Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 137 of 199
Found at i:39935230 original size:30 final size:30
Alignment explanation
Indices: 39935196--39935292 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39935186 AGCTCACTCC
39935196 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
39935226 TAGCTCAACTTCAGCTTAGGAGTTTACCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
39935256 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
39935286 TAGCTCA
1 TAGCTCA
39935293 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39936222 original size:22 final size:20
Alignment explanation
Indices: 39936190--39936238 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
39936180 GTCGAATTTA
39936190 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
39936213 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
39936233 TGAACA
1 TGAACA
39936239 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:39938072 original size:40 final size:40
Alignment explanation
Indices: 39937975--39938183 Score: 244
Period size: 40 Copynumber: 5.3 Consensus size: 40
39937965 TCCTCGTTCA
* * *
39937975 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
39938013 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
39938053 AATGCTTTCGGGACCTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
39938093 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * * * *
39938133 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGG-ATTTAATAACTCGCACG
39938173 AATGCCTTCGG
1 AATGCCTTCGG
39938184 ATCTTAGTCC
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 22 0.14
39 12 0.08
40 115 0.75
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:39938196 original size:80 final size:80
Alignment explanation
Indices: 39937940--39938236 Score: 245
Period size: 80 Copynumber: 3.7 Consensus size: 80
39937930 AAATCACGTA
* ** * *
39937940 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG--TTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
39938001 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * * * *
39938017 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCTTTCGGGACCTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
39938080 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
39938097 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
39938161 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
39938177 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
39938237 CAGCATTCAA
Statistics
Matches: 179, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
76 1 0.01
77 12 0.07
78 30 0.17
79 21 0.12
80 102 0.57
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:39938196 original size:120 final size:119
Alignment explanation
Indices: 39937975--39938236 Score: 280
Period size: 120 Copynumber: 2.2 Consensus size: 119
39937965 TCCTCGTTCA
* *
39937975 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * * *
39938039 TAACAACTCGCACGAATGCTTTCGGGACCTAACCCGGATTTAATAAC-TCGCAC
66 TAACAACTCGCACAAATGCCTTCGGGACCTAACCCGGATATAATAACTTAGCAC
* * * * *
39938092 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
** * * ** * *
39938157 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAACAACTCGCACAAATGCCTTCGGGA-CCTAACCCGGATATAATAACTTAGCAC
*
39938213 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39938237 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
118 21 0.18
119 16 0.14
120 72 0.61
121 9 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAACAACTCGCACAAATGCCTTCGGGACCTAACCCGGATATAATAACTTAGCAC
Found at i:39938245 original size:41 final size:41
Alignment explanation
Indices: 39938168--39938245 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39938158 TTTGTATCTC
* * *
39938168 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39938209 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39938246 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39945631 original size:40 final size:40
Alignment explanation
Indices: 39945534--39945742 Score: 244
Period size: 40 Copynumber: 5.3 Consensus size: 40
39945524 TCCTCGTTCA
* * *
39945534 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
39945572 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
39945612 AATGCTTTCGGGACCTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
39945652 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * * * *
