Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 140 of 290
Found at i:47574020 original size:27 final size:27
Alignment explanation
Indices: 47573972--47574111 Score: 167
Period size: 27 Copynumber: 5.2 Consensus size: 27
47573962 GGGCAAAACA
* * *
47573972 ATCATTTTACCTTACAGGGGTATTAC-
1 ATCATTTTACCCTATAGGGGTATTTCG
* * *
47573998 AGTCATTTTACCCCATAGAGGTATTTTG
1 A-TCATTTTACCCTATAGGGGTATTTCG
* *
47574026 GTCA-TTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATAGGGGTATTTCG
47574052 ATCATTTTACCCTATAGGGGTATTTCG
1 ATCATTTTACCCTATAGGGGTATTTCG
*
47574079 ATCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATAGGGGTATTTCG
*
47574106 GTCATT
1 ATCATT
47574112 ATTTCATCCC
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
26 22 0.23
27 74 0.77
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (27 bp):
ATCATTTTACCCTATAGGGGTATTTCG
Found at i:47574057 original size:53 final size:54
Alignment explanation
Indices: 47573972--47574111 Score: 176
Period size: 53 Copynumber: 2.6 Consensus size: 54
47573962 GGGCAAAACA
* ** * *
47573972 ATCATTTTACCTTACAGGGGTATTAC-AGTCATTTTACCCCATAGAGGTATTTTG
1 ATCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCCATAGAGGTATTTCG
* * *
47574026 GTCA-TTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCCATAGAGGTATTTCG
*
47574079 ATCATTTTACCCTATGGGGGTATTTCGGTCATT
1 ATCATTTTACCCTATGGGGGTATTTCGATCATT
47574112 ATTTCATCCC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 43 0.58
54 31 0.42
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (54 bp):
ATCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCCATAGAGGTATTTCG
Found at i:47576898 original size:40 final size:40
Alignment explanation
Indices: 47576815--47577077 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
47576805 TTGAATGCTG
* * * * * *
47576815 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
47576855 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
47576895 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
47576935 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
47576975 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
47577015 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
47577054 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47577078 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:47577097 original size:79 final size:80
Alignment explanation
Indices: 47576854--47577112 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
47576844 AAGTGAATAT
* * * * * *
47576854 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
47576918 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
47576934 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
47576999 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
47577014 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
47577078 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
47577093 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
47577113 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:47584848 original size:40 final size:40
Alignment explanation
Indices: 47584765--47585107 Score: 485
Period size: 40 Copynumber: 8.6 Consensus size: 40
47584755 TTGAATGCTG
* * * * * *
47584765 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
47584805 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
47584845 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
47584885 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
47584925 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
47584965 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
47585005 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
47585045 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
47585084 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47585108 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:47589191 original size:22 final size:22
Alignment explanation
Indices: 47589166--47589212 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47589156 GAGATTCTTG
*
47589166 CATTCAACTTATTATGTTGCGA
1 CATTCAACTTATTATGTTGCAA
* * *
47589188 CATTGAACTTCTTGTGTTGCAA
1 CATTCAACTTATTATGTTGCAA
47589210 CAT
1 CAT
47589213 AGCGACTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (22 bp):
CATTCAACTTATTATGTTGCAA
Found at i:47594564 original size:14 final size:14
Alignment explanation
Indices: 47594545--47594571 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47594535 CCGAAACTAG
47594545 AAAGAAAAAAAAAC
1 AAAGAAAAAAAAAC
47594559 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
47594572 TGCTCATCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:47595744 original size:39 final size:40
Alignment explanation
Indices: 47595649--47595910 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
47595639 TTGAATGATG
*
47595649 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
47595687 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
47595728 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
47595767 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
47595806 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
47595845 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
47595884 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
47595911 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:47598658 original size:24 final size:25
Alignment explanation
Indices: 47598624--47598701 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 25
47598614 TATGACATTC
*
47598624 TGCTAAGTGAAATAAGACCATGGCA
1 TGCTAAGTGAAATAAGTCCATGGCA
47598649 T-CTAAGTGAAATAAGTCCATGGCAA
1 TGCTAAGTGAAATAAGTCCATGGC-A
*
47598674 TGTGCTAAGTGAAATAAGTTCATGGCA
1 --TGCTAAGTGAAATAAGTCCATGGCA
47598701 T
1 T
47598702 TGTGCTAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
24 21 0.45
25 3 0.06
27 2 0.04
28 21 0.45
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (25 bp):
TGCTAAGTGAAATAAGTCCATGGCA
Found at i:47598690 original size:28 final size:28
Alignment explanation
Indices: 47598624--47598713 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 28
47598614 TATGACATTC
*
47598624 TGCTAAGTGAAATAAGACCATGGC-A--
1 TGCTAAGTGAAATAAGTCCATGGCAATG
47598649 T-CTAAGTGAAATAAGTCCATGGCAATG
1 TGCTAAGTGAAATAAGTCCATGGCAATG
* *
47598676 TGCTAAGTGAAATAAGTTCATGGCATTG
1 TGCTAAGTGAAATAAGTCCATGGCAATG
47598704 TGCTAAGTGA
1 TGCTAAGTGA
47598714 GAAATTTCTC
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
24 21 0.36
25 2 0.03
27 1 0.02
28 34 0.59
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (28 bp):
TGCTAAGTGAAATAAGTCCATGGCAATG
Found at i:47598834 original size:37 final size:37
Alignment explanation
Indices: 47598781--47598864 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
47598771 TGTGAAGGCC
47598781 ACTTTGTGAATATAATAGCTTTGGACACAAGTGTGGT
1 ACTTTGTGAATATAATAGCTTTGGACACAAGTGTGGT
* *
47598818 ACTTTGTGAATTTAATATCTTTGGACACAAGTGTGGT
1 ACTTTGTGAATATAATAGCTTTGGACACAAGTGTGGT
*
47598855 ACTATGTGAA
1 ACTTTGTGAA
47598865 GGCCACTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.37
Consensus pattern (37 bp):
ACTTTGTGAATATAATAGCTTTGGACACAAGTGTGGT
Found at i:47598873 original size:51 final size:51
Alignment explanation
Indices: 47598818--47599023 Score: 342
Period size: 51 Copynumber: 4.0 Consensus size: 51
47598808 CAAGTGTGGT
** *
47598818 ACTTTGTGAATTTAATATCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
1 ACTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
*
47598869 ACTTTGTGAATAAAATAGCTTTGGACATAAGTGTGGTACTATGTGAAGGCC
1 ACTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
47598920 ACTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
1 ACTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
* *
47598971 ACTTTGTAAATAAAATAGCTTTGG-CTACAAGGGTGGTACTATGTGAAGGCC
1 ACTTTGTGAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCC
47599022 AC
1 AC
47599024 CATGTATCTA
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
50 1 0.01
51 146 0.99
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (51 bp):
ACTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCC
Found at i:47598901 original size:88 final size:88
Alignment explanation
Indices: 47598743--47598915 Score: 301
Period size: 88 Copynumber: 2.0 Consensus size: 88
47598733 TTAGGAATAA
*
47598743 AATAGCTTTGGACACAAGTGTAGTACTATGTGAAGGCCACTTTGTGAATATAATAGCTTTGGACA
1 AATAGCTTTGGACACAAGTGTAGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTTTGGACA
*
47598808 CAAGTGTGGTACTTTGTGAATTT
66 CAAGTGTGGTACTATGTGAATTT
* *
47598831 AATATCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTTTGGACA
1 AATAGCTTTGGACACAAGTGTAGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTTTGGACA
*
47598896 TAAGTGTGGTACTATGTGAA
66 CAAGTGTGGTACTATGTGAA
47598916 GGCCACTTTG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (88 bp):
AATAGCTTTGGACACAAGTGTAGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTTTGGACA
CAAGTGTGGTACTATGTGAATTT
Found at i:47613421 original size:93 final size:93
Alignment explanation
Indices: 47613258--47613428 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
47613248 CCCATAAGTG
* * * *
47613258 AACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAGGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
47613323 AAGTTCGGATGCCTAGTTACATTTCACA
66 AAGTTCGGATGCCTAGTTACATTTCACA
* *
47613351 AACTCGGACTCAACTCAATGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
47613416 GAGTTCGGATGCC
66 AAGTTCGGATGCC
47613429 CAAATATCCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
AAGTTCGGATGCCTAGTTACATTTCACA
Found at i:47613424 original size:46 final size:46
Alignment explanation
Indices: 47613249--47613424 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
47613239 TGTAACCCGC
* * * *
47613249 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTAGCAT
* * * *
47613295 CCATAGGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTAGCAT
* * ** * *
47613341 ACATTTCA-CAAACTCGGACTCAACTCAATGAGTTCGGACGCTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTAGCAT
47613388 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
47613425 TGCCCAAATA
Statistics
Matches: 102, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
45 2 0.02
46 67 0.66
47 32 0.31
48 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTAGCAT
Found at i:47613443 original size:46 final size:46
Alignment explanation
