Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 81 of 235
Found at i:28019016 original size:40 final size:40
Alignment explanation
Indices: 28018986--28019155 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
28018976 GGACTAAGAT
* *
28018986 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* *
28019026 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** * *
28019066 CCGAAGGCATTCGTGCGAGTTGTTTAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
28019106 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
28019145 CCGAAGGCATT
1 CCGAAGGCATT
28019156 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 33 0.28
40 84 0.72
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:28019070 original size:80 final size:79
Alignment explanation
Indices: 28018933--28019157 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 79
28018923 TTGAATGCTG
* * * * * * *
28018933 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
28018997 TGTGCGAGATACTAAA
64 TGTGCGAGATACTAAA
* * *
28019013 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTT
* ** *
28019078 GTGCGAGTTGTTTAA
65 GTGCGAGATACTAAA
* * * * *
28019093 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
28019158 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 36 0.30
80 82 0.67
81 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:28019175 original size:79 final size:80
Alignment explanation
Indices: 28019011--28019190 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 80
28019001 CGAGATACTA
* * *
28019011 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** ** *
28019076 TCGTGCGAGTTGTTT
66 TCGAACGAGGAGTAT
* * *
28019091 AATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAT
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
28019155 TTGAACGAGGAGCTAT
66 TCGAACGAGGAG-TAT
*
28019171 -ATCC-GGTTAAATCCCGAAGG
1 AATCCGGGTTAAGTCCCGAAGG
28019191 TAATGAATGA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
78 14 0.16
79 44 0.52
80 27 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
TCGAACGAGGAGTAT
Found at i:28021353 original size:34 final size:34
Alignment explanation
Indices: 28021302--28021368 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
28021292 AGATACGCTT
*
28021302 GGGAATGTGTTTCGTCCGAGGCTATCATGTGTAG
1 GGGAATGGGTTTCGTCCGAGGCTATCATGTGTAG
*
28021336 GGGAATGGGTTTTGTCCGAGGCTATCATGTGTA
1 GGGAATGGGTTTCGTCCGAGGCTATCATGTGTA
28021369 AACGCTTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.13, G:0.36, T:0.33
Consensus pattern (34 bp):
GGGAATGGGTTTCGTCCGAGGCTATCATGTGTAG
Found at i:28026323 original size:25 final size:24
Alignment explanation
Indices: 28026279--28026355 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 24
28026269 GCCTAGCCTC
* *
28026279 TTTTAATAACTGGGGTAAAGCCCT
1 TTTTGATAACTGGGGCAAAGCCCT
28026303 TTTTGATAACCTGGGGCAAAGCCCT
1 TTTTGATAA-CTGGGGCAAAGCCCT
* * *
28026328 TTTCGGTAAATTGGGGCAAAGCCCT
1 TTTTGAT-AACTGGGGCAAAGCCCT
28026353 TTT
1 TTT
28026356 AGCACTTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.17
25 36 0.78
26 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (24 bp):
TTTTGATAACTGGGGCAAAGCCCT
Found at i:28026590 original size:27 final size:27
Alignment explanation
Indices: 28026561--28026721 Score: 232
Period size: 27 Copynumber: 6.0 Consensus size: 27
28026551 GGGCAAAATG
* * * *
28026561 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
28026588 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
28026615 GTAATTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
28026642 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
28026669 GTAATTCTACCCTACATGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * *
28026696 GTAATTCTACCTTATAGGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
28026722 GATATTTTAC
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:28026853 original size:81 final size:81
Alignment explanation
Indices: 28026766--28026918 Score: 227
Period size: 81 Copynumber: 1.9 Consensus size: 81
28026756 CACAGATCAA
* * *
28026766 GGGTATTTTGGTAATTTTAC-AAGCCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTA
1 GGGTATTTTGGTAATTTTACTAA-CCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTA
28026830 GTAATTTTACAAACAAG
65 GTAATTTTACAAACAAG
* ** *
28026847 GGGTATTTTGGTAATTTTACTAATCAAGGGTATTTTGGTAATTTTGTAAACCAATGGTATTTTAG
1 GGGTATTTTGGTAATTTTACTAACCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAG
28026912 TAATTTT
66 TAATTTT
28026919 GTAAATCGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACTAACCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAG
TAATTTTACAAACAAG
Found at i:28026923 original size:27 final size:27
Alignment explanation
Indices: 28026725--28026918 Score: 201
Period size: 27 Copynumber: 7.2 Consensus size: 27
28026715 GTATTTCGAT
* * * * *
28026725 ATTTTACAAATCGAGAGTATTTCGATA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* * *
28026752 ATTTCACAGATCAAGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* *
28026779 ATTTTACAAGCCAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* * *
28026806 ATTTTACAAACTAGGGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
28026833 ATTTTACAAA-CAAGGGGTATTTTGGTA
1 ATTTTACAAACCAA-GGGTATTTTGGTA
* *
28026860 ATTTTACTAATCAAGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
** * *
28026887 ATTTTGTAAACCAATGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
28026914 ATTTT
1 ATTTT
28026919 GTAAATCGAG
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 137 0.97
28 3 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
ATTTTACAAACCAAGGGTATTTTGGTA
Found at i:28026932 original size:27 final size:27
Alignment explanation
Indices: 28026725--28027107 Score: 191
Period size: 27 Copynumber: 14.2 Consensus size: 27
28026715 GTATTTCGAT
* * *
28026725 ATTTTACAAATCGAGAGT-ATTTCGATA
1 ATTTTATAAATCGAGGGTAATTT-GGTA
* * * * *
28026752 ATTTCACAGATCAAGGGTATTTTGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* * * *
28026779 ATTTTA-CAAGCCAGGGGTATTTTGGTA
1 ATTTTATAAATCGA-GGGTAATTTGGTA
* * * *
28026806 ATTTTACAAA-CTAGGGGTATTTTAGTA
1 ATTTTATAAATCGA-GGGTAATTTGGTA
* * *
28026833 ATTTTACAAA-CAAGGGGTATTTTGGTA
1 ATTTTATAAATCGA-GGGTAATTTGGTA
* *
28026860 ATTTTACT-AATCAAGGGTATTTTGGTA
1 ATTTTA-TAAATCGAGGGTAATTTGGTA
* * * * * *
28026887 ATTTTGTAAACCAATGGTATTTTAGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* ***
28026914 ATTTTGTAAATCGAGGGTAAAACGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* ** *
28026941 ATTCTATAAATCGAGGGTAAAATAGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* **
28026968 ATTCTATAAATCGAGGGTAAAATGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* **
28026995 ATTCTATAAATCGAGGGTAAAATGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* * * ****
28027022 ATTCTGTAAATCGAGGATAAAACAGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* ***
28027049 ATTCTATAAATCGAGGGTAAAACGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
* * *
28027076 ATTCTGTAAATCGAGGGTACTTTGGTA
1 ATTTTATAAATCGAGGGTAATTTGGTA
28027103 ATTTT
1 ATTTT
28027108 CCAAATTGAG
Statistics
Matches: 303, Mismatches: 47, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.01
27 291 0.96
28 8 0.03
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (27 bp):
ATTTTATAAATCGAGGGTAATTTGGTA
Found at i:28026958 original size:81 final size:81
Alignment explanation
Indices: 28026793--28027037 Score: 215
Period size: 81 Copynumber: 3.0 Consensus size: 81
28026783 TACAAGCCAG
* * * * * ***
28026793 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAA-CAAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAATCGA-GGGTAAAATG
* *
28026857 GTAATTTTACT-AATCAA
65 GTAATTCTA-TAAATCGA
* * * *
28026874 GGGTATTTTGGTAATTTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACGG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGG
28026939 TAATTCTATAAATCGA
66 TAATTCTATAAATCGA
*** * * * * *** * *
28026955 GGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGG
*
28027020 TAATTCTGTAAATCGA
66 TAATTCTATAAATCGA
28027036 GG
1 GG
28027038 ATAAAACAGT
Statistics
Matches: 131, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
80 1 0.01
81 128 0.98
82 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGG
TAATTCTATAAATCGA
Found at i:28027105 original size:54 final size:54
Alignment explanation
Indices: 28026911--28027094 Score: 305
Period size: 54 Copynumber: 3.4 Consensus size: 54
28026901 TGGTATTTTA
* *
28026911 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
* *
28026965 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
* * *
28027019 GTAATTCTGTAAATCGAGGATAAAACAGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
28027073 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
28027095 CTTTGGTAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
Found at i:28027122 original size:81 final size:81
Alignment explanation
Indices: 28026911--28027094 Score: 305
Period size: 81 Copynumber: 2.3 Consensus size: 81
28026901 TGGTATTTTA
* * * *
28026911 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGATAAAACAGTAATTCTATA
*
28026976 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAACG
* *
28026992 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGATAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGATAAAACAGTAATTCTATA
28027057 AATCGAGGGTAAAACG
66 AATCGAGGGTAAAACG
28027073 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
28027095 CTTTGGTAAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGATAAAACAGTAATTCTATA
AATCGAGGGTAAAACG
Found at i:28027129 original size:81 final size:81
Alignment explanation
Indices: 28026911--28027132 Score: 282
Period size: 81 Copynumber: 2.7 Consensus size: 81
28026901 TGGTATTTTA
* * * ** * *
28026911 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATA
1 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTCCAAATCGAGGATAAAACAGTAATTCTATA
*
28026976 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAACG
**
28026992 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGATAAAACAGTAATTCTATA
1 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTCCAAATCGAGGATAAAACAGTAATTCTATA
28027057 AATCGAGGGTAAAACG
66 AATCGAGGGTAAAACG
* *** * * **
28027073 GTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTCCAAATTGAGGATAATTCAGTAATT
