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 160 of 290
Found at i:54701962 original size:11 final size:11
Alignment explanation
Indices: 54701946--54701970 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54701936 AAAATTATAA
54701946 AAACTAATATT
1 AAACTAATATT
54701957 AAACTAATATT
1 AAACTAATATT
54701968 AAA
1 AAA
54701971 GGAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAACTAATATT
Found at i:54724099 original size:20 final size:20
Alignment explanation
Indices: 54724074--54724120 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54724064 TTATGAATTC
*
54724074 ATCATGTGCATTTCATA-CA
1 ATCATGTGCATATCATATCA
54724093 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
54724114 ATCATGT
1 ATCATGT
54724121 ATATTATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:54732007 original size:25 final size:26
Alignment explanation
Indices: 54731979--54732075 Score: 162
Period size: 26 Copynumber: 3.8 Consensus size: 26
54731969 CCTCTTTAAT
54731979 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
54732004 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54732029 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54732055 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54732076 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 33 0.49
26 34 0.51
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:54732050 original size:51 final size:51
Alignment explanation
Indices: 54731979--54732075 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
54731969 CCTCTTTAAT
54731979 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
54732029 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
54732076 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 10 0.22
51 25 0.56
52 10 0.22
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (51 bp):
AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:54732150 original size:20 final size:20
Alignment explanation
Indices: 54732125--54732199 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
54732115 TTATGAATTC
*
54732125 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
54732145 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54732165 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
54732185 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
54732200 TCCCACGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54732156 original size:11 final size:11
Alignment explanation
Indices: 54732125--54732180 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54732115 TTATGAATTC
54732125 ATCATGTGCAT
1 ATCATGTGCAT
* *
54732136 TTCA--TACAT
1 ATCATGTGCAT
54732145 ATCATGTGCAT
1 ATCATGTGCAT
*
54732156 ATCA--TACAT
1 ATCATGTGCAT
54732165 ATCATGTGCAT
1 ATCATGTGCAT
54732176 ATCAT
1 ATCAT
54732181 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54732197 original size:9 final size:10
Alignment explanation
Indices: 54732142--54732198 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
54732132 GCATTTCATA
54732142 CATATCATGT
1 CATATCATGT
*
54732152 GCATATCAT-A
1 -CATATCATGT
54732162 CATATCATGT
1 CATATCATGT
*
54732172 GCATATCATAT
1 -CATATCATGT
54732183 CA-ATCATGT
1 CATATCATGT
54732192 -ATATCAT
1 CATATCAT
54732199 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:54742149 original size:13 final size:13
Alignment explanation
Indices: 54742131--54742159 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54742121 GGTTGTTTAT
54742131 TAAACTAATTAAC
1 TAAACTAATTAAC
54742144 TAAACTAATTAAC
1 TAAACTAATTAAC
54742157 TAA
1 TAA
54742160 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:54748923 original size:61 final size:61
Alignment explanation
Indices: 54748784--54748952 Score: 159
Period size: 60 Copynumber: 2.8 Consensus size: 61
54748774 AATTTTACAT
* * * *
54748784 GGCCTAAGCCCTATT-CAGAAATCAGAGT-TAACTGGGACTTAGCCCATATCAATATTAATCTG
1 GGCCTTAGCCCTATTACAG-TATCAGAGTAT-ACTGGG-CCTAGCCCATATCAATATCAATCTG
* * * * *
54748846 GGCCATGGCCC-CTTACAGTATCAGAGTATACTGGGCCTAGCCCATGTCAGTATCAATCTG
1 GGCCTTAGCCCTATTACAGTATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTG
* * *
54748906 GGCCTTAGCCCTATTACAAGT-TGAGA-TATATTGGGCCTTGCCCATAT
1 GGCCTTAGCCCTATTAC-AGTATCAGAGTATACTGGGCCTAGCCCATAT
54748953 TAACACAGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
60 48 0.55
61 24 0.28
62 15 0.17
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (61 bp):
GGCCTTAGCCCTATTACAGTATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTG
Found at i:54748970 original size:20 final size:19
Alignment explanation
Indices: 54748945--54748988 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
54748935 ATTGGGCCTT
54748945 GCCCATATT-AACACAGTTGG
1 GCCCAT-TTCAACACAGTT-G
*
54748965 GCCCATTTCAATACAGTTG
1 GCCCATTTCAACACAGTTG
54748984 GCCCA
1 GCCCA
54748989 GAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (19 bp):
GCCCATTTCAACACAGTTG
Found at i:54757959 original size:27 final size:26
Alignment explanation
Indices: 54757908--54757996 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 26
54757898 CCCCAGTTTT
* * *
54757908 TAAAATGACCGAATACCCTTGTAGGG
1 TAAAATGACCTAATACCCCTATAGGG
54757934 TAAAATGACCATAATACCCCTATAGGG
1 TAAAATGACC-TAATACCCCTATAGGG
* *
54757961 TAAAATGACTGTAATACCCCTATATGG
1 TAAAATGAC-CTAATACCCCTATAGGG
54757988 TAAAATGAC
1 TAAAATGAC
54757997 GATTATGCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 10 0.18
27 46 0.82
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (26 bp):
TAAAATGACCTAATACCCCTATAGGG
Found at i:54759752 original size:39 final size:40
Alignment explanation
Indices: 54759709--54759874 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 40
54759699 CTCGTTCAAG
* * * *
54759709 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
54759748 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
54759788 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
54759828 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
54759868 TGCCTTC
1 TGCCTTC
54759875 AGATCTTAGT
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.24
40 79 0.72
41 3 0.03
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:54759860 original size:80 final size:80
Alignment explanation
Indices: 54759744--54759929 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
54759734 AGTAACTCAT
* * * *
54759744 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-AGATCTTAACCCG
*
54759808 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
54759823 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCAGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCAGATCTTAACCC
54759887 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
54759904 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
54759930 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 10 0.11
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCAGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:54759889 original size:40 final size:40
Alignment explanation
Indices: 54759746--54759874 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
54759736 TAACTCATAC
* *
54759746 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
54759786 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
54759826 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
54759866 AATGCCTTC
1 AATGCCTTC
54759875 AGATCTTAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.04
40 77 0.96
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54759923 original size:40 final size:40
Alignment explanation
Indices: 54759749--54759929 Score: 154
Period size: 40 Copynumber: 4.5 Consensus size: 40
54759739 CTCATACAAT
* * * * *
54759749 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGA-ATTAATAACTAGCACAAAG
* * * *
54759789 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAGCCCGGAATTAATAACTAGCACAAAG
* * *
54759829 GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAATAACTAGCACAAAG
* * * *
54759869 GCCTTC-AGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-
1 GCCTTCGGGA-CTTAGCCCGGAAT-TAATAAC-TAGCACAAAG
54759909 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGCCCGGA
54759930 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
39 7 0.06
40 102 0.86
41 10 0.08
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGAATTAATAACTAGCACAAAG
Found at i:54764769 original size:40 final size:41
Alignment explanation
Indices: 54764685--54764780 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
54764675 GACTATGTTC
54764685 GGCACTAAGTGTGCG-GTTCGAAATAGCTTCAGCTACAAAT
1 GGCACTAAGTGTGCGAGTTCGAAATAGCTTCAGCTACAAAT
* * * *
54764725 GGCACTAATTGTGCGAGTT-GGAATAGCTTCGGCTATAAGA-
1 GGCACTAAGTGTGCGAGTTCGAAATAGCTTCAGCTACAA-AT
*
54764765 GGCACCAAGTGTGCGA
1 GGCACTAAGTGTGCGA
54764781 TACTGAGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
GGCACTAAGTGTGCGAGTTCGAAATAGCTTCAGCTACAAAT
Found at i:54774660 original size:38 final size:38
Alignment explanation
Indices: 54774617--54774689 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
54774607 TTCATCCTTT
54774617 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
54774655 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAG
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAG
54774690 TTCTTGCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:54775968 original size:40 final size:39
Alignment explanation
Indices: 54775874--54776018 Score: 173
Period size: 40 Copynumber: 3.6 Consensus size: 39
54775864 TACTCGAATG
*
54775874 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCT-AGCGACT
* *
54775915 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAGCGACT
* * *
54775955 ATATCCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCC-GAAGGCATTTGTGCTAGCGACT
* *
54775995 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAG-TCCGAAGGC
54776019 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
39 3 0.03
40 57 0.63
41 30 0.33
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGCGACT
Found at i:54779070 original size:25 final size:25
Alignment explanation
Indices: 54779042--54779092 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
54779032 ATCAAACATG
54779042 TTAGTCACAAAAATCTCCATATCAA
1 TTAGTCACAAAAATCTCCATATCAA
54779067 TTAGTCACAAAAATCTCCATATCAA
1 TTAGTCACAAAAATCTCCATATCAA
54779092 T
1 T
54779093 CAAGTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (25 bp):
TTAGTCACAAAAATCTCCATATCAA
Found at i:54782141 original size:32 final size:32
Alignment explanation
Indices: 54782084--54782146 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
54782074 CTGATTGCAT
54782084 ACTGTATTGTTACTGTAATGGGCTTAGGCCCC
1 ACTGTATTGTTACTGTAATGGGCTTAGGCCCC
54782116 ACTGATATTGTTACTG-AATGGGCTTAGGCCC
1 ACTG-TATTGTTACTGTAATGGGCTTAGGCCC
54782147 AGATTACTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (32 bp):
ACTGTATTGTTACTGTAATGGGCTTAGGCCCC
Found at i:54785808 original size:66 final size:66
Alignment explanation
Indices: 54785719--54786605 Score: 1731
Period size: 66 Copynumber: 13.4 Consensus size: 66
54785709 ACGGCTACCA
* *
54785719 GACACGCCTATGT-CACAGACCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCA
1 GACACGCCCATGTGC-CAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCA
54785783 AG
65 AG
54785785 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54785850 G