Indices: 47613301--47613443 Score: 107
Period size: 46 Copynumber: 3.1 Consensus size: 46
47613291 GCATCCATAG
* * * *
47613301 GTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACATTTCACA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATATCCCA
* * * ** *
47613351 ---AACTCGGACTCAACTCAATGAGTTCGGACGCTC--GCATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCC--CA
47613394 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCCA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCCA
47613440 GTGA
1 GTGA
47613444 CATGCCACTT
Statistics
Matches: 70, Mismatches: 16, Indels: 18
0.67 0.15 0.17
Matches are distributed among these distances:
41 2 0.03
43 1 0.01
46 35 0.50
47 28 0.40
48 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCCA
Found at i:47629369 original size:18 final size:17
Alignment explanation
Indices: 47629346--47629380 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47629336 GATGGGTCGA
47629346 AATGGGCCGTGTGGGCCC
1 AATGGG-CGTGTGGGCCC
*
47629364 AATGGGCTTGTGGGCCC
1 AATGGGCGTGTGGGCCC
47629381 CACACGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.20
Consensus pattern (17 bp):
AATGGGCGTGTGGGCCC
Found at i:47630672 original size:34 final size:33
Alignment explanation
Indices: 47630610--47630682 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
47630600 GTTACAGCCG
*
47630610 TGGTC-TTTTATTCACATGCCATAACCCAGTTA
1 TGGTCTTTTTATTCACATGCCATAACCCAGCTA
** *
47630642 TGGTCTTTTTATTCGATTTGCCATAGCCCAGCTA
1 TGGTCTTTTTATTC-ACATGCCATAACCCAGCTA
47630676 TGGTCTT
1 TGGTCTT
47630683 GATCGGCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 5 0.14
33 8 0.23
34 22 0.63
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.41
Consensus pattern (33 bp):
TGGTCTTTTTATTCACATGCCATAACCCAGCTA
Found at i:47637967 original size:32 final size:33
Alignment explanation
Indices: 47637931--47638004 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
47637921 AAGCCCTACC
* *
47637931 ATGGTCTTTTGTTC-ACATGCCATAACCCGGCT
1 ATGGTCTTTTATTCGACATGCCATAACCCAGCT
** *
47637963 ATGGTCTTTTTATTCGATTTGCCATAGCCCAGCT
1 ATGGTC-TTTTATTCGACATGCCATAACCCAGCT
47637997 ATGGTCTT
1 ATGGTCTT
47638005 AATCGGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 6 0.17
33 9 0.26
34 20 0.57
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (33 bp):
ATGGTCTTTTATTCGACATGCCATAACCCAGCT
Found at i:47642875 original size:21 final size:21
Alignment explanation
Indices: 47642796--47642930 Score: 67
Period size: 21 Copynumber: 6.5 Consensus size: 21
47642786 CCGTAAGGGT
* *
47642796 TAAACAGAATCTCAGAAGAGC
1 TAAACTGAAACTCAGAAGAGC
* * * * * *
47642817 TGAACGGAAACCCACAAGGGT
1 TAAACTGAAACTCAGAAGAGC
** * *
47642838 TAATTTGAAGCTTAGAAGAGC
1 TAAACTGAAACTCAGAAGAGC
* *
47642859 TAAACTGAAACTCAGAAGGGT
1 TAAACTGAAACTCAGAAGAGC
* * *
47642880 TAAAATGAAACTCATATGAG-
1 TAAACTGAAACTCAGAAGAGC
* *
47642900 TTAACTGAAGCTCATG-AGAGC
1 TAAACTGAAACTCA-GAAGAGC
*
47642921 TAAACGGAAA
1 TAAACTGAAA
47642931 GAAAACATGA
Statistics
Matches: 77, Mismatches: 35, Indels: 4
0.66 0.30 0.03
Matches are distributed among these distances:
20 14 0.18
21 63 0.82
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (21 bp):
TAAACTGAAACTCAGAAGAGC
Found at i:47649655 original size:27 final size:27
Alignment explanation
Indices: 47649623--47649794 Score: 254
Period size: 27 Copynumber: 6.4 Consensus size: 27
47649613 CTCTTATAAG
*
47649623 ATAGAATTACCATTTTACCCTTGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* * * *
47649650 ACAGAAATACCGTTTTTCCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
47649677 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
47649704 ATAGAATTACCATCTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
47649731 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
47649758 ATAGAATTACAATTTTACCCTCAATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
47649785 ACAAAATTAC
1 ATAGAATTAC
47649795 TGAAATACCC
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 130 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (27 bp):
ATAGAATTACCATTTTACCCTCGATTT
Found at i:47649893 original size:27 final size:27
Alignment explanation
Indices: 47649464--47649912 Score: 251
Period size: 27 Copynumber: 16.6 Consensus size: 27
47649454 TTAGTTTACC
** * *
47649464 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
47649491 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * * *
47649518 AAGTTACCCAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * **
47649545 AAATCACCGAAATACCCTC-AGTTTGCA
1 AAATTACCAAAATACCCTCGA-TTTATA
* *
47649572 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
** * * **
47649599 AAATTACTGAAATACTCT-TATAAGATA
1 AAATTACCAAAATACCCTCGAT-TTATA
* *** * *
47649626 GAATTACCATTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
**** *
47649653 GAAA-TACCGTTTTTCCCTCGATTTATA
1 -AAATTACCAAAATACCCTCGATTTATA
* ***
47649680 GAATTACCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* ***
47649707 GAATTACCATCTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* ***
47649734 GAATTACCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* ** * *
47649761 GAATTA-CAATTTTACCCTCAATTTACA
1 AAATTACCAA-AATACCCTCGATTTATA
** * * *
47649788 AAATTACTGAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
**
47649815 AAATTACCAAAATACCCTCGATCAATA
1 AAATTACCAAAATACCCTCGATTTATA
* *
47649842 AAATTACCAAAATACACCT-GGTTTGTA
1 AAATTACCAAAATAC-CCTCGATTTATA
* * *
47649869 AAATTACCAAAATACCCTTGATTTGTG
1 AAATTACCAAAATACCCTCGATTTATA
*
47649896 AAATTACCGAAATACCC
1 AAATTACCAAAATACCC
47649913 CTGTAGGGTA
Statistics
Matches: 339, Mismatches: 73, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
26 10 0.03
27 320 0.94
28 9 0.03
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:47649927 original size:27 final size:27
Alignment explanation
Indices: 47649897--47650040 Score: 198
Period size: 27 Copynumber: 5.3 Consensus size: 27
47649887 TGATTTGTGA
47649897 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
47649924 AATTACTTAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
47649951 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
47649978 AATTATCGAAATACCCTTGTAGAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
47650005 AAATACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
47650032 AATTACCGA
1 AATTACCGA
47650041 GTACCTTTGT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 101 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:47649928 original size:54 final size:53
Alignment explanation
Indices: 47649816--47650038 Score: 191
Period size: 54 Copynumber: 4.1 Consensus size: 53
47649806 TGGTTTACAA
* * * * * ** *
47649816 AATTACCAAAATACCCTCGATCAATAAAATTACCAAAATACACCTGGT-TTGTAA
1 AATTACCAAAATACCCTTG-TTAGTGAAATTACCAAAATACCCCT-GTAGGGTAG
* *
47649870 AATTACCAAAATACCCTTGATTTGTGAAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTTG-TTAGTGAAATTACCAAAATACCCCTGTAGGGTAG
** * *
47649924 AATTACTTAAATACCCTTG-TAGGGTAGAATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTTGTTAGTG-A-AATTACCAAAATACCCCTGTAGGGTAG
* * * * *
47649978 AATTATCGAAATACCCTTGTAGAGTAGAAA-TACCGAAATACCCCTATAGGGTAG
1 AATTACCAAAATACCCTTGT-TAGT-GAAATTACCAAAATACCCCTGTAGGGTAG
47650032 AATTACC
1 AATTACC
47650039 GAGTACCTTT
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
52 3 0.02
53 3 0.02
54 126 0.91
55 2 0.01
56 3 0.02
57 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (53 bp):
AATTACCAAAATACCCTTGTTAGTGAAATTACCAAAATACCCCTGTAGGGTAG
Found at i:47650512 original size:19 final size:19
Alignment explanation
Indices: 47650471--47650514 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47650461 TCTGATTTTG
* *
47650471 ATTCTGTTACCCGATACTG
1 ATTCTGTCACCCGATACTA
* *
47650490 ATTCTGTCACCTGATTCTA
1 ATTCTGTCACCCGATACTA
47650509 ATTCTG
1 ATTCTG
47650515 ATTCTGATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (19 bp):
ATTCTGTCACCCGATACTA
Found at i:47650518 original size:6 final size:6
Alignment explanation
Indices: 47650500--47650552 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
47650490 ATTCTGTCAC
*
47650500 CTGATT CTAATT CTGATT CTGATT CTGATT CTGATT CTGATT CT-AGTT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CTGATT CTGATT CTGA-TT
47650548 CTGAT
1 CTGAT
47650553 AATGGTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
CTGATT
Found at i:47654723 original size:25 final size:25
Alignment explanation
Indices: 47654695--47654744 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
47654685 AATGCTAAAC
47654695 CAGTATTTCTTCAGCAAATTTGTGA
1 CAGTATTTCTTCAGCAAATTTGTGA
47654720 CAGTATTTCTTCAGCAAATTTGTGA
1 CAGTATTTCTTCAGCAAATTTGTGA
47654745 AGCTCAGAAA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (25 bp):
CAGTATTTCTTCAGCAAATTTGTGA
Found at i:47661689 original size:42 final size:42
Alignment explanation
Indices: 47661637--47661760 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
47661627 GGGCTGCATA
* * *
47661637 GAAGCACATAAGTGCTAAACGGAAACCCGTAAGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
* * * * *
47661679 GAAGCTCATAAGAGCTTAACGAAAACCTATAAGGGTTAATCT
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
* * *
47661721 AAAGCTCAGAAGAGCTGAAA-TGAAACCCATAAGGGTTAAA
1 GAAGCTCATAAGAGCT-AAACGGAAACCCATAAGGGTTAAA
47661761 TTGAAACTCA
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.18
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACG
Found at i:47661690 original size:21 final size:21
Alignment explanation
Indices: 47661637--47661699 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
47661627 GGGCTGCATA
*
47661637 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGGGCTAAACG
* * * *
47661658 GAAACCCGTAAGGGTTAAACG
1 GAAGCACATAAGGGCTAAACG
* * *
47661679 GAAGCTCATAAGAGCTTAACG
1 GAAGCACATAAGGGCTAAACG
47661700 AAAACCTATA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
GAAGCACATAAGGGCTAAACG
Found at i:47663651 original size:42 final size:42
Alignment explanation
Indices: 47663604--47663695 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
47663594 TGGCCCTTAG
* * * *
47663604 GCCCATTTCAATATCGCATGTAATATCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
47663646 GCCCATTTCAATATCACATGAAATACCAATGAATGTCTGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
47663688 GCCCATTT
1 GCCCATTT
47663696 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:47663873 original size:26 final size:26