1 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTCCAAATCGAGGATAAAACAGTAATT
28027133 TGGTAAACTA
Statistics
Matches: 124, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 124 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (81 bp):
GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTCCAAATCGAGGATAAAACAGTAATTCTATA
AATCGAGGGTAAAACG
Found at i:28029348 original size:24 final size:25
Alignment explanation
Indices: 28029321--28029397 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
28029311 GCCTAGCCTC
*
28029321 TTTTAAT-AACTAGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
28029345 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* * *
28029370 TTTCAGTAAACTGGGGCAAAGTCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
28029395 TTT
1 TTT
28029398 AGCACTTCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 6 0.13
25 40 0.87
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:28029635 original size:27 final size:27
Alignment explanation
Indices: 28029605--28029740 Score: 209
Period size: 27 Copynumber: 5.0 Consensus size: 27
28029595 GGGGCAAAAT
* * *
28029605 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28029632 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28029659 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28029686 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28029713 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28029740 G
1 G
28029741 ATATTTTACA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28029790 original size:27 final size:26
Alignment explanation
Indices: 28029730--28029791 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
28029720 CTACCCTACA
*
28029730 AGGG-TATTTCGATATTTTACAAATC
1 AGGGATATTTCGATATTTCACAAATC
* *
28029755 -GAGAGTATTTCGATAATTTCACAGATC
1 AGGGA-TATTTCGAT-ATTTCACAAATC
28029782 AGGGATATTT
1 AGGGATATTT
28029792 TAGTAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
24 2 0.07
26 9 0.31
27 15 0.52
28 3 0.10
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (26 bp):
AGGGATATTTCGATATTTCACAAATC
Found at i:28029798 original size:27 final size:27
Alignment explanation
Indices: 28029781--28029857 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
28029771 TTTCACAGAT
*
28029781 CAGGGATATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTAGTAATTTTACAAAC
28029808 CAGGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTAGTAATTTTACAAAC
*
28029835 CAGGGGTATTTTGGTAATTTTAC
1 CAGGGGTATTTTAGTAATTTTAC
28029858 TGATCGATGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTAGTAATTTTACAAAC
Found at i:28029997 original size:27 final size:27
Alignment explanation
Indices: 28029874--28029986 Score: 199
Period size: 27 Copynumber: 4.2 Consensus size: 27
28029864 ATGGTATTTT
28029874 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
28029901 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
** *
28029928 GAATAAAACGGTAATTTTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
28029955 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
28029982 GGGTA
1 GGGTA
28029987 CTTTGGTAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTATAAATCGA
Found at i:28035207 original size:46 final size:46
Alignment explanation
Indices: 28035106--28035193 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
28035096 TGTAACCCGC
* * * *
28035106 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
28035152 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
28035194 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:28052592 original size:40 final size:40
Alignment explanation
Indices: 28052407--28052643 Score: 246
Period size: 40 Copynumber: 5.9 Consensus size: 40
28052397 CTGTGTTCCA
* * *
28052407 GTTGGATCAACTTTTACGAGCTTCTATTTGGCGTGTTACG
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTGTTACG
* * * *
28052447 ATTGGATCAACTTTTATGAGCTTTTATTTGGCGTGTTACG
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTGTTACG
* * *
28052487 GTTGGATCAACTCTTATGAGCATCTGTTTTGCGCT-TTTCG
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCG-TGTTACG
*
28052527 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTACG
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTGTTACG
* * * *
28052567 GTTGGATCAACTTTTATAAGCTTCTGTTTAGTGTGCTT-CAG
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTG-TTAC-G
* * * * *
28052608 G-TGGATCAGCTCTTATAAGTTTCTGTCTGGTGTGTT
1 GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTGTT
28052644 CTGTTGATCT
Statistics
Matches: 169, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.02
40 161 0.95
41 5 0.03
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (40 bp):
GTTGGATCAACTCTTATGAGCTTCTGTTTGGCGTGTTACG
Found at i:28052621 original size:120 final size:120
Alignment explanation
Indices: 28052407--28052623 Score: 303
Period size: 120 Copynumber: 1.8 Consensus size: 120
28052397 CTGTGTTCCA
* * *
28052407 GTTGGATCAACTTTTACGAGCTTCTATTTGGCGTGTTACGATTGGATCAACTTTTATGAGCTTTT
1 GTTGGATCAACTCTTACGAGCTTCTATTTGGCGTGTTACGATTGGATCAACTTTTATAAGCTTCT
*
28052472 ATTTGGCGTGTTACGGTTGGATCAACTCTTATGAGCATCTGTTTTGCGCTTTTCG
66 ATTTAGCGTGTTACGGTTGGATCAACTCTTATGAGCATCTGTTTTGCGCTTTTCG
* * * *
28052527 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTACGGTTGGATCAACTTTTATAAGCTTCT
1 GTTGGATCAACTCTTACGAGCTTCTATTTGGCGTGTTACGATTGGATCAACTTTTATAAGCTTCT
* * *
28052592 GTTTAGTGTGCTT-CAGG-TGGATCAGCTCTTAT
66 ATTTAGCGTG-TTAC-GGTTGGATCAACTCTTAT
28052624 AAGTTTCTGT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 80 0.95
121 4 0.05
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (120 bp):
GTTGGATCAACTCTTACGAGCTTCTATTTGGCGTGTTACGATTGGATCAACTTTTATAAGCTTCT
ATTTAGCGTGTTACGGTTGGATCAACTCTTATGAGCATCTGTTTTGCGCTTTTCG
Found at i:28053355 original size:20 final size:20
Alignment explanation
Indices: 28053307--28053362 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
28053297 AGTTTATGCT
** * *
28053307 AAGTAAATAAAATGGAAAGT
1 AAGTAAATGGAATGGTAAGA
28053327 AAGTAAATGGAATGGTAAGA
1 AAGTAAATGGAATGGTAAGA
*
28053347 AAGTAAATGGAGTGGT
1 AAGTAAATGGAATGGT
28053363 TCATAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (20 bp):
AAGTAAATGGAATGGTAAGA
Found at i:28070346 original size:75 final size:75
Alignment explanation
Indices: 28070199--28070349 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
28070189 CCATCTTGTC
* *
28070199 AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTGAATCTTCCACTGCTTTACCATCA
1 AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
*
28070264 ACTAAGTTTG
66 ACAAAGTTTG
* **
28070274 AAGACTATCTACAATTGTATTTTCTTCCCAGGGAATATGTTCAAACTTCCACTGCTTTACCATTG
1 AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
28070339 ACAAAGTTTG
66 ACAAAGTTTG
28070349 A
1 A
28070350 TGAATTCTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (75 bp):
AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
ACAAAGTTTG
Found at i:28076441 original size:25 final size:23
Alignment explanation
Indices: 28076413--28076464 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
28076403 TTTATGAGCG
*
28076413 TCCTAATATAAGCTCTTCTTGAACT
1 TCCTAATAT-AGCTC-ACTTGAACT
*
28076438 TCCTAATATGGCTCACTTGAACT
1 TCCTAATATAGCTCACTTGAACT
28076461 TCCT
1 TCCT
28076465 GTTATATGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 4 0.16
25 9 0.36
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (23 bp):
TCCTAATATAGCTCACTTGAACT
Found at i:28080265 original size:40 final size:40
Alignment explanation
Indices: 28080210--28080386 Score: 275
Period size: 40 Copynumber: 4.4 Consensus size: 40
28080200 TGGAGGATAA
* * * *
28080210 CCGGGCCAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
28080250 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28080290 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28080330 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28080370 CCGGGCTATGTCCCGAA
1 CCGGGCTAAGTCCCGAA
28080387 TGTATTCGAG
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 126 0.99
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28080400 original size:40 final size:40
Alignment explanation
Indices: 28080210--28080410 Score: 255
Period size: 40 Copynumber: 5.0 Consensus size: 40
28080200 TGGAGGATAA
* * * *
28080210 CCGGGCCAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTA-TAT
28080250 CCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTTACTATAT
* *
28080290 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT
*
28080330 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT
* * * *
28080370 CCGGGCTATGTCCCGAATGTATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTA-CTATAT
28080410 C
1 C
28080411 TGGTTCAATC
Statistics
Matches: 145, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 142 0.98
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT
Found at i:28088414 original size:40 final size:40
Alignment explanation
Indices: 28088312--28088486 Score: 180
Period size: 40 Copynumber: 4.4 Consensus size: 40
28088302 AGGATAACCA
* * **
28088312 GGCTAAGTCCCGAAGGCATTTGCGCTAGCGACTAGT-TCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCG
28088352 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
**
28088392 GGCTAAGTCCCGAAGGCATTTGTGCG-GTTTACTATATTGG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAG-TTACTATATCCG
* * * * *
28088432 GGCTATGTCCCGAAGGTATTCGAGCGAG-TAGCTATATCTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
28088472 GTGC-AA-TCCCGAAGG
1 G-GCTAAGTCCCGAAGG
28088487 TACTTGGCTC
Statistics
Matches: 117, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 13 0.11
40 101 0.86
41 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:28094394 original size:56 final size:56
Alignment explanation
Indices: 28094308--28094414 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
28094298 TTGTATATTT
* * *
28094308 TCAACAATAGAAGAGTTATAGTATATATAACCAATAATACATGAAGCTTTATAGGG
1 TCAACAATAGAAGAGTTACAGTATATATAACCAACAACACATGAAGCTTTATAGGG
* * *
28094364 TCAACAATAGAGGAGTTACAGTATATATAACCTACAACACATTAAGCTTTA
1 TCAACAATAGAAGAGTTACAGTATATATAACCAACAACACATGAAGCTTTA
28094415 CAAGGAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (56 bp):
TCAACAATAGAAGAGTTACAGTATATATAACCAACAACACATGAAGCTTTATAGGG
Found at i:28094524 original size:56 final size:57
Alignment explanation
Indices: 28094445--28094551 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 57