66 G
54785851 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54785916 G
66 G
54785917 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54785982 G
66 G
54785983 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786048 G
66 G
54786049 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786114 G
66 G
54786115 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786180 G
66 G
54786181 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786246 G
66 G
54786247 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786312 G
66 G
54786313 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786378 G
66 G
54786379 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786444 G
66 G
54786445 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786510 G
66 G
54786511 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
54786576 G
66 G
*
54786577 GACACGCCCATGTGCCAGACCGTGTGAAA
1 GACACGCCCATGTGCCAGGCCGTGTGAAA
54786606 TCTAAGGAGG
Statistics
Matches: 817, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
66 816 1.00
67 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (66 bp):
GACACGCCCATGTGCCAGGCCGTGTGAAAACAGGGCATACATACTGACTTGCCTGACACGGCCAA
G
Found at i:54787831 original size:43 final size:42
Alignment explanation
Indices: 54787777--54787900 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
54787767 AGCTCATATA
* *
54787777 ATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCATATCCCAGATATGGTCTTACATGTAATCACATAACG
* * * *
54787819 ATGCCACTATCCCAGATAGGGTCTTACACGAAATCGA-TTAACG
1 ATGCCA-TATCCCAGATATGGTCTTACATGTAATC-ACATAACG
* * *
54787862 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACAT
1 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCACAT
54787901 GTAACACCCC
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
42 7 0.11
43 56 0.86
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGTAATCACATAACG
Found at i:54797556 original size:43 final size:42
Alignment explanation
Indices: 54797502--54797625 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
54797492 AGCTCATATA
* *
54797502 ATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCATATCCCAGATATGGTCTTACATGTAATCACATAACG
* * * *
54797544 ATGCCACTATCCCAGATAGGGTCTTACACGAAATCGA-TTAACG
1 ATGCCA-TATCCCAGATATGGTCTTACATGTAATC-ACATAACG
* * *
54797587 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACAT
1 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCACAT
54797626 GTAACACCCC
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
42 7 0.11
43 56 0.86
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGTAATCACATAACG
Found at i:54808190 original size:40 final size:40
Alignment explanation
Indices: 54808145--54808296 Score: 225
Period size: 40 Copynumber: 3.8 Consensus size: 40
54808135 ATAACCACAA
* * * *
54808145 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
54808185 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
54808225 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
*
54808265 GCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
54808297 CATTCAAATG
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 98 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:54813757 original size:256 final size:256
Alignment explanation
Indices: 54813302--54813813 Score: 862
Period size: 256 Copynumber: 2.0 Consensus size: 256
54813292 CTAAGGTTTC
54813302 ACATATGTAAGAATGAGTAGAACCAGGGTCAATCAAAGCAATCACATTAGTATCAAAGAGAGTAA
1 ACATATGTAAGAATGAGTAGAACCAGGGTCAATCAAAGCAATCACATTAGTATCAAAGAGAGTAA
* * * * * * *
54813367 AAGTACCGGTAATAACATCTGGTGAGGAAGCATCCTCGCGTGCGCGTATAGTATAAGCCCTAGTA
66 AAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGGATAAGCCCTAGCA
* *
54813432 GGAGCACGAGCCTCAGATCTGGTCGTAGCATCCCTAGATCCTCTCTTACCACCACTAGCATTGCC
131 GGAGCACGAGCCTCAGATCTGGTCGTAGAATCCCTAGATCCTCTCTGACCACCACTAGCATTGCC
* * *
54813497 CGTATTTCTAGATGGTCTACCTCGAGTAGTGGTAGCACCCGGTTTCCCACTCTGATTTACA
196 CGTATTTCTAGATGGTCGACCTCAAGTAGTGGTAGCACCCGGATTCCCACTCTGATTTACA
* *
54813558 ACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTAA
1 ACATATGTAAGAATGAGTAGAACCAGGGTCAATCAAAGCAATCACATTAGTATCAAAGAGAGTAA
*
54813623 AAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGGATAAGCTCTAGCA
66 AAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGGATAAGCCCTAGCA
* * *
54813688 GGCGCACGAGCCTCGGATCTGGTCGTAGAATCTCTAGATCCTCTCTGACCACCACTAGCATTGCC
131 GGAGCACGAGCCTCAGATCTGGTCGTAGAATCCCTAGATCCTCTCTGACCACCACTAGCATTGCC
54813753 CGTATTTCTAGATGGTCGACCTCAAGTAGTGGTAGCACCCGGATTCCCACTCTGATTTACA
196 CGTATTTCTAGATGGTCGACCTCAAGTAGTGGTAGCACCCGGATTCCCACTCTGATTTACA
54813814 TTCTGTTCAG
Statistics
Matches: 238, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
256 238 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (256 bp):
ACATATGTAAGAATGAGTAGAACCAGGGTCAATCAAAGCAATCACATTAGTATCAAAGAGAGTAA
AAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGGATAAGCCCTAGCA
GGAGCACGAGCCTCAGATCTGGTCGTAGAATCCCTAGATCCTCTCTGACCACCACTAGCATTGCC
CGTATTTCTAGATGGTCGACCTCAAGTAGTGGTAGCACCCGGATTCCCACTCTGATTTACA
Found at i:54816485 original size:40 final size:40
Alignment explanation
Indices: 54816424--54816670 Score: 309
Period size: 40 Copynumber: 6.2 Consensus size: 40
54816414 CGGAATTTAG
* * * *
54816424 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
54816464 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
54816504 CCGGAT-ATATCAACTCGCACAAATGCCTTCGAGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
*
54816544 CCGGATAAAATCACTAGCACAAATGCCTTTGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
*
54816584 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
54816624 CCGGATAAAATCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
54816664 CCGGATA
1 CCGGATA
54816671 TCATTCAAAT
Statistics
Matches: 184, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 178 0.97
41 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:54820435 original size:285 final size:285
Alignment explanation
Indices: 54819925--54820493 Score: 1030
Period size: 285 Copynumber: 2.0 Consensus size: 285
54819915 AGGTCAAATA
* * *
54819925 AGCCCCCAGTTGACAGAATCCGAAAACATGAGGCTACTGAATTTAAAGCTACGGATAGCGACGAT
1 AGCCCCCAGTTGACAGAATCCGAAAACACGAGGCTACTAAATTTAAAGCTACGCATAGCGACGAT
* * *
54819990 GCCGAGCAAGCTGAATTTTGGTTGGACAACACTATCTGGGTACTCGATGAGCTATCTTGTACACC
66 GCCGAGCAAGCTGAATTTTGGTTGGACAACACTATCCGGGTACTCGACGAGCTATCTTGCACACC
*
54820055 CGATGAATGCCTAAAGTGTACTATCTCCTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGT
131 CGATGAATGCCTAAACTGTACTATCTCCTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGT
54820120 TGACTTCTGTTGTGCCCAGCGAGCAAGTAACTTGGGAGTTTTTCCAAACCGAGTTTCGAAAGAAG
196 TGACTTCTGTTGTGCCCAGCGAGCAAGTAACTTGGGAGTTTTTCCAAACCGAGTTTCGAAAGAAG
54820185 TATATCAGTCAGAGATTCAATGACT
261 TATATCAGTCAGAGATTCAATGACT
* * *
54820210 AGCCCCCAGTTGACAGAATCCGAAAACACGGGGCTACTAAATTTAAGGCTACGCATAGCGATGAT
1 AGCCCCCAGTTGACAGAATCCGAAAACACGAGGCTACTAAATTTAAAGCTACGCATAGCGACGAT
*
54820275 GCCGAGCAAGCTGAATTTTGGTTGGGCAACACTATCCGGGTACTCGACGAGCTATCTTGCACACC
66 GCCGAGCAAGCTGAATTTTGGTTGGACAACACTATCCGGGTACTCGACGAGCTATCTTGCACACC
*
54820340 CGATGAGTGCCTAAACTGTACTATCTCCTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGT
131 CGATGAATGCCTAAACTGTACTATCTCCTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGT
54820405 TGACTTCTGTTGTGCCCAGCGAGCAAGTAACTTGGGAGTTTTTCCAAACCGAGTTTCGAAAGAAG
196 TGACTTCTGTTGTGCCCAGCGAGCAAGTAACTTGGGAGTTTTTCCAAACCGAGTTTCGAAAGAAG
54820470 TATATCAGTCAGAGATTCAATGAC
261 TATATCAGTCAGAGATTCAATGAC
54820494 CAAAAACGGA
Statistics
Matches: 272, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
285 272 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (285 bp):
AGCCCCCAGTTGACAGAATCCGAAAACACGAGGCTACTAAATTTAAAGCTACGCATAGCGACGAT
GCCGAGCAAGCTGAATTTTGGTTGGACAACACTATCCGGGTACTCGACGAGCTATCTTGCACACC
CGATGAATGCCTAAACTGTACTATCTCCTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGT
TGACTTCTGTTGTGCCCAGCGAGCAAGTAACTTGGGAGTTTTTCCAAACCGAGTTTCGAAAGAAG
TATATCAGTCAGAGATTCAATGACT
Found at i:54826549 original size:39 final size:41
Alignment explanation
Indices: 54826444--54826651 Score: 216
Period size: 40 Copynumber: 5.2 Consensus size: 41
54826434 TATTCGAATG
* * *
54826444 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT-
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA
*
54826485 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
* *
54826526 AT-TCCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTACTA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* ** *
54826565 A-ATCCGGGTTAAGTCCTAAAGGCATTTGTGTGAGTTAC-A
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* * *
54826604 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT-
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTA
54826644 ATATCCGG
1 ATATCCGG
54826652 TTAAATTCCG
Statistics
Matches: 138, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
39 38 0.28
40 69 0.50
41 30 0.22
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
Found at i:54826587 original size:79 final size:79
Alignment explanation
Indices: 54826504--54826655 Score: 211
Period size: 79 Copynumber: 1.9 Consensus size: 79
54826494 CTAAGATCCG
*
54826504 AAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTA-CTAA
1 AAGGCATTTGTGCGAGTTAC-AATAACCGGGCTAAGTCCCGAAGGCATTGGAGCGAG-TAGCTAA
54826566 ATCCGGGTTAAGTCCTA
64 ATCC-GGTTAAGTCCTA
* * * *
54826583 AAGGCATTTGTGTGAGTTACAATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTATAT
1 AAGGCATTTGTGCGAGTTACAATAACCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAGCTAAAT
54826648 CCGGTTAA
66 CCGGTTAA
54826656 ATTCCGAAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
78 3 0.05
79 36 0.55
80 26 0.40
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACAATAACCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAGCTAAAT
CCGGTTAAGTCCTA
Found at i:54829337 original size:15 final size:16
Alignment explanation
Indices: 54829317--54829351 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54829307 TTTCAAGAAT
54829317 AACTA-TGTTTGGAAC
1 AACTATTGTTTGGAAC
54829332 AACTATTGTTTGGAAC
1 AACTATTGTTTGGAAC
54829348 AACT
1 AACT
54829352 TATATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (16 bp):
AACTATTGTTTGGAAC
Found at i:54853709 original size:12 final size:13
Alignment explanation
Indices: 54853692--54853729 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
54853682 TTCCTGAAAT
54853692 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
54853704 ATTAAGAACACATA
1 ATTAAGAACA-AGA
54853718 ATTAAGAACAAG
1 ATTAAGAACAAG
54853730 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:54860659 original size:33 final size:33
Alignment explanation
Indices: 54860553--54860659 Score: 126
Period size: 33 Copynumber: 3.3 Consensus size: 33
54860543 GCCAATCCCT
* *
54860553 CCAACA-ACCAATGCTCAGAATAGCTAATCCAA
1 CCAACACACCAATGCTCATAAAAGCTAATCCAA
*
54860585 CCAACAAACCAATGCTCATAAAAGCTAATCCAA
1 CCAACACACCAATGCTCATAAAAGCTAATCCAA
* * * * *
54860618 CCATCACACCAGTGCTTATAAGAGCTAGTCCAA
1 CCAACACACCAATGCTCATAAAAGCTAATCCAA
*
54860651 CCAGCACAC
1 CCAACACAC
54860660 TAACAGATAG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.16
Consensus pattern (33 bp):
CCAACACACCAATGCTCATAAAAGCTAATCCAA