Alignment explanation
Indices: 47663850--47664014 Score: 242
Period size: 26 Copynumber: 6.4 Consensus size: 26
47663840 AACCGGGACA
** *
47663850 AAGCCCTTTTCGGTAAACTGGGG-AA
1 AAGCCCTTTTCAATAAACTGGGGCAT
* *
47663875 AAACCATTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
47663901 AAGCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
**
47663927 AAGCCCTTTTCGGTAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
47663953 AAGCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
**
47663979 AAGCCCTTTTCGGTAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
47664005 AAGCCCTTTT
1 AAGCCCTTTT
47664015 GCACTTCCTC
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 19 0.15
26 107 0.85
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
AAGCCCTTTTCAATAAACTGGGGCAT
Found at i:47663981 original size:78 final size:77
Alignment explanation
Indices: 47663850--47664014 Score: 276
Period size: 78 Copynumber: 2.1 Consensus size: 77
47663840 AACCGGGACA
47663850 AAGCCCTTTTCGGTAAACTGGGGAAAAACCATTTTCAATAAACTGGGGCATAAGCCCTTTTCAAT
1 AAGCCCTTTTCGGTAAACTGGGGAAAAACCATTTTCAATAAACTGGGGCATAAGCCCTTTTCAAT
47663915 AAACTGGGGCAT
66 AAACTGGGGCAT
* * * **
47663927 AAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGG
1 AAGCCCTTTTCGGTAAACTGGGG-AAAAACCATTTTCAATAAACTGGGGCATAAGCCCTTTTCAA
47663992 TAAACTGGGGCAT
65 TAAACTGGGGCAT
47664005 AAGCCCTTTT
1 AAGCCCTTTT
47664015 GCACTTCCTC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 23 0.28
78 59 0.72
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (77 bp):
AAGCCCTTTTCGGTAAACTGGGGAAAAACCATTTTCAATAAACTGGGGCATAAGCCCTTTTCAAT
AAACTGGGGCAT
Found at i:47664846 original size:26 final size:27
Alignment explanation
Indices: 47664817--47664899 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
47664807 GGGCATATTC
* *
47664817 GTCATTTTACCATATA-GGG-TATTACG
1 GTCAATTTACCATACAGGGGCT-TTACG
* *
47664843 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCAATTTACCATACAGGGGCTTTACG
*
47664870 GTCAATTTACCCTACAGGGGCTTTACG
1 GTCAATTTACCATACAGGGGCTTTACG
47664897 GTC
1 GTC
47664900 TTTTTGCCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 13 0.25
27 37 0.73
28 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (27 bp):
GTCAATTTACCATACAGGGGCTTTACG
Found at i:47664916 original size:27 final size:27
Alignment explanation
Indices: 47664838--47664899 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
47664828 ATATAGGGTA
*
47664838 TTACGGTCACTTTACCCTACAGGGGCT
1 TTACGGTCAATTTACCCTACAGGGGCT
47664865 TTACGGTCAATTTACCCTACAGGGGCT
1 TTACGGTCAATTTACCCTACAGGGGCT
47664892 TTACGGTC
1 TTACGGTC
47664900 TTTTTGCCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (27 bp):
TTACGGTCAATTTACCCTACAGGGGCT
Found at i:47664981 original size:27 final size:27
Alignment explanation
Indices: 47664951--47665003 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
47664941 GGGTGTTTTG
47664951 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * * *
47664978 GTAATTTTATAAACCAATGGTATTTC
1 GTAAATCTACAAACCAAGGGTATTTC
47665004 TATAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:47665009 original size:27 final size:27
Alignment explanation
Indices: 47664961--47665295 Score: 151
Period size: 27 Copynumber: 12.4 Consensus size: 27
47664951 GTAAATCTAC
47664961 AAACCAAGGGTATTTCAGTAATTTTAT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
47664988 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * * *
47665016 AAAGTCAAGGGTATTTCTGTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
** * ** *
47665044 AAATTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
47665071 AAATTGAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
** *
47665098 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTCAGTAATTTTAT
* * ** *
47665125 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
** * * *
47665152 AAATTAAGAGTA--TCGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * * *
47665177 AAACCAGGGGTATTTTAGCAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* **
47665204 AAA-CTAGGGTATTTTGGTAATTTTACT
1 AAACCAAGGGTATTTCAGTAATTTTA-T
* * * ** *
47665231 -GATCGAGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
47665257 AAACCAATGGTATTTTAGTAATTTTAT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
47665284 AAATCGAGGGTA
1 AAACCAAGGGTA
47665296 AAATAGTAAT
Statistics
Matches: 244, Mismatches: 53, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
25 20 0.08
26 22 0.09
27 172 0.70
28 16 0.07
29 14 0.06
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:47665110 original size:54 final size:53
Alignment explanation
Indices: 47664940--47665295 Score: 247
Period size: 54 Copynumber: 6.6 Consensus size: 53
47664930 TCATCCTACA
* * * * * ** *
47664940 AGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTATAAACC
1 AGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACC
* * * * * ** **
47664993 AATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTAAATT
1 -AGGGTATTT-TGGTAA-TTTTACAAA-TCGAGGGTATTT-TGGTAATTTTACAAACC
* * *
47665049 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC
1 A-GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACC
* **
47665103 AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTA
1 AG-GGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTACAAA-CC
* * * * * *
47665158 AGAGTA--TCGGTAATTTTACAAA-CCAGGGGTATTTTAGCAATTTTACAAACT
1 AGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTACAAACC
** **
47665209 AGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACC
1 AGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACC
* * *
47665262 AATGGTATTTTAGTAATTTTATAAATCGAGGGTA
1 -AGGGTATTTTGGTAATTTTACAAATCGAGGGTA
47665296 AAATAGTAAT
Statistics
Matches: 236, Mismatches: 52, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
51 5 0.02
52 39 0.17
53 35 0.15
54 106 0.45
55 19 0.08
56 32 0.14
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (53 bp):
AGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACC
Found at i:47665187 original size:52 final size:52
Alignment explanation
Indices: 47665060--47665254 Score: 171
Period size: 52 Copynumber: 3.7 Consensus size: 52
47665050 GGGGTATTTT
** * * * * *
47665060 GGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTT
1 GGTAATTTTACAAACCAG-GGGTATTTTGGTAATTTTACAAACTAG-AGTA-TTC
* *
47665114 GGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTAAGAGTA-TC
1 GGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACT-AGAGTATTC
* * * *
47665166 GGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAAACTAGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGAGTA-TTC
** *
47665219 GGTAATTTTACTGATC-GAGGGTATTTTGGTAATTTT
1 GGTAATTTTACAAACCAG-GGGTATTTTGGTAATTTT
47665255 GTAAACCAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
51 5 0.04
52 41 0.35
53 30 0.25
54 38 0.32
55 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (52 bp):
GGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGAGTATTC
Found at i:47665200 original size:79 final size:80
Alignment explanation
Indices: 47665048--47665229 Score: 287
Period size: 79 Copynumber: 2.3 Consensus size: 80
47665038 CTTTGTAAAT
* * *
47665048 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTT
1 TAGGGGTATTTTGGTAATTTTACAAATTAAGAGTA-TTCGGTAATTTCACAAACCAGGGGTATTT
* *
47665113 TGGTAATTTTACAAAC
65 TAGCAATTTTACAAAC
*
47665129 TAGGGGTATTTTGGTAATTTTACAAATTAAGAGTA-TCGGTAATTTTACAAACCAGGGGTATTTT
1 TAGGGGTATTTTGGTAATTTTACAAATTAAGAGTATTCGGTAATTTCACAAACCAGGGGTATTTT
47665193 AGCAATTTTACAAAC
66 AGCAATTTTACAAAC
47665208 TA-GGGTATTTTGGTAATTTTAC
1 TAGGGGTATTTTGGTAATTTTAC
47665230 TGATCGAGGG
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
78 20 0.21
79 42 0.44
81 33 0.35
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (80 bp):
TAGGGGTATTTTGGTAATTTTACAAATTAAGAGTATTCGGTAATTTCACAAACCAGGGGTATTTT
AGCAATTTTACAAAC
Found at i:47665302 original size:27 final size:27
Alignment explanation
Indices: 47665272--47665403 Score: 192
Period size: 27 Copynumber: 4.9 Consensus size: 27
47665262 AATGGTATTT
*
47665272 TAGTAATTTTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* *
47665299 TAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
*
47665326 CAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
**
47665353 CGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* *
47665380 TGGTAATTCTATAAATTGAGGGTA
1 TAGTAATTCTATAAATCGAGGGTA
47665404 CTTTGGTAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 96 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (27 bp):
TAGTAATTCTATAAATCGAGGGTAAAA
Found at i:47665305 original size:54 final size:54
Alignment explanation
Indices: 47665209--47665403 Score: 149
Period size: 54 Copynumber: 3.6 Consensus size: 54
47665199 TTTACAAACT
* * *** * *
47665209 AGGGTATTTTGGTAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTA-TAAATCGAGGGTAAAATAGTAATTCTGTAAACCA
* *
47665263 ATGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTAAACCA
**** * ** * * *
47665317 AGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTAAACCA
*** * * *
47665371 AGGGTAAAATGGTAATTCTATAAATTGAGGGTA
1 AGGGTATTTTAGTAATTTTATAAATCGAGGGTA
47665404 CTTTGGTAAT
Statistics
Matches: 118, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
53 1 0.01
54 117 0.99
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTAAACCA
Found at i:47665425 original size:27 final size:27
Alignment explanation
Indices: 47665380--47665442 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
47665370 GAGGGTAAAA
* * *
47665380 TGGTAATTCTATAAATTGAGGGTACTT
1 TGGTAATTTTACAAATTGAGGGCACTT
* *
47665407 TGGTAATTTTACAATTTGAGGGCATTT
1 TGGTAATTTTACAAATTGAGGGCACTT
*
47665434 TAGTAATTT
1 TGGTAATTT
47665443 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (27 bp):
TGGTAATTTTACAAATTGAGGGCACTT
Found at i:47666569 original size:18 final size:18
Alignment explanation
Indices: 47666541--47666584 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
47666531 ATATGCCATT
47666541 CAAAGACACCACAATATAC
1 CAAA-ACACCACAATATAC
47666560 CAAAACACCACAATATAC
1 CAAAACACCACAATATAC
47666578 CAAAACA
1 CAAAACA
47666585 AAAACTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.57, C:0.32, G:0.02, T:0.09
Consensus pattern (18 bp):
CAAAACACCACAATATAC
Found at i:47670833 original size:42 final size:42
