAAGAAAACCTTTGTGGCAG
1 AATATGAAAGAAAGCCTTTGTGG-GG
* * *
53926559 AATTTGAAAAGAACGTCTTTGTGGGG
1 AATATG-AAAGAAAGCCTTTGTGGGG
53926585 AA
1 AA
53926587 ACTCCATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
26 31 0.69
27 14 0.31
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.26
Consensus pattern (25 bp):
AATATGAAAGAAAGCCTTTGTGGGG
Found at i:53927165 original size:52 final size:52
Alignment explanation
Indices: 53927103--53927202 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
53927093 ATTTGAGTAA
*
53927103 GAATCAATAGTGTGGAAAACTATATAAGTATCCACCATATGTATGTGTTCGC
1 GAATCAATAGTGTGAAAAACTATATAAGTATCCACCATATGTATGTGTTCGC
*
53927155 GAATCAATAGTGTGAAAAACTATGTAAGTATCCACCATATGTATGTGT
1 GAATCAATAGTGTGAAAAACTATATAAGTATCCACCATATGTATGTGT
53927203 CTGCCCAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (52 bp):
GAATCAATAGTGTGAAAAACTATATAAGTATCCACCATATGTATGTGTTCGC
Found at i:53929281 original size:11 final size:12
Alignment explanation
Indices: 53929260--53929285 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53929250 GCGGTCCATC
53929260 TTTGTTTTTTTT
1 TTTGTTTTTTTT
53929272 TTTGTTTTTTTT
1 TTTGTTTTTTTT
53929284 TT
1 TT
53929286 AATCTACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTGTTTTTTTT
Found at i:53930844 original size:34 final size:35
Alignment explanation
Indices: 53930768--53930845 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
53930758 ACAGTTCCTG
*
53930768 AAAA-TATTATTTCAAAAAATTCTATCAAATAGCA
1 AAAAGTATTATTTCAAAAAATTCTATCAAACAGCA
*
53930802 AAACGTATT-TTTCAAAAAATT-TATCTAAACA-CTA
1 AAAAGTATTATTTCAAAAAATTCTATC-AAACAGC-A
53930836 AAAAGTATTA
1 AAAAGTATTA
53930846 ACTTATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 5 0.14
34 28 0.76
35 4 0.11
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (35 bp):
AAAAGTATTATTTCAAAAAATTCTATCAAACAGCA
Found at i:53931721 original size:95 final size:95
Alignment explanation
Indices: 53931558--53931748 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
53931548 GAGAAAGAGA
53931558 AAGATGCATGATGGAGGCAGCACTCATTATCTCAAGCAAAAGTTTCAGATTCCGATAAAGGAAAT
1 AAGATGCATGATGGAGGCAGCACTCATTATCTCAAGCAAAAGTTTCAGATTCCGATAAAGGAAAT
53931623 TCAGGGGGGGAAAAAGCTTGAATACAATGC
66 TCAGGGGGGGAAAAAGCTTGAATACAATGC
53931653 AAGATGCATGATGGAGGCAGCACTCATTATCTCAAGCAAAAGTTTCAGATTCCGATAAAGGAAAT
1 AAGATGCATGATGGAGGCAGCACTCATTATCTCAAGCAAAAGTTTCAGATTCCGATAAAGGAAAT
53931718 TCAGGGGGGGAAAAAGCTTGAATACAATGC
66 TCAGGGGGGGAAAAAGCTTGAATACAATGC
53931748 A
1 A
53931749 TGGCACCACT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (95 bp):
AAGATGCATGATGGAGGCAGCACTCATTATCTCAAGCAAAAGTTTCAGATTCCGATAAAGGAAAT
TCAGGGGGGGAAAAAGCTTGAATACAATGC
Found at i:53933582 original size:107 final size:107
Alignment explanation
Indices: 53933388--53933599 Score: 370
Period size: 107 Copynumber: 2.0 Consensus size: 107
53933378 GTACATGTAT
* * *
53933388 TTTAATTTGATTAATTTTAGTCTTTATGTTTTTTGAGTTTTGAAATTTAGTTCTAACGCGATAGT
1 TTTAATTTGATTAATTTGAATCTTTATGCTTTTTGAGTTTTGAAATTTAGTTCTAACGCGATAGT
*
53933453 AACAGTTAAATCTGTTTAGTTAAATTATGTCATTAGTCTTAC
66 AACAGTTAAATCTATTTAGTTAAATTATGTCATTAGTCTTAC
*
53933495 TTTAATTTGATTAATTTGAATCTTTATGCTTTTTGAGTTTTGAAATTTAGTTCTAACGCGATGGT
1 TTTAATTTGATTAATTTGAATCTTTATGCTTTTTGAGTTTTGAAATTTAGTTCTAACGCGATAGT
*
53933560 AACAGTTAAATCTATTTGGTTAAATTATGTCATTAGTCTT
66 AACAGTTAAATCTATTTAGTTAAATTATGTCATTAGTCTT
53933600 GTTTTATATG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (107 bp):
TTTAATTTGATTAATTTGAATCTTTATGCTTTTTGAGTTTTGAAATTTAGTTCTAACGCGATAGT
AACAGTTAAATCTATTTAGTTAAATTATGTCATTAGTCTTAC
Found at i:53942551 original size:31 final size:30
Alignment explanation
Indices: 53942494--53942552 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
53942484 GTAAATACTC
* * * *
53942494 AAAATTTGAGGGATTAAAGTGTAAATATGA
1 AAAAGTTGAAGGACTAAAGTGCAAATATGA
53942524 AAAAGTTGAAGGACTAATAGTGCAAATAT
1 AAAAGTTGAAGGACTAA-AGTGCAAATAT
53942553 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGCAAATATGA
Found at i:53948047 original size:26 final size:25
Alignment explanation
Indices: 53948004--53948086 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 25
53947994 CATGAAATTC
53948004 TTATCATGAACATTTACCTAACCCA
1 TTATCATGAACATTTACCTAACCCA
53948029 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCCA
* *
53948055 TTATCATGGAACACTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCCA
53948081 TTATCA
1 TTATCA
53948087 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
25 8 0.15
26 45 0.83
27 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.33
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCCA
Found at i:53949013 original size:45 final size:45
Alignment explanation
Indices: 53948949--53949266 Score: 305
Period size: 45 Copynumber: 7.3 Consensus size: 45
53948939 TTACCGCTAT
* * *
53948949 TGCTACTGTTACCGATTCGGCACTTTATGTGTCGAATATTGCTAC
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
*
53948994 TGCTATCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
* * * *
53949039 TGTTACCGTTACTGATTTGACACTTTGTGTGTCGAATATTGTTAC
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
* * *
53949084 TG---CCGTTATCGATTCGGCACTATGTGTGTCGAATATTGTTAT
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
* * *
53949126 TGTTACCGTTACC-ATTTCGACACTTTGTGTGTTGAATATTGTTA-
1 TGCTACCGTTACCGA-TTCGGCACTTTGTGTGTCGAATATTGTTAC
* * * *
53949170 --CT---GTTACCAATTCGACACTTTGTGTGTTGAATACTGTTAC
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
* * * * * ** *
53949210 CGTTACTGTTACAGATTCAGCACTTTGTGTGTTAAATACTGTTAC
1 TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
* *
53949255 TGTTACTGTTAC
1 TGCTACCGTTAC
53949267 TGCTATTGTT
Statistics
Matches: 234, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.15
40 1 0.00
42 38 0.16
44 1 0.00
45 160 0.68
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (45 bp):
TGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
Found at i:53949119 original size:87 final size:86
Alignment explanation
Indices: 53948969--53949256 Score: 332
Period size: 87 Copynumber: 3.3 Consensus size: 86
53948959 ACCGATTCGG
* *
53948969 CACTTTATGTGTCGAATATTGCTACTGCTATCGTTACCGATTCGGCACTTTGTGTGTCGAATATT
1 CACTTTGTGTGTCGAATATTGTTACTGC---CGTTACCGATTCGGCACTTTGTGTGTCGAATATT
53949034 GTTACTGTTACCGTTACTGATTTGA
63 GTTACTGTTACCGTTAC-GATTTGA
* *
53949059 CACTTTGTGTGTCGAATATTGTTACTGCCGTTATCGATTCGGCACTATGTGTGTCGAATATTGTT
1 CACTTTGTGTGTCGAATATTGTTACTGCCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTT
* *
53949124 ATTGTTACCGTTACCATTTCGA
66 ACTGTTACCGTTACGATTT-GA
* * * * *
53949146 CACTTTGTGTGTTGAATATTGTTACT---GTTACCAATTCGACACTTTGTGTGTTGAATACTGTT
1 CACTTTGTGTGTCGAATATTGTTACTGCCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTT
* * *
53949208 ACCGTTACTGTTACAGA-TTCA
66 ACTGTTACCGTTAC-GATTTGA
** *
53949229 GCACTTTGTGTGTTAAATACTGTTACTG
1 -CACTTTGTGTGTCGAATATTGTTACTG
53949257 TTACTGTTAC
Statistics
Matches: 174, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
83 1 0.01
84 67 0.39
85 1 0.01
86 4 0.02
87 75 0.43
90 26 0.15
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (86 bp):
CACTTTGTGTGTCGAATATTGTTACTGCCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTT
ACTGTTACCGTTACGATTTGA
Found at i:53949170 original size:33 final size:35
Alignment explanation
Indices: 53949133--53949210 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 35
53949123 TATTGTTACC
* *
53949133 GTTACCATTTCGACACTTTGTGTGTTGAATATTGTTACT
1 GTTACCAATTCGACACTTTGTGTGTTGAATA---TCA-T
53949172 GTTACCAATTCGACACTTTGTGTGTTGAATA-C-T
1 GTTACCAATTCGACACTTTGTGTGTTGAATATCAT