39945692 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGG-ATTTAATAACTCGCACG
39945732 AATGCCTTCGG
1 AATGCCTTCGG
39945743 ATCTTAGTCC
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 22 0.14
39 12 0.08
40 115 0.75
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:39945755 original size:80 final size:80
Alignment explanation
Indices: 39945499--39945795 Score: 245
Period size: 80 Copynumber: 3.7 Consensus size: 80
39945489 AAATCACGTA
* ** * *
39945499 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG--TTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
39945560 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * * * *
39945576 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCTTTCGGGACCTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
39945639 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
39945656 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
39945720 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
39945736 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
39945796 CAGCATTCAA
Statistics
Matches: 179, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
76 1 0.01
77 12 0.07
78 30 0.17
79 21 0.12
80 102 0.57
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:39945755 original size:120 final size:119
Alignment explanation
Indices: 39945534--39945795 Score: 280
Period size: 120 Copynumber: 2.2 Consensus size: 119
39945524 TCCTCGTTCA
* *
39945534 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * * *
39945598 TAACAACTCGCACGAATGCTTTCGGGACCTAACCCGGATTTAATAAC-TCGCAC
66 TAACAACTCGCACAAATGCCTTCGGGACCTAACCCGGATATAATAACTTAGCAC
* * * * *
39945651 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
** * * ** * *
39945716 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAACAACTCGCACAAATGCCTTCGGGA-CCTAACCCGGATATAATAACTTAGCAC
*
39945772 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39945796 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
118 21 0.18
119 16 0.14
120 72 0.61
121 9 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAACAACTCGCACAAATGCCTTCGGGACCTAACCCGGATATAATAACTTAGCAC
Found at i:39945804 original size:41 final size:41
Alignment explanation
Indices: 39945727--39945804 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39945717 TTTGTATCTC
* * *
39945727 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39945768 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39945805 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39962845 original size:15 final size:15
Alignment explanation
Indices: 39962821--39962850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39962811 GATTTCTTGT
39962821 TTTTCATTTATTTAC
1 TTTTCATTTATTTAC
*
39962836 TTTTCTTTTATTTAC
1 TTTTCATTTATTTAC
39962851 CTCCTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTATTTAC
Found at i:39965701 original size:29 final size:29
Alignment explanation
Indices: 39965654--39965943 Score: 185
Period size: 29 Copynumber: 9.9 Consensus size: 29
39965644 TTGATGGTCG
*
39965654 TCACCATCCCTTTTCATAATCGATAG-CC
1 TCACTATCCCTTTTCATAATCGATAGTCC
** * *
39965682 AAAGCTATCCCTTTTCATAATTCGATGGTCT
1 TCA-CTATCCCTTTTCATAA-TCGATAGTCC
* * * * *
39965713 TTACTATCCTTTTTCATAGTTGATGGTCC
1 TCACTATCCCTTTTCATAATCGATAGTCC
* * ** * *
39965742 TCACGATCCCTTTTCATAGTTAATGGTCG
1 TCACTATCCCTTTTCATAATCGATAGTCC
*
39965771 TCACCATCCCCTTTT-ATAATCGATAG-CC
1 TCACTAT-CCCTTTTCATAATCGATAGTCC
** * * *
39965799 GAAGCTATCCCTTTTCATAGTTCGATGGTCA
1 TCA-CTATCCCTTTTCATA-ATCGATAGTCC
*
39965830 TCACCATCCCTTTTCATAATCGATAG--C
1 TCACTATCCCTTTTCATAATCGATAGTCC
* * * *
39965857 TGAATCTATCCCTTTTCATAATTTGATGGTCG
1 T-CA-CTATCCCTTTTCATAA-TCGATAGTCC
* * * *
39965889 TCACCATCCCTTTTCATAGTTGATAGTCG
1 TCACTATCCCTTTTCATAATCGATAGTCC
*
39965918 TCACCATCCCTTTTCATAATCGATAG
1 TCACTATCCCTTTTCATAATCGATAG
39965944 CCAAAACTAT
Statistics
Matches: 204, Mismatches: 45, Indels: 25
0.74 0.16 0.09
Matches are distributed among these distances:
27 1 0.00
28 11 0.05
29 120 0.59
30 66 0.32
31 5 0.02
32 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (29 bp):
TCACTATCCCTTTTCATAATCGATAGTCC
Found at i:39965727 original size:59 final size:58
Alignment explanation
Indices: 39965642--39965937 Score: 319
Period size: 59 Copynumber: 5.1 Consensus size: 58
39965632 TGAAGTGGAA
*
39965642 AATTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCAT
1 AATTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCAT
* * * * * * * ** *
39965700 AATTCGATGGTCTTTACTATCCTTTTTCATAGTTGATGGTCCTCA-CGATCCCTTTTCAT
1 AATT-GATGGTCGTCACCATCCCTTTTCATAATCGATAG-CCGAAGCTATCCCTTTTCAT
* *
39965759 AGTTAATGGTCGTCACCATCCCCTTTT-ATAATCGATAGCCGAAGCTATCCCTTTTCAT
1 AATTGATGGTCGTCACCAT-CCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCAT
* * * *
39965817 AGTTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCTGAATCTATCCCTTTTCAT
1 AATT-GATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCAT
* * * * *
39965876 AATTTGATGGTCGTCACCATCCCTTTTCATAGTTGATAGTCGTCA-CCATCCCTTTTCAT
1 AA-TTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCG-AAGCTATCCCTTTTCAT
39965935 AAT
1 AAT
39965938 CGATAGCCAA
Statistics
Matches: 196, Mismatches: 34, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
57 3 0.02
58 48 0.24
59 139 0.71
60 6 0.03
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (58 bp):
AATTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCAT
Found at i:39965868 original size:88 final size:86
Alignment explanation
Indices: 39965644--39965963 Score: 313
Period size: 88 Copynumber: 3.6 Consensus size: 86
39965634 AAGTGGAAAA
**
39965644 TTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATG
1 TTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCTGAA-CTATCCCTTTTCATAATTCGATG
*** *
39965709 GTCTTTACTATCCTTTTTCATAG
65 G-CCGAACTATCCCTTTTCATAG
* * * ** * * *
39965732 TTGATGGTCCTCACGATCCCTTTTCATAGTTAAT-GGTCGTCACCATCCCCTTTT-ATAA-TCGA
1 TTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCT-G-AACTAT-CCCTTTTCATAATTCGA
*
39965794 TAGCCGAAGCTATCCCTTTTCATAG
63 TGGCCGAA-CTATCCCTTTTCATAG
* *
39965819 TTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCTGAATCTATCCCTTTTCATAATTTGAT
1 TT-GATGGTCGTCACCATCCCTTTTCATAATCGATAGCTGAA-CTATCCCTTTTCATAATTCGAT
* * *
39965884 GGTCGTCACCATCCCTTTTCATAG
64 GGCCG-AACTATCCCTTTTCATAG
* ** *
39965908 TTGATAGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAACTATCCATTTTCAT
1 TTGATGGTCGTCACCATCCCTTTTCATAATCGATAG-CTGAACTATCCCTTTTCAT
39965964 TAGTCGATAT
Statistics
Matches: 188, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
86 2 0.01
87 32 0.17
88 116 0.62
89 37 0.20
90 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (86 bp):
TTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCTGAACTATCCCTTTTCATAATTCGATGG
CCGAACTATCCCTTTTCATAG
Found at i:39965868 original size:117 final size:117
Alignment explanation
Indices: 39965647--39965906 Score: 346
Period size: 117 Copynumber: 2.2 Consensus size: 117
39965637 TGGAAAATTG
39965647 ATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGTC
1 ATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGTC
* * * * * * * *
39965712 TTTACTATCCTTTTTCATAGTTGATGGTCCTCACGATCCCTTTTCAT-AGTTA
66 ATCACCATCCCTTTTCATAATCGATAG-CCTAACGATCCCTTTTCATAAGTTA
* *
39965764 ATGGTCGTCACCATCCCCTTTT-ATAATCGATAGCCGAAGCTATCCCTTTTCATAGTTCGATGGT
1 ATGGTCGTCACCAT-CCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGT
* * *
39965828 CATCACCATCCCTTTTCATAATCGATAG-CTGAATCTATCCCTTTTCATAATTTG
65 CATCACCATCCCTTTTCATAATCGATAGCCT-AA-CGATCCCTTTTCATAAGTTA
39965882 ATGGTCGTCACCATCCCTTTTCATA
1 ATGGTCGTCACCATCCCTTTTCATA
39965907 GTTGATAGTC
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
115 2 0.02
116 1 0.01
117 95 0.76
118 27 0.22
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.38
Consensus pattern (117 bp):
ATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGTC
ATCACCATCCCTTTTCATAATCGATAGCCTAACGATCCCTTTTCATAAGTTA
Found at i:39965955 original size:29 final size:29
Alignment explanation
Indices: 39965652--39965978 Score: 178
Period size: 29 Copynumber: 11.1 Consensus size: 29
39965642 AATTGATGGT
*
39965652 CGTCACCATCCCTTTTCATAATCGATAGC
1 CGTCACTATCCCTTTTCATAATCGATAGC
** * *
39965681 C-AAAGCTATCCCTTTTCATAATTCGATGGT
1 CGTCA-CTATCCCTTTTCATAA-TCGATAGC
* * * * * *
39965711 CTTTACTATCCTTTTTCATAGTTGATGGTC
1 CGTCACTATCCCTTTTCATAATCGATAG-C
* * ** * *
39965741 C-TCACGATCCCTTTTCATAGTTAATGGT
1 CGTCACTATCCCTTTTCATAATCGATAGC
*
39965769 CGTCACCATCCCCTTTT-ATAATCGATAGC
1 CGTCACTAT-CCCTTTTCATAATCGATAGC
* * * *
39965798 CG-AAGCTATCCCTTTTCATAGTTCGATGGT
1 CGTCA-CTATCCCTTTTCATA-ATCGATAGC
* *
39965828 CATCACCATCCCTTTTCATAATCGATAGC
1 CGTCACTATCCCTTTTCATAATCGATAGC
* * * * *
39965857 TG-AATCTATCCCTTTTCATAATTTGATGGT
1 CGTCA-CTATCCCTTTTCATAA-TCGATAGC
* * * *