Alignment explanation
Indices: 47670722--47670842 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 42
47670712 TACCATACCA
* ** * *
47670722 ATGCCATATCCCAGTTATGGTCTTACGTGTAATCTCGTATTG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
* * *
47670764 ATGCCAATAACCCAGCTATGGTTTTACACG-AAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCATATCG
*
47670807 ATGCCATATCTCAGATATGGTCTTACACGTAATCTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTC
47670843 TGTAACCCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
42 31 0.48
43 34 0.52
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:47677213 original size:24 final size:24
Alignment explanation
Indices: 47677186--47677256 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
47677176 CTAGATTTCC
*
47677186 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCTACTCCTAAATCCTA
*
47677210 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCTACTCCTAAATCCTA
*
47677234 TCCCTTATTTACTCCTAAATCCT
1 TCCCTTATCTACTCCTAAATCCT
47677257 CTCTTGACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.24, C:0.37, G:0.01, T:0.38
Consensus pattern (24 bp):
TCCCTTATCTACTCCTAAATCCTA
Found at i:47696196 original size:28 final size:26
Alignment explanation
Indices: 47696140--47696252 Score: 136
Period size: 27 Copynumber: 4.2 Consensus size: 26
47696130 AGCATGGCTG
* *
47696140 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
47696166 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
47696194 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
47696221 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
47696249 CCAG
1 CCAG
47696253 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.08
27 38 0.50
28 32 0.42
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:47696225 original size:55 final size:54
Alignment explanation
Indices: 47696140--47696252 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 54
47696130 AGCATGGCTG
*
47696140 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAGAACCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAACCA
* * * *
47696194 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAACCA
47696249 CCAG
1 CCAG
47696253 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
54 19 0.37
55 33 0.63
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAACCA
Found at i:47699516 original size:30 final size:30
Alignment explanation
Indices: 47699482--47699542 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
47699472 TCCTTAACTC
47699482 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
47699512 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
47699542 A
1 A
47699543 GGCTCGGGAA
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:47702229 original size:42 final size:42
Alignment explanation
Indices: 47702117--47702238 Score: 120
Period size: 43 Copynumber: 2.9 Consensus size: 42
47702107 TACCGTACCA
* * * * *
47702117 ATGCCATATCCTAAATATGGTCTTACATGTAATCTCGTATTG
1 ATGCAATATCCTAGATATGGTCTTACACGTAATCTCATATCG
* * * *
47702159 ATGCCAATAGCCCAGTTATGGTCGTACACG-AAGTCTCATATCG
1 ATG-CAATATCCTAGATATGGTCTTACACGTAA-TCTCATATCG
* *
47702202 ATGCTATATCCTAGATATGGTCTTACACATAATCTCA
1 ATGCAATATCCTAGATATGGTCTTACACGTAATCTCA
47702239 GTAACACTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
42 30 0.48
43 32 0.52
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (42 bp):
ATGCAATATCCTAGATATGGTCTTACACGTAATCTCATATCG
Found at i:47709287 original size:35 final size:35
Alignment explanation
Indices: 47709188--47709288 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 35
47709178 TGATGATATG
* * * * **
47709188 TTGAACTTGTAAATTTGGCTACATGTGATGTTTTA
1 TTGAACTTGTATATTCGGCCAAATGTGATGAATTA
* * * * *
47709223 TTTAACTTGTATTTTCGGTCATATCTGATGAATTA
1 TTGAACTTGTATATTCGGCCAAATGTGATGAATTA
47709258 TTGAACTTGTATATTCGGCCAAATGTGATGA
1 TTGAACTTGTATATTCGGCCAAATGTGATGA
47709289 TATAACGAAC
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.44
Consensus pattern (35 bp):
TTGAACTTGTATATTCGGCCAAATGTGATGAATTA
Found at i:47712093 original size:28 final size:27
Alignment explanation
Indices: 47712041--47712093 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
47712031 AACACAATTT
**
47712041 GGGCCTAAGCCCTTTCAGTCTCAGTTA
1 GGGCCTAAGCCCTTTCAGTAACAGTTA
*
47712068 GGGCCTTAGCCCATTTCAGTAACAGT
1 GGGCCTAAGCCC-TTTCAGTAACAGT
47712094 AACAGTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (27 bp):
GGGCCTAAGCCCTTTCAGTAACAGTTA
Found at i:47712106 original size:34 final size:34
Alignment explanation
Indices: 47712062--47712165 Score: 122
Period size: 34 Copynumber: 3.1 Consensus size: 34
47712052 CTTTCAGTCT
*
47712062 CAGTTAGGGCCTTAGCCCATTTCAGTAACAGTAA
1 CAGTTAGGGCCTAAGCCCATTTCAGTAACAGTAA
* * * *
47712096 CAGTTTGGGCCTGAGCCTATTTCAGTAACAGTAT
1 CAGTTAGGGCCTAAGCCCATTTCAGTAACAGTAA
* * *
47712130 CAG-TGGGGCCTAAGCCCATTACAGTATCAGT-A
1 CAGTTAGGGCCTAAGCCCATTTCAGTAACAGTAA
47712162 CAGT
1 CAGT
47712166 ATGCAATTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
32 3 0.05
33 23 0.39
34 33 0.56
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (34 bp):
CAGTTAGGGCCTAAGCCCATTTCAGTAACAGTAA
Found at i:47724671 original size:12 final size:12
Alignment explanation
Indices: 47724654--47724682 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
47724644 CACACGCCCT
47724654 TGTGCTAGGCTG
1 TGTGCTAGGCTG
47724666 TGTGCTAGGCTG
1 TGTGCTAGGCTG
47724678 TGTGC
1 TGTGC
47724683 CAAATAGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.41, T:0.34
Consensus pattern (12 bp):
TGTGCTAGGCTG
Found at i:47725653 original size:19 final size:20
Alignment explanation
Indices: 47725579--47725662 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
47725569 CACTCTCAAT
* * *
47725579 CATATAAATAGTAAATCATT
1 CATATAAACAGTAATTCATC
*
47725599 CA-AT-AACAGTAACTCATC
1 CATATAAACAGTAATTCATC
* * *
47725617 CGTTTAAACAGTACTTCATC
1 CATATAAACAGTAATTCATC
47725637 CATATAAA-AGTAATTCATC
1 CATATAAACAGTAATTCATC
*
47725656 CGTATAA
1 CATATAA
47725663 CACATAGCTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
18 12 0.24
19 19 0.37
20 20 0.39
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (20 bp):
CATATAAACAGTAATTCATC
Found at i:47728009 original size:45 final size:44
Alignment explanation
Indices: 47727924--47728009 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
47727914 TATGTAATCT
* *
47727924 GAACTCATTGAGTTGTGTCTGATTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATCC
* *
47727968 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATGTATGACA
1 GAACTCATTGAGTTGT-GTCTGAGTTCATGATATATATGACA
47728010 CATGTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 16 0.43
45 21 0.57
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (44 bp):
GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATCC
Found at i:47734104 original size:17 final size:16
Alignment explanation
Indices: 47734053--47734110 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
47734043 TAATATTAGT
47734053 ATATAAATAGAAATAGAA
1 ATATAAA-A-AAATAGAA
47734071 ATATAAAAAAATAGAA
1 ATATAAAAAAATAGAA
* *
47734087 ATATAATAATAGTAGAA
1 ATATAA-AAAAATAGAA
47734104 ATATAAA
1 ATATAAA
47734111 TTGATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.41
17 15 0.41
18 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
ATATAAAAAAATAGAA
Found at i:47734119 original size:14 final size:15
Alignment explanation
Indices: 47734102--47734140 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
47734092 ATAATAGTAG
47734102 AAATATAAATT-GAT
1 AAATATAAATTAGAT
*
47734116 AAATAAAAATTAGAT
1 AAATATAAATTAGAT
47734131 AAATAATAAA
1 AAAT-ATAAA
47734141 CTAGCAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAATATAAATTAGAT
Found at i:47740206 original size:43 final size:43
Alignment explanation
Indices: 47740143--47740308 Score: 226
Period size: 43 Copynumber: 3.9 Consensus size: 43
47740133 TGAATAATAT
* *
47740143 TATCGGGCTACGGGCCTAGCAGGCTATAATGCCGGTGAGATAA
1 TATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGAGATAA
*
47740186 TATCAGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGAGATAA
1 TATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGAGATAA
* * * *
47740229 TATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTGAAATGA
1 TATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGAGATAA
* * * *
47740272 TATCGGGCTTCAAGCATAGCAGGCGA-AATGCCAGTGA
1 TATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGA
47740309 ATGAGTTTAG
Statistics
Matches: 109, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 10 0.09
43 99 0.91
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (43 bp):
TATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGGTGAGATAA
Found at i:47748859 original size:25 final size:25
Alignment explanation
Indices: 47748795--47749015 Score: 139
Period size: 25 Copynumber: 8.9 Consensus size: 25
47748785 CACAACACTT
* * *
47748795 ATGAGCATCCTGATATATGGCACTC
1 ATGAGCTTCCTGTTATATGGCTCTC
* * *
47748820 ACGAGCTTCCCGTTATTTGGCTCTC
1 ATGAGCTTCCTGTTATATGGCTCTC
* *
47748845 ACGAGCTTCCTGTTA-ATTAGCTCTC
1 ATGAGCTTCCTGTTATA-TGGCTCTC
*
47748870 ATGAGCTT-CTCGATTA-ATGGCTCGC
1 ATGAGCTTCCT-G-TTATATGGCTCTC
* * * *
47748895 ATGAGCTTTCTG-AATTTGGCTCTT
1 ATGAGCTTCCTGTTATATGGCTCTC
* *
47748919 TTGAGCTTCCCGTT-TATGGCTCGT-
1 ATGAGCTTCCTGTTATATGGCTC-TC
* * * * *
47748943 ATGAGATTCTTGATATTTGGCTCAC
1 ATGAGCTTCCTGTTATATGGCTCTC
* * * *
47748968 AAGAGCTTCTTGTTACATGGCTCAC
1 ATGAGCTTCCTGTTATATGGCTCTC
*
47748993 ATGAGCTTCCCGTTATATGGCTC
1 ATGAGCTTCCTGTTATATGGCTC
47749016 AAAGGAGCTT
Statistics
Matches: 150, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
23 1 0.01
24 33 0.22
25 110 0.73
26 6 0.04
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (25 bp):
ATGAGCTTCCTGTTATATGGCTCTC
Found at i:47748947 original size:48 final size:50
Alignment explanation
Indices: 47748871--47748965 Score: 124
Period size: 48 Copynumber: 1.9 Consensus size: 50
47748861 TTAGCTCTCA
* *
47748871 TGAGCTTCTCGATTAATGGCTCGCATGAGCTT-TCTGA-ATTTGGCTCTTT
1 TGAGCTTCCCGATTAATGGCTCGCATGAGATTCT-TGATATTTGGCTCTTT
* *
47748920 TGAGCTTCCCG-TTTATGGCTCGTATGAGATTCTTGATATTTGGCTC
1 TGAGCTTCCCGATTAATGGCTCGCATGAGATTCTTGATATTTGGCTC
47748966 ACAAGAGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 20 0.50
49 20 0.50
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (50 bp):
TGAGCTTCCCGATTAATGGCTCGCATGAGATTCTTGATATTTGGCTCTTT