53949205 GTTACC
1 GTTACC
53949211 GTTACTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 7 0.19
39 30 0.81
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (35 bp):
GTTACCAATTCGACACTTTGTGTGTTGAATATCAT
Found at i:53949217 original size:132 final size:128
Alignment explanation
Indices: 53948956--53949209 Score: 334
Period size: 132 Copynumber: 2.0 Consensus size: 128
53948946 TATTGCTACT
* * *
53948956 GTTACCGATTCGGCACTTTATGTGTCGAATATTGCTACTGCTATCGTTACCGATTCGGCACTTTG
1 GTTACCGATTCGGCACTATATGTGTCGAATATTGCTACTGCTACCGTTACCGATTCGACACTTTG
*
53949021 TGTGTCGAATATTGTTACTGTTACCGTTACTGATTTGACACTTTGTGTGTCGAATATTGTTACTG
66 TGTGTCGAATATTGTTACTGTTACC--TAC--ATTCGACACTTTGTGTGTCGAATATTGTTACTG
53949086 CC
127 CC
* * * * *
53949088 GTTATCGATTCGGCACTATGTGTGTCGAATATTGTTATTGTTACCGTTACC-ATTTCGACACTTT
1 GTTACCGATTCGGCACTATATGTGTCGAATATTGCTACTGCTACCGTTACCGA-TTCGACACTTT
* * *
53949152 GTGTGTTGAATATTGTTACTGTTACC-A-ATTCGACACTTTGTGTGTTGAATACTGTTAC
65 GTGTGTCGAATATTGTTACTGTTACCTACATTCGACACTTTGTGTGTCGAATATTGTTAC
53949210 CGTTACTGTT
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
126 28 0.26
129 1 0.01
131 1 0.01
132 79 0.72
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (128 bp):
GTTACCGATTCGGCACTATATGTGTCGAATATTGCTACTGCTACCGTTACCGATTCGACACTTTG
TGTGTCGAATATTGTTACTGTTACCTACATTCGACACTTTGTGTGTCGAATATTGTTACTGCC
Found at i:53949257 original size:6 final size:6
Alignment explanation
Indices: 53949246--53949289 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
53949236 GTGTGTTAAA
* *
53949246 TACTGT TACTGT TACTGT TACTGC TATTGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
53949290 TAGGTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:53949436 original size:2 final size:2
Alignment explanation
Indices: 53949429--53949465 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53949419 ACCGTACTGA
53949429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53949466 AGAAAGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53954509 original size:14 final size:14
Alignment explanation
Indices: 53954486--53954522 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
53954476 TCTAATATAC
53954486 TAAGTACCCTTGAA
1 TAAGTACCCTTGAA
*
53954500 TAAGTTCCCTTGAA
1 TAAGTACCCTTGAA
*
53954514 TAAATACCC
1 TAAGTACCC
53954523 AATTTTAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (14 bp):
TAAGTACCCTTGAA
Found at i:53965956 original size:20 final size:20
Alignment explanation
Indices: 53965931--53965990 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
53965921 TATCCCCTTG
*
53965931 TTTAAACATCTTTTAAATCC-
1 TTTAAA-ATCTTTTAAAACCT
* *
53965951 TTTAAAACCTTTCAAAACCT
1 TTTAAAATCTTTTAAAACCT
*
53965971 TTTAAAATCTCTTAAAACCT
1 TTTAAAATCTTTTAAAACCT
53965991 AAAACTCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAATCTTTTAAAACCT
Found at i:53965967 original size:10 final size:9
Alignment explanation
Indices: 53965942--53965990 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 9
53965932 TTAAACATCT
*
53965942 TTTAAATCC
1 TTTAAAACC
53965951 TTTAAAACC
1 TTTAAAACC
53965960 TTTCAAAACC
1 TTT-AAAACC
*
53965970 TTTTAAAATC
1 -TTTAAAACC
53965980 TCTTAAAACC
1 T-TTAAAACC
53965990 T
1 T
53965991 AAAACTCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 12 0.35
10 19 0.56
11 3 0.09
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (9 bp):
TTTAAAACC
Found at i:53968687 original size:49 final size:49
Alignment explanation
Indices: 53968627--53969027 Score: 652
Period size: 49 Copynumber: 8.3 Consensus size: 49
53968617 ATATGAGATA
*
53968627 TATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
53968676 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
53968725 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
53968774 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
53968823 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
53968872 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* *
53968919 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * * *
53968966 TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
53969013 TATAAATGTGATAAG
1 TATATATGTGATAAG
53969028 TCCCGAAGGG
Statistics
Matches: 339, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
47 100 0.29
48 5 0.01
49 234 0.69
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:53975845 original size:19 final size:19
Alignment explanation
Indices: 53975821--53975861 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53975811 GCTTCATAGC
* *
53975821 TTAGTAAGCTTGTATGTGA
1 TTAGTAAGCTCGTATGCGA
53975840 TTAGTAAGCTCGTATGCGA
1 TTAGTAAGCTCGTATGCGA
53975859 TTA
1 TTA
53975862 AATTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (19 bp):
TTAGTAAGCTCGTATGCGA
Found at i:53976305 original size:19 final size:19
Alignment explanation
Indices: 53976281--53976320 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53976271 GGCCTGAAGG
53976281 CAACAAAATAACCTAATGA
1 CAACAAAATAACCTAATGA
53976300 CAACAAAATAACCTAATGA
1 CAACAAAATAACCTAATGA
53976319 CA
1 CA
53976321 TGTCACTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.23, G:0.05, T:0.15
Consensus pattern (19 bp):
CAACAAAATAACCTAATGA
Found at i:53979808 original size:22 final size:22
Alignment explanation
Indices: 53979783--53979837 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
53979773 AATGGAAGCT
**
53979783 ATGTCACAACACGGATGATTCG
1 ATGTCACAACACAAATGATTCG
*
53979805 ATGTCACGACACAAATGATTCG
1 ATGTCACAACACAAATGATTCG
*
53979827 ATGTCATAACA
1 ATGTCACAACA
53979838 TGGGGAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (22 bp):
ATGTCACAACACAAATGATTCG
Found at i:53983526 original size:25 final size:25
Alignment explanation
Indices: 53983492--53983542 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
53983482 AACTATAAAG
*
53983492 TATGAAATGAGATGTGCGAAATGAA
1 TATGAAATGAGATGTACGAAATGAA
*
53983517 TATGAAATGAGATGTATGAAATGAA
1 TATGAAATGAGATGTACGAAATGAA
53983542 T
1 T
53983543 TTAGTAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.27
Consensus pattern (25 bp):
TATGAAATGAGATGTACGAAATGAA
Found at i:53983534 original size:14 final size:14
Alignment explanation
Indices: 53983491--53983540 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
53983481 TAACTATAAA
53983491 GTATGAAATGAGAT
1 GTATGAAATGAGAT
**
53983505 GTGCGAAATGA-A-
1 GTATGAAATGAGAT
53983517 -TATGAAATGAGAT
1 GTATGAAATGAGAT
53983530 GTATGAAATGA
1 GTATGAAATGA
53983541 ATTTAGTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 1 0.03
14 19 0.66
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.26
Consensus pattern (14 bp):
GTATGAAATGAGAT
Found at i:53996476 original size:40 final size:40
Alignment explanation
Indices: 53996431--53996638 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 40
53996421 CGGAATACAA
*
53996431 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
53996471 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
53996511 CCGGATTTAGCAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * *
53996551 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
** * ** * * *
53996591 CCGGATATAATTACTAGCATAAATGTCTTTGGGACTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
53996631 CCGGATAT
1 CCGGATAT
53996639 CATTCAATTG
Statistics
Matches: 142, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.01
40 138 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:53999181 original size:16 final size:17
Alignment explanation
Indices: 53999162--53999201 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
53999152 AATTTGTGTG
53999162 TTATTTTATTTT-TTCT