39965887 CGTCACCATCCCTTTTCATAGTTGATAGT
1 CGTCACTATCCCTTTTCATAATCGATAGC
*
39965916 CGTCACCATCCCTTTTCATAATCGATAGC
1 CGTCACTATCCCTTTTCATAATCGATAGC
*** * *
39965945 CAAAACTATCCATTTTCATTAGTCGATATGC
1 CGTCACTATCCCTTTTCA-TAATCGATA-GC
39965976 CGT
1 CGT
39965979 TGGATTTTTT
Statistics
Matches: 227, Mismatches: 56, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
28 11 0.05
29 132 0.58
30 78 0.34
31 6 0.03
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (29 bp):
CGTCACTATCCCTTTTCATAATCGATAGC
Found at i:39966046 original size:12 final size:12
Alignment explanation
Indices: 39966029--39966054 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39966019 TAGCATTAAA
39966029 AACATGCAATTT
1 AACATGCAATTT
39966041 AACATGCAATTT
1 AACATGCAATTT
39966053 AA
1 AA
39966055 ACATACGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AACATGCAATTT
Found at i:39970204 original size:27 final size:27
Alignment explanation
Indices: 39970163--39970496 Score: 386
Period size: 27 Copynumber: 12.4 Consensus size: 27
39970153 GTAATAGGCC
**
39970163 TAAAATGACCAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
39970190 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
39970217 TAAAATGACTAAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
** *
39970244 TAAAATGACCAAAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * * *
39970271 TAAAATAACCGATATCCCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
39970298 TAAAATGACTGAAATA-CCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
39970324 TAAAATGA-TCGAAATTCCCTTGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
* * * **
39970351 TAAAATAACCGAAATGCCCTTAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
39970378 TAAAATGACTGAAATACCC-CTGAAGGG
1 TAAAATGACTGAAATACCCTC-GAAGGG
*
39970405 TAAAATGACTGAAATACCTTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
39970432 TAAAATGACCGAAGTACCCCCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
39970459 TAAAATGATTGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
39970486 TAAAATAACTG
1 TAAAATGACTG
39970497 TTATACCCCA
Statistics
Matches: 264, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
25 1 0.00
26 23 0.09
27 239 0.91
28 1 0.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:39970298 original size:81 final size:81
Alignment explanation
Indices: 39970163--39970491 Score: 428
Period size: 81 Copynumber: 4.1 Consensus size: 81
39970153 GTAATAGGCC
* * * *
39970163 TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACTA
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATAACCGAAATCCCCTCGAAGGGTAAAATGACTG
39970228 AAATACCCCCAAAGGG
66 AAATACCCCCAAAGGG
* *
39970244 TAAAATGACCAAAATACCCCCGAAGGGTAAAATAACCGATATCCCCTCGAAGGGTAAAATGACTG
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATAACCGAAATCCCCTCGAAGGGTAAAATGACTG
* *
39970309 AAATA-CCTCGAAGGG
66 AAATACCCCCAAAGGG
* * * * * **
39970324 TAAAATGATCGAAATTCCCTTGAAGGGTAAAATAACCGAAATGCCCTTAAAGGGTAAAATGACTG
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATAACCGAAATCCCCTCGAAGGGTAAAATGACTG
**
39970389 AAATACCCCTGAAGGG
66 AAATACCCCCAAAGGG
** * * * *
39970405 TAAAATGACTGAAATACCTTCGAAGGGTAAAATGACCGAAGTACCCC-CGAAGGGTAAAATGATT
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATAACCGAAAT-CCCCTCGAAGGGTAAAATGACT
39970469 GAAATACCCCCAAAGGG
65 GAAATACCCCCAAAGGG
39970486 TAAAAT
1 TAAAAT
39970492 AACTGTTATA
Statistics
Matches: 214, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
80 69 0.32
81 142 0.66
82 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (81 bp):
TAAAATGACCAAAATACCCTCGAAGGGTAAAATAACCGAAATCCCCTCGAAGGGTAAAATGACTG
AAATACCCCCAAAGGG
Found at i:39970685 original size:27 final size:27
Alignment explanation
Indices: 39970640--39970714 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 27
39970630 ATAGGAGAAG
**
39970640 TATACTG-TACTGGTGGCTTTGCCACA
1 TATACTGTTACTGGCAGCTTTGCCACA
** *
39970666 TATACTGTTACTGGCAGCTTTGCTGCG
1 TATACTGTTACTGGCAGCTTTGCCACA
*
39970693 T-TACTGTTACTGGCAACTTTGC
1 TATACTGTTACTGGCAGCTTTGC
39970715 TGCATCACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 27 0.64
27 15 0.36
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
TATACTGTTACTGGCAGCTTTGCCACA
Found at i:39970697 original size:26 final size:26
Alignment explanation
Indices: 39970668--39970744 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
39970658 TTGCCACATA