Found at i:47748961 original size:49 final size:49
Alignment explanation
Indices: 47748871--47748965 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
47748861 TTAGCTCTCA
* *
47748871 TGAGCTTCTCGATTAATGGCTCGCATGAGCTTTCTGAATTTGGCTCTTT
1 TGAGCTTCCCGATTAATGGCTCGCATGAGATTTCTGAATTTGGCTCTTT
* *
47748920 TGAGCTTCCCG-TTTATGGCTCGTATGAGA-TTCTTGATATTTGGCTC
1 TGAGCTTCCCGATTAATGGCTCGCATGAGATTTC-TGA-ATTTGGCTC
47748966 ACAAGAGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 3 0.08
48 18 0.45
49 19 0.47
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (49 bp):
TGAGCTTCCCGATTAATGGCTCGCATGAGATTTCTGAATTTGGCTCTTT
Found at i:47749023 original size:25 final size:24
Alignment explanation
Indices: 47748960--47749037 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
47748950 TCTTGATATT
**
47748960 TGGCTCACAAGAGCTTCTTGTTACA
1 TGGCTCA-AAGAGCTTCCCGTTACA
* *
47748985 TGGCTCACATGAGCTTCCCGTTATA
1 TGGCTCA-AAGAGCTTCCCGTTACA
*
47749010 TGGCTCAAAGGAGCTTTCCGATTACA
1 TGGCTCAAA-GAGCTTCCCG-TTACA
47749036 TG
1 TG
47749038 CTTGCATAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 37 0.84
26 6 0.14
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (24 bp):
TGGCTCAAAGAGCTTCCCGTTACA
Found at i:47751997 original size:52 final size:52
Alignment explanation
Indices: 47751934--47752037 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
47751924 ATATGTATGC
47751934 GGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
* *
47751986 GGCATCTGAGCTCGTTGAGTTGGTCTGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
47752038 AATTGGGTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (52 bp):
GGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
Found at i:47755988 original size:13 final size:14
Alignment explanation
Indices: 47755970--47755998 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
47755960 AATGCATTCA
47755970 TTAGTTAA-TTTAG
1 TTAGTTAATTTTAG
47755983 TTAGTTAATTTTAG
1 TTAGTTAATTTTAG
47755997 TT
1 TT
47755999 TTAATCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAGTTAATTTTAG
Found at i:47756695 original size:19 final size:19
Alignment explanation
Indices: 47756667--47756708 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
47756657 TCTTGTTTAG
*
47756667 GTTAAGTTTTTTTTACCGA
1 GTTAAATTTTTTTTACCGA
47756686 GTTAAATTTTTTTTACCGA
1 GTTAAATTTTTTTTACCGA
47756705 GTTA
1 GTTA
47756709 TAGTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (19 bp):
GTTAAATTTTTTTTACCGA
Found at i:47757982 original size:13 final size:14
Alignment explanation
Indices: 47757964--47757992 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
47757954 AATGCATTCA
47757964 TTAGTTAA-TTTAG
1 TTAGTTAATTTTAG
47757977 TTAGTTAATTTTAG
1 TTAGTTAATTTTAG
47757991 TT
1 TT
47757993 TTAATCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAGTTAATTTTAG
Found at i:47758689 original size:19 final size:19
Alignment explanation
Indices: 47758661--47758702 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
47758651 TCTTGTTTAG
*
47758661 GTTAAGTTTTTTTTACCGA
1 GTTAAATTTTTTTTACCGA
47758680 GTTAAATTTTTTTTACCGA
1 GTTAAATTTTTTTTACCGA
47758699 GTTA
1 GTTA
47758703 TAGTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (19 bp):
GTTAAATTTTTTTTACCGA
Found at i:47768900 original size:38 final size:38
Alignment explanation
Indices: 47768858--47768971 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
47768848 CAAGAACTCC
47768858 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
47768896 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
47768934 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
47768972 AAAGGATGAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:47773271 original size:26 final size:24
Alignment explanation
Indices: 47773237--47773284 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
47773227 ATATGGTACA
47773237 ATAACTTTTAAATATTTTTAATAATT
1 ATAACTTTT--ATATTTTTAATAATT
*
47773263 ATAATTTTTATATTTTTAATAA
1 ATAACTTTTATATTTTTAATAA
47773285 AATTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
26 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAACTTTTATATTTTTAATAATT
Found at i:47773291 original size:24 final size:25
Alignment explanation
Indices: 47773248--47773296 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
47773238 TAACTTTTAA
*
47773248 ATATTTTTAATAATTATAAT-TTTT
1 ATATTTTTAATAAATATAATATTTT
47773272 ATATTTTTAATAAA-ATTAATATTTT
1 ATATTTTTAATAAATA-TAATATTTT
47773297 TAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 17 0.77
25 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATTTTTAATAAATATAATATTTT
Found at i:47773315 original size:18 final size:18
Alignment explanation
Indices: 47773263--47773316 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
47773253 TTTAATAATT
*
47773263 ATAATTTTTATATTTTTA
1 ATAAATTTTATATTTTTA
* *
47773281 ATAAAATTAATATTTTTA
1 ATAAATTTTATATTTTTA
47773299 ATAAATTTTATACTTTTT
1 ATAAATTTTATA-TTTTT
47773317 CTATATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAAATTTTATATTTTTA
Found at i:47773438 original size:22 final size:21
Alignment explanation
Indices: 47773398--47773533 Score: 74
Period size: 20 Copynumber: 6.7 Consensus size: 21
47773388 AATTTTTTTA
*
47773398 TTTAT-TATAATTTTTAATAAAT
1 TTTATATAT-ATTTTAAAT-AAT
*
47773420 TTTGTATATATTTTAAATAAT
1 TTTATATATATTTTAAATAAT
* *
47773441 TTTAT-TATATTTTATTATATT
1 TTTATATATATTTTA-AATAAT
* * * *
47773462 CTTTTTCTAAATTTTAATTAAT
1 -TTTATATATATTTTAAATAAT
*
47773484 TTTA-ATATATTTT-TATATAT
1 TTTATATATATTTTAAATA-AT
*
47773504 TTT-TA-A-ATTTTTAATAAT
1 TTTATATATATTTTAAATAAT
47773522 TTT-TATAT-TTTT
1 TTTATATATATTTT
47773534 CTAGATTTAT
Statistics
Matches: 89, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
18 12 0.13
19 11 0.12
20 22 0.25
21 14 0.16
22 19 0.21
23 11 0.12
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTATATATATTTTAAATAAT
Found at i:47773447 original size:43 final size:40
Alignment explanation
Indices: 47773398--47773533 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 40
47773388 AATTTTTTTA
47773398 TTTATTATAATTTTTAATAAATTTTGTATATATTTTAAATAAT
1 TTTATTAT-ATTTTTAATAAATTTT-TATA-ATTTTAAATAAT
* ** * *
47773441 TTTATTATATTTTATTATATTCTTTTTCTAAATTTTAATTAAT
1 TTTATTATATTTT-TAATA-AATTTTTAT-AATTTTAAATAAT
* * *
47773484 TTTAATATATTTTT-ATATATTTTTA-AATTTTTAATAA-
1 TTTATTATATTTTTAATAAATTTTTATAATTTTAAATAAT
47773521 TTT-TTATATTTTT
1 TTTATTATATTTTT
47773534 CTAGATTTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 13
0.77 0.11 0.13
Matches are distributed among these distances:
36 9 0.11
37 3 0.04
38 10 0.13
40 6 0.08
41 3 0.04
42 6 0.08
43 37 0.47
44 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTATTATATTTTTAATAAATTTTTATAATTTTAAATAAT
Found at i:47773513 original size:8 final size:9
Alignment explanation
Indices: 47773388--47773533 Score: 64
Period size: 10 Copynumber: 14.8 Consensus size: 9
47773378 ATTTAAAAGG
47773388 AATTTTT-T
1 AATTTTTAT
*
47773396 TATTTATTAT
1 AATTT-TTAT
47773406 AATTTTTAAT
1 AATTTTT-AT
47773416 AAATTTTGTAT
1 -AATTTT-TAT
*
47773427 ATATTTTAAAT
1 A-ATTTT-TAT
47773438 AATTTTATTAT
1 AA-TTT-TTAT
*
47773449 ATTTTATTAT
1 AATTT-TTAT
* *
47773459 ATTCTTTTTCT
1 A--ATTTTTAT
*
47773470 AAATTTTAATT
1 -AATTTTTA-T
*
47773481 AATTTTAAT
1 AATTTTTAT
47773490 ATATTTTTAT
1 A-ATTTTTAT
47773500 ATATTTTTA-
1 A-ATTTTTAT
47773509 AATTTTTAAT
1 AATTTTT-AT
47773519 AATTTTTAT
1 AATTTTTAT
47773528 -ATTTTT
1 AATTTTT
47773534 CTAGATTTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 30
0.73 0.08 0.20
Matches are distributed among these distances:
8 16 0.14
9 10 0.09
10 53 0.48
11 26 0.23
12 6 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:47773515 original size:18 final size:18
Alignment explanation
Indices: 47773464--47773533 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
47773454 ATTATATTCT
47773464 TTTTCTAAA-TTTTAATTAA
1 TTTT-TAAATTTTTAA-TAA
*
47773483 -TTTTAATATATTTTTATATA
1 TTTTTAA-AT-TTTTAATA-A
47773503 TTTTTAAATTTTTAATAA
1 TTTTTAAATTTTTAATAA
*
47773521 TTTTTATATTTTT
1 TTTTTAAATTTTT
47773534 CTAGATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
17 3 0.07
18 17 0.40
19 9 0.21
20 8 0.19
21 6 0.14
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTTTTAATAA
Found at i:47773541 original size:28 final size:28
Alignment explanation
Indices: 47773483--47773569 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
47773473 TTTTAATTAA
*
47773483 TTTTAATATATTTTTATATATTTT-TAAAT
1 TTTTAATA-ATTTTTATAT-TTTTCTAGAT
47773512 TTTTAATAATTTTTATATTTTTCTAGATT
1 TTTTAATAATTTTTATATTTTTCTAGA-T
* * *
47773541 TATTTTATAACTTTTATTTTTTTCT-GAT
1 T-TTTAATAATTTTTATATTTTTCTAGAT
47773569 T
1 T
47773570 ATTATTATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
27 4 0.08
28 15 0.29
29 12 0.24
30 20 0.39
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTTAATAATTTTTATATTTTTCTAGAT
Found at i:47773575 original size:31 final size:30
Alignment explanation
Indices: 47773512--47773577 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
47773502 ATTTTTAAAT
*
47773512 TTTTAATAATTTTTATATTTTTCTAGATTTA
1 TTTT-ATAACTTTTATATTTTTCTAGATTTA
*
47773543 TTTTATAACTTTTATTTTTTTCT-GA-TTA
1 TTTTATAACTTTTATATTTTTCTAGATTTA
47773571 TTATTAT
1 TT-TTAT
47773578 TATTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 6 0.19
30 17 0.53
31 4 0.12
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTTATAACTTTTATATTTTTCTAGATTTA
Found at i:47774208 original size:6 final size:6
Alignment explanation
Indices: 47774197--47774222 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47774187 AGTACTCGTG
47774197 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
47774223 GTTTACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:47781309 original size:22 final size:22
Alignment explanation
Indices: 47781284--47781328 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47781274 TTTAATAAAA
47781284 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
47781306 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
47781328 A
1 A
47781329 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:47785143 original size:22 final size:22
Alignment explanation
Indices: 47785118--47785162 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47785108 TTTAATAAAA
47785118 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