1 TTATTTTATTTTATTCT
*
53999178 TTATTTTATTTTATTTT
1 TTATTTTATTTTATTCT
53999195 TTATTTT
1 TTATTTT
53999202 TTTCACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (17 bp):
TTATTTTATTTTATTCT
Found at i:53999188 original size:21 final size:20
Alignment explanation
Indices: 53999162--53999204 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
53999152 AATTTGTGTG
*
53999162 TTATTTTATTTTTTCTTTATT
1 TTATTTTATTTTTTATTT-TT
53999183 TTATTTTATTTTTTATTTTT
1 TTATTTTATTTTTTATTTTT
53999203 TT
1 TT
53999205 CACAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (20 bp):
TTATTTTATTTTTTATTTTT
Found at i:54008007 original size:16 final size:15
Alignment explanation
Indices: 54007971--54008014 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54007961 TAAAAACATA
*
54007971 ATAATATAAAATGAC
1 ATAATATAAAATAAC
*
54007986 ATAATATAAAATAATT
1 ATAATATAAAATAA-C
*
54008002 ATAATATATAATA
1 ATAATATAAAATA
54008015 TGAAAGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAATATAAAATAAC
Found at i:54008081 original size:45 final size:44
Alignment explanation
Indices: 54007977--54008088 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 44
54007967 CATAATAATA
*
54007977 TAAAATGACATAATATA-AAATAATTATAATATATAATATGAAAG
1 TAAAATAACATAATATATAAATAATTATAATATATAATA-GAAAG
* ** *
54008021 T-ATAT-ATGTATATATATAAATAATTAATAATATATAATA-CAAG
1 TAAAATAACATA-ATATATAAATAATT-ATAATATATAATAGAAAG
54008064 TAAAATAACAATAATATATAAATAA
1 TAAAATAAC-ATAATATATAAATAA
54008089 GAATGTGAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
42 3 0.05
43 12 0.22
44 12 0.22
45 26 0.47
46 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (44 bp):
TAAAATAACATAATATATAAATAATTATAATATATAATAGAAAG
Found at i:54008161 original size:13 final size:16
Alignment explanation
Indices: 54008122--54008163 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
54008112 TGAAAAAGTG
54008122 ATATATAATAACAATA
1 ATATATAATAACAATA
54008138 ATATATAATAA-AATA
1 ATATATAATAACAATA
54008153 ATTATATAATA
1 A-TATATAATA
54008164 TGGTATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATAATAACAATA
Found at i:54011234 original size:20 final size:20
Alignment explanation
Indices: 54011189--54011234 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
54011179 CATCCAAACA
*
54011189 CCAGAAAAGTAAATCATTTT
1 CCAGAAAACTAAATCATTTT
54011209 -CAGAAAACTAAATCATTTT
1 CCAGAAAACTAAATCATTTT
54011228 CCAGAAA
1 CCAGAAA
54011235 TCATTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (20 bp):
CCAGAAAACTAAATCATTTT
Found at i:54013279 original size:43 final size:43
Alignment explanation
Indices: 54013134--54013280 Score: 156
Period size: 43 Copynumber: 3.4 Consensus size: 43
54013124 TATCCTAGTT
* * * *
54013134 ATGGTCTTACATGTTATCAC-ATATCGATGCTATTGTCCCAAAC
1 ATGGTCTTACATGTAATCTCAATA-CGATGCTAATGTCCCAGAC
* * * *
54013177 AGGGTCTTACA-GCAAATCAT-AATACGATGCCAATGTCCTAGAC
1 ATGGTCTTACATG-TAATC-TCAATACGATGCTAATGTCCCAGAC
* *
54013220 ATGGTCTTACACGTAATCTCAATACAATGCTAATGTCCCAGAC
1 ATGGTCTTACATGTAATCTCAATACGATGCTAATGTCCCAGAC
54013263 ATGGTCTTACATGTAATC
1 ATGGTCTTACATGTAATC
54013281 ACATCTCGGT
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.02
43 79 0.93
44 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCTCAATACGATGCTAATGTCCCAGAC
Found at i:54015076 original size:40 final size:40
Alignment explanation
Indices: 54015034--54015187 Score: 184
Period size: 40 Copynumber: 3.9 Consensus size: 40
54015024 ATCATGATTT
* *
54015034 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* **
54015074 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * * * *
54015114 GCATAAATGTCC-TCGGGACTTAGCCCGGATGTAGCCACTA
1 GCACAAATG-CCTTCGGGTCTTAGCCCGGATATAACAACTA
* *
54015154 GCACAATTGCCTTCGGGTCTTAACCCGGATATAA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAA
54015188 TTTCCAGCAT
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 2 0.02
40 90 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
Found at i:54015102 original size:80 final size:80
Alignment explanation
Indices: 54015002--54015223 Score: 232
Period size: 80 Copynumber: 2.8 Consensus size: 80
54014992 CCGCACCAAG
* * * * * * *
54015002 GCCTACGGGACTTAACCCGGATATCATGATTTGCACAAATG-CCTTCGGGTCTTAGCCCGGATTT
1 GCCTTCGGGTCTTAACCCGGATATAATGACTAGCACAAATGTCC-TCGGGACTTAGCCCGGATGT
*
54015066 AACAACTTGCACGAA-T
65 AACAACTAGCAC-AATT
* * *
54015082 GCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAAATGTCCTCGGGACTTAGCCCGGATGTA
1 GCCTTCGGGTCTTAACCCGGATATAATGACTAGCACAAATGTCCTCGGGACTTAGCCCGGATGTA
* *
54015147 GCCACTAGCACAATT
66 ACAACTAGCACAATT
** * ** * *
54015162 GCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATTAACGTCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGTCTTAACCCGGATATAATGACTAGCACAAATGTCCTCGGGACTTAGCCCGGAT
54015224 ATCATTCAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 117 0.97
81 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (80 bp):
GCCTTCGGGTCTTAACCCGGATATAATGACTAGCACAAATGTCCTCGGGACTTAGCCCGGATGTA
ACAACTAGCACAATT
Found at i:54022487 original size:93 final size:93
Alignment explanation
Indices: 54022328--54022499 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
54022318 GCCCATAAGT
* * *
54022328 GAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCATCCATGAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54022393 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
54022421 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
54022485 ACGAGTTCGGATGCC
65 ACGAGTTCGGATGCC
54022500 CAAATATCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54022495 original size:46 final size:46
Alignment explanation
Indices: 54022320--54022495 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
54022310 TGTAACCCGC
* * *
54022320 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * * *
54022366 CCATGAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
54022416 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
54022459 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54022496 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 60 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:54022514 original size:46 final size:46
Alignment explanation
Indices: 54022371--54022514 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 46
54022361 CGCATCCATG
* * * *
54022371 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TATATCCC
* * *
54022419 A-CGAACTCGGACTCAACTCAACGAGTTCGGA----CATTTGCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATAT--ATCC--C
*
54022464 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCC
54022510 AGTGA
1 AGTGA
54022515 CATGTCACTC
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
41 1 0.01
43 4 0.05
45 1 0.01
46 34 0.45
47 28 0.37
48 5 0.07
50 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCC
Found at i:54031782 original size:26 final size:26
Alignment explanation
Indices: 54031746--54031880 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
54031736 CATGAAATTC
54031746 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
**
54031772 TTATCATGAAACATTTACCTAATACA
1 TTATCATGAAACATTTACCTAACCCA
*
54031798 TTATCATAAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
54031824 TTATCATGAAACATTTACCTAACACA
1 TTATCATGAAACATTTACCTAACCCA
*
54031850 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
54031875 TTATCA
1 TTATCA
54031881 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 21 0.21
26 79 0.79
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:54035047 original size:39 final size:39
Alignment explanation