28094435 TCCTATAATC
*
28094445 AAGGATTGACTCAATCCTAAAGAAAGAAATA-AATAAAATCTCATCAAATTATAACT
1 AAGGATTGACTCAATCCTAAAGAAAGAAAAATAATAAAATCTCATCAAATTATAACT
*
28094501 AAGGATTGACTCCATCCTAAAGAAAGAAAAATAATAAAATCTCATCAAATT
1 AAGGATTGACTCAATCCTAAAGAAAGAAAAATAATAAAATCTCATCAAATT
28094552 TGTCTCAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 29 0.60
57 19 0.40
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.24
Consensus pattern (57 bp):
AAGGATTGACTCAATCCTAAAGAAAGAAAAATAATAAAATCTCATCAAATTATAACT
Found at i:28106507 original size:15 final size:17
Alignment explanation
Indices: 28106476--28106508 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28106466 GAAGGATCTG
28106476 ATCGATAACAGTGAAAC
1 ATCGATAACAGTGAAAC
28106493 ATCGAT-ACA-TGAAAC
1 ATCGATAACAGTGAAAC
28106508 A
1 A
28106509 CATTGTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (17 bp):
ATCGATAACAGTGAAAC
Found at i:28108813 original size:42 final size:42
Alignment explanation
Indices: 28108754--28108907 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 42
28108744 TCAGTATCAG
*
28108754 TATGAG-TTATCATGTAAGACCATATCTGGGATATGGTGTTGA
1 TATGAGATT-TCATGTAAGACCATATCTGGGATATGGCGTTGA
* * * * *
28108796 TATGAGATTTCGTGTAAGATCATGTCTGGGACATGGCGTCGA
1 TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTTGA
* * * * * *
28108838 AATGAGAATTCTTATAAGACCATATCTGAGATATGGCATTGA
1 TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTTGA
* ** *
28108880 TGTGAGATCCCATGTAAGACCATGTCTG
1 TATGAGATTTCATGTAAGACCATATCTG
28108908 AGACATGGAA
Statistics
Matches: 87, Mismatches: 24, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 85 0.98
43 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTTGA
Found at i:28111000 original size:37 final size:37
Alignment explanation
Indices: 28110959--28111032 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
28110949 CCAAGACCAT
28110959 TCAATGATGCATCACTGA-AAATCACAAACTCTTTCCC
1 TCAATGATGCATCACT-ATAAATCACAAACTCTTTCCC
* * * *
28110996 TCAATGATGTATCGCTATAAATTACAAATTCTTTCCC
1 TCAATGATGCATCACTATAAATCACAAACTCTTTCCC
28111033 CGACTCAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (37 bp):
TCAATGATGCATCACTATAAATCACAAACTCTTTCCC
Found at i:28118870 original size:55 final size:54
Alignment explanation
Indices: 28118775--28118924 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
28118765 CTACTTTGTT
* ** * *
28118775 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
28118829 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
28118884 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
28118925 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:28118887 original size:27 final size:27
Alignment explanation
Indices: 28118747--28118924 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
28118737 TAAATTGTAC
28118747 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
28118774 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
28118800 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
28118828 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
28118856 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
28118883 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
28118910 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28118925 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:28118888 original size:82 final size:81
Alignment explanation
Indices: 28118748--28118903 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
28118738 AAATTGTACA
* * * *
28118748 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
28118813 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
28118829 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
28118892 TGTGCGAGTTGA
63 TGTGCGAATTGA
28118904 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:28121601 original size:43 final size:43
Alignment explanation
Indices: 28121532--28121623 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 43
28121522 CTAAGTAAGC
* *
28121532 AAAAGAAATAATAAAGCAACAGGGAGGGAAAAAAGAAAGAACA
1 AAAAGAAATAATAAAGAAACAAGGAGGGAAAAAAGAAAGAACA
*
28121575 AAAAGAAATAATAAAGAAATAAGGAGGGAAAAAAGAAAGAACA
1 AAAAGAAATAATAAAGAAACAAGGAGGGAAAAAAGAAAGAACA
28121618 AAAAGA
1 AAAAGA
28121624 GTGGGAGGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.68, C:0.04, G:0.22, T:0.05
Consensus pattern (43 bp):
AAAAGAAATAATAAAGAAACAAGGAGGGAAAAAAGAAAGAACA
Found at i:28123755 original size:28 final size:28
Alignment explanation
Indices: 28123700--28123802 Score: 109
Period size: 28 Copynumber: 3.7 Consensus size: 28
28123690 TGGCCCCTTT
* *
28123700 AGGCCCAATCTCATTCATATGACCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
28123728 -GTGCCCAATCACAATCATATGGCTCATC
1 AG-GCCCAATCACATTCATATGGCCCATC
* * * *
28123756 AGGCCCAATAACTTTCATATGGCCCTTT
1 AGGCCCAATCACATTCATATGGCCCATC
*
28123784 AGGCCCAATCACACTCATA
1 AGGCCCAATCACATTCATA
28123803 GTCATGCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
27 1 0.02
28 58 0.97
29 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:28129118 original size:27 final size:27
Alignment explanation
Indices: 28129012--28129123 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 27
28129002 AGCATGGCTG
** *
28129012 CCAGAACAGATAA-TGTAACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
28129038 CCAGATACAAATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
* *
28129066 CCAGAACAGAT-ATATATGGTAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
28129093 CTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
28129120 CCAG
1 CCAG
28129124 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
26 7 0.10
27 44 0.66
28 16 0.24
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:28129553 original size:8 final size:8
Alignment explanation
Indices: 28129536--28129568 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
28129526 TCTCAAAATA
28129536 TCGGCTTT
1 TCGGCTTT
*
28129544 TCGGCATT
1 TCGGCTTT
28129552 TCGGCTTT
1 TCGGCTTT
28129560 TCGGCTTT
1 TCGGCTTT
28129568 T
1 T
28129569 GCCGATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.48
Consensus pattern (8 bp):
TCGGCTTT
Found at i:28132448 original size:30 final size:30
Alignment explanation
Indices: 28132414--28132474 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28132404 TCCTTAACTC
28132414 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
28132444 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
28132474 A
1 A
28132475 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:28133664 original size:36 final size:36
Alignment explanation
Indices: 28133602--28133673 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
28133592 TGATGCTTAG
*
28133602 CTTTCACTTGCTGGCATATCAGACATTTCCCTACAA
1 CTTTCACTTGCTGGCATATCAAACATTTCCCTACAA
* * * *
28133638 CTTTCACTTGTTGGCGTGTCAAACATTTTCCTACAA
1 CTTTCACTTGCTGGCATATCAAACATTTCCCTACAA
28133674 ACTCCGTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (36 bp):
CTTTCACTTGCTGGCATATCAAACATTTCCCTACAA
Found at i:28135947 original size:30 final size:30
Alignment explanation
Indices: 28135889--28135949 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28135879 TTCCCAAGCC
*
28135889 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATACAAAAGTT
* * * *
28135919 TAGGGGCAAAATTGTAATTTTACCAAAGTT
1 TAGGGGCAAAAGTGTAAATATACAAAAGTT
28135949 T
1 T
28135950 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATACAAAAGTT
Found at i:28138942 original size:68 final size:67
Alignment explanation
Indices: 28138870--28139019 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28138860 CATCATGTGT
* * * *
28138870 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28138932 ATGTAG
62 ATGTAG
** * *
28138938 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28139003 AG
66 AG
28139005 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28139020 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28138975 original size:64 final size:64
Alignment explanation
Indices: 28138894--28139077 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28138884 AGACATTATG
* *
28138894 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28138958 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28139023 AA
63 AA
* * * *
28139025 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28139078 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28142603 original size:30 final size:30
Alignment explanation
Indices: 28142545--28142605 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28142535 TTCCCAAGCC
*
28142545 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATACAAAAGTT
* * * *
28142575 TAGGGGCAAAATTGTAATTTTACCAAAGTT
1 TAGGGGCAAAAGTGTAAATATACAAAAGTT
28142605 T
1 T
28142606 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATACAAAAGTT
Found at i:28143111 original size:59 final size:59
Alignment explanation
Indices: 28143036--28143153 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
28143026 GGATATTATG
* *
28143036 GGAAATTGTAAATTCATATGATTTTTAATAAGGCAATGTGTAATTTAATGTTATTGCCT
1 GGAAATTGTAAATTCATATGATTTCTAATAAGACAATGTGTAATTTAATGTTATTGCCT
*
28143095 GGAAATTGTAAGTTCATATGATTTCTAATAAGACAATGTGTAATTTAATGTTATTGCCT
1 GGAAATTGTAAATTCATATGATTTCTAATAAGACAATGTGTAATTTAATGTTATTGCCT
28143154 TGATATTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.42
Consensus pattern (59 bp):
GGAAATTGTAAATTCATATGATTTCTAATAAGACAATGTGTAATTTAATGTTATTGCCT
Found at i:28144169 original size:86 final size:86
Alignment explanation
Indices: 28144037--28144207 Score: 288
Period size: 86 Copynumber: 2.0 Consensus size: 86
28144027 TAAAAGAAAC
* * * *
28144037 AGAGAAAGAAATTAAGTTCTGTATTTTTAGATATTTATGTTTTTTTGAGAATGGTTCAGAATGAT
1 AGAGAAAGAAAATAAGTTCTATATATTTAGATATTTATGTTTTTTTGAGAATGGTCCAGAATGAT
28144102 TACGTGATCCCCTGTTCTGAT
66 TACGTGATCCCCTGTTCTGAT
*
28144123 AGAGAAAGAAAATAAGTTCTATATATTTAGATATTTATGTTTTTTTGAGACTGGTCCAGAATGAT
1 AGAGAAAGAAAATAAGTTCTATATATTTAGATATTTATGTTTTTTTGAGAATGGTCCAGAATGAT
*
28144188 TATGTGATCCCCTGTTCTGA
66 TACGTGATCCCCTGTTCTGA
28144208 CTTTGGAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (86 bp):
AGAGAAAGAAAATAAGTTCTATATATTTAGATATTTATGTTTTTTTGAGAATGGTCCAGAATGAT
TACGTGATCCCCTGTTCTGAT
Found at i:28151497 original size:27 final size:27
Alignment explanation
Indices: 28151462--28151518 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
28151452 AGCATGGCTG
*