Found at i:54862374 original size:57 final size:57
Alignment explanation
Indices: 54862292--54862457 Score: 190
Period size: 57 Copynumber: 2.9 Consensus size: 57
54862282 CTAGTAAAAG
* * * * * *
54862292 GTTTACCACGAAGGCTTACCCTTCTAGAGTTTTGCCACAAAAGTTGTCCTTTAACAT
1 GTTTGCCACAAAGGCTTGCCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTTTAACAC
* * * *
54862349 GTTCT-CCACAAAGGCTTGCCTTTCTAGAGTTTTTCCATAAAGGTTGTTCTATAACAC
1 GTT-TGCCACAAAGGCTTGCCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTTTAACAC
* * * *
54862406 GTTTGCCACAAAGGTTTGCCTCTCCAGAGTTTTGCCACAAAGGCTGTCCTTT
1 GTTTGCCACAAAGGCTTGCCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTTT
54862458 TACTAGTGTT
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
56 1 0.01
57 88 0.98
58 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (57 bp):
GTTTGCCACAAAGGCTTGCCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTTTAACAC
Found at i:54865843 original size:47 final size:47
Alignment explanation
Indices: 54865774--54865881 Score: 162
Period size: 47 Copynumber: 2.3 Consensus size: 47
54865764 TGTCTGAACA
* * *
54865774 AAGACACATTAAAATGCTATACTAAGTAAGACATAATTAATAGACTT
1 AAGACACATTAAAATGCTATACTAAATAAGACACAATTAATAAACTT
* *
54865821 AAGACACATTAAAATGCTATACTAAATAGGACACAATTAGTAAACTT
1 AAGACACATTAAAATGCTATACTAAATAAGACACAATTAATAAACTT
*
54865868 ATGACACATTAAAA
1 AAGACACATTAAAA
54865882 ATGTTCAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (47 bp):
AAGACACATTAAAATGCTATACTAAATAAGACACAATTAATAAACTT
Found at i:54867064 original size:12 final size:13
Alignment explanation
Indices: 54867047--54867075 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54867037 TTTTGTATTA
54867047 TTTTCTTTTT-AT
1 TTTTCTTTTTGAT
54867059 TTTTCTTTTTGAT
1 TTTTCTTTTTGAT
54867072 TTTT
1 TTTT
54867076 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTGAT
Found at i:54873959 original size:24 final size:24
Alignment explanation
Indices: 54873932--54873981 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
54873922 CCCTTAAGAA
54873932 GCCCTTTTGTAGCCTATAAGCTCT
1 GCCCTTTTGTAGCCTATAAGCTCT
*
54873956 GCCCTTTTGTAGCCTATAGGCTCT
1 GCCCTTTTGTAGCCTATAAGCTCT
54873980 GC
1 GC
54873982 TAGGTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (24 bp):
GCCCTTTTGTAGCCTATAAGCTCT
Found at i:54874125 original size:14 final size:14
Alignment explanation
Indices: 54874106--54874135 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54874096 AAGAAATTTG
54874106 TTTCTTTAAAATAT
1 TTTCTTTAAAATAT
54874120 TTTCTTTAAAATAT
1 TTTCTTTAAAATAT
54874134 TT
1 TT
54874136 GCCTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTCTTTAAAATAT
Found at i:54878659 original size:24 final size:24
Alignment explanation
Indices: 54878627--54878677 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
54878617 TTATTTTTCA
54878627 TTCTAATGTATAAAAACCAATTCT
1 TTCTAATGTATAAAAACCAATTCT
54878651 TTCTAATGTATAAAAACCAATTCT
1 TTCTAATGTATAAAAACCAATTCT
54878675 TTC
1 TTC
54878678 ATATTGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (24 bp):
TTCTAATGTATAAAAACCAATTCT
Found at i:54879808 original size:15 final size:15
Alignment explanation
Indices: 54879788--54879819 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54879778 TTTATTTTTT
54879788 GAATGAATATAGTTG
1 GAATGAATATAGTTG
54879803 GAATGAATATAGTTG
1 GAATGAATATAGTTG
54879818 GA
1 GA
54879820 TTTATTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (15 bp):
GAATGAATATAGTTG
Found at i:54881039 original size:14 final size:14
Alignment explanation
Indices: 54881020--54881046 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54881010 TTGGTAATTT
54881020 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
54881034 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
54881047 AGGTTTTTCT
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:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:54883840 original size:11 final size:11
Alignment explanation
Indices: 54883820--54883859 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
54883810 GCTATATTAA
*
54883820 AAAATAATTTT
1 AAAATTATTTT
54883831 AAAATTATTTTTT
1 AAAATTA--TTTT
54883844 AAAATTATTTT
1 AAAATTATTTT
54883855 AAAAT
1 AAAAT
54883860 CATCGTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:54883843 original size:13 final size:13
Alignment explanation
Indices: 54883827--54883854 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54883817 TAAAAAATAA
54883827 TTTTAAAATTATT
1 TTTTAAAATTATT
54883840 TTTTAAAATTATT
1 TTTTAAAATTATT
54883853 TT
1 TT
54883855 AAAATCATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:54885825 original size:25 final size:25
Alignment explanation
Indices: 54885797--54885848 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
54885787 AAAGAATACA
54885797 ATCATCTGTGAACAATAAATGCGAT
1 ATCATCTGTGAACAATAAATGCGAT
54885822 ATCATCTGTGAACAATAAATGCGAT
1 ATCATCTGTGAACAATAAATGCGAT
54885847 AT
1 AT
54885849 TTTTGGACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCATCTGTGAACAATAAATGCGAT
Found at i:54887476 original size:47 final size:46
Alignment explanation
Indices: 54887329--54887544 Score: 185
Period size: 47 Copynumber: 4.7 Consensus size: 46
54887319 TGATTTGTGT
* * * * *
54887329 GCCAGTGTAAGACGTGTTTGGGACATGCTTTGGC-CACATTATGA-GA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACA-GA-GATGA
*
54887375 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG--CACAGAGATGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTCACAGAGATGA
* *
54887421 GTGTCAGTGTAAGATATGTCTGGGACATGCATCGGCCTCGACAGAGAT-A
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTC-ACAGAGATGA
* * * *
54887470 GCCAGTGTAAGACGTGTCTGGGGCATGCATCGGCT-A-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACAGAGATGA
* *
54887514 GCTAGTGTAAGACATATCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
54887545 AGCCCGCGTA
Statistics
Matches: 141, Mismatches: 19, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
43 5 0.04
44 28 0.20
45 2 0.01
46 23 0.16
47 58 0.41
48 15 0.11
49 2 0.01
50 8 0.06
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACAGAGATGA
Found at i:54887538 original size:91 final size:95
Alignment explanation
Indices: 54887374--54887544 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 95
54887364 ACATTATGAG
* *
54887374 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGTGTCAGTGTAAGATATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGTGTCAGTGTAAGACATA
54887439 TCTGGGACATGCATCGGCCTCGACAGAGAT
66 TCTGGGACATGCATCGGCCTCGACAGAGAT
* * * *
54887469 AGCCAGTGTAAGA-CGTGTCTGGGGCAT-GCATCGGCTA-AGAG-T-TGTG-CTAGTGTAAGACA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACAGAGATGAGTGTC-AGTGTAAGACA
54887528 TATCTGGGACATGCATC
64 TATCTGGGACATGCATC
54887545 AGCCCGCGTA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
90 1 0.01
91 29 0.43
92 1 0.01
93 11 0.16
94 13 0.19
95 13 0.19
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (95 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGTGTCAGTGTAAGACATA
TCTGGGACATGCATCGGCCTCGACAGAGAT
Found at i:54890986 original size:17 final size:19
Alignment explanation
Indices: 54890944--54890987 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54890934 ATGAAATTTT
*
54890944 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
54890963 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
54890981 AA-TATTA
1 AATTATTA
54890988 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:54891030 original size:54 final size:54
Alignment explanation
Indices: 54890961--54891135 Score: 181
Period size: 54 Copynumber: 3.3 Consensus size: 54
54890951 ATTATGAGAT
54890961 AAAATTATTATTATTAGAAAAATATTACTGTATGTATGTTTGAAAAATTTTATG
1 AAAATTATTATTATTAGAAAAATATTACTGTATGTATGTTTGAAAAATTTTATG
* * * *
54891015 AAAATTATTATTATT------A-CTTACTGTATGAAAT-TTT-AATTAGTATTATGA-G
1 AAAATTATTATTATTAGAAAAATATTACTGTATG-TATGTTTGAA--A-AATT-TTATG
54891064 ATAAAATTATTATTATTAGAAAAATATTACTGTATGTATGTTTGAAAAATTTTATG
1 --AAAATTATTATTATTAGAAAAATATTACTGTATGTATGTTTGAAAAATTTTATG
54891120 AAAATTATTATTATTA
1 AAAATTATTATTATTA
54891136 ATTATTGTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 34
0.70 0.06 0.25
Matches are distributed among these distances:
46 2 0.02
47 13 0.14
48 4 0.04
49 4 0.04
50 2 0.02
51 15 0.16
54 31 0.32
55 2 0.02
56 4 0.04
57 4 0.04
58 13 0.14
59 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (54 bp):
AAAATTATTATTATTAGAAAAATATTACTGTATGTATGTTTGAAAAATTTTATG
Found at i:54891079 original size:105 final size:105
Alignment explanation
Indices: 54890933--54891145 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 105
54890923 TTTAAATTTT
54890933 TATGAAATTTTAATTAGTATTATGAGATAAAATTATTATTATTAGAAAAATATTACTGTATGTAT
1 TATGAAATTTTAATTAGTATTATGAGATAAAATTATTATTATTAGAAAAATATTACTGTATGTAT
*
54890998 GTTTGAAAAATTTTATGAAAATTATTATTATTACTTACTG
66 GTTTGAAAAATTTTATGAAAATTATTATTATTAATTACTG
54891038 TATGAAATTTTAATTAGTATTATGAGATAAAATTATTATTATTAGAAAAATATTACTGTATGTAT
1 TATGAAATTTTAATTAGTATTATGAGATAAAATTATTATTATTAGAAAAATATTACTGTATGTAT
*
54891103 GTTTGAAAAATTTTATGAAAATTATTATTATTAATTATTG
66 GTTTGAAAAATTTTATGAAAATTATTATTATTAATTACTG
54891143 TAT
1 TAT
54891146 TATTGATATT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (105 bp):
TATGAAATTTTAATTAGTATTATGAGATAAAATTATTATTATTAGAAAAATATTACTGTATGTAT
GTTTGAAAAATTTTATGAAAATTATTATTATTAATTACTG
Found at i:54891091 original size:17 final size:19
Alignment explanation
Indices: 54891049--54891092 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54891039 ATGAAATTTT
*
54891049 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
54891068 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
54891086 AA-TATTA
1 AATTATTA
54891093 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:54896550 original size:79 final size:81
Alignment explanation
Indices: 54896414--54896598 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
54896404 TTGAATGATG
* * *
54896414 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
*
54896478 TGTGCGAGATGCTA-A
66 TGTGCGAGATACTATA
* * * **
54896493 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
54896555 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
54896573 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54896599 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:54896605 original size:40 final size:40
Alignment explanation
Indices: 54896414--54896598 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
54896404 TTGAATGATG
* * * * *
54896414 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
54896454 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATGCTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54896494 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54896533 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54896574 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54896599 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54896620 original size:79 final size:79
Alignment explanation
Indices: 54896467--54896631 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
54896457 GGACTAAGAT
* * * **
54896467 CCGAAGGCATTTGTGCGAGATGCTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
54896532 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