39970668 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
39970694 TACTGTTACTGGCAACTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * * *
39970720 CACTATTTCTGGTAGCTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGCTGCG
39970745 ATTTTAGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:39976626 original size:27 final size:27
Alignment explanation
Indices: 39976595--39976769 Score: 181
Period size: 27 Copynumber: 6.4 Consensus size: 27
39976585 TAAATTGTAC
*
39976595 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39976622 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39976648 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39976676 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
39976704 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39976731 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39976758 AGCACTGAGTGT
1 AGCACTAAGTGT
39976770 ACGGGCTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39976656 original size:54 final size:55
Alignment explanation
Indices: 39976596--39976746 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 55
39976586 AAATTGTACA
*
39976596 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATG-TG
* * ** * *
39976650 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
* *
39976705 GCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGA
39976747 GTTGATTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 41 0.49
55 42 0.51
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (55 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:39976711 original size:82 final size:81
Alignment explanation
Indices: 39976596--39976751 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39976586 AAATTGTACA
* * * *
39976596 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39976660 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39976677 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39976742 TGCGAGTTGA
65 TGCGAATTGA
39976752 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39976763 original size:82 final size:81
Alignment explanation
Indices: 39976592--39976769 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 81
39976582 GATTAAATTG
* * * *
39976592 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39976657 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39976673 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39976737 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39976755 TATAGCACTGAGTGT
1 TACAGCACTAAGTGT
39976770 ACGGGCTCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.23
82 61 0.77
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39984870 original size:27 final size:27
Alignment explanation
Indices: 39984839--39985013 Score: 181
Period size: 27 Copynumber: 6.4 Consensus size: 27
39984829 TAAATTGTAC
*
39984839 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39984866 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39984892 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39984920 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
39984948 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39984975 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39985002 AGCACTGAGTGT
1 AGCACTAAGTGT
39985014 ACGGGCTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39984900 original size:54 final size:55
Alignment explanation
Indices: 39984840--39984990 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 55
39984830 AAATTGTACA
*
39984840 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATG-TG
* * ** * *
39984894 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
* *
39984949 GCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGA
39984991 GTTGATTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 41 0.49
55 42 0.51
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (55 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:39984955 original size:82 final size:81
Alignment explanation
Indices: 39984840--39984995 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39984830 AAATTGTACA
* * * *
39984840 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39984904 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39984921 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39984986 TGCGAGTTGA
65 TGCGAATTGA
39984996 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39985007 original size:82 final size:81