Indices: 54034933--54035114 Score: 229
Period size: 39 Copynumber: 4.6 Consensus size: 39
54034923 GTTCAAAACA
* * ** * *
54034933 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* * *
54034973 CCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
54035013 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* * *
54035052 CCTTCGGGCTTAGCCCGGATATCGTAATTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
54035091 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
54035115 CTCGAACATT
Statistics
Matches: 124, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
39 85 0.69
40 39 0.31
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:54035094 original size:78 final size:79
Alignment explanation
Indices: 54034963--54035114 Score: 252
Period size: 78 Copynumber: 1.9 Consensus size: 79
54034953 TATGGTAACC
54034963 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTGCCTTCGGGCTTAGCC
54035028 CGGATATCATAGCT
66 CGGATATCATAGCT
* * ** *
54035042 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCGTAATTTGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTGCCTTCGGGCTTAGCC
54035106 CGGATATCA
66 CGGATATCA
54035115 CTCGAACATT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 51 0.75
79 17 0.25
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (79 bp):
CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTTGCACAATTGCCTTCGGGCTTAGCC
CGGATATCATAGCT
Found at i:54043038 original size:40 final size:40
Alignment explanation
Indices: 54042994--54043137 Score: 175
Period size: 39 Copynumber: 3.6 Consensus size: 40
54042984 GTTCAAAACA
* * ***
54042994 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * *
54043034 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
** *
54043074 CCTTCGGG-CTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
54043113 CCTTCGGG-CTTAGCCCGGATATCAC
1 CCTTCGGGACTTAGCCCGGATATCAC
54043138 TCGAACATTC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 54 0.57
40 40 0.43
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
Found at i:54043106 original size:39 final size:39
Alignment explanation
Indices: 54043024--54043137 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 39
54043014 TATGGTAACC
* *
54043024 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
*
54043064 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
54043103 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
54043138 TCGAACATTC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 54 0.76
40 17 0.24
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54056134 original size:40 final size:40
Alignment explanation
Indices: 54055888--54056134 Score: 291
Period size: 40 Copynumber: 6.2 Consensus size: 40
54055878 CGGAATACAA
* * *
54055888 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
*
54055928 CC-GATAGAACGACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
* *
54055967 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
54056007 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
54056047 CCGGATGTAGTCG-CTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACGACTTGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54056087 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
54056127 CCGGATAT
1 CCGGATAT
54056135 CATTCAATTG
Statistics
Matches: 178, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 35 0.20
40 142 0.80
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACGACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:54062741 original size:40 final size:38
Alignment explanation
Indices: 54062655--54062829 Score: 179
Period size: 40 Copynumber: 4.4 Consensus size: 38
54062645 CGACTTGATC
* *
54062655 GTCTTAGCCCGGATAGAACGACTTGCACAATGCCTTCGG
1 GTCTTAGCCCGGATATAAC-ACTAGCACAATGCCTTCGG
* * *
54062694 GTATTAGCCCGGATTTAACAACTTGCACGAATGCCTTCGG
1 GTCTTAGCCCGGATATAAC-ACTAGCAC-AATGCCTTCGG
* *
54062734 GTCTTAGCCCGGATGTAGTCACTAGCACAATTGCCTTCGG
1 GTCTTAGCCCGGATATA-ACACTAGCACAA-TGCCTTCGG
* * * *
54062774 GTCTTAACCCGGATATAATTACTAGCATAAATGTCTTCGG
1 GTCTTAGCCCGGATATAA-CACTAGCA-CAATGCCTTCGG
*
54062814 GACTTAGCCCGGATAT
1 GTCTTAGCCCGGATAT
54062830 CATTCAATTG
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
39 26 0.23
40 86 0.75
41 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (38 bp):
GTCTTAGCCCGGATATAACACTAGCACAATGCCTTCGG
Found at i:54062812 original size:80 final size:79
Alignment explanation
Indices: 54062679--54062827 Score: 199
Period size: 80 Copynumber: 1.9 Consensus size: 79
54062669 AGAACGACTT
* * * * *
54062679 GCACAATGCCTTCGGGTATTAGCCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCC
1 GCACAATGCCTTCGGGTATTAACCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCCC
54062744 GGATGTAGTCACTA
66 GGATGTAGTCACTA
* ** * *
54062758 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCC
1 GCACAA-TGCCTTCGGGTATTAACCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCC
54062823 CGGAT
65 CGGAT
54062828 ATCATTCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
79 6 0.10
80 53 0.90
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (79 bp):
GCACAATGCCTTCGGGTATTAACCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCCC
GGATGTAGTCACTA
Found at i:54070687 original size:40 final size:40
Alignment explanation
Indices: 54070642--54070889 Score: 289
Period size: 40 Copynumber: 6.2 Consensus size: 40
54070632 CGGAATACAA
* *
54070642 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* *
54070682 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
54070722 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
54070762 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* ** * * * *
54070802 CCGGATGTAGTCGCTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54070842 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
54070882 CCGGATAT
1 CCGGATAT
54070890 CATTCAATTG
Statistics
Matches: 180, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 180 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:54070866 original size:120 final size:120
Alignment explanation
Indices: 54070642--54070889 Score: 331
Period size: 120 Copynumber: 2.1 Consensus size: 120
54070632 CGGAATACAA
* *
54070642 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
* *
54070707 CCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTA-TTAGC
66 CCTTCGGGTCTTAACCCGGATAGAACGACTAGCACAAATGCCTTCGGG-ACTTAGC
* * * *
54070762 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGTCG-CTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-A-ACGACTAGCACAAA
* ** * *
54070825 TGCCTTCGGGTCTTAACCCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
64 TGCCTTCGGGTCTTAACCCGGATAGAACGACTAGCACAAATGCCTTCGGGACTTAGC
54070882 CCGGATAT
1 CCGGATAT
54070890 CATTCAATTG
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
119 2 0.02
120 107 0.96
121 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (120 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
CCTTCGGGTCTTAACCCGGATAGAACGACTAGCACAAATGCCTTCGGGACTTAGC
Found at i:54079689 original size:26 final size:26
Alignment explanation
Indices: 54079659--54079709 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
54079649 AACACAGTAG
*
54079659 GAAAGAAA-ACCTTTGTAGCATAATAT
1 GAAAGAAAGA-CTTTGTAGCAGAATAT
*
54079685 GAAAGAAAGACTTTGTGGCAGAATA
1 GAAAGAAAGACTTTGTAGCAGAATA
54079710 CGGAAGGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (26 bp):
GAAAGAAAGACTTTGTAGCAGAATAT
Found at i:54080995 original size:37 final size:37
Alignment explanation
Indices: 54080932--54081040 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