54896546 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
54896609 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
54896625 CCGAAGG
1 CCGAAGG
54896632 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54902202 original size:84 final size:84
Alignment explanation
Indices: 54902061--54902227 Score: 325
Period size: 84 Copynumber: 2.0 Consensus size: 84
54902051 GTTCATGGGA
*
54902061 ATGGTATTTACCTTTGATTGAATTCGCTTACAACAGTAGTTTTCAATCAAGTATTAAGATGGCAC
1 ATGGTATTTACCTTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTATTAAGATGGCAC
54902126 CTTACGAGGCTTTGTACGG
66 CTTACGAGGCTTTGTACGG
54902145 ATGGTATTTACCTTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTATTAAGATGGCAC
1 ATGGTATTTACCTTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTATTAAGATGGCAC
54902210 CTTACGAGGCTTTGTACG
66 CTTACGAGGCTTTGTACG
54902228 ATCGTAAATG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (84 bp):
ATGGTATTTACCTTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTATTAAGATGGCAC
CTTACGAGGCTTTGTACGG
Found at i:54903643 original size:86 final size:86
Alignment explanation
Indices: 54903498--54903664 Score: 307
Period size: 86 Copynumber: 1.9 Consensus size: 86
54903488 TGAGATTCAT
*
54903498 GCATGTTTTTAGTTGCTAGCTTGAGTTCTAATTAGCCCATGGTTCAAATCTTTGCTATGTCATGG
1 GCATGTTTTTAGTTGCTAGCTTGAGTTCTAATTAGCCCATAGTTCAAATCTTTGCTATGTCATGG
54903563 GGATGATATTCGGCCTAGGTG
66 GGATGATATTCGGCCTAGGTG
* *
54903584 GCATGTTTTTAGTTGCTAGCTTGAGTTCTAATTATCTCATAGTTCAAATCTTTGCTATGTCATGG
1 GCATGTTTTTAGTTGCTAGCTTGAGTTCTAATTAGCCCATAGTTCAAATCTTTGCTATGTCATGG
54903649 GGATGATATTCGGCCT
66 GGATGATATTCGGCCT
54903665 TGGTAGATTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.40
Consensus pattern (86 bp):
GCATGTTTTTAGTTGCTAGCTTGAGTTCTAATTAGCCCATAGTTCAAATCTTTGCTATGTCATGG
GGATGATATTCGGCCTAGGTG
Found at i:54904651 original size:39 final size:39
Alignment explanation
Indices: 54904555--54904733 Score: 172
Period size: 40 Copynumber: 4.6 Consensus size: 39
54904545 ATGATGTCCG
* * *
54904555 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
*
54904594 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
54904634 GAGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
54904673 GGGT-AGTCCCGAAGGCAATTGTGCGAGTTACT-ATAACC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
54904711 GGGCTATGTCCCGAAGGCATTTG
1 -GGCTAAGTCCCGAAGGCATTTG
54904734 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
37 3 0.03
38 28 0.24
39 34 0.29
40 41 0.35
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:54904740 original size:40 final size:38
Alignment explanation
Indices: 54904604--54904733 Score: 165
Period size: 39 Copynumber: 3.3 Consensus size: 38
54904594 GGACTAAGAT
* * *
54904604 CCGAAGGCATTTGTGCGAGATACTAATTCCGAGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCG-GGT-AGTC
54904643 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
*
54904681 CCGAAGGCAATTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGG-TA-GTC
54904721 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54904734 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
37 2 0.02
38 32 0.39
39 33 0.40
40 15 0.18
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
Found at i:54904747 original size:40 final size:38
Alignment explanation
Indices: 54904604--54904733 Score: 149
Period size: 38 Copynumber: 3.3 Consensus size: 38
54904594 GGACTAAGAT
* * *
54904604 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGAGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTATA-ACCG-GGT-AGTC
54904643 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGTAGTC
*
54904681 CCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGG-TA-GTC
54904721 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54904734 AACGAGTAGC
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
37 2 0.02
38 32 0.40
39 32 0.40
40 15 0.19
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGTAGTC
Found at i:54912754 original size:176 final size:176
Alignment explanation
Indices: 54912460--54912810 Score: 666
Period size: 176 Copynumber: 2.0 Consensus size: 176
54912450 AACGAAAATG
*
54912460 AAATACGAATGTGCCATGATTTACTGTTAAATGTGCATGGTTATTTGAATGATGTCTGGGCTAAG
1 AAATACGAATGTGCCATGATTTACTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAG
54912525 TCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGATAC
66 TCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGATAC
*
54912590 TAATTCCGGGCTAAGCCCGAAGGCATTTGTCCGAGTTACTAAATCT
131 TAATTCCGAGCTAAGCCCGAAGGCATTTGTCCGAGTTACTAAATCT
54912636 AAATACGAATGTGCCATGATTTACTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAG
1 AAATACGAATGTGCCATGATTTACTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAG
*
54912701 TCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATAC
66 TCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGATAC
*
54912766 TAATTCCGAGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
131 TAATTCCGAGCTAAGCCCGAAGGCATTTGTCCGAGTTACTAAATC
54912811 CGGGTAGTCC
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 171 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (176 bp):
AAATACGAATGTGCCATGATTTACTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAG
TCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGATAC
TAATTCCGAGCTAAGCCCGAAGGCATTTGTCCGAGTTACTAAATCT
Found at i:54912790 original size:39 final size:39
Alignment explanation
Indices: 54912694--54912872 Score: 172
Period size: 40 Copynumber: 4.6 Consensus size: 39
54912684 ATGATGTCCG
* * *
54912694 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
*
54912733 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
54912773 GAGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
54912812 GGGT-AGTCCCGAAGGCAATTGTGCGAGTTACT-ATAACC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
54912850 GGGCTATGTCCCGAAGGCATTTG
1 -GGCTAAGTCCCGAAGGCATTTG
54912873 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
37 3 0.03
38 28 0.24
39 34 0.29
40 41 0.35
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:54912879 original size:40 final size:38
Alignment explanation
Indices: 54912743--54912872 Score: 165
Period size: 39 Copynumber: 3.3 Consensus size: 38
54912733 GGACTAAGAT
* * *
54912743 CCGAAGGCATTTGTGCGAGATACTAATTCCGAGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCG-GGT-AGTC
54912782 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
*
54912820 CCGAAGGCAATTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGG-TA-GTC
54912860 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54912873 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
37 2 0.02
38 32 0.39
39 33 0.40
40 15 0.18
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAGTC
Found at i:54912886 original size:40 final size:38
Alignment explanation
Indices: 54912743--54912872 Score: 149
Period size: 38 Copynumber: 3.3 Consensus size: 38
54912733 GGACTAAGAT
* * *
54912743 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGAGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTATA-ACCG-GGT-AGTC
54912782 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGTAGTC
*
54912820 CCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGG-TA-GTC
54912860 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54912873 AACGAGTAGC
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
37 2 0.02
38 32 0.40
39 32 0.40
40 15 0.19
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGTAGTC
Found at i:54924862 original size:35 final size:36
Alignment explanation
Indices: 54924822--54924904 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 36
54924812 CTTCTTGATA
* * *
54924822 TTAATTGGAAGAAGTATTGATGTTCT-T-GTAGGATG
1 TTAATTGAAAGAAGTATCGATGTT-TGTGGCAGGATG
*
54924857 TTAATTGAAAGAAGTATCGGTGTTTGTGGCAGGATG
1 TTAATTGAAAGAAGTATCGATGTTTGTGGCAGGATG
54924893 TTAATTGAAAGA
1 TTAATTGAAAGA
54924905 GGACTGGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.02
35 22 0.52
36 19 0.45
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (36 bp):
TTAATTGAAAGAAGTATCGATGTTTGTGGCAGGATG
Found at i:54929958 original size:6 final size:6
Alignment explanation
Indices: 54929947--54930054 Score: 64
Period size: 6 Copynumber: 18.0 Consensus size: 6
54929937 AGATCAATTG
* * *
54929947 AAAGAA AAAG-A AAA-AA AATGAA AATGAGGA AAAG-A AAAG-A AAATAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA--AGAA AAAGAA AAAGAA AAAGAA
* * * *
54929993 CAAGAG AAAGATA AAAGAA AATGAGA AAAGAA AAAGAA AAA-AA GGAAGAA
1 AAAGAA AAAGA-A AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA -AAAGAA
*
54930043 AAGGAA AAAGAA
1 AAAGAA AAAGAA
54930055 TATGAGAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
5 18 0.23
6 44 0.56
7 12 0.15
8 4 0.05
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:54929979 original size:24 final size:24
Alignment explanation
Indices: 54929952--54930032 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
54929942 AATTGAAAGA
54929952 AAAAGAAAA-AAAATGAAAATGAGG
1 AAAAGAAAAGAAAATGAAAA-GAGG
54929976 AAAAGAAAAGAAAAT-AACAAGA-G
1 AAAAGAAAAGAAAATGAA-AAGAGG
* *
54929999 AAAGATAAAAGAAAATGAGAAA-AGA
1 AAA-AGAAAAGAAAATGA-AAAGAGG
54930024 AAAAGAAAA
1 AAAAGAAAA
54930033 AAAGGAAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 4 0.08
24 30 0.62
25 13 0.27
26 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (24 bp):
AAAAGAAAAGAAAATGAAAAGAGG
Found at i:54929988 original size:19 final size:19
Alignment explanation
Indices: 54929956--54930032 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 19
54929946 GAAAGAAAAA
54929956 GAAAA-AAAATGAAAATGAG
1 GAAAAGAAAA-GAAAATGAG
*
54929975 GAAAAGAAAAGAAAATAACAAG
1 GAAAAGAAAAGAAAAT---GAG
*
54929997 AGAAAGATAAAAGAAAATGA-
1 -GAAA-AGAAAAGAAAATGAG
54930017 GAAAAGAAAAAGAAAA
1 GAAAAG-AAAAGAAAA
54930033 AAAGGAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
18 1 0.02
19 24 0.51
20 4 0.09
21 1 0.02
22 2 0.04
23 4 0.09
24 11 0.23
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.06
Consensus pattern (19 bp):
GAAAAGAAAAGAAAATGAG
Found at i:54930052 original size:43 final size:41
Alignment explanation
Indices: 54929955--54930064 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 41
54929945 TGAAAGAAAA
*
54929955 AGAAA-AAAAATGAAAATGAGGAAAAGAAAAGAAAATAACAAG
1 AGAAAGAAAAA-GAAAATGA-GAAAAGAAAAGAAAAAAACAAG
*
54929997 AGAAAGATAAAAGAAAATGAGAAAAGAAAAAGAAAAAAAGGAAG
1 AGAAAGA-AAAAGAAAATGAGAAAAG-AAAAGAAAAAAA-CAAG
*
54930041 A-AAAGGAAAAAGAATATGAGAAAA
1 AGAAA-GAAAAAGAAAATGAGAAAA
54930065 AATGTTTGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
42 11 0.18
43 39 0.65
44 10 0.17
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (41 bp):
AGAAAGAAAAAGAAAATGAGAAAAGAAAAGAAAAAAACAAG
Found at i:54931577 original size:12 final size:12
Alignment explanation
Indices: 54931560--54931584 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54931550 TAAATTGCTA
54931560 GGTGAGATATTT
1 GGTGAGATATTT
54931572 GGTGAGATATTT
1 GGTGAGATATTT
54931584 G
1 G
54931585 CTGCTTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (12 bp):
GGTGAGATATTT
Found at i:54937754 original size:24 final size:25
Alignment explanation
Indices: 54937708--54937781 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
54937698 GTATGCTGAC