28151462 CCAGAACAGATAAT-GTGACAGAGTCA
1 CCAGAACAGATAATCGTGACAGAGCCA
*
28151488 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATCGTGACAGAGCCA
28151516 CCA
1 CCA
28151519 ATATATGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 5 0.19
27 9 0.33
28 13 0.48
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.14
Consensus pattern (27 bp):
CCAGAACAGATAATCGTGACAGAGCCA
Found at i:28151556 original size:48 final size:49
Alignment explanation
Indices: 28151474--28151566 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
28151464 AGAACAGATA
*
28151474 ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAG-AGCCACCAATAT
1 ATGTGACAGAGCCACCAGATACAGATAATCGTGGC-GTAGCCACCAATAT
* * * *
28151523 ATGTGGCAGAGCCACTAGAT-CATATAATTGTGGCGTAGCCACCA
1 ATGTGACAGAGCCACCAGATACAGATAATCGTGGCGTAGCCACCA
28151567 GGACGCTTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 1 0.03
48 20 0.53
49 17 0.45
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (49 bp):
ATGTGACAGAGCCACCAGATACAGATAATCGTGGCGTAGCCACCAATAT
Found at i:28151998 original size:8 final size:8
Alignment explanation
Indices: 28151982--28152013 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28151972 CTCAAAATAC
28151982 CGGCTTTT
1 CGGCTTTT
*
28151990 CGGCATTT
1 CGGCTTTT
28151998 CGGCTTTT
1 CGGCTTTT
28152006 CGGCTTTT
1 CGGCTTTT
28152014 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:28163324 original size:22 final size:22
Alignment explanation
Indices: 28163299--28163369 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
28163289 CCACTAGTCT
28163299 ATTCTATACATGCCATAAAATA
1 ATTCTATACATGCCATAAAATA
* ** **
28163321 ATTCTAAACATAACAGTAACAAGCG
1 ATTCTATACATGCCA-TAA-AA-TA
*
28163346 ATTCTATACATGCCATAAGATA
1 ATTCTATACATGCCATAAAATA
28163368 AT
1 AT
28163370 CCAAAACGTA
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
22 14 0.40
23 4 0.11
24 5 0.14
25 12 0.34
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.28
Consensus pattern (22 bp):
ATTCTATACATGCCATAAAATA
Found at i:28163987 original size:37 final size:37
Alignment explanation
Indices: 28163924--28164032 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
28163914 AGCTCAGACG
* * *
28163924 AAATCTCCACACGAAGTTATCAGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
28163961 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
28163998 TAATCTCCACACGTAGTCGTCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28164033 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:28164429 original size:47 final size:47
Alignment explanation
Indices: 28164377--28164562 Score: 273
Period size: 47 Copynumber: 4.0 Consensus size: 47
28164367 TTTCACACTA
* * * *
28164377 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
28164424 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
28164471 GCCATTCGACCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * **
28164518 GCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
28164563 AAAATCCTAA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:28164489 original size:22 final size:22
Alignment explanation
Indices: 28164462--28164533 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
28164452 GCTCACATTC
28164462 ATCACATTGGCCATTCGACCTT
1 ATCACATTGGCCATTCGACCTT
* *
28164484 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
*
28164508 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
28164531 ATC
1 ATC
28164534 TCATATATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
22 13 0.34
23 7 0.18
24 8 0.21
25 10 0.26
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:28167701 original size:13 final size:13
Alignment explanation
Indices: 28167683--28167707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28167673 TGTGTGATAT
28167683 GTGTGAAAATTTC
1 GTGTGAAAATTTC
28167696 GTGTGAAAATTT
1 GTGTGAAAATTT
28167708 TATCATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:28177956 original size:40 final size:40
Alignment explanation
Indices: 28177924--28178235 Score: 489
Period size: 40 Copynumber: 7.8 Consensus size: 40
28177914 CCAGCATGAT
* * *
28177924 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
28177964 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
28178004 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
28178044 TGCTCTTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
28178084 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
28178124 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
28178164 TGCTCTTTGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
28178204 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
28178236 CTCAATTCTC
Statistics
Matches: 245, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 245 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:28179517 original size:37 final size:37
Alignment explanation
Indices: 28179470--28179614 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
28179460 ACCTTTAGCT
* * *
28179470 CGGACGAAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
28179507 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
*
28179544 CGGGCAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
***
28179581 CGGACATCCTCTCCACACGTAGTCATCGGGTCTT
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTT
28179615 TAGAGCTCGG
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (37 bp):
CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:28179804 original size:47 final size:47
Alignment explanation
Indices: 28179744--28181060 Score: 2418
Period size: 47 Copynumber: 28.0 Consensus size: 47
28179734 TTATCAAATT
* * ** * * * *
28179744 TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28179791 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
* * *
28179838 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
* * * * *
28179885 TATACACTTTCCCATTCATCACATCGGCTATTAGGCCTTGTCACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28179932 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
* *
28179979 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180026 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
* *
28180073 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180120 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180167 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180214 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180261 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180308 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180355 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180402 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180449 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180496 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180543 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180590 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180637 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180684 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180731 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180778 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180825 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180872 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180919 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28180966 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
** * *
28181013 TATACACTTTCACATTCATCACATTGGCTATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
28181060 T
1 T
28181061 TGTAACACCC
Statistics
Matches: 1240, Mismatches: 30, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 1240 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (47 bp):
TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATGACATA
Found at i:28195955 original size:20 final size:20
Alignment explanation
Indices: 28195930--28195967 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28195920 GTAACATATA
28195930 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
28195950 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
28195968 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:28202482 original size:29 final size:29
Alignment explanation
Indices: 28202436--28202731 Score: 215
Period size: 29 Copynumber: 10.2 Consensus size: 29
28202426 GTGTGTTAAA
* * *
28202436 CGATGGTTGTAACTATCCCTTTTCATATT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* ** * *
28202465 TGATGGTCGAAATCATCCCTTTTCATTAAT
1 CGATGGTCGTCACCATCCCTTTTCA-TATT
* *
28202495 CGATGGTTGTCACCATCCCTTTCCATAGTT
1 CGATGGTCGTCACCATCCCTTTTCATA-TT
*
28202525 -GATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* * * * * * *
28202553 CAATAGCCG-AAGCTATCCTTTTTCATTTT
1 CGATGGTCGTCA-CCATCCCTTTTCATATT
* * ** *
28202582 TGATAGTC-AAAGCTATCCCTTTTCATATT
1 CGATGGTCGTCA-CCATCCCTTTTCATATT
* *
28202611 CAATGGTCATCACCATCCCTTTTCATATT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* *
28202640 TGATGGTCGTCACCATCCCTTTTCGTAGTT
1 CGATGGTCGTCACCATCCCTTTTCATA-TT
*
28202670 -GATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* * * *
28202698 CGATAGCCG-AAGCTATCCCTTTTCATATT
1 CGATGGTCGTCA-CCATCCCTTTTCATATT
28202727 CGATG
1 CGATG
28202732 ATCGCTAATA
Statistics
Matches: 211, Mismatches: 47, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
28 4 0.02
29 181 0.86
30 26 0.12
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.39
Consensus pattern (29 bp):
CGATGGTCGTCACCATCCCTTTTCATATT
Found at i:28202653 original size:116 final size:117
Alignment explanation
Indices: 28202448--28202663 Score: 319
Period size: 116 Copynumber: 1.9 Consensus size: 117
28202438 ATGGTTGTAA
* * * **
28202448 CTATCCCTTTTCATATTTGATGGTCGAAATCATCCCTTTTCATTAATCGATGGTTGTCACCATCC
1 CTATCCCTTTTCATATTTGATAGTCGAAAGCATCCCTTTTCATTAATCAATGGTCATCACCATCC
28202513 CTTTCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAG
66 CTTTCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAG
* * *
28202565 CTATCCTTTTTCATTTTTGATAGTC-AAAGCTATCCCTTTTCA-TATTCAATGGTCATCACCATC
1 CTATCCCTTTTCATATTTGATAGTCGAAAGC-ATCCCTTTTCATTAATCAATGGTCATCACCATC
* *
28202628 CCTTTTCATATTTGATGGTCGTCACCATCCCTTTTC
65 CCTTTCCATAGTTGATGGTCGTCACCATCCCTTTTC
28202664 GTAGTTGATG
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 55 0.62
117 33 0.38
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.40
Consensus pattern (117 bp):