54080922 TGCTCAGACG
* * *
54080932 AAATCTCCACACGAAGTTATCAGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
54080969 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
54081006 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
54081041 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:54081302 original size:97 final size:96
Alignment explanation
Indices: 54081187--54081369 Score: 298
Period size: 97 Copynumber: 1.9 Consensus size: 96
54081177 GCACATCGCC
* *
54081187 TACATATTTTACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATT
54081252 -GACCATTCGGC-TTACCACATATGCATATCTCA
64 AG-CCATTCGGCTTTACCACATATGCATATCTCA
*
54081284 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
54081349 CCATTCGGCTTTACCACATAT
66 CCATTCGGCTTTACCACATAT
54081370 ATGCATGTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
95 24 0.30
96 12 0.15
97 45 0.56
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCTTTACCACATATGCATATCTCA
Found at i:54081334 original size:48 final size:48
Alignment explanation
Indices: 54081187--54081370 Score: 291
Period size: 48 Copynumber: 3.8 Consensus size: 48
54081177 GCACATCGCC
* *
54081187 TACATATTTTACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
54081237 TATATATTTCACATT-GACCATTCGGC-TTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
54081284 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
54081332 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
54081371 TGCATGTTCA
Statistics
Matches: 125, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
47 24 0.19
48 60 0.48
49 20 0.16
50 21 0.17
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:54081419 original size:47 final size:47
Alignment explanation
Indices: 54081340--54081627 Score: 432
Period size: 47 Copynumber: 6.1 Consensus size: 47
54081330 CATACATATT
* * * *
54081340 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
54081387 CCACATTGGCCATTCGTCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
54081434 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
54081481 CCACATTGGCCATTCGGCCTTATCACACATATGCATGGTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
54081528 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
54081575 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
54081622 TCACAT
1 TCACAT
54081628 AAAATCCTAA
Statistics
Matches: 217, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 217 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:54081554 original size:22 final size:22
Alignment explanation
Indices: 54081527--54081598 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
54081517 GGTCACATTC
54081527 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
54081549 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
54081573 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
54081596 ATC
1 ATC
54081599 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:54083983 original size:40 final size:40
Alignment explanation
Indices: 54083925--54084052 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
54083915 CAATTGAATG
* * *
54083925 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTT
1 ATATCCGGGCTAATACCCGAAGGCAATTGTGCAAGTTG--TT
54083966 -TATCCGGGCTAATACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAATACCCGAAGGCAATT-GTGCAAGTTGTT
* * * *
54084005 ATATCCGGGCTAATACTCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAATACCCGAAGGCAATTGTGCAAGTTGTT
54084045 ATATCCGG
1 ATATCCGG
54084053 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
39 5 0.07
40 67 0.88
41 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAATACCCGAAGGCAATTGTGCAAGTTGTT
Found at i:54092013 original size:39 final size:39
Alignment explanation
Indices: 54091893--54092059 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 39
54091883 CAATTGAATG
* *
54091893 ATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTG--TT
* *
54091934 -TATCCGGGCTAATACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG-TGTT
* *
54091973 ATATCCGGGCTAATA-CCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGT-GTT
*
54092012 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGT-GTT
54092052 ATATCCGG
1 ATATCCGG
54092060 TTGTATTCCG
Statistics
Matches: 112, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.01
39 39 0.35
40 70 0.62
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGTT
Found at i:54092030 original size:79 final size:79
Alignment explanation
Indices: 54091893--54092059 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 79
54091883 CAATTGAATG
* * *
54091893 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAATACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
54091958 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
54091973 ATATCCGGGCTAATA-CCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
54092036 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
54092052 ATATCCGG
1 ATATCCGG
54092060 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
78 2 0.03
79 61 0.79
80 14 0.18
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:54099653 original size:13 final size:12
Alignment explanation
Indices: 54099617--54099663 Score: 85
Period size: 12 Copynumber: 3.8 Consensus size: 12
54099607 AAATACGTTG
54099617 AACATTCTCTTT
1 AACATTCTCTTT
54099629 AACATTCTCTTT
1 AACATTCTCTTT
54099641 AACATTCCTCTTT
1 AACATT-CTCTTT
54099654 AACATTCTCT
1 AACATTCTCT
54099664 CCTCGGGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 22 0.65
13 12 0.35
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (12 bp):
AACATTCTCTTT
Found at i:54099654 original size:25 final size:24
Alignment explanation
Indices: 54099617--54099663 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
54099607 AAATACGTTG
54099617 AACATTCTCTTTAACATTCTCTTT
1 AACATTCTCTTTAACATTCTCTTT
54099641 AACATTCCTCTTTAACATTCTCT
1 AACATT-CTCTTTAACATTCTCT
54099664 CCTCGGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (24 bp):
AACATTCTCTTTAACATTCTCTTT
Found at i:54100009 original size:24 final size:21
Alignment explanation
Indices: 54099951--54100015 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 21
54099941 CATGTATCGC
54099951 ATCCATAATGAACTCGGACCA
1 ATCCATAATGAACTCGGACCA
* * *
54099972 ATTC--AACGAGCTCGGATGCTCA
1 ATCCATAATGAACTCGGA--C-CA
54099994 ATCCATAATGAACTCGGACCA
1 ATCCATAATGAACTCGGACCA
54100015 A
1 A
54100016 CTCAAAGAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 10 0.30
21 7 0.21
22 6 0.18
24 10 0.30
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCCATAATGAACTCGGACCA
Found at i:54100012 original size:43 final size:43
Alignment explanation
Indices: 54099951--54100033 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
54099941 CATGTATCGC
* *
54099951 ATCCATAATGAACTCGGACCAATTCAACGAGCTCGGATGCTCA
1 ATCCATAATGAACTCGGACCAACTCAAAGAGCTCGGATGCTCA
*
54099994 ATCCATAATGAACTCGGACCAACTCAAAGAGCTTGGATGC
1 ATCCATAATGAACTCGGACCAACTCAAAGAGCTCGGATGC
54100034 CTTATACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (43 bp):
ATCCATAATGAACTCGGACCAACTCAAAGAGCTCGGATGCTCA
Found at i:54105147 original size:49 final size:48
Alignment explanation
Indices: 54105094--54105316 Score: 317
Period size: 47 Copynumber: 4.7 Consensus size: 48
54105084 GATTCTACGC
* * *
54105094 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTAT-AATATGTGATAAGGCCTAATGGCCAATGT
* *
54105143 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCAATGT
54105192 GATGAATGTGAAAGTGTAT-ATATGTGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAATGT
* * * *
54105239 GATGAATGTGAAAGTGTAT-ATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAATGT
*
54105286 GATGGATGTGAAAGTGTATAA-ATGTGATAAG
1 GATGAATGTGAAAGTGTATAATATGTGATAAG
54105317 TCCCGAAGGG
Statistics
Matches: 161, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
47 97 0.60
48 2 0.01
49 62 0.39
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (48 bp):
GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAATGT
Found at i:54114100 original size:46 final size:46
Alignment explanation
Indices: 54114029--54114120 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
54114019 GCATATAGCC
*
54114029 ACACCTTAACCTTATGACTCGTCCACGGTCGCAATTAATTAATTAA
1 ACACCTTAACCTTATGACTCATCCACGGTCGCAATTAATTAATTAA
54114075 ACACCTTAACCTTATGACTCATCCACGGTCGCAATTAATTAATTAA
1 ACACCTTAACCTTATGACTCATCCACGGTCGCAATTAATTAATTAA
54114121 GTTTTATGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (46 bp):
ACACCTTAACCTTATGACTCATCCACGGTCGCAATTAATTAATTAA
Found at i:54114479 original size:78 final size:78
Alignment explanation
Indices: 54114350--54114507 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
54114340 ATGTCGTATG
54114350 TAGCGACCAATTATCATTTATGCTTTCATAACAACCAATAAGTATATAACTCATAATAACAAGAA
1 TAGCGACCAATTATCATTTATGCTTTCATAACAACCAATAAGTATATAACTCATAATAACAAGAA
54114415 AACATTTATCACA
66 AACATTTATCACA
54114428 TAGCGACCAATTATCATTTATGCTTTCATAACAACCAATAAGTATATAACTCATAATAACAAGAA
1 TAGCGACCAATTATCATTTATGCTTTCATAACAACCAATAAGTATATAACTCATAATAACAAGAA
54114493 AACATTTATCACA
66 AACATTTATCACA
54114506 TA
1 TA
54114508 ATATCAGAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (78 bp):
TAGCGACCAATTATCATTTATGCTTTCATAACAACCAATAAGTATATAACTCATAATAACAAGAA
AACATTTATCACA
Found at i:54118404 original size:19 final size:19
Alignment explanation
Indices: 54118380--54118417 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54118370 ATGCGATTAA
54118380 TTGAAGGGTGATATCATTT
1 TTGAAGGGTGATATCATTT
*
54118399 TTGAAGGTTGATATCATTT
1 TTGAAGGGTGATATCATTT
54118418 GTAGGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (19 bp):
TTGAAGGGTGATATCATTT
Found at i:54118788 original size:29 final size:29
Alignment explanation
Indices: 54118746--54118838 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
54118736 CTGAGCAAGA
* *
54118746 ATAT-AAGGTGATTTGGGCCTAACGGGCC
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
*
54118774 ATATAAAGGTGATTTGGACCTGATGGGCC
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
* * * * *
54118803 ATATGAATGTGAATTGGGTCTGATGGGCT
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
54118832 ATATAAA
1 ATATAAA
54118839 TAAGATTGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 4 0.07
29 50 0.93
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATAAAGGTGATTTGGGCCTGATGGGCC
Found at i:54126544 original size:29 final size:29
Alignment explanation
Indices: 54126487--54126579 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
54126477 GTGAGAATGA
* * *
54126487 ATAT-AAGGTGATTTGGGCCTAACGTGCC
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
*
54126515 ATATAAAGGTGATTTGGGCCCGATGGGCC
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
* *** *
54126544 ATATAAATGTGGCGTAGGCCTGATGGGCC
1 ATATAAAGGTGATTTGGGCCTGATGGGCC
54126573 ATATAAA
1 ATATAAA
54126580 TGAGATTGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 4 0.07
29 50 0.93
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
ATATAAAGGTGATTTGGGCCTGATGGGCC
Found at i:54129794 original size:56 final size:56
Alignment explanation
Indices: 54129702--54129809 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
54129692 TGAAAAAAAA
54129702 AAAAGAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCG-AATGTACTAAGGAAAG
1 AAAAGAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAAT-TACTAAGGAAAG
** ***
54129758 AAAAGAAAAATTTGTTCATCCTT-TCTCATCTTCTTGGCCGAAATTACTAAGG
1 AAAAGAAAAAAATGTTCATCCTTCTC-CATAGGCTTGGCCGAAATTACTAAGG
54129810 GAAAAGGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 40 0.89
57 3 0.07
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (56 bp):
AAAAGAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAATTACTAAGGAAAG
Found at i:54131071 original size:40 final size:40
Alignment explanation
Indices: 54131005--54131171 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
54130995 AAATTGAATG
* * *
54131005 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
54131044 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54131084 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
54131124 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
54131164 ATATCCGG
1 ATATCCGG
54131172 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54132843 original size:37 final size:38
Alignment explanation
Indices: 54132771--54132870 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 38
54132761 CAGTTGGACT
** *
54132771 AGCTCTTCGGAACAATTGGCGTG-TTATCGAGTGGATG
1 AGCTCTTATGAACATTTGGCGTGTTTATCGAGTGGATG
* * * * *
54132808 AGTTGTTATGAGCATTTGGCGTGTTTA-CGATTGGATT
1 AGCTCTTATGAACATTTGGCGTGTTTATCGAGTGGATG
*
54132845 AGCTCTTATGAACATTTGGCATGTTT
1 AGCTCTTATGAACATTTGGCGTGTTT
54132871 TTGGTGGATT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
37 47 0.94
38 3 0.06
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (38 bp):
AGCTCTTATGAACATTTGGCGTGTTTATCGAGTGGATG
Found at i:54133335 original size:25 final size:25
Alignment explanation
Indices: 54133301--54133349 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
54133291 ATTATATGTC
54133301 ATGTAATAGGATTATTTTGACCTTT
1 ATGTAATAGGATTATTTTGACCTTT
54133326 ATGTAATAGGATTATTTTGACCTT
1 ATGTAATAGGATTATTTTGACCTT
54133350 ACTTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (25 bp):
ATGTAATAGGATTATTTTGACCTTT
Found at i:54138758 original size:44 final size:44
Alignment explanation
Indices: 54138694--54138777 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
54138684 ATGTGATTTG
* *
54138694 AACTCATGAGTTGTGATCTGAGTTCATGATATATTTGACATCTA
1 AACTCATAAGTTGTGATCTGAGTTCATGATATATATGACATCTA
* *
54138738 AACTCATAAGTTGTGGTCTGAGTTCATTATATATATGACA
1 AACTCATAAGTTGTGATCTGAGTTCATGATATATATGACA
54138778 CATGTTTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (44 bp):
AACTCATAAGTTGTGATCTGAGTTCATGATATATATGACATCTA
Found at i:54145381 original size:10 final size:10
Alignment explanation
Indices: 54145327--54145396 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
54145317 TCGTACGGTT
54145327 TATAATATGA
1 TATAATATGA
54145337 TATATATAT-A
1 TATA-ATATGA
54145347 TATATATATGA
1 TATA-ATATGA
* **
54145358 AATGTTTGATGA
1 TAT-AAT-ATGA
54145370 TATAATATGA
1 TATAATATGA
54145380 TATAATA-GA
1 TATAATATGA
54145389 TAT-ATATG
1 TATAATATG
54145397 TTTTATTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 3 0.06
9 6 0.12
10 25 0.51
11 9 0.18
12 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (10 bp):
TATAATATGA
Found at i:54151777 original size:50 final size:50
Alignment explanation
Indices: 54151617--54151765 Score: 243
Period size: 50 Copynumber: 3.1 Consensus size: 50
54151607 ACAGGACAAA
* * *
54151617 AATGAGCCATGTAAGTCCATATCAG----ATATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
54151663 AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
54151713 AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
54151763 AAT
1 AAT
54151766 AATTCATGTA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
46 23 0.24
50 73 0.76
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (50 bp):
AATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGAGACAGG
Found at i:54154052 original size:24 final size:21
Alignment explanation
Indices: 54154020--54154066 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
54154010 AAAAATTCCA
54154020 TGGAACAGGGTCACACGCCCATG
1 TGGAACAGGG--ACACGCCCATG
54154043 TGGACACAGGGACACGCCCATG
1 TGGA-ACAGGGACACGCCCATG
54154065 TG
1 TG
54154067 CCCTCGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.57
23 4 0.17
24 6 0.26
ACGTcount: A:0.26, C:0.30, G:0.32, T:0.13
Consensus pattern (21 bp):
TGGAACAGGGACACGCCCATG
Found at i:54154362 original size:21 final size:21
Alignment explanation
Indices: 54154338--54154377 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54154328 TTAATCCCTT
54154338 ACACAT-TTATACACATCAAAG
1 ACACATATTATA-ACATCAAAG
54154359 ACACATATTATAACATCAA
1 ACACATATTATAACATCAA
54154378 TTTAATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.25
Consensus pattern (21 bp):
ACACATATTATAACATCAAAG
Found at i:54155671 original size:50 final size:50
Alignment explanation
Indices: 54155572--54155746 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
54155562 AGGCCGTATT
*
54155572 CCAGATATGGTCTTACATGGGA--TCACATA-CTGATGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGATCTCACATATC-GATGCCAATGCCATGTC
* * * * *
54155620 CCAGACATGGTCCTACATGGGATCTCACATATCAATGCCACTGTCAGGTC
1 CCAGACATGGTCTTACATGGGATCTCACATATCGATGCCAATGCCATGTC
54155670 CCAGACATGGTCTTACATGGGATCTCACATATCGATGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGATCTCACATATCGATGCCAATGCCATGTC
* *
54155720 CCAAACATGGTTTTACATGGGATCTCA
1 CCAGACATGGTCTTACATGGGATCTCA
54155747 TACATGGGAT
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
48 20 0.18
50 90 0.81
51 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (50 bp):
CCAGACATGGTCTTACATGGGATCTCACATATCGATGCCAATGCCATGTC
Found at i:54155948 original size:20 final size:20
Alignment explanation
Indices: 54155911--54155949 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54155901 GTCACATATA
* *
54155911 TCATGAACTCAGACCACAAC
1 TCATGAACTCAAAACACAAC
*
54155931 TCATGAGCTCAAAACACAA
1 TCATGAACTCAAAACACAA
54155950 ATTTCCTAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (20 bp):
TCATGAACTCAAAACACAAC
Found at i:54158368 original size:40 final size:39
Alignment explanation
Indices: 54158323--54158530 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
54158313 CGGAATACAA
*
54158323 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54158363 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54158403 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
54158443 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
54158483 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
54158523 CCGGATAT
1 CCGGATAT
54158531 CATTTAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:54158470 original size:80 final size:81
Alignment explanation
Indices: 54158323--54158528 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
54158313 CGGAATACAA
* * * *
54158323 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
54158387 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
54158403 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAG-TC-ACTAGCATAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAGAACGACTAGCACAAA
*
54158466 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* * ** * *
54158483 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
54158529 ATCATTTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 104 0.95
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:54166355 original size:40 final size:39
Alignment explanation
Indices: 54166310--54166517 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
54166300 CGGAATACAA
*
54166310 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54166350 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
54166390 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
54166430 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
54166470 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
54166510 CCGGATAT
1 CCGGATAT
54166518 CATTTAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:54166457 original size:80 final size:81
Alignment explanation
Indices: 54166310--54166515 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
54166300 CGGAATACAA
* * * *
54166310 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
54166374 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
54166390 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAG-TC-ACTAGCATAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAGAACGACTAGCACAAA
*
54166453 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* * ** * *
54166470 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
54166516 ATCATTTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 104 0.95
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:54170300 original size:15 final size:15
Alignment explanation
Indices: 54170280--54170308 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54170270 GAAAACTAAG
54170280 ATAGAGGAATCCAAA
1 ATAGAGGAATCCAAA
54170295 ATAGAGGAATCCAA
1 ATAGAGGAATCCAA
54170309 GATACGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.14
Consensus pattern (15 bp):
ATAGAGGAATCCAAA
Found at i:54179132 original size:27 final size:27
Alignment explanation
Indices: 54179091--54179171 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
54179081 GATGGGTCAT
* *
54179091 AAATACCCCCAATTTGCAAAATTATCA
1 AAATACCCCCAATTTGAAAAATTACCA
* *
54179118 AAATACCCCCGATTTGAAAAATTACCG
1 AAATACCCCCAATTTGAAAAATTACCA
* * * *
54179145 AAATACCCCTAGTTTGTAAAATGACCA
1 AAATACCCCCAATTTGAAAAATTACCA
54179172 TAATGCCCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (27 bp):
AAATACCCCCAATTTGAAAAATTACCA
Found at i:54179217 original size:27 final size:28
Alignment explanation
Indices: 54179159--54179220 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
54179149 ACCCCTAGTT
* * *
54179159 TGTAAAATGACCATAATGCCCTTGTAAG
1 TGTAAAATGACCAGAATACCCTTATAAG
54179187 -GTAAAATGACCAGAATACCCTTAT-AG
1 TGTAAAATGACCAGAATACCCTTATAAG
54179213 TGTAAAAT
1 TGTAAAAT
54179221 TATTGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (28 bp):
TGTAAAATGACCAGAATACCCTTATAAG
Found at i:54182268 original size:18 final size:18
Alignment explanation
Indices: 54182247--54182281 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54182237 TTACGTAGAA
54182247 CCAAACACCATCCATTCG
1 CCAAACACCATCCATTCG
**
54182265 CCAAATGCCATCCATTC
1 CCAAACACCATCCATTC
54182282 ATACTCATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.43, G:0.06, T:0.20
Consensus pattern (18 bp):
CCAAACACCATCCATTCG
Found at i:54182906 original size:56 final size:56
Alignment explanation
Indices: 54182817--54182975 Score: 246
Period size: 56 Copynumber: 2.8 Consensus size: 56
54182807 TACAGACATT
* * *
54182817 TCATATCATGACATGGGTCTTAACCACATGGTCTTACATATGTTCATTCAGTCATA
1 TCATATCTTGCCATGGGTCTTAACCACATGGTCTTACATATATTCATTCAGTCATA
* * * *
54182873 TCATATCTTGCCATGTGTCTTAACCTCAAGGTCTTACATATATTCATTTAGTCATA
1 TCATATCTTGCCATGGGTCTTAACCACATGGTCTTACATATATTCATTCAGTCATA
*
54182929 TCATATTTTGCCATGGGTCTTAACCACATGGTCTTACATATATTCAT
1 TCATATCTTGCCATGGGTCTTAACCACATGGTCTTACATATATTCAT
54182976 GTATCTTAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 92 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (56 bp):
TCATATCTTGCCATGGGTCTTAACCACATGGTCTTACATATATTCATTCAGTCATA
Found at i:54185117 original size:29 final size:29
Alignment explanation
Indices: 54185085--54185162 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
54185075 ATACCCTCCG