* * * *
54937708 ACGAGCTTTGAATCGGTATGCTCTT
1 ACGAGCTGTAAATCGGTAAGCTCAT
54937733 ACGAGCTGTAAAT-GGTAAGCTCAT
1 ACGAGCTGTAAATCGGTAAGCTCAT
*
54937757 CCGAGC--TAAATAACGGTAAGCTCAT
1 ACGAGCTGTAAAT--CGGTAAGCTCAT
54937782 GCAAGCTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 5 0.12
24 14 0.34
25 22 0.54
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (25 bp):
ACGAGCTGTAAATCGGTAAGCTCAT
Found at i:54939047 original size:11 final size:11
Alignment explanation
Indices: 54939031--54939055 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54939021 GGGTCCCTTT
54939031 ATATACAATAA
1 ATATACAATAA
54939042 ATATACAATAA
1 ATATACAATAA
54939053 ATA
1 ATA
54939056 CAATAATCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATACAATAA
Found at i:54944806 original size:16 final size:15
Alignment explanation
Indices: 54944784--54944828 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
54944774 TTAAGTCTAT
54944784 ATTAATTATGTCTTA
1 ATTAATTATGTCTTA
*
54944799 ATTTAATTAGTGTATTA
1 A-TTAATTA-TGTCTTA
54944816 ATTAA-TATGTCTT
1 ATTAATTATGTCTT
54944829 GATGTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 5 0.19
15 3 0.12
16 11 0.42
17 7 0.27
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (15 bp):
ATTAATTATGTCTTA
Found at i:54944818 original size:17 final size:16
Alignment explanation
Indices: 54944785--54944818 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54944775 TAAGTCTATA
*
54944785 TTAATTATGTCTTAAT
1 TTAATTATGTATTAAT
54944801 TTAATTAGTGTATTAAT
1 TTAATTA-TGTATTAAT
54944818 T
1 T
54944819 AATATGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (16 bp):
TTAATTATGTATTAAT
Found at i:54946119 original size:15 final size:16
Alignment explanation
Indices: 54946099--54946132 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54946089 AAAAAAATAT
54946099 AATTGAA-GTAAAAAA
1 AATTGAATGTAAAAAA
*
54946114 AATTGAATTTAAAAAA
1 AATTGAATGTAAAAAA
54946130 AAT
1 AAT
54946133 AGGAGAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTGAATGTAAAAAA
Found at i:54948052 original size:50 final size:53
Alignment explanation
Indices: 54947961--54948083 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 53
54947951 CCCATGTAAT
* * *
54947961 ACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT-CCCACATAAG
1 ACCATGTCTGGGACATGGCATTGG-A-GACTGAGG-TATGAGAAGTGCCC-CATAAG
*
54948017 ACCATGTCTGGGACATGGCATTGG-GACTGA-G-ATGAGAAGTGCCCCGTAAG
1 ACCATGTCTGGGACATGGCATTGGAGACTGAGGTATGAGAAGTGCCCCATAAG
*
54948067 ACCATGTCGGGGACATG
1 ACCATGTCTGGGACATG
54948084 AAATGGGCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 29 0.48
51 3 0.05
52 1 0.02
53 4 0.07
56 24 0.39
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (53 bp):
ACCATGTCTGGGACATGGCATTGGAGACTGAGGTATGAGAAGTGCCCCATAAG
Found at i:54948371 original size:20 final size:20
Alignment explanation
Indices: 54948346--54948384 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54948336 TGAGTTATTT
54948346 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
54948366 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
54948385 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:54951105 original size:17 final size:17
Alignment explanation
Indices: 54951082--54951122 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54951072 AGAGCAAATG
*
54951082 AGAAAAAAAAATAAAAA
1 AGAAAAAAAAAGAAAAA
* *
54951099 TGAAAAAGAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
54951116 AGAAAAA
1 AGAAAAA
54951123 TAGAGAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:54951131 original size:23 final size:23
Alignment explanation
Indices: 54951081--54951133 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
54951071 TAGAGCAAAT
*
54951081 GAGAAAAAAAAATAAAAATGAAA
1 GAGAAAAAAAAAGAAAAATGAAA
* *
54951104 AAGAAAGAAAAAAGAAAAAT-AGA
1 GAGAAA-AAAAAAGAAAAATGAAA
54951127 GAGAAAA
1 GAGAAAA
54951134 TAAATTGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 12 0.48
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (23 bp):
GAGAAAAAAAAAGAAAAATGAAA
Found at i:54970566 original size:23 final size:23
Alignment explanation
Indices: 54970522--54970566 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54970512 TCCTTTGTAA
* *
54970522 TTTTAGTTTTTAGTTTTTCTTTC
1 TTTTAGTTTTTAGGTTTACTTTC
54970545 TTTTAGGTTTTT-GGTTTACTTT
1 TTTTA-GTTTTTAGGTTTACTTT
54970567 TAGTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.71
Consensus pattern (23 bp):
TTTTAGTTTTTAGGTTTACTTTC
Found at i:54974158 original size:14 final size:14
Alignment explanation
Indices: 54974141--54974172 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
54974131 TAATAAGAAT
*
54974141 GAAATTAAAGTAAA
1 GAAATTAAAGAAAA
54974155 GAAATTAAAGAAAA
1 GAAATTAAAGAAAA
54974169 GAAA
1 GAAA
54974173 GAGAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
GAAATTAAAGAAAA
Found at i:54983796 original size:50 final size:50
Alignment explanation
Indices: 54983674--54983866 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
54983664 TAATAATATT
* ** * * *
54983674 CCAATGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCTTGTAC--TG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTG
* * **
54983723 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
54983773 CCCATGCCATGTCCCAGACATGGTC-TA-ATGGGGGACCTCTCATCTTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAT--GGGACCTCTCATATCGGTG
* *
54983823 CCAATGCCATGTCCCCGATATGGTCTTACATGGGACCTCTCATA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
54983867 ATCTCAATGA
Statistics
Matches: 119, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
48 3 0.03
49 39 0.33
50 73 0.61
51 2 0.02
52 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:54984302 original size:30 final size:29
Alignment explanation
Indices: 54984255--54984314 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
54984245 GCCCTCGACT
*
54984255 CTAAATTTTGCAAAATTACGA-TTTTGCCC
1 CTAAATTTTACAAAATTAC-ACTTTTGCCC
*
54984284 CTAAACTTTTACATAATTACACTTTTGCCC
1 CTAAA-TTTTACAAAATTACACTTTTGCCC
54984314 C
1 C
54984315 AAAGCTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (29 bp):
CTAAATTTTACAAAATTACACTTTTGCCC
Found at i:54990679 original size:41 final size:40
Alignment explanation
Indices: 54990621--54990880 Score: 213
Period size: 41 Copynumber: 6.3 Consensus size: 40
54990611 ATTACACCGA
54990621 CACAGAGCCTGATATAAATCACCGCTACTAAGCCTAG-TA-G
1 CACAGAGCCTGATATAAATCACCGC-ACTAAGCCT-GCTAGG
*
54990661 CTACAGAGCCTGATATAAATCACCGGCACCAAGCCTGCTAGG
1 C-ACAGAGCCTGATATAAATCACC-GCACTAAGCCTGCTAGG
* * * *
54990703 CACTGAACCTAATATAAATCACTGACACTAAGCCTGCTAGG
1 CACAGAGCCTGATATAAATCACCG-CACTAAGCCTGCTAGG
* * *
54990744 CATAGAGCCTGATATAAATCATCGACACGAA-CCTTGCTAGG
1 CACAGAGCCTGATATAAATCACCG-CACTAAGCC-TGCTAGG
* * * * * *
54990785 CATAGAGCCTAATATAAATCACTGGCACGAAGACTGCTAGT
1 CACAGAGCCTGATATAAATCAC-CGCACTAAGCCTGCTAGG
* ** * * * *
54990826 CACTA-AGCCAGATATAAATCATAGGCACGAAACCTGGTATG
1 CAC-AGAGCCTGATATAAATCA-CCGCACTAAGCCTGCTAGG
54990867 CACAGAGCCTGATA
1 CACAGAGCCTGATA
54990881 GAACATGCTG
Statistics
Matches: 181, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
40 6 0.03
41 168 0.93
42 7 0.04
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
CACAGAGCCTGATATAAATCACCGCACTAAGCCTGCTAGG
Found at i:54990782 original size:82 final size:81
Alignment explanation
Indices: 54990632--54990861 Score: 245
Period size: 82 Copynumber: 2.8 Consensus size: 81
54990622 ACAGAGCCTG
* * * *
54990632 ATATAAATCACCGCTACTAAGCCTAG-TA-GCTACAGAGCCTGATATAAATCACCGGCACCAAGC
1 ATATAAATCACTGC-ACTAAGCCT-GCTAGGC-ATAGAGCCTGATATAAATCATCGGCACGAAGC
54990695 CTGCTAGGCACT-GAACCTA
63 CTGCTAGGCA-TAGAACCTA
*
54990714 ATATAAATCACTGACACTAAGCCTGCTAGGCATAGAGCCTGATATAAATCATCGACACGAA-CCT
1 ATATAAATCACTG-CACTAAGCCTGCTAGGCATAGAGCCTGATATAAATCATCGGCACGAAGCC-
*
54990778 TGCTAGGCATAGAGCCTA
64 TGCTAGGCATAGAACCTA
* * * * * *
54990796 ATATAAATCACTGGCACGAAGACTGCTAGTCACTA-AGCCAGATATAAATCATAGGCACGAAACC
1 ATATAAATCACT-GCACTAAGCCTGCTAGGCA-TAGAGCCTGATATAAATCATCGGCACGAAGCC
54990860 TG
64 TG
54990862 GTATGCACAG
Statistics
Matches: 128, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
81 4 0.03
82 116 0.91
83 8 0.06
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (81 bp):
ATATAAATCACTGCACTAAGCCTGCTAGGCATAGAGCCTGATATAAATCATCGGCACGAAGCCTG
CTAGGCATAGAACCTA
Found at i:54990874 original size:82 final size:82
Alignment explanation
Indices: 54990665--54990876 Score: 257
Period size: 82 Copynumber: 2.6 Consensus size: 82
54990655 TAGTAGCTAC
* * * * *
54990665 AGAGCCTGATATAAATCACCGGCACCAAGCCTGCTAGGCACTGAACCTAATATAAATCACTGACA
1 AGAGCCTGATATAAATCATCGGCACGAAACCTGCTAGGCACAGAGCCTAATATAAATCACTGACA
* *
54990730 CTAAGCCTGCTAGGCAT
66 CGAAGACTGCTAGGCAT
* * *
54990747 AGAGCCTGATATAAATCATCGACACG-AACCTTGCTAGGCATAGAGCCTAATATAAATCACTGGC
1 AGAGCCTGATATAAATCATCGGCACGAAACC-TGCTAGGCACAGAGCCTAATATAAATCACTGAC
*
54990811 ACGAAGACTGCTAGTCACT
65 ACGAAGACTGCTAGGCA-T
* * * *
54990830 A-AGCCAGATATAAATCATAGGCACGAAACCTGGTATGCACAGAGCCT
1 AGAGCCTGATATAAATCATCGGCACGAAACCTGCTAGGCACAGAGCCT
54990877 GATAGAACAT
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
81 3 0.03
82 101 0.92
83 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (82 bp):
AGAGCCTGATATAAATCATCGGCACGAAACCTGCTAGGCACAGAGCCTAATATAAATCACTGACA
CGAAGACTGCTAGGCAT
Found at i:54990905 original size:123 final size:123
Alignment explanation
Indices: 54990621--54990945 Score: 290
Period size: 123 Copynumber: 2.6 Consensus size: 123
54990611 ATTACACCGA
* * * *
54990621 CACAGAGCCTGATATAAATCACCG-CTACTAAGCCTAG-TAG-CTACAGAGCCTGATATAAATCA
1 CACAGAGCCTGATAGAAATCATCGAC-ACGAA-CCTTGCTAGAC-ACAGAGCCTGATATAAATCA
* * * *
54990683 CCGGCACCAAGCCTGCTAGGCACTGAACCTAATATAAATCACTGACACTAAGCCTGCTAGG
63 CTGGCACGAAGCCTGCTAGGCACTGAACCTAATATAAATCACTGACACGAAACCTGCTAGG
* * * * *
54990744 CATAGAGCCTGATATAAATCATCGACACGAACCTTGCTAGGCATAGAGCCTAATATAAATCACTG
1 CACAGAGCCTGATAGAAATCATCGACACGAACCTTGCTAGACACAGAGCCTGATATAAATCACTG
* * * * *
54990809 GCACGAAGACTGCTAGTCACT-AAGCC-AGATATAAATCA-TAGGCACGAAACCTGGTATG
66 GCACGAAGCCTGCTAGGCACTGAA-CCTA-ATATAAATCACT-GACACGAAACCTGCTAGG
* * * * *
54990867 CACAGAGCCTGATAG-AA-CATGCTGACACGGA-GTCTGCTAGACACAAAACCTGATGTAAATCA
1 CACAGAGCCTGATAGAAATCAT-C-GACACGAACCT-TGCTAGACACAGAGCCTGATATAAATCA
*
54990929 CTGGCATGAAGCCTGCT
63 CTGGCACGAAGCCTGCT
54990946 GGACTCAAAG
Statistics
Matches: 166, Mismatches: 27, Indels: 18
0.79 0.13 0.09
Matches are distributed among these distances:
121 3 0.02
122 12 0.07
123 149 0.90
124 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (123 bp):
CACAGAGCCTGATAGAAATCATCGACACGAACCTTGCTAGACACAGAGCCTGATATAAATCACTG
GCACGAAGCCTGCTAGGCACTGAACCTAATATAAATCACTGACACGAAACCTGCTAGG
Found at i:54995169 original size:14 final size:14
Alignment explanation
Indices: 54995136--54995172 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
54995126 TCCAAGTCAG
*
54995136 ATAAAACAATTCAA
1 ATAAAATAATTCAA
54995150 AT-AAATAATTCAA
1 ATAAAATAATTCAA
54995163 ATAAAATAAT
1 ATAAAATAAT
54995173 AAATCAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTCAA
Found at i:54997109 original size:45 final size:44
Alignment explanation
Indices: 54997014--54997110 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
54997004 TTTTCATTTT
* * *
54997014 CATTTTCTTTTTCCACTTGAGAACTCTCTAATTTTTCTAGCTTTT