Alignment explanation
Indices: 39984836--39985013 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 81
39984826 GATTAAATTG
* * * *
39984836 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39984901 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39984917 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39984981 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39984999 TATAGCACTGAGTGT
1 TACAGCACTAAGTGT
39985014 ACGGGCTCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.23
82 61 0.77
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39986708 original size:29 final size:29
Alignment explanation
Indices: 39986662--39986976 Score: 265
Period size: 29 Copynumber: 10.8 Consensus size: 29
39986652 AATCACGATT
39986662 GTCGTCACCATCCCTTTTCATAGTTGATG
1 GTCGTCACCATCCCTTTTCATAGTTGATG
* * * *
39986691 GTTGTCACCATCCTTTTTCATAATTCAATG
1 GTCGTCACCATCCCTTTTCATAGTT-GATG
* * **
39986721 GTTGCCACCATCTTTTTTCATAGTTGATG
1 GTCGTCACCATCCCTTTTCATAGTTGATG
* *
39986750 GTCTTCCCCATCCCTTTTCATAGTTGATG
1 GTCGTCACCATCCCTTTTCATAGTTGATG
* * * * *
39986779 GTCGTCACCGTCCCTTTTTATAATCGATA
1 GTCGTCACCATCCCTTTTCATAGTTGATG
* * *
39986808 GTCG-AAGCTATCCCTTTTCATAATTCGATG
1 GTCGTCA-CCATCCCTTTTCATAGTT-GATG
* *
39986838 GTCATCACCATCCCTTTTCATGGTTGATG
1 GTCGTCACCATCCCTTTTCATAGTTGATG
* * ** *
39986867 GTCATCACCATCCCTTTTCATAATCAATA
1 GTCGTCACCATCCCTTTTCATAGTTGATG
*** * * *
39986896 G-CCAAAGCTATCCATTTTCATAATTCGATG
1 GTCGTCA-CCATCCCTTTTCATAGTT-GATG
** *
39986926 GTCGTCACCATATCTTTTCATAGTTGACG
1 GTCGTCACCATCCCTTTTCATAGTTGATG
39986955 GTCGTCACCATCCCTTTTCATA
1 GTCGTCACCATCCCTTTTCATA
39986977 ATCGATAGCC
Statistics
Matches: 223, Mismatches: 56, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.01
29 155 0.70
30 62 0.28
31 3 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (29 bp):
GTCGTCACCATCCCTTTTCATAGTTGATG
Found at i:39986838 original size:88 final size:88
Alignment explanation
Indices: 39986657--39987004 Score: 396
Period size: 88 Copynumber: 4.0 Consensus size: 88
39986647 AGTGGAATCA
* * * * *
39986657 CGATTGTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCCTTTTTCATAATTCAATGG
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAA-TCAATAG
* * * ** *
39986722 TTGCCA-CCATCTTTTTTCATAGTT
65 TCG-AAGCTATCCATTTTCATAATT
* * * * *
39986746 -GATGGTCTTCCCCATCCCTTTTCATAGTTGATGGTCGTCACCGTCCCTTTTTATAATCGATAGT
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGT
*
39986810 CGAAGCTATCCCTTTTCATAATT
66 CGAAGCTATCCATTTTCATAATT
* * *
39986833 CGATGGTCATCACCATCCCTTTTCATGGTTGATGGTCATCACCATCCCTTTTCATAATCAATAGC
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGT
*
39986898 CAAAGCTATCCATTTTCATAATT
66 CGAAGCTATCCATTTTCATAATT
* ** * *
39986921 CGATGGTCGTCACCATATCTTTTCATAGTTGACGGTCGTCACCATCCCTTTTCATAATCGATAG-
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGT
* *
39986985 CCACAACTATCCATTTTCAT
66 CGA-AGCTATCCATTTTCAT
39987005 TGGTCGATGA
Statistics
Matches: 222, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
86 1 0.00
87 23 0.10
88 198 0.89
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (88 bp):
CGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCAATAGT
CGAAGCTATCCATTTTCATAATT
Found at i:39986976 original size:59 final size:58
Alignment explanation
Indices: 39986662--39986978 Score: 244
Period size: 59 Copynumber: 5.4 Consensus size: 58
39986652 AATCACGATT
* * *
39986662 GTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCAT-CCTTTTTCATAATTCAATG
1 GTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATACC-TTTTCATAATT-GATG
* * ** * * * * *
39986721 GTTGCCACCATCTTTTTTCATAGTTGATGGTCTTCCCCATCCCTTTTCATAGTTGATG
1 GTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATACCTTTTCATAATTGATG
* * * * * * *
39986779 GTCGTCACCGTCCCTTTTTATAATCGATAGTCG-AAGCTATCCCTTTTCATAATTCGATG
1 GTCGTCACCATCCCTTTTCATAATTGATGGTCGTCA-CCATACCTTTTCATAATT-GATG
* ** * * ** *
39986838 GTCATCACCATCCCTTTTCATGGTTGATGGTCATCACCATCCCTTTTCATAATCAATA
1 GTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATACCTTTTCATAATTGATG
*** * * * * *
39986896 G-CCAAAGCTATCCATTTTCATAATTCGATGGTCGTCACCATATCTTTTCATAGTTGACG
1 GTCGTCA-CCATCCCTTTTCATAATT-GATGGTCGTCACCATACCTTTTCATAATTGATG
39986955 GTCGTCACCATCCCTTTTCATAAT
1 GTCGTCACCATCCCTTTTCATAAT
39986979 CGATAGCCAC
Statistics
Matches: 195, Mismatches: 56, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