** *
54185085 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
54185114 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
54185143 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
54185163 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:54187907 original size:18 final size:20
Alignment explanation
Indices: 54187870--54187907 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
54187860 AAATAAAACT
*
54187870 AAAATACAATGTTCAAATTA
1 AAAATACAATGTTAAAATTA
54187890 AAAATA-AAT-TTAAAATTA
1 AAAATACAATGTTAAAATTA
54187908 TTCAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATACAATGTTAAAATTA
Found at i:54192885 original size:47 final size:47
Alignment explanation
Indices: 54192763--54192892 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 47
54192753 GTGTGAATAA
* * ** *
54192763 TACCTTGATTTGGCTACAGGCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGAGAGAAGT
* *
54192810 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGAGAGAAGT
* * *
54192857 TACCTTGATTTGGCTACAGGCTACGGTATATGTACT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
54192893 TATCGATTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCCGAGAGAAGT
Found at i:54196484 original size:40 final size:40
Alignment explanation
Indices: 54196279--54196486 Score: 172
Period size: 40 Copynumber: 5.2 Consensus size: 40
54196269 CAATTGAATG
* * ** **
54196279 ATATCCGGGCTAAGTCCCGAAGACATTTATGC-TGGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAT-GTGGTT
* * **
54196319 ATATCCGGGTTAAGACCCGAAGGAAATT-GTGC-TAGTGACT
1 ATATCCGGGCTAAGACCCGAAGG-CATTCGTGCAT-GTGGTT
* *
54196359 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGC-ATGTGGTT
* * * * * *
54196399 AAATCTGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
* *
54196439 CTATCCGGGCTAAGACCCGAAGGCATTCATGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
54196479 ATATCCGG
1 ATATCCGG
54196487 TCGTATTCTG
Statistics
Matches: 135, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
39 4 0.03
40 128 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
Found at i:54202381 original size:27 final size:27
Alignment explanation
Indices: 54202351--54202422 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
54202341 TATTTTGATT
*
54202351 ATTTGATCACATAAGGGCAAAATCGTC
1 ATTTTATCACATAAGGGCAAAATCGTC
*
54202378 ATTTTAACACATAAGGGCAAAATCGTC
1 ATTTTATCACATAAGGGCAAAATCGTC
*
54202405 ATTTTATCACATGAGGGC
1 ATTTTATCACATAAGGGC
54202423 TCAGGTACGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (27 bp):
ATTTTATCACATAAGGGCAAAATCGTC
Found at i:54216159 original size:29 final size:28
Alignment explanation
Indices: 54216125--54216227 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
54216115 TACTCAATCA
*
54216125 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
54216154 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
54216183 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
54216212 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
54216228 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:54224177 original size:29 final size:28
Alignment explanation
Indices: 54224143--54224245 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
54224133 TACTCAATCA
*
54224143 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
54224172 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
54224201 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
54224230 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
54224246 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:54229227 original size:27 final size:27
Alignment explanation
Indices: 54229169--54229687 Score: 688
Period size: 27 Copynumber: 19.3 Consensus size: 27
54229159 CCAAAATAAT
* * *
54229169 TAAAATAACCGTAAT-GCCCTTTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* * * *
54229195 TAAAATGACTGTAATGCCCTTATAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*
54229222 TAAAATGACCGTAATACCCCTATAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* * * *
54229249 TAAAATAACCATAATGCCCCTATAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
54229276 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* * *
54229303 TAAAATGACCGTAATGCCCCTATAGGT
1 TAAAATGACCGTAATACCCCTGTAGGG
54229330 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*
54229357 TAAAATGACCGTAATGCCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
54229384 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*
54229411 TAAAATGATCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
54229438 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*
54229465 TAAAATGACCGTAAT-GCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* * *
54229491 TAAAAAGACCGTAATACCCCTATATGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*** *
54229518 TAAAATGATTATAATGCCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
54229545 TAAAATGACCGTAATACCCCTGT-GTGG
1 TAAAATGACCGTAATACCCCTGTAG-GG
* *
54229572 TAAAATGA-CGATTATGCCCCTGTAGGG
1 TAAAATGACCG-TAATACCCCTGTAGGG
* * *
54229599 TAAAATGATCGTAATACCTCTGTAAGG
1 TAAAATGACCGTAATACCCCTGTAGGG
*
54229626 TAAAATGACCGTAATGCCCCTGT-GGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* *
54229652 TAAAATGACCGTAATACCCCTATATGG
1 TAAAATGACCGTAATACCCCTGTAGGG
54229679 TAAAATGAC
1 TAAAATGAC
54229688 GATTATGCCC
Statistics
Matches: 432, Mismatches: 54, Indels: 13
0.87 0.11 0.03
Matches are distributed among these distances:
26 63 0.15
27 366 0.85
28 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
TAAAATGACCGTAATACCCCTGTAGGG
Found at i:54232658 original size:28 final size:27
Alignment explanation
Indices: 54232595--54232664 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54232585 ATAGTGAGTC
*
54232595 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54232622 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54232650 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54232665 GTACAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54238686 original size:17 final size:18
Alignment explanation
Indices: 54238664--54238700 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
54238654 AAGCCAGAAC
54238664 TCGGCCCTTTC-GCATCA
1 TCGGCCCTTTCGGCATCA
54238681 TCGGCCCTTTCGGCATCA
1 TCGGCCCTTTCGGCATCA
54238699 TC
1 TC
54238701 AGTAACTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.11, C:0.41, G:0.19, T:0.30
Consensus pattern (18 bp):
TCGGCCCTTTCGGCATCA
Found at i:54240604 original size:28 final size:27
Alignment explanation
Indices: 54240541--54240610 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54240531 ATAGTGAGTC
*
54240541 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
54240568 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54240596 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54240611 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54243192 original size:5 final size:5
Alignment explanation
Indices: 54243182--54243207 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54243172 ATTTACTAAC
54243182 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
54243208 TCATAACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:54248062 original size:14 final size:14
Alignment explanation
Indices: 54248043--54248071 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54248033 AGGAATAGTT
54248043 AGGATACAAATGTC
1 AGGATACAAATGTC
54248057 AGGATACAAATGTC
1 AGGATACAAATGTC
54248071 A
1 A
54248072 TGACATTAGG
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:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGGATACAAATGTC
Done.