CTATCCCTTTTCATATTTGATAGTCGAAAGCATCCCTTTTCATTAATCAATGGTCATCACCATCC
CTTTCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAG
Found at i:28202692 original size:116 final size:116
Alignment explanation
Indices: 28202450--28202727 Score: 317
Period size: 116 Copynumber: 2.4 Consensus size: 116
28202440 GGTTGTAACT
* * * * **
28202450 ATCCCTTTTCATATTTGATGGTCGAAATC-ATCCCTTTTCATTAATCGATGGTTGTCACCATCCC
1 ATCCCTTTTCATATTTGATAGTC-AAAGCTATCCCTTTTCA-TATTCAATGGTCATCACCATCCC
*
28202514 TTTCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAGCT
64 TTTCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAGCC
* *
28202567 ATCCTTTTTCATTTTTGATAGTCAAAGCTATCCCTTTTCATATTCAATGGTCATCACCATCCCTT
1 ATCCCTTTTCATATTTGATAGTCAAAGCTATCCCTTTTCATATTCAATGGTCATCACCATCCCTT
* * * * ** * * *
28202632 TTCATATTTGATGGTCGTCACCATCCCTTTTCGTAGTTGATGGTCGTCA-CC
66 TCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCG-AAGCC
* * * *
28202683 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTC
1 ATCCCTTTTCATATTTGATAGTCAAAGCTATCCCTTTTCATATTC
28202728 GATGATCGCT
Statistics
Matches: 135, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
116 103 0.76
117 32 0.24
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.39
Consensus pattern (116 bp):
ATCCCTTTTCATATTTGATAGTCAAAGCTATCCCTTTTCATATTCAATGGTCATCACCATCCCTT
TCCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGCCGAAGCC
Found at i:28208542 original size:48 final size:48
Alignment explanation
Indices: 28208444--28208654 Score: 230
Period size: 48 Copynumber: 4.4 Consensus size: 48
28208434 TGCCAACAAA
* * * * * * *
28208444 CCAGCTATGGTCTTACACGA-AGTCTTATAACGGTGCTGATTCCATGTC
1 CCAGATATGGTCTTACACGAGA-TCTCATATCGATGCCGATGCCATATC
* * * *
28208492 CCAGACATGGTCTTATACGGGA-CTTCATATCGATGCCAATGCCATATC
1 CCAGATATGGTCTTACACGAGATC-TCATATCGATGCCGATGCCATATC
*
28208540 CCAGATATGGTCTTACATGAGATCTCATA-CTGATGCCGATGCCATATC
1 CCAGATATGGTCTTACACGAGATCTCATATC-GATGCCGATGCCATATC
* * * *
28208588 CCAGATATGGTCTTATACAAGATCTCTTATCGATGTCGATGCCATATC
1 CCAGATATGGTCTTACACGAGATCTCATATCGATGCCGATGCCATATC
28208636 CCAGATATGGTCTTACACG
1 CCAGATATGGTCTTACACG
28208655 GGACCTCAAT
Statistics
Matches: 135, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
47 2 0.01
48 130 0.96
49 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (48 bp):
CCAGATATGGTCTTACACGAGATCTCATATCGATGCCGATGCCATATC
Found at i:28218026 original size:30 final size:29
Alignment explanation
Indices: 28217963--28218050 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
28217953 TGTGCTAAAT
* * *
28217963 GATGGTTGTAATCGTCCCTTTTTATATTC
1 GATGGTTGTAATCATCCCTTTTCATAATC
*
28217992 GATGGTTGAAATCATCCCTTTTCATTAATC
1 GATGGTTGTAATCATCCCTTTTCA-TAATC
* * *
28218022 GATGGTCGTCACCATCCCTTTTCATAATC
1 GATGGTTGTAATCATCCCTTTTCATAATC
28218051 AATAGCCTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 26 0.52
30 24 0.48
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (29 bp):
GATGGTTGTAATCATCCCTTTTCATAATC
Found at i:28248608 original size:49 final size:49
Alignment explanation
Indices: 28248549--28249063 Score: 914
Period size: 49 Copynumber: 10.6 Consensus size: 49
28248539 TATTTGAATA
28248549 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248598 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248647 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248696 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248745 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28248794 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248843 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28248892 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
28248941 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
28248990 AATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAG-GCCTAATGGCCGATGTGATG
*
28249037 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
28249064 TCCCGAAGGG
Statistics
Matches: 451, Mismatches: 11, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
46 2 0.00
47 44 0.10
48 3 0.01
49 402 0.89
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:28249238 original size:37 final size:37
Alignment explanation
Indices: 28249182--28249260 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
28249172 CCGAGCTCTA
* * *
28249182 AAGACCCGATGACTACGTGTGGGGA-TATTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTA-TGTCCGGGT
*
28249219 AAGACCCAATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
28249256 AAGAC
1 AAGAC
28249261 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28260875 original size:47 final size:46
Alignment explanation
Indices: 28260812--28261074 Score: 200
Period size: 47 Copynumber: 5.6 Consensus size: 46
28260802 GTGTGAGCTG
*
28260812 GTGTAAGACATGTCTGGGACAT-GCATCAGCCATATTATGAGAGCCA
1 GTGTAAGACATGTCTGGGACATGGCATC-GCCATATGATGAGAGCCA
* * *
28260858 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGACGAGAGCTA
1 GTGTAAGA-CATGTCTGGGACATGGCATCGCCATAT--GATGAGAGCCA
* *
28260906 GTGTAAGACATGTCTGGTACAT-GCATCGGCC-T-CGA-GAAGTAAGCCA
1 GTGTAAGACATGTCTGGGACATGGCATC-GCCATATGATG-AG--AGCCA
* * * * * **
28260952 ATGTAAGACATGTCTGGGACAT-GCATCGACTACAAGATGATAGTTA
1 GTGTAAGACATGTCTGGGACATGGCATCG-CCATATGATGAGAGCCA
* * *
28260998 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-GATGTGAGCCA
1 GTGTAAGA-CATGTCTGGGACATGGCATCGCCAT-ATGATGAGAGCCA
* *
28261045 GTGTAAGACCGTGTTTGGGACATGGCATCG
1 GTGTAAGA-CATGTCTGGGACATGGCATCG
28261075 GTACCTTACC
Statistics
Matches: 175, Mismatches: 27, Indels: 29
0.76 0.12 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.02
45 1 0.01
46 55 0.31
47 82 0.47
48 31 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGGCATCGCCATATGATGAGAGCCA
Found at i:28261068 original size:140 final size:141
Alignment explanation
Indices: 28260813--28261075 Score: 361
Period size: 140 Copynumber: 1.9 Consensus size: 141
28260803 TGTGAGCTGG
* **
28260813 TGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGGGA
1 TGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAGTGTAAGACCATGTCTGGGA
* * *
28260878 CATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGGTACAT-GCATCGGCCTCGAG
66 CATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAG
28260942 AAGTAAGCCAA
131 AAGTAAGCCAA
* * **
28260953 TGTAAGACATGTCTGGGACATGCATC-GACTACAAGATGATAGTTAGTGTAAGACCATGTCTGGG
1 TGTAAGACATGTCTGGGACATGCATCAG-CCACAAGATGAGAGCCAGTGTAAGACCATGTCTGGG
* * * *
28261017 ACATGGCATCGAC-TTGAGATGTGAGCCAGTGTAAGACCGTGTTTGGGACATGGCATCGG
65 ACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGG
28261076 TACCTTACCC
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
139 21 0.20
140 78 0.74
141 7 0.07
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (141 bp):
TGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAGTGTAAGACCATGTCTGGGA
CATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAG
AAGTAAGCCAA
Found at i:28268714 original size:46 final size:46
Alignment explanation
Indices: 28268586--28268847 Score: 205
Period size: 46 Copynumber: 5.6 Consensus size: 46
28268576 AGGCCGACGC
* *
28268586 CATGTCCCAGACATGTTCTTACACTAGCTCTCACATATTCGT-GCCGATG
1 CATGTCCCAGACATG-TCTTACACTGGCT-T-ACAT-CTCGTAGCCGATG
*
28268635 CCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCGTAGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGTAGCCGATG
* * *
28268681 CATGTCCCAGACATGTCTTACATTGGCTTACATCTC-AAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTA-GCCGATG
* * * * *
28268727 CATGTCCCAGATATGTCTTACACTAGCTCT-CGTCTC-AATGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGTA-GCCGATG
* * * *
28268773 CCATGTCCCATACATGGTCTTACACTGGCTTTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTTACAT-CTCGTAGCCGATG
* **
28268821 CATGTACTTGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
28268848 ACATAAATAA
Statistics
Matches: 175, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
44 11 0.06
45 19 0.11
46 74 0.42
47 24 0.14
48 21 0.12
49 1 0.01
50 24 0.14
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGCCGATG
Found at i:28268821 original size:94 final size:91
Alignment explanation
Indices: 28268584--28268851 Score: 231
Period size: 94 Copynumber: 2.9 Consensus size: 91
28268574 CGAGGCCGAC
* * * *
28268584 GCCATGTCCCAGACATGTTCTTACACTAGCTCTCACATATTCGTGCCGATGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATA-ATT-G-GCCGATG-CATGTCCCAGACA
* *
28268649 TGGTCTTACACTGACACATCTCGTAGCCGAT
62 T-GTCTTACACTGACACATCTCATAGCCAAT
* * * *
28268680 G-CATGTCCCAGACAT-GTCTTACATTGGCTTACATCTCAA--GGCTGATGCATGTCCCAGATAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCA--T-AATTGGCCGATGCATGTCCCAGACAT
* * *
28268741 GTCTTACACTAGCTCTCGTCTCA-ATGCCAAT
63 GTCTTACACT-G-ACACATCTCATA-GCCAAT
* * **
28268772 GCCATGTCCCATACATGGTCTTACACTGGCTTTCATAATGTGGCCGATGCATGTACTTGACATGT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAAT-TGGCCGATGCATGTCCCAGACATGT
*
28268837 CTTACACTGGCACAT
65 CTTACACTGACACAT
28268852 AAATAACCCA
Statistics
Matches: 137, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
90 10 0.07
91 17 0.12
92 22 0.16
93 15 0.11
94 56 0.41
95 14 0.10
96 2 0.01
97 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (91 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATTGGCCGATGCATGTCCCAGACATGTC
TTACACTGACACATCTCATAGCCAAT
Found at i:28268834 original size:140 final size:140
Alignment explanation
Indices: 28268586--28268847 Score: 325
Period size: 140 Copynumber: 1.9 Consensus size: 140
28268576 AGGCCGACGC
* * *
28268586 CATGTCCCAGACATGTTCTTACACTAGCTCTCACATATTCGTGCCGATGCCATGTCCCAGACATG
1 CATGTCCCAGACATGTTCTTACACTAGCTCT-ACATACTCATGCCAATGCCATGTCCCAGACATG
* * *
28268651 GTCTTACACTGACACATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACATTGGCTTACATCT
65 GTCTTACACTGACACATATCGTAGCCGATGCATGTACCAGACATGTCTTACACTGGCTTACATCT
28268716 CAAGGCTGATG
130 CAAGGCTGATG
* * *
28268727 CATGTCCCAGATATG-TCTTACACTAGCTCT-CGT-CTCAATGCCAATGCCATGTCCCATACATG
1 CATGTCCCAGACATGTTCTTACACTAGCTCTACATACTC-ATGCCAATGCCATGTCCCAGACATG
* * * **
28268789 GTCTTACACTGGCTTTCATAAT-GTGGCCGATGCATGTACTTGACATGTCTTACACTGGC
65 GTCTTACACTGAC--ACAT-ATCGTAGCCGATGCATGTACCAGACATGTCTTACACTGGC
28268848 ACATAAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
137 2 0.02
138 36 0.35
140 50 0.49
141 15 0.15
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (140 bp):
CATGTCCCAGACATGTTCTTACACTAGCTCTACATACTCATGCCAATGCCATGTCCCAGACATGG