47785140 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
47785162 A
1 A
47785163 CACTTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:47785951 original size:22 final size:22
Alignment explanation
Indices: 47785905--47785960 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
47785895 TGTTATCAAT
* *
47785905 TATCTGCTTATTTTAAGACTTG
1 TATCTGATTATTTTAAGACTAG
47785927 TATCTGATATATTTTAAG-CTAG
1 TATCTGAT-TATTTTAAGACTAG
*
47785949 TATTCTTATTAT
1 TA-TCTGATTAT
47785961 CTAATGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (22 bp):
TATCTGATTATTTTAAGACTAG
Found at i:47787799 original size:26 final size:26
Alignment explanation
Indices: 47787742--47787803 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
47787732 CTCGAAAAAA
*
47787742 TTATTATTTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATTAATAT
*
47787768 TT-TTAATTTATCGATAAGTTAATAT
1 TTATTAATTTATCGATAAATTAATAT
47787793 TTATTAATTTA
1 TTATTAATTTA
47787804 GTAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATTAATAT
Found at i:47790935 original size:20 final size:20
Alignment explanation
Indices: 47790912--47790971 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
47790902 TAACATGCAA
47790912 ATTATTTTTATAATATTTTT
1 ATTATTTTTATAATATTTTT
*
47790932 ATTATATTTTAGAA-ATTTTT
1 ATTAT-TTTTATAATATTTTT
* **
47790952 ATGATTTAAATAATATTTTT
1 ATTATTTTTATAATATTTTT
47790972 TATAGCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 5 0.15
20 21 0.64
21 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTATTTTTATAATATTTTT
Found at i:47790981 original size:22 final size:21
Alignment explanation
Indices: 47790947--47790989 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
47790937 ATTTTAGAAA
47790947 TTTTTATGATTTA-AATAATAT
1 TTTTTATGATTTATAA-AATAT
*
47790968 TTTTTATAGCTTTATAAAATAT
1 TTTTTAT-GATTTATAAAATAT
47790990 ATATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTATGATTTATAAAATAT
Found at i:47795401 original size:18 final size:18
Alignment explanation
Indices: 47795380--47795418 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
47795370 GATTGAGAGT
* *
47795380 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
47795398 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
47795416 GAA
1 GAA
47795419 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:47799404 original size:39 final size:40
Alignment explanation
Indices: 47799350--47799564 Score: 242
Period size: 40 Copynumber: 5.4 Consensus size: 40
47799340 AAACCAAGTA
** *
47799350 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
47799389 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
47799429 CCTTCGGGACTTTGCCCGGTTATAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
47799469 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** * *
47799509 -CTCTCGGG-CTTAGAGCGGA-ATTAGTCACTAGCACAAATG
1 CCT-TCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
47799548 CATTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
47799565 AGTTATCATC
Statistics
Matches: 152, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 43 0.28
40 108 0.71
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:47807343 original size:358 final size:357
Alignment explanation
Indices: 47806645--47807363 Score: 1402
Period size: 358 Copynumber: 2.0 Consensus size: 357
47806635 ATTCATCAAG
*
47806645 GTTCGATTACATAATTCATTCAATATTTAATTCCATTCTACTATTTTTAGTGATTTTTCACATCC
1 GTTCGATTACATAATTCATTCAATATTTAATTCCATTCTAATATTTTTAGTGATTTTTCACATCC
47806710 ACATCACTGCTGCTGTCAGCATCTATTTTTAAGGTAAACTTTACCTATTTCATGATCCTCCAGGG
66 ACATCACTGCTGCTGTCAGCATCTATTTTTAAGGTAAACTTTACCTATTTCATGATCCTCCAGGG
47806775 ATCAACTAGAGTTTGTCATACATAGCACCAAAATGATCATGAATAACCATTCCAATGGCTAATCG
131 ATCAACTAGAGTTTGTCATACATAGCACCAAAATGATCATGAATAACCATTCCAATGGCTAATCG
47806840 TTACCAACATTTCCATACCTCTCAACGAACAACATACAAACGATTATAATGCTATGATCAAAGTA
196 TTACCAACATTTCCATACCTCTCAACGAACAACATACAAACGATTATAATGCTATGATCAAAGTA
47806905 TATTTAAGCCATTTTCGCATGGCTATCCAAATTTACACAAAACCAAGGGTACATGACCAACAACA
261 TATTTAAGCCATTTTCGCATGGCTATCCAAATTTACACAAAACCAAGGGTACATGACCAACAACA
47806970 AAAAGGATAGTCCTATACATGCCATTTTCAGA
326 AAAAGGATAGTCCTATACATGCCATTTTCAGA
*
47807002 GTTCGATTACATAATTCATTCACTATTTAATTCCATTCCTAATATTTTTAGTGATTTTTCACATC
1 GTTCGATTACATAATTCATTCAATATTTAATTCCATT-CTAATATTTTTAGTGATTTTTCACATC
47807067 CACATCACTGCTGCTGTCAGCATCTATTTTTAAGGTAAACTTTACCTATTTCATGATCCTCCAGG
65 CACATCACTGCTGCTGTCAGCATCTATTTTTAAGGTAAACTTTACCTATTTCATGATCCTCCAGG
47807132 GATCAACTAGAGTTTGTCATACATAGCACCAAAATGATCATGAATAACCATTCCAATGGCTAATC
130 GATCAACTAGAGTTTGTCATACATAGCACCAAAATGATCATGAATAACCATTCCAATGGCTAATC
47807197 GTTACCAACATTTCCATACCTCTCAACGAACAACATACAAACGATTATAATGCTATGATCAAAGT
195 GTTACCAACATTTCCATACCTCTCAACGAACAACATACAAACGATTATAATGCTATGATCAAAGT
47807262 ATATTTAAGCCATTTTCGCATGGCTATCCAAATTTACACAAAACCAAGGGTACATGACCAACAAC
260 ATATTTAAGCCATTTTCGCATGGCTATCCAAATTTACACAAAACCAAGGGTACATGACCAACAAC
*
47807327 AAAAAGGGTAGTCCTATACATGCCATTTTCAGA
325 AAAAAGGATAGTCCTATACATGCCATTTTCAGA
47807360 GTTC
1 GTTC
47807364 AACCAAAAGT
Statistics
Matches: 358, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
357 36 0.10
358 322 0.90
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (357 bp):
GTTCGATTACATAATTCATTCAATATTTAATTCCATTCTAATATTTTTAGTGATTTTTCACATCC
ACATCACTGCTGCTGTCAGCATCTATTTTTAAGGTAAACTTTACCTATTTCATGATCCTCCAGGG
ATCAACTAGAGTTTGTCATACATAGCACCAAAATGATCATGAATAACCATTCCAATGGCTAATCG
TTACCAACATTTCCATACCTCTCAACGAACAACATACAAACGATTATAATGCTATGATCAAAGTA
TATTTAAGCCATTTTCGCATGGCTATCCAAATTTACACAAAACCAAGGGTACATGACCAACAACA
AAAAGGATAGTCCTATACATGCCATTTTCAGA
Found at i:47820968 original size:44 final size:44
Alignment explanation
Indices: 47820905--47822127 Score: 1651
Period size: 44 Copynumber: 28.2 Consensus size: 44
47820895 GACCTGAAAT
47820905 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
47820949 AGATAACAGATTTGGCGTCTCTGCAGTGGCAGACAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
47820993 AGATAACAGATTTGACGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
47821037 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
47821081 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCACATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
47821125 AGATAGCAGATTTGGCGTCTCTGTAGCGGCGGCGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
47821169 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCACATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
47821213 AGATAGCAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
47821257 AGATAACAGATTTGACGTCTCTGTAGCGGCAGAGAACAGGTCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
47821301 AGATAGA-TGATTTGGCATCTCTGTAGCGGCGGAGAGCAAATCGA
1 AGATA-ACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
47821345 AGAT----GAATTGGCATCTCTGTAACGGCGGAGAGCAGATTGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
**
47821385 AGATAACAGATTTGGCGTCTCTGTAGCGGTAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
47821429 AGATAGCAGATTTGGCGTCTCTGTAGCGGTGGAGAGCAGATCAA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
47821473 AGATAACAGATTTGGCATCTCTGTAGCGGTGGAGAGCAAATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* **
47821517 AGATAACAGATTTGGCATCTCTGTAGCGGTAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* ***
47821561 AGAT----GATTTGGCATCTCTGTAGCGATAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
47821601 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* **
47821645 AGAT----GATTTGGCATCTCTGTAGCAACGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
47821685 AGATAACAGATTTGACGTCTCTGTAGCGGCAGAGAACAGGTCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
47821729 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCAA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* **
47821773 AGATAACAGATTTGGCGTCTCTGTAGGGGTAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
47821817 AGAT----GATTTGGCATCTCTGTAGCGACGGAGAGCAGATTGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
47821857 AGATAACAGATCTGGCATCTCTGTAGCGGTGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
** * *
47821901 AGATAACAGATTTGATGTCTCTGTAGCGGCGGAGAACAGGTCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
47821945 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCAA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* **
47821989 AGATAACAGATTTGGCGTCTCTGTAGGGGTAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* **
47822033 AGAT----GATTTGGCATCTCTGTAGCAACGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
47822073 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
47822117 AAATAACAGAT
1 AGATAACAGAT
47822128 CGGTGTTCCT
Statistics
Matches: 1039, Mismatches: 119, Indels: 42
0.87 0.10 0.04
Matches are distributed among these distances:
40 179 0.17
44 859 0.83
45 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (44 bp):
AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
Found at i:47821478 original size:216 final size:217
Alignment explanation
Indices: 47820912--47822127 Score: 1679
Period size: 216 Copynumber: 5.6 Consensus size: 217
47820902 AATAGATAAC
* * *
47820912 AGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGCAGTG
1 AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
* *
47820977 GCAGACAGCAGATCGAAGATAACAGATTTGACGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATA
66 GCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATA
* * * *
47821042 ACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAG
131 ACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTGTAG
* *
47821107 CGGCAGAGAGCACATCGAAGAT
196 CGGCGGAGAGCAGATCGAAGAT
* *
47821129 AGCAGATTTGGCGTCTCTGTAGCGGCGGCGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
1 ---AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
* *
47821194 GCGGCAGAGAGCACATCGAAGATAGCAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAG
63 GCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAG
* *
47821259 ATAACAGATTTGACGTCTCTGTAGCGGCAGAGAACAGGTCGAAGATAGA-TGATTTGGCATCTCT
128 ATAACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATA-ACAGATTTGGCATCTCT
*
47821323 GTAGCGGCGGAGAGCAAATCGAAGAT
192 GTAGCGGCGGAGAGCAGATCGAAGAT
* * * * *
47821349 -GAATTGGCATCTCTGTAACGGCGGAGAGCAGATTGAAGATAACAGATTTGGCGTCTCTGTAGCG
1 AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
* * * *