1 CATTTTCTTTTTCCACTTGAGAACTCTCTAATTTTCCTA-CTATG
54997059 CATTTTCTTTTTCCACTTGAGAACTCTCTAATTTTACCT-CATATG
1 CATTTTCTTTTTCCACTTGAGAACTCTCTAATTTT-CCTAC-TATG
*
54997104 GATTTTC
1 CATTTTC
54997111 ACTCACCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 1 0.02
45 43 0.93
46 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.51
Consensus pattern (44 bp):
CATTTTCTTTTTCCACTTGAGAACTCTCTAATTTTCCTACTATG
Found at i:55000352 original size:16 final size:17
Alignment explanation
Indices: 55000323--55000355 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55000313 TTAACTGTCA
55000323 AATTAAATTAAATTAAT
1 AATTAAATTAAATTAAT
*
55000340 AATT-AATTTAATTAAT
1 AATTAAATTAAATTAAT
55000356 CTTACGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATTAAATTAAT
Found at i:55012108 original size:20 final size:20
Alignment explanation
Indices: 55012085--55012123 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
55012075 ACTTTATTTT
55012085 TAAAGTTAAAATA-ATATTAA
1 TAAAG-TAAAATATATATTAA
55012105 TAAAGTAAAATATATATTA
1 TAAAGTAAAATATATATTA
55012124 TCATCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAGTAAAATATATATTAA
Found at i:55016720 original size:40 final size:40
Alignment explanation
Indices: 55016675--55016912 Score: 191
Period size: 40 Copynumber: 6.0 Consensus size: 40
55016665 CGAATACACG
* * * *
55016675 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * * * *
55016715 ACACCAGCACGAATGCTCTTTGGAACATAGCCCGGAAACA
1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * * *
55016755 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATA
1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
55016795 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATTTA
1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * *
55016835 GTAACTC-GCACCAATGC-CTTCGG-GCTTAGCCCGGA-ATTA
1 -TCAC-CAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-TA
* * * *
55016874 GTAACTC-GCACAAATGC-CTTCGGATCTTAGTCCGGATAT
1 -TCAC-CAGCACGAATGCTCTTCGGAACTTAGCCCGGATAT
55016913 GGTCACTTAG
Statistics
Matches: 164, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
39 35 0.21
40 116 0.71
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
Found at i:55016813 original size:80 final size:80
Alignment explanation
Indices: 55016675--55016830 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 80
55016665 CGAATACACG
* *
55016675 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGAA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
55016740 CATAGCCCGGAAACA
66 CATAGCCCGGAAACA
* * * * *
55016755 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATATCACTAGCACGAATGCTCTTCGGAA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
*
55016820 CTTAGCCCGGA
66 CATAGCCCGGA
55016831 TTTAGTAACT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
CATAGCCCGGAAACA
Found at i:55016856 original size:80 final size:78
Alignment explanation
Indices: 55016692--55016945 Score: 246
Period size: 80 Copynumber: 3.2 Consensus size: 78
55016682 CATGATTGCT
* * * * * * *
55016692 CTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGAACATAGCCCGGAAACA-T
1 CTTCGGGACTTAGCCCGGTTAT-ACACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATAGT
*
55016756 CACTAGCATGAATGC
65 CACTAGCA-CAATGC
*
55016771 TCTTCGGGACTTAGCCCGGTTATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATTTAG
1 -CTTCGGGACTTAGCCCGGTTATA-CACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATAG
* *
55016836 TAACTCGCACCAATGC
64 TCACTAGCA-CAATGC
* * * * *
55016852 CTTCGGG-CTTAGCCCGGAATTAGTA-ACTCGCACAAATGC-CTTCGGATCTTAGTCCGGATATG
1 CTTCGGGACTTAGCCCGG--TTA-TACACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
55016914 GTCACTTAGCACAAAGC
63 GTCAC-TAGCACAATGC
55016931 CTTCGGGACTTAGCC
1 CTTCGGGACTTAGCC
55016946 TGGACATCAT
Statistics
Matches: 146, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
79 46 0.32
80 83 0.57
81 15 0.10
82 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (78 bp):
CTTCGGGACTTAGCCCGGTTATACACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATAGTC
ACTAGCACAATGC
Found at i:55016943 original size:40 final size:39
Alignment explanation
Indices: 55016772--55016945 Score: 158
Period size: 40 Copynumber: 4.4 Consensus size: 39
55016762 CATGAATGCT
* * *
55016772 CTTCGGGACTTAGCCCGGTTATA-TCACTAGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCAC-AAAGC
* * * *
55016811 TCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCAATGC
1 -CTTCGGGACTTAGCCCGGATATAGTAACTAGCA-CAAAGC
*
55016852 CTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAA-GC
* * *
55016891 CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCACAAAGC
55016931 CTTCGGGACTTAGCC
1 CTTCGGGACTTAGCC
55016946 TGGACATCAT
Statistics
Matches: 112, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
38 5 0.04
39 29 0.26
40 53 0.47
41 24 0.21
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAAGC
Found at i:55017291 original size:29 final size:29
Alignment explanation
Indices: 55017252--55017330 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
55017242 CTTAATAATC
*
55017252 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
55017282 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
55017311 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
55017331 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:55019392 original size:40 final size:40
Alignment explanation
Indices: 55019189--55019392 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
55019179 CGGAATTTAA
** *
55019189 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55019229 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
55019269 CCGGATTTAATAACTCGCACCACTGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55019308 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55019348 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55019388 CCGGA
1 CCGGA
55019393 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 30 0.22
40 91 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55029131 original size:27 final size:27
Alignment explanation
Indices: 55029101--55029308 Score: 160
Period size: 27 Copynumber: 7.7 Consensus size: 27
55029091 TTACCCTATG
*
55029101 GGGGTATTTCAATAATTTTACCCATTA
1 GGGGTATTTCGATAATTTTACCCATTA
* *
55029128 GGGGTATTT-TAGTAATTTTACAC-TTCA
1 GGGGTATTTCGA-TAATTTTACCCATT-A
* * * *
55029155 AGGGTATTTTGATAATTTTAGCCA-TC
1 GGGGTATTTCGATAATTTTACCCATTA
* *
55029181 GAGGGTATTTCGATAATTTTATCC-TTCG
1 G-GGGTATTTCGATAATTTTACCCATT-A
* *
55029209 GGGGAATTTCGATAATTTTACCCA-TC
1 GGGGTATTTCGATAATTTTACCCATTA
* *
55029235 GGAGGTATTTCGGTAATTTTACCCA-TC
1 GG-GGTATTTCGATAATTTTACCCATTA
*
55029262 GAGGGTATTTCGGTAATTTTACCC-TTCA
1 G-GGGTATTTCGATAATTTTACCCATT-A
* *
55029290 AGGGTATTTCAATAATTTT
1 GGGGTATTTCGATAATTTT
55029309 TACGACCTTT
Statistics
Matches: 149, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
26 5 0.03
27 141 0.95
28 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCGATAATTTTACCCATTA
Found at i:55029172 original size:54 final size:52
Alignment explanation
Indices: 55029102--55029308 Score: 200
Period size: 54 Copynumber: 3.8 Consensus size: 52
55029092 TACCCTATGG
* * *
55029102 GGGTATTTCAATAATTTTACCCATTAGGGGTATTTTAGTAATTTTACACTTCAA
1 GGGTATTTCGATAATTTTACCCA-TAGGGGTATTTCAGTAATTTTAC-CTTCGA
* * * *
55029156 GGGTATTTTGATAATTTTAGCCATCGAGGGTATTTC-GATAATTTTATCCTTCGG
1 GGGTATTTCGATAATTTTACCCATAG-GGGTATTTCAG-TAATTTTA-CCTTCGA
* * * *
55029210 GGGAATTTCGATAATTTTACCCATCGGAGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATAGG-GGTATTTCAGTAATTTTA-CCTTCGA
* * * *
55029264 GGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCAATAATTTT
1 GGGTATTTCGATAATTTTACCCAT-AGGGGTATTTCAGTAATTTT
55029309 TACGACCTTT
Statistics
Matches: 127, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
53 4 0.03
54 120 0.94
55 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (52 bp):
GGGTATTTCGATAATTTTACCCATAGGGGTATTTCAGTAATTTTACCTTCGA
Found at i:55029242 original size:81 final size:81
Alignment explanation
Indices: 55029102--55029308 Score: 229
Period size: 81 Copynumber: 2.6 Consensus size: 81
55029092 TACCCTATGG
* * * * * * * * *
55029102 GGGTATTTCAATAATTTTACCCATT-AGGGGTATTTTAGTAATTTTACACTTC-AAGGGTATTTT
1 GGGTATTTCGATAATTTTACCC-TTCAAGGGAATTTCAATAATTTTACCCATCGGA-GGTATTTC
*
55029165 GATAATTTTAGCCATCGA
64 GATAATTTTACCCATCGA
* ** * *
55029183 GGGTATTTCGATAATTTTATCCTTCGGGGGAATTTCGATAATTTTACCCATCGGAGGTATTTCGG
1 GGGTATTTCGATAATTTTACCCTTCAAGGGAATTTCAATAATTTTACCCATCGGAGGTATTTCGA
55029248 TAATTTTACCCATCGA
66 TAATTTTACCCATCGA
* *
55029264 GGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCAATAATTTT
1 GGGTATTTCGATAATTTTACCCTTCAAGGGAATTTCAATAATTTT
55029309 TACGACCTTT
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
80 2 0.02
81 102 0.97
82 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (81 bp):
GGGTATTTCGATAATTTTACCCTTCAAGGGAATTTCAATAATTTTACCCATCGGAGGTATTTCGA
TAATTTTACCCATCGA
Found at i:55029537 original size:17 final size:18
Alignment explanation
Indices: 55029515--55029549 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55029505 TATCTGTGTG
*
55029515 GGGCCCACGA-GCCCATT
1 GGGCCCACAAGGCCCATT
55029532 GGGCCCACAAGGCCCATT
1 GGGCCCACAAGGCCCATT
55029550 TCGGCCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.40, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGCCCACAAGGCCCATT
Found at i:55030745 original size:25 final size:25
Alignment explanation
Indices: 55030696--55030749 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
55030686 TGAACCTCTA
*
55030696 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTATGACGCC
* **
55030721 ACCTCCTTGCCACACCTATTTCGCC
1 ACCTCCTTACCACACCTATGACGCC
55030746 ACCT
1 ACCT
55030750 TGCCACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.48, G:0.09, T:0.24
Consensus pattern (25 bp):
ACCTCCTTACCACACCTATGACGCC
Found at i:55035010 original size:656 final size:658
Alignment explanation
Indices: 55033752--55036906 Score: 5253
Period size: 656 Copynumber: 4.8 Consensus size: 658
55033742 TTATAGAGAT
* *
55033752 TTTAACAATTAAGCCTCTTTAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
1 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
*
55033817 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTTTGAATTGGGTTTAAT
66 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
* *
55033882 CTTTCTTTTCTTTAAATTAATATAAACATATTTGCTATGTGTTCTTTGTTCTTGTTGACAACAAT
131 CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACAAT
*
55033947 GTTAGCTTAACTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
196 GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
55034012 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTA-TT-ATTCATAC
261 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATAC
* *
55034075 GTGATTGAAATACACCTGAATTAGCTAAGTGATCCTAACCAGATGACGGCTAATGGATGCATAAT
326 GTGATTGAAATACACCTGAATTAGCTGAGTGATCCTAACCAGATGACGGCTAATGGACGCATAAT
*
55034140 TGAAATCTGCATGCTTAATTTAGATCCTGACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
391 TGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
55034205 CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
456 CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