TCTTACACTGACACATATCGTAGCCGATGCATGTACCAGACATGTCTTACACTGGCTTACATCTC
AAGGCTGATG
Found at i:28270296 original size:21 final size:22
Alignment explanation
Indices: 28270250--28270303 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28270240 TACAAGGCTC
**
28270250 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGACCCAAGGG
*
28270272 ACACGCCCGTGTGACCCTA-GG
1 ACACGCCCGTGTGACCCAAGGG
28270293 ACACGCCCGTG
1 ACACGCCCGTG
28270304 CTGCAGGCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.19, C:0.37, G:0.31, T:0.13
Consensus pattern (22 bp):
ACACGCCCGTGTGACCCAAGGG
Found at i:28273420 original size:96 final size:96
Alignment explanation
Indices: 28273256--28273443 Score: 268
Period size: 96 Copynumber: 2.0 Consensus size: 96
28273246 GTTACTTTCT
* * * * *
28273256 TCTCTAGTTGGATATTTAATTGGACATTGGATACCGTTATGATATTCTGCACTACACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGACATTCTGAACTACACCAACAACA
*
28273321 TTGCACAAAAGGTGATATCTCAATCGTCTTC
66 TTGCACAAAAGGTGATAACTCAATCGTCTTC
* * * * *
28273352 TCTCTATTTGGATATTTAATTGGGCATTGGAAACCCTTATGACCTTTTGAACTACACCAACAATA
1 TCTCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGACATTCTGAACTACACCAACAACA
*
28273417 TTGCACAAAATGTGATAACTCAATCGT
66 TTGCACAAAAGGTGATAACTCAATCGT
28273444 GTTTCTCCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (96 bp):
TCTCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGACATTCTGAACTACACCAACAACA
TTGCACAAAAGGTGATAACTCAATCGTCTTC
Found at i:28274465 original size:15 final size:17
Alignment explanation
Indices: 28274445--28274481 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28274435 GCACATAATT
28274445 TTTTTTTTC-T-TTTTC
1 TTTTTTTTCGTATTTTC
28274460 TTTTTTTTCGTATTTTC
1 TTTTTTTTCGTATTTTC
28274477 TTTTT
1 TTTTT
28274482 CTGTACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 10 0.50
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCGTATTTTC
Found at i:28274465 original size:16 final size:18
Alignment explanation
Indices: 28274444--28274481 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
28274434 CGCACATAAT
28274444 TTTTTTTTTC-T-TTTTC
1 TTTTTTTTTCGTATTTTC
28274460 -TTTTTTTTCGTATTTTC
1 TTTTTTTTTCGTATTTTC
28274477 TTTTT
1 TTTTT
28274482 CTGTACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 5 0.26
18 4 0.21
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTCGTATTTTC
Found at i:28278962 original size:17 final size:16
Alignment explanation
Indices: 28278931--28278964 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28278921 ATAAACAGGC
*
28278931 AGAAAGTAAAGAGCAA
1 AGAAAATAAAGAGCAA
28278947 AGAAAATAAGAGAGCAA
1 AGAAAATAA-AGAGCAA
28278964 A
1 A
28278965 AGAGAGAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.06, G:0.24, T:0.06
Consensus pattern (16 bp):
AGAAAATAAAGAGCAA
Found at i:28280642 original size:49 final size:49
Alignment explanation
Indices: 28280589--28280685 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
28280579 ACTCAATATC
* * * *
28280589 CAGATAAGATGGGCCATTGGTAGGGCATGGTAGTTGCTAACTAGATTGA
1 CAGATAAGATAGACCATTGGAAGGGCATGGTAGTTGCTAACCAGATTGA
** * *
28280638 CAGATGTGATAGACCATTGGAATGGCATGGTTGTTGCTAACCAGATTG
1 CAGATAAGATAGACCATTGGAAGGGCATGGTAGTTGCTAACCAGATTG
28280686 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (49 bp):
CAGATAAGATAGACCATTGGAAGGGCATGGTAGTTGCTAACCAGATTGA
Found at i:28281597 original size:47 final size:46
Alignment explanation
Indices: 28281534--28281633 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 46
28281524 GTCTTAAATA
* *
28281534 TGTCTTAAGTCTATTAATGCATG-T-TAATTAGTACATCATTTTAATG
1 TGTCTTAAGTCTATTAAT--ATGTTATAATAAGTACAACATTTTAATG
* *
28281580 TGTCTTAAGTTTAATTAATATGTTATAATAAGTACAACTTTTTAATG
1 TGTCTTAAGTCT-ATTAATATGTTATAATAAGTACAACATTTTAATG
28281627 TGTCTTA
1 TGTCTTA
28281634 GATTAAGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 3 0.06
46 12 0.26
47 32 0.68
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (46 bp):
TGTCTTAAGTCTATTAATATGTTATAATAAGTACAACATTTTAATG
Found at i:28284710 original size:138 final size:138
Alignment explanation
Indices: 28284548--28284824 Score: 527
Period size: 138 Copynumber: 2.0 Consensus size: 138
28284538 GCATGAATTG
28284548 TATACATTTTTTTATGAAATTGATTAATGACGATTTTGATGAAGTTTTGAGAAACGAGAAATCCT
1 TATACATTTTTTTATGAAATTGATTAATGACGATTTTGATGAAGTTTTGAGAAACGAGAAATCCT
**
28284613 GATTTAACCTTAAGGGTAGAATACAAATGTCTAGGATATGACATCGGTATGTGATTTTGTATAAG
66 GATTTAACCTTAAGGGTAGAATACAAACATCTAGGATATGACATCGGTATGTGATTTTGTATAAG
28284678 ACCATGTC
131 ACCATGTC
28284686 TATACATTTTTTTATGAAATTGATTAATGACGATTTTGATGAAGTTTTGAGAAACGAGAAATCCT
1 TATACATTTTTTTATGAAATTGATTAATGACGATTTTGATGAAGTTTTGAGAAACGAGAAATCCT
*
28284751 GATTTAACCTTAAGGGTAGAATACAAACATCTAGGATATGACATTGGTATGTGATTTTGTATAAG
66 GATTTAACCTTAAGGGTAGAATACAAACATCTAGGATATGACATCGGTATGTGATTTTGTATAAG
28284816 ACCATGTC
131 ACCATGTC
28284824 T
1 T
28284825 GGGATATGGC
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (138 bp):
TATACATTTTTTTATGAAATTGATTAATGACGATTTTGATGAAGTTTTGAGAAACGAGAAATCCT
GATTTAACCTTAAGGGTAGAATACAAACATCTAGGATATGACATCGGTATGTGATTTTGTATAAG
ACCATGTC
Found at i:28284843 original size:42 final size:42
Alignment explanation
Indices: 28284784--28284870 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
28284774 CAAACATCTA
* *
28284784 GGATATGACATTGGTATGTGATTTTGTATAAGACCATGTCTG
1 GGATATGACATCGGTATGTGATTTTGTATAAGACCATGTCAG
*
28284826 GGATATGGCATCGGTATGTGATTTTGTATAAGACCATGTCAG
1 GGATATGACATCGGTATGTGATTTTGTATAAGACCATGTCAG
28284868 GGA
1 GGA
28284871 CATAGCATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.34
Consensus pattern (42 bp):
GGATATGACATCGGTATGTGATTTTGTATAAGACCATGTCAG
Found at i:28285785 original size:7 final size:8
Alignment explanation
Indices: 28285767--28285795 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28285757 GAATGAGTAG
28285767 AAATCTTA
1 AAATCTTA
28285775 AAATC-TA
1 AAATCTTA
28285782 AAATCTTA
1 AAATCTTA
28285790 AAATCT
1 AAATCT
28285796 AATTCCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATCTTA
Found at i:28285787 original size:15 final size:15
Alignment explanation
Indices: 28285767--28285797 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28285757 GAATGAGTAG
28285767 AAATCTTAAAATCTA
1 AAATCTTAAAATCTA
28285782 AAATCTTAAAATCTA
1 AAATCTTAAAATCTA
28285797 A
1 A
28285798 TTCCAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATCTTAAAATCTA
Found at i:28294040 original size:13 final size:13
Alignment explanation
Indices: 28294024--28294048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28294014 CTTTACATAC
28294024 TGTCTTCAACAGG
1 TGTCTTCAACAGG
28294037 TGTCTTCAACAG
1 TGTCTTCAACAG
28294049 CTCGCACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:28294940 original size:25 final size:25
Alignment explanation
Indices: 28294906--28294955 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28294896 ATAGGAAGTT
28294906 GGTTTATATTCTTTTCTGGTAGTAA
1 GGTTTATATTCTTTTCTGGTAGTAA
28294931 GGTTTATATTCTTTTCTGGTAGTAA
1 GGTTTATATTCTTTTCTGGTAGTAA
28294956 TACATGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (25 bp):
GGTTTATATTCTTTTCTGGTAGTAA
Found at i:28297631 original size:21 final size:21
Alignment explanation
Indices: 28297605--28297646 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28297595 ACAAATCGGT
28297605 TAGAAAGGAATTTTGAATATC
1 TAGAAAGGAATTTTGAATATC
*
28297626 TAGAAAGTAATTTTGAATATC
1 TAGAAAGGAATTTTGAATATC
28297647 CTTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.36
Consensus pattern (21 bp):
TAGAAAGGAATTTTGAATATC
Found at i:28298434 original size:42 final size:42
Alignment explanation
Indices: 28298380--28298489 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
28298370 TTATTAATTA
* *
28298380 AGATTTTATTTGCAAGTGAAGCATG-TCGACTATGATAAACTG
1 AGATTTGATTTGCAAGTTAAGCATGCT-GACTATGATAAACTG
* * * * * *
28298422 ATATTTGATTTGCATGTTAAGCATGCTGACTATGTTGATCTT
1 AGATTTGATTTGCAAGTTAAGCATGCTGACTATGATAAACTG
*
28298464 AGATTTGATTTGCACGTTAAGCATGC
1 AGATTTGATTTGCAAGTTAAGCATGC
28298490 CTACTAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (42 bp):
AGATTTGATTTGCAAGTTAAGCATGCTGACTATGATAAACTG
Found at i:28300342 original size:24 final size:24
Alignment explanation
Indices: 28300315--28300412 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
28300305 AAGGCTGTCA
*
28300315 GGAGAAGATATAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
28300339 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
28300363 GGAGAGGATTTAAGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
28300387 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
28300412 G
1 G
28300413 AGCAGGAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
24 63 0.95
25 3 0.05
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.19
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:28302107 original size:33 final size:32
Alignment explanation
Indices: 28302030--28302122 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
28302020 TATGGGCCAT
* * *
28302030 ACTGTTAACTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAA-AA-GGGCTTAGGCCCAGTTC
* * *
28302064 AATGTAATCTGAAAAGGGCTTTGGCCCAGTATC
1 ACTGTTATCTGAAAAGGGCTTAGGCCCAGT-TC
*
28302097 ACTGTTATCTG-AATGGGCTTAGGCCC
1 ACTGTTATCTGAAAAGGGCTTAGGCCC
28302123 GATGGGCTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
32 26 0.54
33 12 0.25
34 10 0.21
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (32 bp):
ACTGTTATCTGAAAAGGGCTTAGGCCCAGTTC
Found at i:28308284 original size:24 final size:24
Alignment explanation
Indices: 28308257--28308354 Score: 133
Period size: 24 Copynumber: 4.0 Consensus size: 24
28308247 AAGGCTGTCA
28308257 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
**
28308281 GGAGGGGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * * *
28308305 TGAGAGGATTTAGAAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
28308329 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
28308354 G
1 G
28308355 AGCAGGAGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
24 60 0.95
25 3 0.05
ACGTcount: A:0.36, C:0.05, G:0.38, T:0.21
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:28315979 original size:40 final size:40
Alignment explanation
Indices: 28315935--28316196 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28315925 GCTCCTCGTT
* *
28315935 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