47821413 GTAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTAGCGGTGGAGAGCAGATCAAAGATA
66 GCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATA
* * * * **
47821478 ACAGATTTGGCATCTCTGTAGCGGTGGAGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTAG
131 ACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTGTAG
**
47821543 CGGTAGAGAGCAGATCGAAGAT
196 CGGCGGAGAGCAGATCGAAGAT
* **
47821565 -GATTTGGCATCTCTGTAGCGATAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
1 AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
* **
47821629 GCAGAGAGCAGATCGAAGAT----GATTTGGCATCTCTGTAGCAACGGAGAGCAGATCGAAGATA
66 GCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATA
*
47821690 ACAGATTTGACGTCTCTGTAGCGGCAGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTGTAG
131 ACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTGTAG
*
47821755 CGGCGGAGAGCAGATCAAAGAT
196 CGGCGGAGAGCAGATCGAAGAT
* * *
47821777 AACAGATTTGGCGTCTCTGTAGGGGTAGAGAGCAGATCGAAGAT----GATTTGGCATCTCTGTA
1 ---AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
* * * * * *
47821838 GCGACGGAGAGCAGATTGAAGATAACAGATCTGGCATCTCTGTAGCGGTGGAGAGCAGATCGAAG
63 GCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAG
*
47821903 ATAACAGATTTGATGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTG
128 ATAACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTG
*
47821968 TAGCGGCGGAGAGCAGATCAAAGAT
193 TAGCGGCGGAGAGCAGATCGAAGAT
* * *
47821993 AACAGATTTGGCGTCTCTGTAGGGGTAGAGAGCAGATCGAAGAT----GATTTGGCATCTCTGTA
1 ---AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
** * * *
47822054 GCAACGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAA
63 GCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAG
47822119 ATAACAGAT
128 ATAACAGAT
47822128 CGGTGTTCCT
Statistics
Matches: 909, Mismatches: 77, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
212 149 0.16
215 1 0.00
216 558 0.61
220 200 0.22
221 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.22
Consensus pattern (217 bp):
AGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
GCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATA
ACAGATTTGACGTCTCTGTAGCGGCGGAGAACAGGTCGAAGATAACAGATTTGGCATCTCTGTAG
CGGCGGAGAGCAGATCGAAGAT
Found at i:47823687 original size:24 final size:24
Alignment explanation
Indices: 47823631--47823687 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
47823621 TATTTTCATG
* *
47823631 ATTATTATTGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
* *
47823655 ACTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
47823679 ATTAGTATT
1 ATTATTATT
47823688 ATAATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:47825510 original size:8 final size:8
Alignment explanation
Indices: 47825499--47825523 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47825489 CCCTTTTTTT
47825499 TTTTTAAA
1 TTTTTAAA
47825507 TTTTTAAA
1 TTTTTAAA
47825515 TTTTTAAA
1 TTTTTAAA
47825523 T
1 T
47825524 CAAGGAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTTAAA
Found at i:47829483 original size:19 final size:19
Alignment explanation
Indices: 47829459--47829499 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
47829449 TTAAATTGTT
*
47829459 TTATAATATGAAATGAATA
1 TTATAATATGAAAGGAATA
*
47829478 TTATAATATTAAAGGAATA
1 TTATAATATGAAAGGAATA
47829497 TTA
1 TTA
47829500 ATATTATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (19 bp):
TTATAATATGAAAGGAATA
Found at i:47846917 original size:35 final size:35
Alignment explanation
Indices: 47846878--47846948 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
47846868 CATCTCCAGA
*
47846878 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* *
47846913 GCTTGGCAAATATGGAAGGGGATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
47846948 G
1 G
47846949 TGATCCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:47854380 original size:27 final size:28
Alignment explanation
Indices: 47854350--47854407 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
47854340 TCTGTGTATT
47854350 TGTGAAA-TAGGGACTAAACTGTAAAAA
1 TGTGAAACTAGGGACTAAACTGTAAAAA
* *
47854377 TGTGAAACTTAGGGGCTAAAGTGTAAAAA
1 TGTGAAAC-TAGGGACTAAACTGTAAAAA
47854406 TG
1 TG
47854408 CCCAAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
29 20 0.74
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (28 bp):
TGTGAAACTAGGGACTAAACTGTAAAAA
Found at i:47854795 original size:43 final size:43
Alignment explanation
Indices: 47854747--47854917 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 43
47854737 GTTACCGAGA
* *
47854747 TGTGATTACATGTAAGATCATATCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
* * * *
47854790 TGTGATTACGTGTAAGACCATGTCTGGGGCATTGGCGTCGTTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCG-TAT
* *** * * *
47854834 T-CGATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
* * * *
47854875 ATGTGATAACATGTAATACCATATCTGGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
47854918 GAGCTTTATG
Statistics
Matches: 101, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.02
42 8 0.08
43 87 0.86
44 4 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.35
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT
Found at i:47865557 original size:41 final size:41
Alignment explanation
Indices: 47865512--47865661 Score: 144
Period size: 41 Copynumber: 3.6 Consensus size: 41
47865502 GAGCTTGGTC
47865512 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
47865553 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAATCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
47865595 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
* *
47865636 TGGAAGGGCTTTTGAGCCTGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
47865662 GAGTCGGACT
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 4 0.05
40 9 0.10
41 35 0.40
42 27 0.31
43 12 0.14
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:47865624 original size:40 final size:41
Alignment explanation
Indices: 47865513--47865624 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
47865503 AGCTTGGTCT
* * * * *
47865513 CGAAGGGCT-TTTGAGCCAGTGCTAATAACCGAACTTAGTTT
1 CGAAGGGCTCTTAGAGCCAGTG-TCATAATCGGACTTAGTTC
*
47865554 CGAAGGGCTTTTTAGAGCCAGTGTCATAATCGGACTTAGTTC
1 CGAAGGGC-TCTTAGAGCCAGTGTCATAATCGGACTTAGTTC
*
47865596 CGAAGGGC-CTTCGAGCCAGTAGTC-TAATC
1 CGAAGGGCTCTTAGAGCCAGT-GTCATAATC
47865625 CGAGCTTGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
40 15 0.25
41 11 0.18
42 24 0.39
43 11 0.18
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (41 bp):
CGAAGGGCTCTTAGAGCCAGTGTCATAATCGGACTTAGTTC
Found at i:47871607 original size:39 final size:40
Alignment explanation
Indices: 47871512--47871734 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
47871502 TTGAATGATG
*
47871512 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
47871550 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
47871591 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
47871630 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
47871669 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* * *
47871708 AACCGGGCTATGTCCCAAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
47871735 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 58 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:47871698 original size:79 final size:81
Alignment explanation
Indices: 47871512--47871734 Score: 273
Period size: 79 Copynumber: 2.8 Consensus size: 81
47871502 TTGAATGATG
* * *
47871512 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
47871574 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
47871591 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
47871652 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * * *
47871669 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCAAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
47871733 TG
66 TG
47871735 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 46 0.37
79 56 0.44
80 24 0.19
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:47871756 original size:79 final size:79
Alignment explanation
Indices: 47871512--47871767 Score: 199
Period size: 79 Copynumber: 3.3 Consensus size: 79
47871502 TTGAATGATG
* * * * *
47871512 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCAAAGGCA
** *
47871573 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* * *
47871591 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTG
** *
47871655 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
47871669 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCAAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCAAAGGCAT
*
47871732 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
47871749 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47871768 TACGTGATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 35 0.23
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTG
AACGAGTGACTAAA
Found at i:47877094 original size:41 final size:41
Alignment explanation
Indices: 47877049--47877198 Score: 135
Period size: 41 Copynumber: 3.6 Consensus size: 41
47877039 GAGCTTGGTC
*
47877049 TCGAAGGGCTTTTGAGCCAGTGCTAATAACTGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
47877090 TCGAAGGGCTTTTTAGAGCCAATG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
47877132 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
**
47877173 TCGAAGGGCTTTTGAGCTGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
47877199 GAGTCGGACT
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
39 4 0.05
40 8 0.09
41 36 0.42
42 27 0.31
43 11 0.13
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:47883604 original size:33 final size:33
Alignment explanation
Indices: 47883556--47883659 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
47883546 ATTAGGATGT
* *
47883556 AAACACAGAACAGAGACAGTCTGCTGGGATAGC
1 AAACACAAAACAGAGACAGTCAGCTGGGATAGC
* * *
47883589 AAACACAAAATAGAGATAGTCAGCTGGGATAGT
1 AAACACAAAACAGAGACAGTCAGCTGGGATAGC
* * * *
47883622 AAAAACAAAACAGAGATAACTCA-CTGGGATAGT
1 AAACACAAAACAGAGA-CAGTCAGCTGGGATAGC
47883655 AAACA
1 AAACA
47883660 TAGAAAGAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 56 0.93
34 4 0.07
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (33 bp):
AAACACAAAACAGAGACAGTCAGCTGGGATAGC
Found at i:47886018 original size:15 final size:15
Alignment explanation