55034270 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAATAA
521 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAATAA
55034335 GACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCATT
586 GACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCATT
55034400 CCCACGCG
651 CCCACGCG
*
55034408 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACTATCAGCAAAGGAGC
1 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
*
55034473 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTTTGAATTGGGTTTAAT
66 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
* *
55034538 CTTTCTTTTCTTTAAATTAATATAAACATATTTGCTATGTGTTCTTTGTTCTTGTTGACAACAAT
131 CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACAAT
*
55034603 GTTAGCTTAACTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
196 GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
55034668 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTA-TT-ATTCATAC
261 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATAC
* *
55034731 GTGATTGAAATACACCTGAATTAGCTAAGTGATCCTAACCAGATGACGGCTAATGGATGCATAAT
326 GTGATTGAAATACACCTGAATTAGCTGAGTGATCCTAACCAGATGACGGCTAATGGACGCATAAT
*
55034796 TGAAATCTGCATGCTTAATTTAGATCCTGACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
391 TGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
55034861 CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
456 CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
55034926 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAATAA
521 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAATAA
55034991 GACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCATT
586 GACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCATT
55035056 CCCACGCG
651 CCCACGCG
*
55035064 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACTATCAGCAAAGGAGC
1 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
*
55035129 AAAGCAAAGGAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
66 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
* *
55035194 CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTTTTATTGTTTACAACAAT
131 CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACAAT
55035259 GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
196 GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
55035324 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATAC
261 TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATAC
* * * * *
55035389 GAGAATGAAGTACACCTAAATTAGCTGAGCGATCCTAACCAGATGACGGCTAATGGACGCATAAT
326 GTGATTGAAATACACCTGAATTAGCTGAGTGATCCTAACCAGATGACGGCTAATGGACGCATAAT
*
55035454 TGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCCAAC
391 TGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
* ** * *
55035519 CAAGCTTTGTTATCTGCATAGTTTTTACATTTGTGTGATTAAATTATGGCCGGCCACCCATGGAA
456 CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
* *
55035584 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTCTCTCTCTCTCTCCTCACCTATAAAG
521 GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAA--CTATCTCTCTCTCCTCACCTATAAAT
* * * * *
55035649 AAGACCCTCTCATCCCTCAAGCATCAATCAAACATCATTCCCTCTCTTTCTCTTAGCCTTTTCCA
584 AAGACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCA
55035714 TTCCCACGCCTAGTATCATTTTTTCATAGAG
649 TTCCCA---C--G-----------C-----G
55035745 ATTTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGA
1 --TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGA
* *** *
55035810 GCAAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGAGAAACACTCTAAATTGGGTTTA
64 GCAAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTA
* * *
55035875 ATCTTTCTTTTCTTTAAATTAATATAAAGATGTTTTCTTTGTGTTCTTTGTTCTTGTTTACAACA
129 ATCTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACA
* *
55035940 ATTTTAGCTTAATTTTATTTAAGCCAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCAT
194 ATGTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCAT
* * * *
55036005 GATTATAATGTTTGTGCCTCAATCGATCATGTTTTTAATTAAAATCATGTCTGTATTTCATTCAT
259 GCTTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCAT
* * * * **
55036070 ACGTGATTGAAATACACCTAAATTAGCTGAGCGATACTAACTAGACAACGGCTAATGGACGCATA
324 ACGTGATTGAAATACACCTGAATTAGCTGAGTGATCCTAACCAGATGACGGCTAATGGACGCATA
* * *
55036135 ATTGAATTGTGCATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTA
389 ATTGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTA
* *
55036200 ACCAAGCTTTGTTATCTGCATAGTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATGG
454 ACCAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAG
55036265 AAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAAT
519 AAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAAT
55036330 AAGACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCA
584 AAGACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCA
55036395 TTCCCACGCG
649 TTCCCACGCG
*
55036405 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAACAAAGGAGC
1 TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
* * *
55036470 AAAGCAAAGGAACGAAGGAGTCCCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAAT
66 AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
* * *
55036535 ATTTCTTTTCTTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGCTCTTGTTTACAACAAT
131 CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACAAT
*
55036600 GTTAGCTTAATTTTTTTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
196 GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
* * * *
55036665 TTATAATGTTTATGGC-TCAATCGATCATGTTTTCAATTAAAATGAAGTCTGTATTTCGTTCAGA
261 TTATAATGTTTGT-GCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATA
* * * *
55036729 CGTTATTGAAATACACTTGAATTAGCTGA-TCGATCCTAACCAGACGACAGCTAATGGACGCATA
325 CGTGATTGAAATACACCTGAATTAGCTGAGT-GATCCTAACCAGATGACGGCTAATGGACGCATA
* *
55036793 ATTGAAATGTGCATGCTCAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTA
389 ATTGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTA
* *
55036858 ACCATGGTTTGTTATCTGCATAGTTTTTT-GATTTGTGTGATTAAATTAT
454 ACCAAGCTTTGTTATCTGCATA-TTTTTTGGATTTGTGTGATTAAATTAT
55036907 TTCAAACCTA
Statistics
Matches: 2364, Mismatches: 105, Indels: 58
0.94 0.04 0.02
Matches are distributed among these distances:
656 959 0.41
657 2 0.00
658 683 0.29
659 7 0.00
660 91 0.04
663 1 0.00
665 2 0.00
676 2 0.00
678 1 0.00
681 91 0.04
683 525 0.22
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (658 bp):
TTTAGCAATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGC
AAAGCAAAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGGGCCACTCTGAATTGGGTTTAAT
CTTTCTTTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTTACAACAAT
GTTAGCTTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGC
TTATAATGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATAC
GTGATTGAAATACACCTGAATTAGCTGAGTGATCCTAACCAGATGACGGCTAATGGACGCATAAT
TGAAATCTGCATGCTTAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTAAC
CAAGCTTTGTTATCTGCATATTTTTTGGATTTGTGTGATTAAATTATGGCCGACCACCCATAGAA
GATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACTATCTCTCTCTCCTCACCTATAAATAA
GACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTCTCTCTTTTTGTCTTAGCCTTTTCCATT
CCCACGCG
Found at i:55053212 original size:39 final size:40
Alignment explanation
Indices: 55053098--55053223 Score: 155
Period size: 40 Copynumber: 3.2 Consensus size: 40
55053088 CAAAAGGTCG
* * * *
55053098 AGCATTAGTGGCACTTTTTGAAAAATGCCGCTATAGATCG
1 AGCATTAGTGGCGCGTTTTGAAAAACGCCGCTATAGATCA
* * *
55053138 AGCATTAGCGGTGCGTTTTGAAAAACGTCGCTATAGATCA
1 AGCATTAGTGGCGCGTTTTGAAAAACGCCGCTATAGATCA
* * *
55053178 AGCATTAGTGGCGC-TTTTCAAAAACACCGTTATAGATCA
1 AGCATTAGTGGCGCGTTTTGAAAAACGCCGCTATAGATCA
55053217 AGCATTA
1 AGCATTA
55053224 CCAGTGCTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 28 0.38
40 45 0.62
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (40 bp):
AGCATTAGTGGCGCGTTTTGAAAAACGCCGCTATAGATCA
Found at i:55053233 original size:39 final size:39
Alignment explanation
Indices: 55053125--55053247 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
55053115 TTGAAAAATG
* * *
55053125 CCGCTATAGATCGAGCATTAGCGGTGCGTTTTGAAAAACG
1 CCGCTATAGATCAAGCATTAGCGGTGC-TTTTCAAAAACA
* * *
55053165 TCGCTATAGATCAAGCATTAGTGGCGCTTTTCAAAAACA
1 CCGCTATAGATCAAGCATTAGCGGTGCTTTTCAAAAACA
* * * *
55053204 CCGTTATAGATCAAGCATTACCAGTGCTTTTCGTAAAACA
1 CCGCTATAGATCAAGCATTAGCGGTGCTTTTC-AAAAACA
55053244 CCGC
1 CCGC
55053248 AAAAAAAGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 36 0.53
40 32 0.47
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (39 bp):
CCGCTATAGATCAAGCATTAGCGGTGCTTTTCAAAAACA
Found at i:55053388 original size:155 final size:149
Alignment explanation
Indices: 55053153--55053745 Score: 487
Period size: 155 Copynumber: 3.9 Consensus size: 149
55053143 TAGCGGTGCG
* * * * * * * *
55053153 TTTTGAAAAACGTCGCTATAGATCAAGCATTAGTGGCGCTT-TTCAAAAACACCGTTATAGATCA
1 TTTTAAAAAACGCCGCAATAGATCAAGAATTAGTGGCGCTTGTTGAAAAACGCCGCTATAGATCG
* * * * *
55053217 AGCATTA-CCAGTGCTTTTCGTAAAACACCGCAAAAAAAGTTAAGCAAAACACGTCATTTGTTGT
66 AGCATTAGCTA-CGCTTTTTG-AAAACGCCGC-AAAAAAGTTGAGCAAAACACGTCATTTGTTGT
55053281 TGAGCTTTAGTGGCGTTAGTGGCGCT
128 TGAGCTTTAGTGGC--TAG-GGC-CT
* ** *
55053307 TTTTAAAAAACGCCGCAATAGATCAAGCATTAGTGATGCTAT-TTGAAAAACGCCTCTATAGATC
1 TTTTAAAAAACGCCGCAATAGATCAAGAATTAGTGGCGCT-TGTTGAAAAACGCCGCTATAGATC
* * * *
55053371 GAGCATTAGCTACGCTTTTTGGAAAATGCCGCAAAAAATTTGAGCAAAATAGCGTCGTTTGTTGT
65 GAGCATTAGCTACGCTTTTT-GAAAACGCCGCAAAAAAGTTGAGCAAAACA-CGTCATTTGTTGT
55053436 TGAGCTTTAGTGGC-A----C-
128 TGAGCTTTAGTGGCTAGGGCCT
* * *
55053452 TTTTAAAAAATGCCGCAATAGATCAAGAATTAGTGGCGCTTGTCGAAAAACGCCGATATAGATCG
1 TTTTAAAAAACGCCGCAATAGATCAAGAATTAGTGGCGCTTGTTGAAAAACGCCGCTATAGATCG
* * * *
55053517 AGCATTAGCGGTA--TTTTTTGGAAACGCC-CTAAAAAGTTGAGCAAAATGACGTCATTT-TT-T
66 AGCATTAGC--TACGCTTTTTGAAAACGCCGCAAAAAAGTTGAGCAAAA-CACGTCATTTGTTGT
*
55053577 TTAGCTTTAGTGGCATAAGCGGCACTT
128 TGAGCTTTAGTGGC-T-AG-GGC-C-T
* * * * * *
55053604 TTTTAAGAAATGCCGCAATAGATCGAGAATTAGTGGTGCTTGTTGAAAAATGTCGCTATAGATCG
1 TTTTAAAAAACGCCGCAATAGATCAAGAATTAGTGGCGCTTGTTGAAAAACGCCGCTATAGATCG
* ** * * * ** * **
55053669 AGCATTAGCGACGCTTTTAACAAAACTCCGTAAAAAGGTTGAG-AAATTGATGTTGTTTGTTGTT
66 AGCATTAGCTACGCTTTT-TGAAAACGCCGCAAAAAAGTTGAGCAAA-ACACGTCATTTGTTGTT
55053733 GAGCTTTAGTGGC
129 GAGCTTTAGTGGC
55053746 ATTTTCAAAA
Statistics
Matches: 358, Mismatches: 55, Indels: 51
0.77 0.12 0.11
Matches are distributed among these distances:
141 14 0.04
142 2 0.01
143 23 0.06
144 10 0.03
145 70 0.20
146 1 0.00
147 2 0.01
150 2 0.01
152 72 0.20
153 16 0.04
154 63 0.18
155 80 0.22
156 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (149 bp):
TTTTAAAAAACGCCGCAATAGATCAAGAATTAGTGGCGCTTGTTGAAAAACGCCGCTATAGATCG
AGCATTAGCTACGCTTTTTGAAAACGCCGCAAAAAAGTTGAGCAAAACACGTCATTTGTTGTTGA
GCTTTAGTGGCTAGGGCCT
Found at i:55053946 original size:21 final size:21
Alignment explanation
Indices: 55053922--55053961 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55053912 TTAAAGTTTG
* *
55053922 TAGTTTGGGGTTTATTATTTA
1 TAGTTAGGGGTTTAGTATTTA
*
55053943 TAGTTAGGGTTTTAGTATT
1 TAGTTAGGGGTTTAGTATT
55053962 GTTCATGGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (21 bp):
TAGTTAGGGGTTTAGTATTTA
Found at i:55054168 original size:28 final size:28
Alignment explanation