28315975 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28316015 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28316054 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28316093 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
28316132 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
28316173 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28316197 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:28323158 original size:2 final size:2
Alignment explanation
Indices: 28323151--28323179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28323141 CTATGAACTT
28323151 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28323180 TCTATCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28327837 original size:40 final size:40
Alignment explanation
Indices: 28327786--28328818 Score: 1854
Period size: 40 Copynumber: 25.8 Consensus size: 40
28327776 ATTTGAATTT
* * * * *
28327786 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGATTT
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGA-TA
*
28327826 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28327866 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
* *
28327906 TATCCGGGCTAAGACCCGCAGGTATTTGTGCGTGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28327946 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28327986 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328026 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328066 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328106 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328146 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328186 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328226 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328266 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328306 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328346 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328386 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328426 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328466 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328506 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328546 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328586 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328626 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
28328666 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTG--ATA
* * *
28328708 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
* * *
28328748 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTA
1 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
* * * *
28328788 T-GCCTGGGTTAAGACCCGAAGGCAATTGTGC
1 TATCC-GGGCTAAGACCCGCAGGCATTTGTGC
28328819 TTGTGGTAAT
Statistics
Matches: 969, Mismatches: 20, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
39 2 0.00
40 927 0.96
41 3 0.00
42 37 0.04
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
Found at i:28330663 original size:20 final size:20
Alignment explanation
Indices: 28330635--28330695 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 20
28330625 ATTCATTTTT
*
28330635 ATTCGTATAAACTGTAATTC
1 ATTCATATAAACTGTAATTC
*
28330655 ATTCATAT-AACTAGTAGTTC
1 ATTCATATAAACT-GTAATTC
* * *
28330675 A-TCCTATAACCAGTAATTC
1 ATTCATATAAACTGTAATTC
28330694 AT
1 AT
28330696 CAGTAATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
ATTCATATAAACTGTAATTC
Found at i:28330682 original size:19 final size:19
Alignment explanation
Indices: 28330648--28330755 Score: 69
Period size: 20 Copynumber: 5.5 Consensus size: 19
28330638 CGTATAAACT
* *
28330648 GTAATTCATTCATATAACTA
1 GTAATTCA-TCCTATAACCA
*
28330668 GTAGTTCATCCTATAACCA
1 GTAATTCATCCTATAACCA
*
28330687 GTAATTCATCAGTAATAA-CA
1 GTAATTCATC-CT-ATAACCA
* *
28330707 GTAATTTATCTGTATCAA-CA
1 GTAATTCATC-CTAT-AACCA
*
28330727 GTAATTCATCTGTATCAA-CA
1 GTAATTCATC-CTAT-AACCA
28330747 GTAATTCAT
1 GTAATTCAT
28330756 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
19 20 0.26
20 53 0.69
21 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (19 bp):
GTAATTCATCCTATAACCA
Found at i:28330766 original size:20 final size:20
Alignment explanation
Indices: 28330685--28330755 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
28330675 ATCCTATAAC
*
28330685 CAGTAATTCATCAGTAAT-AA
1 CAGTAATTCATCTGT-ATCAA
*
28330705 CAGTAATTTATCTGTATCAA
1 CAGTAATTCATCTGTATCAA
28330725 CAGTAATTCATCTGTATCAA
1 CAGTAATTCATCTGTATCAA
28330745 CAGTAATTCAT
1 CAGTAATTCAT
28330756 TCATTTCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.04
20 45 0.96
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
CAGTAATTCATCTGTATCAA
Found at i:28330766 original size:40 final size:40
Alignment explanation
Indices: 28330639--28330755 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
28330629 ATTTTTATTC
* * *
28330639 GTATAAACTGTAATTCATTCA-T-ATAACTAGTAGTTCATC-
1 GTATCAACAGTAATTCA-TCAGTAATAAC-AGTAATTCATCT
* *
28330678 CTAT-AACCAGTAATTCATCAGTAATAACAGTAATTTATCT
1 GTATCAA-CAGTAATTCATCAGTAATAACAGTAATTCATCT
*
28330718 GTATCAACAGTAATTCATCTGT-ATCAACAGTAATTCAT
1 GTATCAACAGTAATTCATCAGTAAT-AACAGTAATTCAT
28330756 TCATTTCAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
38 5 0.08
39 24 0.37
40 34 0.52
41 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (40 bp):
GTATCAACAGTAATTCATCAGTAATAACAGTAATTCATCT
Found at i:28333588 original size:25 final size:25
Alignment explanation
Indices: 28333560--28333627 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
28333550 GACCCATTTC
*
28333560 ATAACTCATGTGAACATTTACAGTT
1 ATAACTCGTGTGAACATTTACAGTT
* * *
28333585 ATAACTCGTGTGAGCAGTTACCGTT
1 ATAACTCGTGTGAACATTTACAGTT
* *
28333610 ACAACTTGTGTGAACATT
1 ATAACTCGTGTGAACATT
28333628 CTCCCTCCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (25 bp):
ATAACTCGTGTGAACATTTACAGTT
Found at i:28334457 original size:48 final size:47
Alignment explanation
Indices: 28334395--28334538 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 47
28334385 ACTCAAGAGT
* * * *
28334395 CTCGCACCCTAAGTGCCAATATCATGACACGAAGCCAAATCAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGC-CGAAGCCAAATCAATGAAA
* *
28334443 CTCGCACCCGAAGTGCTAATATCATGGCCTGAAGTCAAATTAATGAAA
1 CTCGCACCCGAAGTGCTAATATCATGGCC-GAAGCCAAATCAATGAAA
* * *
28334491 CTCGCACCCGAAGTGCTAATATCTTGGCTCGAAGCCATATAAATGAAA
1 CTCGCACCCGAAGTGCTAATATCATGGC-CGAAGCCAAATCAATGAAA
28334539 TTGAATTTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 82 0.98
49 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (47 bp):
CTCGCACCCGAAGTGCTAATATCATGGCCGAAGCCAAATCAATGAAA
Found at i:28344997 original size:43 final size:43
Alignment explanation
Indices: 28344914--28345061 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 43
28344904 TCATAAGCTC
* * * * *
28344914 ATACAATGCCAACGTCCTAGAC-GTGGTCTTACATGT-AATCAA
1 ATACGATGCCAATGTCCCAGACAG-GGTCGTACACGTAAATCAA
* * *
28344956 ATGCCGATGCCACTGTCCCAGACAGGGTCGTACACG-AAATCAT
1 AT-ACGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCAA
* * * * *
28344999 ATACGATGTCAATGTCCTAGACATGGTCTTACATGTAAATCAA
1 ATACGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCAA
* *
28345042 AAATTGATGCCAATGTCCCA
1 ATA-CGATGCCAATGTCCCA
28345062 AACGTGGTCT
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
42 28 0.35
43 39 0.48
44 14 0.17
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
ATACGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCAA
Found at i:28345015 original size:42 final size:43
Alignment explanation
Indices: 28344960--28345061 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
28344950 AATCAAATGC
*
28344960 CGATGCCACTGTCCCAGACAGGGTCGTACACG-AAATCATATA
1 CGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCATATA
* * * * * * *
28345002 CGATGTCAATGTCCTAGACATGGTCTTACATGTAAATCAAAAA
1 CGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCATATA
*
28345045 TTGATGCCAATGTCCCA
1 -CGATGCCAATGTCCCA
28345062 AACGTGGTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
42 26 0.55
43 8 0.17
44 13 0.28
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACAGGGTCGTACACGTAAATCATATA
Found at i:28345590 original size:73 final size:73
Alignment explanation
Indices: 28345506--28345647 Score: 275
Period size: 73 Copynumber: 1.9 Consensus size: 73
28345496 CTTTTGCCCT
28345506 TGACATTTCACATTTTTCACAATTTAGTCCCTATTTCACAAAACACAAAATATTCAAAATTCGAC
1 TGACATTTCACATTTTTCACAATTTAGTCCCTATTTCACAAAACACAAAATATTCAAAATTCGAC
28345571 CACACCCC
66 CACACCCC
*
28345579 TGACATTTCACATTTTTCACAATTTAGTCCCTATTTCACAAAACACAAAATATTCAAAATTTGAC
1 TGACATTTCACATTTTTCACAATTTAGTCCCTATTTCACAAAACACAAAATATTCAAAATTCGAC
28345644 CACA
66 CACA
28345648 ACCATGCTTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (73 bp):
TGACATTTCACATTTTTCACAATTTAGTCCCTATTTCACAAAACACAAAATATTCAAAATTCGAC
CACACCCC
Found at i:28351736 original size:42 final size:43
Alignment explanation
Indices: 28351634--28351791 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
28351624 AGCTCATACA
* * *
28351634 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCAAATATCG
* *
28351677 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCATATAT-G
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
* * *
28351719 ATGCCAATG-CCTTAGACATGGTCTTACACGTAAATCACAA-ATCA
1 ATGCCAATGTCC-CAGACAGGGTCTTACACG-AAATCA-AATATCG
**
28351763 ATGCCAATGTCCCAGACTTGGTCTTACAC
1 ATGCCAATGTCCCAGACAGGGTCTTACAC
28351792 CATAACACAT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.02
42 25 0.26
43 42 0.43
44 26 0.27
45 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
Found at i:28355945 original size:40 final size:40
Alignment explanation
Indices: 28355887--28356071 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 40
28355877 AAACCAAGTA
* *
28355887 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* * * * *
28355926 CCTTTGGGACTTAACCCGGATATAGTAACTCACACACATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* * * *** *
28355966 CCTTCGGGTCTTAGCCCAGAAATAGTTGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* *
28356006 CCTTCGGGACTTAGCCTGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATG
28356049 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28356072 CATCCGAATA
Statistics
Matches: 114, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 11 0.10