Indices: 47885994--47886023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47885984 AGTGTTTACA
47885994 CCTAAAAAATGGATG
1 CCTAAAAAATGGATG
*
47886009 CCTAATAAATGGATG
1 CCTAAAAAATGGATG
47886024 ATTATCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (15 bp):
CCTAAAAAATGGATG
Found at i:47886333 original size:27 final size:27
Alignment explanation
Indices: 47886295--47886387 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
47886285 ATACCACAGA
47886295 TCACCCAACTATTGCCCTTTTTATTTG
1 TCACCCAACTATTGCCCTTTTTATTTG
*****
47886322 TCACCCAACTATCATTTTTTTTAATTTGG
1 TCACCCAACTATTGCCCTTTTT-ATTT-G
47886351 TCACCCAACTATTGCCCTTTTT-TTTG
1 TCACCCAACTATTGCCCTTTTTATTTG
47886377 TCACCCAACTA
1 TCACCCAACTA
47886388 ATCCAAATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
26 12 0.22
27 20 0.37
28 4 0.07
29 18 0.33
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (27 bp):
TCACCCAACTATTGCCCTTTTTATTTG
Found at i:47886406 original size:56 final size:55
Alignment explanation
Indices: 47886295--47886408 Score: 160
Period size: 56 Copynumber: 2.0 Consensus size: 55
47886285 ATACCACAGA
* *
47886295 TCACCCAACTATTGCCCTTTTTATTTGTCACCCAACTATCATTTTTTTTAATTTGG
1 TCACCCAACTATTGCCCTTTTTATTTGTCACCCAACTATCAATTGTTTT-ATTTGG
47886351 TCACCCAACTATTGCCCTTTTT-TTTGTCACCCAACTAATCCAAATTGTTTT-TTTGG
1 TCACCCAACTATTGCCCTTTTTATTTGTCACCCAACT-AT-C-AATTGTTTTATTTGG
47886407 TC
1 TC
47886409 CATTCTGTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
55 14 0.26
56 31 0.58
57 1 0.02
58 7 0.13
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (55 bp):
TCACCCAACTATTGCCCTTTTTATTTGTCACCCAACTATCAATTGTTTTATTTGG
Found at i:47889123 original size:55 final size:55
Alignment explanation
Indices: 47889062--47889171 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
47889052 ATGGAGAACT
47889062 AGTGGATGGATTAAGGAGGAATTCTTCAAACCTCTTACGACAGTTAGAAAGAGTG
1 AGTGGATGGATTAAGGAGGAATTCTTCAAACCTCTTACGACAGTTAGAAAGAGTG
*
47889117 AGTGGATGGATTAAGGAGGAATTCTTCAAACCTCTTACGACAGTTAGGAAGAGTG
1 AGTGGATGGATTAAGGAGGAATTCTTCAAACCTCTTACGACAGTTAGAAAGAGTG
47889172 TGTAACCTGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (55 bp):
AGTGGATGGATTAAGGAGGAATTCTTCAAACCTCTTACGACAGTTAGAAAGAGTG
Found at i:47896483 original size:30 final size:30
Alignment explanation
Indices: 47896449--47896509 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
47896439 TCCTTAACTC
47896449 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
47896479 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
47896509 A
1 A
47896510 GGCTCGGGAA
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:47904486 original size:22 final size:21
Alignment explanation
Indices: 47904461--47904501 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
47904451 TCGAATTAGT
*
47904461 CACACGGGTGTGTTGCCCCTCC
1 CACACGAGTGTG-TGCCCCTCC
47904483 CACACGAGTGTGTGCCCCT
1 CACACGAGTGTGTGCCCCT
47904502 GCATCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.39, G:0.27, T:0.22
Consensus pattern (21 bp):
CACACGAGTGTGTGCCCCTCC
Found at i:47909475 original size:80 final size:80
Alignment explanation
Indices: 47909342--47909687 Score: 504
Period size: 80 Copynumber: 4.3 Consensus size: 80
47909332 TTGAATGATG
* * * * *
47909342 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGA-GTTACTAAATCCGGACTAAGATCCGAAGGCAT
47909405 TTGTACGAGTTACTAAA
64 TTGTACGAGTTACTAAA
*
47909422 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGATCCGAAGGCATTT
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
47909487 GTACGAGTTACTAAA
66 GTACGAGTTACTAAA
*
47909502 TCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
47909567 GTACGAGTTACTAAA
66 GTACGAGTTACTAAA
**
47909582 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATT
*
47909646 TGTGCGAGTTACTATAA
65 TGTACGAGTTACTA-AA
* *
47909663 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGACTAAGAT-CCGAAGGCATTTG
47909688 AACGAGTAGC
Statistics
Matches: 247, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
79 2 0.01
80 234 0.95
81 11 0.04
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (80 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAA
Found at i:47909555 original size:120 final size:120
Alignment explanation
Indices: 47909342--47909694 Score: 509
Period size: 120 Copynumber: 2.9 Consensus size: 120
47909332 TTGAATGATG
* * * *
47909342 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGA-GTTACTAAATCCGGACTAAGATCCGAAGGCAT
*
47909405 TTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
64 TTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
*
47909462 TCCGGGCTAAGATCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
47909527 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
* **
47909582 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATT
* * * *
47909646 TGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGT
65 TGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGT
47909695 AGCTATATCC
Statistics
Matches: 214, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
119 2 0.01
120 202 0.94
121 10 0.05
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:47909701 original size:40 final size:40
Alignment explanation
Indices: 47909381--47909694 Score: 499
Period size: 40 Copynumber: 7.8 Consensus size: 40
47909371 AGGTGACCAT
47909381 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
*
47909421 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
*
47909461 ATCCGGGCTAAGATCCGAAGGCATTTGTACGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
47909501 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
47909541 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
*
47909581 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
** *
47909621 ATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTA-A
* * *
47909662 A-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGT
1 ATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGT
47909695 AGCTATATCC
Statistics
Matches: 261, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 1 0.00
40 258 0.99
41 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAA
Found at i:47916298 original size:18 final size:19
Alignment explanation
Indices: 47916257--47916298 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
47916247 AGAGATAGTG
*
47916257 GGTTAGTGGGTTAGTGGGA
1 GGTTAGTGGGTTAGAGGGA
*
47916276 -TTTAGT-GGTTAGAGGGA
1 GGTTAGTGGGTTAGAGGGA
47916293 GGTTAG
1 GGTTAG
47916299 GATAGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.33
Consensus pattern (19 bp):
GGTTAGTGGGTTAGAGGGA
Found at i:47917107 original size:18 final size:18
Alignment explanation
Indices: 47917084--47917120 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
47917074 GGGCAGTGAA
*
47917084 CCACACGGACGTGTGGGC
1 CCACACGGACATGTGGGC
47917102 CCACACGGACATGTGGGC
1 CCACACGGACATGTGGGC
47917120 C
1 C
47917121 TATAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.35, G:0.35, T:0.11
Consensus pattern (18 bp):
CCACACGGACATGTGGGC
Found at i:47922991 original size:17 final size:18
Alignment explanation
Indices: 47922956--47922992 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
47922946 AAGGAGTTGA
*
47922956 GATTTAGTGGGTTAGTGG
1 GATTTAGTGGGTTAATGG
47922974 GATTTAGT-GGTTAATGG
1 GATTTAGTGGGTTAATGG
47922991 GA
1 GA
47922993 GGTTAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (18 bp):
GATTTAGTGGGTTAATGG
Found at i:47931402 original size:21 final size:21
Alignment explanation
Indices: 47931376--47931436 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
47931366 ATTCTGGTGG
*
47931376 TCAGCTCTTTTGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
* *
47931397 TTAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTAT
*
47931418 TCAACTCTTATGAGCTTCT
1 TCAGCTCTTATGAGCTTCT
47931437 GTTGGCGTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:47932278 original size:26 final size:26
Alignment explanation
Indices: 47932243--47932298 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
47932233 TATGCATAAC
* *
47932243 AGCCCAGTGCATCGCTTCCTTGGCAT
1 AGCCCAGTGCATAGCTGCCTTGGCAT
* *
47932269 AGCCCGGTGCATAGCTGCCTTGGCGT
1 AGCCCAGTGCATAGCTGCCTTGGCAT
47932295 AGCC
1 AGCC
47932299 TTGGCACCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (26 bp):
AGCCCAGTGCATAGCTGCCTTGGCAT
Found at i:47932549 original size:16 final size:16
Alignment explanation
Indices: 47932530--47932560 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47932520 CCCTTTCTTT
*
47932530 GGCGTACCGTACTTAG
1 GGCGTACCATACTTAG
47932546 GGCGTACCATACTTA
1 GGCGTACCATACTTA
47932561 ACATCTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (16 bp):
GGCGTACCATACTTAG
Found at i:47933062 original size:29 final size:29
Alignment explanation
Indices: 47933030--47933095 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
47933020 GGGATTGCCG
** * *
47933030 CAAAGGCTTTCTTATAACGGAGATCTCTA
1 CAAAGGCTTTCTTATAACAAAGATCACCA
47933059 CAAAGGCTTTCTTATAACAAAGATCACCA
1 CAAAGGCTTTCTTATAACAAAGATCACCA
47933088 CAAAGGCT
1 CAAAGGCT
47933096 CACTTTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (29 bp):
CAAAGGCTTTCTTATAACAAAGATCACCA
Found at i:47933111 original size:58 final size:58
Alignment explanation
Indices: 47933058--47933180 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
47933048 GGAGATCTCT
**
47933058 ACAAAGGCTTTCTTATAACAAAGATCA-CCACAAAGGCTCACTTTTAACTGAGATAGCC
1 ACAAAGGCTCACTTATAACAAAGAT-AGCCACAAAGGCTCACTTTTAACTGAGATAGCC
* * ** *
47933116 ACAAATGCTCACTTTTAACTGAGATAGCCACAAAGGCTCACTTTTAACTGAGATAGTC
1 ACAAAGGCTCACTTATAACAAAGATAGCCACAAAGGCTCACTTTTAACTGAGATAGCC
*
47933174 ATAAAGG
1 ACAAAGG
47933181 AATCCTTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 1 0.02
58 54 0.98
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (58 bp):
ACAAAGGCTCACTTATAACAAAGATAGCCACAAAGGCTCACTTTTAACTGAGATAGCC
Found at i:47933188 original size:29 final size:29
Alignment explanation
Indices: 47933085--47933180 Score: 165
Period size: 29 Copynumber: 3.3 Consensus size: 29
47933075 ACAAAGATCA
47933085 CCACAAAGGCTCACTTTTAACTGAGATAG
1 CCACAAAGGCTCACTTTTAACTGAGATAG
*
47933114 CCACAAATGCTCACTTTTAACTGAGATAG
1 CCACAAAGGCTCACTTTTAACTGAGATAG
47933143 CCACAAAGGCTCACTTTTAACTGAGATAG
1 CCACAAAGGCTCACTTTTAACTGAGATAG
* *
47933172 TCATAAAGG
1 CCACAAAGG
47933181 AATCCTTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTCACTTTTAACTGAGATAG
Done.