Indices: 55054115--55054224 Score: 77
Period size: 28 Copynumber: 4.0 Consensus size: 28
55054105 TTAGGGTGTA
*
55054115 GGTTTATGATTTGGGGTTTAAGGTTTAG
1 GGTTTATGATTTAGGGTTTAAGGTTTAG
* *
55054143 GGTTTATGATTTAGTG-TTAAGAGTTTAA
1 GGTTTATGATTTAGGGTTTAAG-GTTTAG
* * * *
55054171 TGTTTA-CAGTTTAGGGTGT-AGGTTTATT
1 GGTTTATGA-TTTAGGGTTTAAGGTTTA-G
*
55054199 GG-TTAGTG-TTTAGGGTTTATGGTTTA
1 GGTTTA-TGATTTAGGGTTTAAGGTTTA
55054225 TGATTTAGGG
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
27 23 0.37
28 39 0.62
29 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (28 bp):
GGTTTATGATTTAGGGTTTAAGGTTTAG
Found at i:55054204 original size:20 final size:20
Alignment explanation
Indices: 55054181--55054222 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
55054171 TGTTTACAGT
55054181 TTAGGGTGTA-GGTTTATTGG
1 TTAGGGTGTAGGGTTTA-TGG
* *
55054201 TTAGTGTTTAGGGTTTATGG
1 TTAGGGTGTAGGGTTTATGG
55054221 TT
1 TT
55054223 TATGATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (20 bp):
TTAGGGTGTAGGGTTTATGG
Found at i:55054223 original size:14 final size:14
Alignment explanation
Indices: 55054115--55054224 Score: 57
Period size: 14 Copynumber: 7.9 Consensus size: 14
55054105 TTAGGGTGTA
* *
55054115 GGTTTATGATTTGG
1 GGTTTATGGTTTAG
*
55054129 GGTTTAAGGTTTAG
1 GGTTTATGGTTTAG
*
55054143 GGTTTATGATTTAG
1 GGTTTATGGTTTAG
* * *
55054157 TG-TTAAGAGTTTAA
1 GGTTTATG-GTTTAG
* **
55054171 TGTTTACAGTTTAG
1 GGTTTATGGTTTAG
* *
55054185 GGTGTA-GGTTTATT
1 GGTTTATGGTTTA-G
55054199 GG-TTA-GTGTTTAG
1 GGTTTATG-GTTTAG
55054212 GGTTTATGGTTTA
1 GGTTTATGGTTTA
55054225 TGATTTAGGG
Statistics
Matches: 72, Mismatches: 18, Indels: 12
0.71 0.18 0.12
Matches are distributed among these distances:
13 14 0.19
14 54 0.75
15 4 0.06
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (14 bp):
GGTTTATGGTTTAG
Found at i:55054706 original size:18 final size:18
Alignment explanation
Indices: 55054683--55054738 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
55054673 TCCCAACCCA
55054683 TCTGTTGCATCGCCCTCC
1 TCTGTTGCATCGCCCTCC
*
55054701 TCTGTTGCATCGCCTTCC
1 TCTGTTGCATCGCCCTCC
* *
55054719 TCTGCTGCATCGCGCTCC
1 TCTGTTGCATCGCCCTCC
55054737 TC
1 TC
55054739 GACCCGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.43, G:0.18, T:0.34
Consensus pattern (18 bp):
TCTGTTGCATCGCCCTCC
Found at i:55056469 original size:9 final size:9
Alignment explanation
Indices: 55056457--55056751 Score: 151
Period size: 9 Copynumber: 32.1 Consensus size: 9
55056447 AAATATATAT
55056457 CATAACTTA
1 CATAACTTA
55056466 CATAACTTA
1 CATAACTTA
*
55056475 CATAATTTA
1 CATAACTTA
55056484 CATAAC-TA
1 CATAACTTA
55056492 -A-AACTTA
1 CATAACTTA
* * *
55056499 TAAAATATATA
1 CATAA-CT-TA
55056510 TCATAACTTA
1 -CATAACTTA
55056520 CATAACTTA
1 CATAACTTA
*
55056529 CATAATTTA
1 CATAACTTA
55056538 CATAACTTA
1 CATAACTTA
*
55056547 CATAAATATA
1 CATAACT-TA
*
55056557 TATAA--TA
1 CATAACTTA
*
55056564 GCAAAACTTA
1 -CATAACTTA
55056574 CATAACTTA
1 CATAACTTA
*
55056583 CATAATTTA
1 CATAACTTA
55056592 CATAACTTTA
1 CATAAC-TTA
* *
55056602 AAGAA-TTAA
1 CATAACTT-A
* *
55056611 AAAAATCTTTGGA
1 CATAA-C-TT--A
*
55056624 TCTTAACTTA
1 -CATAACTTA
55056634 -ATAACTTA
1 CATAACTTA
*
55056642 TAT-A--TA
1 CATAACTTA
* * *
55056648 TATATCATA
1 CATAACTTA
*
55056657 TCATAACTTC
1 -CATAACTTA
*
55056667 CATAACTCA
1 CATAACTTA
*
55056676 CAAAACTTA
1 CATAACTTA
*
55056685 CGTAACTTA
1 CATAACTTA
55056694 CATAACTTA
1 CATAACTTA
* *
55056703 TATATATCATA
1 CATA-A-CTTA
55056714 TCATAACTTA
1 -CATAACTTA
*
55056724 CATAACTCA
1 CATAACTTA
55056733 CATAACTTA
1 CATAACTTA
55056742 CATAACTTA
1 CATAACTTA
55056751 C
1 C
55056752 GTAAGTTAAT
Statistics
Matches: 220, Mismatches: 41, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
6 8 0.04
7 5 0.02
8 16 0.07
9 143 0.65
10 27 0.12
11 7 0.03
12 10 0.05
13 2 0.01
14 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:55056518 original size:54 final size:54
Alignment explanation
Indices: 55056436--55056598 Score: 244
Period size: 54 Copynumber: 3.0 Consensus size: 54
55056426 TAAATATTTT
55056436 TAAAACTTATAAAATATATATCATAACTTACATAACTTACATAATTTACATAAC
1 TAAAACTTATAAAATATATATCATAACTTACATAACTTACATAATTTACATAAC
55056490 TAAAACTTATAAAATATATATCATAACTTACATAACTTACATAATTTACATAAC
1 TAAAACTTATAAAATATATATCATAACTTACATAACTTACATAATTTACATAAC
* *
55056544 T--TAC--ATAAATATATATAATAGCAAAACTTACATAACTTACATAATTTACATAAC
1 TAAAACTTATAAA-ATATAT-AT--CATAACTTACATAACTTACATAATTTACATAAC
55056598 T
1 T
55056599 TTAAAGAATT
Statistics
Matches: 103, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
50 5 0.05
51 6 0.06
52 4 0.04
54 88 0.85
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.35
Consensus pattern (54 bp):
TAAAACTTATAAAATATATATCATAACTTACATAACTTACATAATTTACATAAC
Found at i:55056718 original size:57 final size:57
Alignment explanation
Indices: 55056644--55056751 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
55056634 ATAACTTATA
* *
55056644 TATATATATCATATCATAACTTCCATAACTCACAAAACTTACGTAACTTACATAACT
1 TATATATATCATATCATAACTTACATAACTCACAAAACTTACATAACTTACATAACT
*
55056701 TATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTAC
1 TATATATATCATATCATAACTTACATAACTCACAAAACTTACATAACTTAC
55056752 GTAAGTTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (57 bp):
TATATATATCATATCATAACTTACATAACTCACAAAACTTACATAACTTACATAACT
Found at i:55062505 original size:43 final size:43
Alignment explanation
Indices: 55062457--55062589 Score: 123
Period size: 42 Copynumber: 3.1 Consensus size: 43
55062447 TAAACGCCAT
55062457 TAAAGAAT-AGTATTTTTAGCGGCGATTGTGATAAAAGAGCCGC
1 TAAAG-ATCAGTATTTTTAGCGGCGATTGTGATAAAAGAGCCGC
* * * * * *
55062500 TAAAGATCA-TGTTTTTAGCAGAGTTTGTGAAAAAAGTGCCGC
1 TAAAGATCAGTATTTTTAGCGGCGATTGTGATAAAAGAGCCGC
* *
55062542 TAAAGGTCATGCTA--TTTAGCGGC-ATTTGTGATAAAAGCGCCGC
1 TAAAGATCA-G-TATTTTTAGCGGCGA-TTGTGATAAAAGAGCCGC
55062585 TAAAG
1 TAAAG
55062590 GTCATGTTCT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
42 37 0.51
43 34 0.47
45 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (43 bp):
TAAAGATCAGTATTTTTAGCGGCGATTGTGATAAAAGAGCCGC
Found at i:55062640 original size:43 final size:43
Alignment explanation
Indices: 55062482--55062642 Score: 191
Period size: 43 Copynumber: 3.8 Consensus size: 43
55062472 TTAGCGGCGA
* *
55062482 TTGTGATAAAAGAGCCGCTAAAGATCATGTT-TTTAGCAGA-GT
1 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAG-AGACGT
* * * * * * *
55062524 TTGTGAAAAAAGTGCCGCTAAAGGTCATGCTATTTAGCGGCAT
1 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGAGACGT
*
55062567 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGACGT
1 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGAGACGT
* *
55062610 TTGTGATAATAGCGCCACTAAAGGTCATGTTCT
1 TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCT
55062643 ATAGCGGCGT
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 28 0.28
43 73 0.72
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
TTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGAGACGT
Found at i:55062649 original size:86 final size:85
Alignment explanation
Indices: 55062473--55062651 Score: 227
Period size: 86 Copynumber: 2.1 Consensus size: 85
55062463 ATAGTATTTT
*
55062473 TAGCGGCGATTGTGATAAAAGAGCCGCTAAAGATCATGTTTTTAGCAGAGTTTGTGAAAAAAGTG
1 TAGCGGCGATTGTGATAAAAGAGCCGCTAAAGATCATGTTTTTAGCAGAGTTTGTGAAAAAAGCG
* *
55062538 CCGCTAAAGGTCATGCTATT
66 CCACTAAAGGTCATGCTATA
* * * * *
55062558 TAGCGGC-ATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAG-TGACGTTTGTGATAATA
1 TAGCGGCGA-TTGTGATAAAAGAGCCGCTAAAGATCATGTT-TTTAGCAGA-GTTTGTGAAAAAA
* *
55062621 GCGCCACTAAAGGTCATGTTCTA
63 GCGCCACTAAAGGTCATGCTATA
55062644 TAGCGGCG
1 TAGCGGCG
55062652 TTATTTCACA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
84 1 0.01
85 38 0.47
86 41 0.51
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (85 bp):
TAGCGGCGATTGTGATAAAAGAGCCGCTAAAGATCATGTTTTTAGCAGAGTTTGTGAAAAAAGCG
CCACTAAAGGTCATGCTATA
Found at i:55062703 original size:15 final size:15
Alignment explanation
Indices: 55062683--55062712 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55062673 AAATTTAACA
55062683 GCGTTATCTATAGCG
1 GCGTTATCTATAGCG
55062698 GCGTTATCTATAGCG
1 GCGTTATCTATAGCG
55062713 TCGCTATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
GCGTTATCTATAGCG
Found at i:55065465 original size:11 final size:11
Alignment explanation
Indices: 55065451--55065509 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
55065441 CACCACTTCT
55065451 CCACCATAACA
1 CCACCATAACA
* *
55065462 CCACTATACCA
1 CCACCATAACA
* **
55065473 CCACCCTAGTA
1 CCACCATAACA
*
55065484 CCACTATAACA
1 CCACCATAACA
*
55065495 CCACCATAGCA
1 CCACCATAACA
55065506 CCAC
1 CCAC
55065510 TATATCACTA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.37, C:0.46, G:0.03, T:0.14
Consensus pattern (11 bp):
CCACCATAACA
Found at i:55065476 original size:22 final size:22
Alignment explanation
Indices: 55065451--55065513 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
55065441 CACCACTTCT
* *
55065451 CCACCATAACACCACTATACCA
1 CCACCATAGCACCACTATAACA
* *
55065473 CCACCCTAGTACCACTATAACA
1 CCACCATAGCACCACTATAACA
55065495 CCACCATAGCACCACTATA
1 CCACCATAGCACCACTATA
55065514 TCACTACCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.43, G:0.03, T:0.16
Consensus pattern (22 bp):
CCACCATAGCACCACTATAACA
Found at i:55071809 original size:18 final size:18
Alignment explanation
Indices: 55071786--55071821 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55071776 AAGAAAGGAA
55071786 CTCAAACCTCTATAATAT
1 CTCAAACCTCTATAATAT
55071804 CTCAAACCTCTATAATAT
1 CTCAAACCTCTATAATAT
55071822 GCTTTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCAAACCTCTATAATAT
Found at i:55074128 original size:40 final size:40
Alignment explanation
Indices: 55073945--55074114 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
55073935 TCCTCGTTCA
* * * * * *
55073945 AATGTCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55073984 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55074024 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55074064 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55074104 AAGGCCTTCGG
1 AATGCCTTCGG
55074115 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 33 0.28
40 85 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55074151 original size:80 final size:79
Alignment explanation
Indices: 55073950--55074167 Score: 206
Period size: 80 Copynumber: 2.7 Consensus size: 79
55073940 GTTCAAATGT
* * * * * *
55073950 CTTCGGGACATAGCCCGGTTTTAGTAACTCA-CACAATGCCTTCGGGACATAACCCGGATTTAAC
1 CTTCGGGACTTAACCCGGATATAATAACT-AGCACAATGCCTTCGGGACTTAACCCGGATTTAAC
* *
55074014 AACTCGCACGAATGC
65 AACTCGCACAAAGGC
* * **
55074029 CTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGT
1 CTTCGGGACTTAACCCGGATATAATAACTAGCAC-AATGCCTTCGGGACTTAACCCGGATTTAAC
*
55074094 ATCTCGCACAAAGGC
65 AACTCGCACAAAGGC
** * * * * *
55074109 CTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCAGGACTTAGCCCGGA
1 CTTCGGGA-CTTAACCCGGATATAATAAC-TAGCACAATGCCTTCGGGACTTAACCCGGA
55074168 CAGCATTCAA
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 31 0.27
80 79 0.69
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAACCCGGATATAATAACTAGCACAATGCCTTCGGGACTTAACCCGGATTTAACA
ACTCGCACAAAGGC
Done.