57 2 0.01
58 59 0.30
59 129 0.66
60 5 0.03
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (58 bp):
GTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATACCTTTTCATAATTGATG
Found at i:39989220 original size:36 final size:36
Alignment explanation
Indices: 39989165--39989238 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
39989155 AATAAACTCT
* * * *
39989165 ATTCAGTTTAGCAGTCTTTCATATCTATTCTGATTG
1 ATTCAGTTCAGCAGCCTTTCAAATCTATTCTGACTG
*
39989201 ATTCAGTTCAGTAGCCTTTCAAATCTATTCTGACTG
1 ATTCAGTTCAGCAGCCTTTCAAATCTATTCTGACTG
39989237 AT
1 AT
39989239 GCACTTCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
ATTCAGTTCAGCAGCCTTTCAAATCTATTCTGACTG
Found at i:39989988 original size:27 final size:27
Alignment explanation
Indices: 39989954--39990008 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
39989944 ATTAACATGA
39989954 AATCATATAAAATATGTAAAAAAAATC
1 AATCATATAAAATATGTAAAAAAAATC
39989981 AATCATATAAAATATGTAAAAAAAATC
1 AATCATATAAAATATGTAAAAAAAATC
39990008 A
1 A
39990009 TGTAATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (27 bp):
AATCATATAAAATATGTAAAAAAAATC
Found at i:39992081 original size:87 final size:87
Alignment explanation
Indices: 39991986--39992235 Score: 277
Period size: 87 Copynumber: 2.9 Consensus size: 87
39991976 CGATCAATGA
* * ** *
39991986 AAAAGGGATGGTTTTGACCATCGTA-TATAAAAAGGGATAGTTTCAACTATCGACTATGAAAAGG
1 AAAAGGGATGGTTTCGACCATCG-ACTATAAAAAGGGATGGTGACAACCATCGACTATGAAAAGG
*
39992050 GATAGTTTCGACTATCGACTATG
65 GATAGTTTCGACTATAGACTATG
** * * * * *
39992073 AAAAGGGATGGTGGCGACCATCAACTATGAAAAGGGATGGTGACCACCAGCAACTATGAAAAGGG
1 AAAAGGGATGGTTTCGACCATCGACTATAAAAAGGGATGGTGACAACCATCGACTATGAAAAGGG
** **
39992138 ATTTTTTTTACTATAGACTATG
66 ATAGTTTCGACTATAGACTATG
* * * *
39992160 AAAAGGGATAGTTTCAACTATCGACTATAAAAAGGGATGGTGACAACCATCGAATATGAAAAGGG
1 AAAAGGGATGGTTTCGACCATCGACTATAAAAAGGGATGGTGACAACCATCGACTATGAAAAGGG
* *
39992225 ATGGTTACGAC
66 ATAGTTTCGAC
39992236 CATTTTTAGC
Statistics
Matches: 129, Mismatches: 33, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
86 1 0.01
87 128 0.99
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (87 bp):
AAAAGGGATGGTTTCGACCATCGACTATAAAAAGGGATGGTGACAACCATCGACTATGAAAAGGG
ATAGTTTCGACTATAGACTATG
Found at i:39992206 original size:29 final size:29
Alignment explanation
Indices: 39991986--39992230 Score: 213
Period size: 29 Copynumber: 8.4 Consensus size: 29
39991976 CGATCAATGA
** * *
39991986 AAAAGGGATGGTTTTGACCATCGTA-TATA
1 AAAAGGGATGGTTTCAACTATCG-ACTATG
*
39992015 AAAAGGGATAGTTTCAACTATCGACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
* *
39992044 AAAAGGGATAGTTTCGACTATCGACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * * *
39992073 AAAAGGGATGGTGGCGACCATCAACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * * * *
39992102 AAAAGGGATGGTGACCACCAGCAACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** ** *
39992131 AAAAGGGATTTTTTTTACTATAGACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
* *
39992160 AAAAGGGATAGTTTCAACTATCGACTATA
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * *
39992189 AAAAGGGATGGTGACAACCATCGAATATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
39992218 AAAAGGGATGGTT
1 AAAAGGGATGGTT
39992231 ACGACCATTT
Statistics
Matches: 178, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
28 1 0.01
29 177 0.99
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (29 bp):
AAAAGGGATGGTTTCAACTATCGACTATG
Found at i:39993225 original size:12 final size:12
Alignment explanation
Indices: 39993208--39993255 Score: 96
Period size: 12 Copynumber: 4.0 Consensus size: 12
39993198 AGTTAAACGA
39993208 CCTAGCACACGG
1 CCTAGCACACGG
39993220 CCTAGCACACGG
1 CCTAGCACACGG
39993232 CCTAGCACACGG
1 CCTAGCACACGG
39993244 CCTAGCACACGG
1 CCTAGCACACGG
39993256 GCGTGTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.42, G:0.25, T:0.08
Consensus pattern (12 bp):
CCTAGCACACGG
Found at i:39997419 original size:7 final size:7
Alignment explanation
Indices: 39997407--39997454 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
39997397 AAGATATTAG
39997407 TAAATGT
1 TAAATGT
39997414 TAAATGT
1 TAAATGT
*
39997421 TAAATAT
1 TAAATGT
39997428 TAAATGT
1 TAAATGT
*
39997435 TCAATGT
1 TAAATGT
*
39997442 TCAATGT
1 TAAATGT
*
39997449 TCAATG
1 TAAATG
39997455 AATTACTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (7 bp):
TAAATGT