40 71 0.62
43 32 0.28
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
Found at i:28364445 original size:44 final size:45
Alignment explanation
Indices: 28364321--28364465 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 45
28364311 CCCGGACGTA
* * * *
28364321 GTCTTACATGT-AA-TTCAGTA-TCGATGCCTCTGTCCCAGACAGG
1 GTCTTACACGTAAATTTCA-TATTCGATGTCTGTGTCCCAGACATG
* *
28364364 GTCTTATACG-AAA--TCATATACGATGTC-GATGTCCCAGACATG
1 GTCTTACACGTAAATTTCATATTCGATGTCTG-TGTCCCAGACATG
*
28364406 GTCTTACACGTAAATTTCA-ATTCGATGTCTGTGTCCCAGACATA
1 GTCTTACACGTAAATTTCATATTCGATGTCTGTGTCCCAGACATG
*
28364450 GTCTTACACGTTAATT
1 GTCTTACACGTAAATT
28364466 CAGATCAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
41 2 0.02
42 30 0.35
43 13 0.15
44 36 0.42
45 4 0.05
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (45 bp):
GTCTTACACGTAAATTTCATATTCGATGTCTGTGTCCCAGACATG
Found at i:28369192 original size:18 final size:17
Alignment explanation
Indices: 28369169--28369202 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28369159 AATAACTCAT
28369169 TTATTAATCTAAAATGAG
1 TTATTAA-CTAAAATGAG
*
28369187 TTATTAACTAAGATGA
1 TTATTAACTAAAATGA
28369203 ACTCAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
TTATTAACTAAAATGAG
Found at i:28381672 original size:10 final size:10
Alignment explanation
Indices: 28381657--28381708 Score: 77
Period size: 10 Copynumber: 5.1 Consensus size: 10
28381647 TAATTTTAGG
*
28381657 ATTTATTTTC
1 ATTTATTTTT
28381667 ATTTATTTTT
1 ATTTATTTTT
*
28381677 ATTTATCTTT
1 ATTTATTTTT
28381687 ATTTATTTTT
1 ATTTATTTTT
28381697 ATTTATCTTTT
1 ATTTAT-TTTT
28381708 A
1 A
28381709 GAATTTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
10 33 0.87
11 5 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:28385022 original size:29 final size:29
Alignment explanation
Indices: 28384980--28385080 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28384970 CATGAAATTG
28384980 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28385009 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
28385038 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28385066 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
28385081 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:28400076 original size:42 final size:43
Alignment explanation
Indices: 28399997--28400098 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
28399987 TCCCGGATGT
* * **
28399997 GGTCTTACATATAATTCAGTATCGATGCCTCTGTCCCAAACAG
1 GGTCTTACACATAAATCAGTATCGATGCCGATGTCCCAAACAG
* *
28400040 GGTCTTACACA-AAATCAG-ATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACATAAATCAGTAT-CGATGCCGATGTCCCAAACAG
* *
28400082 AGTCTTACACTTAAATC
1 GGTCTTACACATAAATC
28400099 TCAAATTAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.04
42 32 0.65
43 15 0.31
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
GGTCTTACACATAAATCAGTATCGATGCCGATGTCCCAAACAG
Found at i:28401649 original size:46 final size:45
Alignment explanation
Indices: 28401596--28401763 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
28401586 ACATCTAGCT
*
28401596 GATGCATGTCCTAGACATGTCTTACACTTGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTTGCTT-CGTCTCGAGGCC
* * *
28401642 GATGCATGTCCCAGACATGTCTTACA-TTAGCACTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTT-GC-TTCGTCTCGAGGCC
* * * * * *
28401688 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTTGCT-TCGT-CTCGAGGCC
28401736 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
28401764 AGCTCACACA
Statistics
Matches: 101, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.02
46 51 0.50
47 27 0.27
48 19 0.19
49 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTTGCTTCGTCTCGAGGCC
Found at i:28401740 original size:94 final size:92
Alignment explanation
Indices: 28401596--28401766 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 92
28401586 ACATCTAGCT
* * *
28401596 GATGCATGTCCTAGACATGTCTTACACTTGCTTACGTCTCGAGGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCTAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAGACATG
*
28401661 TCTTACATTAGCACTCGTCTCAATGCC
66 TCTTACACTAGCACTCGTCTCAATGCC
* *
28401688 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCTGATGCATGTCCCAGA
1 GATG-CATGTCCTAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCGATGCATGTCCCAGA
28401751 CATGTCTTACACTAGC
62 CATGTCTTACACTAGC
28401767 TCACACAACT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
92 4 0.06
93 14 0.20
94 49 0.71
95 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCTAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAGACATG
TCTTACACTAGCACTCGTCTCAATGCC
Found at i:28408024 original size:20 final size:21
Alignment explanation
Indices: 28407999--28408038 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28407989 TCTTTGAAAT
28407999 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
*
28408019 AGGGCAACACGCTCGTGTGG
1 AGGGCAACACGCCCGTGTGG
28408039 CTATTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:28419526 original size:92 final size:93
Alignment explanation
Indices: 28419411--28419580 Score: 245
Period size: 92 Copynumber: 1.8 Consensus size: 93
28419401 TATCTGTGTT
* *
28419411 GATGCCATGTCCTAGACATGGTCTTACACTGACACATC-T-CGTAGCTGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACAC-TCATACGTAGCTGATACATGTCCCAGACA
28419474 TGTCTTACACTAGGACTCGTCTCAATGCC
65 TGTCTTACACTAGGACTCGTCTCAATGCC
* * * *
28419503 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATACATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACTCAT-ACGTAGCTGATACATGTCCCAGACA
*
28419568 TGTCTTACGCTAG
65 TGTCTTACACTAG
28419581 CTCACACAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
91 2 0.03
92 33 0.49
94 33 0.49
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACTCATACGTAGCTGATACATGTCCCAGACAT
GTCTTACACTAGGACTCGTCTCAATGCC
Found at i:28429589 original size:23 final size:22
Alignment explanation
Indices: 28429559--28429602 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
28429549 AAAATCCTCT
28429559 CCTGCTGAAATTCTCTGCAACC
1 CCTGCTGAAATTCTCTGCAACC
28429581 NCCTGCTGAAATTCTCTGCAAC
1 -CCTGCTGAAATTCTCTGCAAC
28429603 TCCCCTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.27
Consensus pattern (22 bp):
CCTGCTGAAATTCTCTGCAACC
Found at i:28430604 original size:38 final size:39
Alignment explanation
Indices: 28430513--28430607 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
28430503 TGGTACCATT
* * *
28430513 TGGTATGTAGGGTTGGATGGGTAGATTTTATCCCTATACT
1 TGGTGTGTAGGGTTGGATGGGTAGATTCTATCCC-ATACA
* *
28430553 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCC-TACA
1 TGGTGTGTAGGGTTGGATGGGTAGATTCTATCCCATACA
*
28430591 TGGTGTGTCGGGTTGGA
1 TGGTGTGTAGGGTTGGA
28430608 CAGAGATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 18 0.38
40 30 0.62
ACGTcount: A:0.15, C:0.12, G:0.37, T:0.37
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGGGTAGATTCTATCCCATACA
Found at i:28436595 original size:13 final size:13
Alignment explanation
Indices: 28436577--28436603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28436567 TGGTTCGGCA
28436577 GGGACACGCCCGT
1 GGGACACGCCCGT
28436590 GGGACACGCCCGT
1 GGGACACGCCCGT
28436603 G
1 G
28436604 TGCGATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.41, T:0.07
Consensus pattern (13 bp):
GGGACACGCCCGT
Found at i:28447403 original size:5 final size:5
Alignment explanation
Indices: 28447397--28447461 Score: 87
Period size: 5 Copynumber: 12.6 Consensus size: 5
28447387 ATTTTATGTT
*
28447397 TTATT TTATTA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-A
1 TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
28447447 TATATTA TTATA TTA
1 T-TA-TA TTATA TTA
28447462 ATTTCTTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
4 2 0.04
5 45 0.82
6 6 0.11
7 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:28447414 original size:8 final size:8
Alignment explanation
Indices: 28447397--28447461 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
28447387 ATTTTATGTT
*
28447397 TTATTTTA
1 TTATTATA
28447405 TTATTATA
1 TTATTATA
28447413 TTA-TAT-
1 TTATTATA
28447419 TATATTATA
1 T-TATTATA
28447428 TTA-TAT-
1 TTATTATA
28447434 TATATTATA
1 T-TATTATA
*
28447443 TTAATATA
1 TTATTATA
28447451 TTATTATA
1 TTATTATA
28447459 TTA
1 TTA
28447462 ATTTCTTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 2 0.04
7 10 0.21
8 34 0.71
9 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:28449550 original size:106 final size:106
Alignment explanation
Indices: 28449365--28449578 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 106
28449355 TTTTTTTTGT
* *
28449365 TTGTGTTTGTTTGTTTTCTATTTAGATTTCCTTGACCCATTTTGCGTGTTTGGATCATCGTCAAA
1 TTGTGTTTATTTGTTTTCTATTTAGATTTCCTTGACCCATTTTGCGTGTTTGGATCATCATCAAA
28449430 GTCATCACACCAGCTTGCAATGTTTTGGTATCTTTTCTTAG
66 GTCATCACACCAGCTTGCAATGTTTTGGTATCTTTTCTTAG
28449471 TTGTGTTTATTTGTTTTCTATTTAGATTTCCTTGACCCATTTTGCGTGTTTGGATCATCATCAAA
1 TTGTGTTTATTTGTTTTCTATTTAGATTTCCTTGACCCATTTTGCGTGTTTGGATCATCATCAAA
28449536 GTCATCACACCAGCTTGCAATGTTTTGGTATCTTTTCTTAG
66 GTCATCACACCAGCTTGCAATGTTTTGGTATCTTTTCTTAG
28449577 TT
1 TT
28449579 ATATAGGTGA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.48
Consensus pattern (106 bp):
TTGTGTTTATTTGTTTTCTATTTAGATTTCCTTGACCCATTTTGCGTGTTTGGATCATCATCAAA
GTCATCACACCAGCTTGCAATGTTTTGGTATCTTTTCTTAG
Found at i:28470711 original size:59 final size:59
Alignment explanation
Indices: 28470641--28470757 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
28470631 AAAAGGGCTC
28470641 TGGCCCAGTACCACTGTTACCTGAATGGGCTTAGGCCCAATAGGCTTGAGCTGACTTGA
1 TGGCCCAGTACCACTGTTACCTGAATGGGCTTAGGCCCAATAGGCTTGAGCTGACTTGA
* * *
28470700 TGGCCCAGTACCATTGTTACTTGAATGGGCTTAGGCCCAATGGGCTTGAGCTGACTTG
1 TGGCCCAGTACCACTGTTACCTGAATGGGCTTAGGCCCAATAGGCTTGAGCTGACTTG
28470758 GGCTTTGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (59 bp):
TGGCCCAGTACCACTGTTACCTGAATGGGCTTAGGCCCAATAGGCTTGAGCTGACTTGA
Found at i:28474535 original size:26 final size:26
Alignment explanation
Indices: 28474498--28474555 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
28474488 TGATACAAAT
28474498 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28474524 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28474550 TGATAA
1 TGATAA
28474556 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Done.