Found at i:40004539 original size:36 final size:36
Alignment explanation
Indices: 40004492--40004565 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
40004482 AATAAACTCT
* *
40004492 ATTCAGTTCAGCAGCCTTTCGGATCTATTCTGACTG
1 ATTCAGTTCAGCACCCTTTCGGATCCATTCTGACTG
*
40004528 ATTCAGTTCAGCACCCTTTTGGATCCATTCTGACTG
1 ATTCAGTTCAGCACCCTTTCGGATCCATTCTGACTG
40004564 AT
1 AT
40004566 GCACTCCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (36 bp):
ATTCAGTTCAGCACCCTTTCGGATCCATTCTGACTG
Found at i:40004740 original size:21 final size:21
Alignment explanation
Indices: 40004694--40004741 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
40004684 CAATGGAAGG
*
40004694 AAAAGGGAAATGGAATGTAAA
1 AAAATGGAAATGGAATGTAAA
*
40004715 AAAATGGAAATGGAATGTAGA
1 AAAATGGAAATGGAATGTAAA
40004736 AAAATG
1 AAAATG
40004742 CTAATGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (21 bp):
AAAATGGAAATGGAATGTAAA
Found at i:40004747 original size:21 final size:21
Alignment explanation
Indices: 40004701--40004747 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40004691 AGGAAAAGGG
*
40004701 AAATGGAATGTAAAAAAATGG
1 AAATGGAATGTAAAAAAATGC
*
40004722 AAATGGAATGTAGAAAAATGC
1 AAATGGAATGTAAAAAAATGC
*
40004743 TAATG
1 AAATG
40004748 AGAGAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATGGAATGTAAAAAAATGC
Found at i:40010790 original size:119 final size:120
Alignment explanation
Indices: 40010608--40010830 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
40010598 TACTCGTTCA
*
40010608 AATGCCTTCAGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
40010673 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
40010728 AATGCCTTC-GGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCAGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
40010790 ATATGGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
40010831 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 69 0.77
120 17 0.19
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:40010830 original size:40 final size:40
Alignment explanation
Indices: 40010587--40010830 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
40010577 CGGAATTTAA
** * *
40010587 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40010627 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40010667 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40010707 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40010746 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
40010786 CCGGATATGGTAACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40010826 CCGGA
1 CCGGA
40010831 CATCATTCGA
Statistics
Matches: 179, Mismatches: 18, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.18
40 133 0.74
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40012026 original size:56 final size:56
Alignment explanation
Indices: 40011959--40012078 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40011949 TATTAGTTTA
40011959 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
40012015 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
40012071 TTGCCCAT
1 TTGCCCAT
40012079 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:40018207 original size:47 final size:46
Alignment explanation
Indices: 40018111--40018208 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 46
40018101 GTCGAATTGG
* * * *
40018111 ATATATGTGGTCAAGCCACTATATTGCAGCCAAGCTACCAGAACAA
1 ATATATGTGATCAAGCCACTATATTGCAGACAAACTACCAGAAAAA
* * *
40018157 ATATATGTGATCGAGCCACTATAATTGCAGACAAACTGCTAGAAAAA
1 ATATATGTGATCAAGCCACTAT-ATTGCAGACAAACTACCAGAAAAA
40018204 ATATA
1 ATATA
40018209 GATGAACCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 20 0.45
47 24 0.55
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (46 bp):
ATATATGTGATCAAGCCACTATATTGCAGACAAACTACCAGAAAAA
Found at i:40021777 original size:3 final size:3
Alignment explanation
Indices: 40021771--40021802 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40021761 CTTGTGTTCT
40021771 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40021803 GCATATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40031426 original size:10 final size:11
Alignment explanation
Indices: 40031411--40031435 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40031401 AGACTAATAA
40031411 TTTTTTTAATT
1 TTTTTTTAATT
40031422 TTTTTTTAATT
1 TTTTTTTAATT
40031433 TTT
1 TTT
40031436 AGAGTTAGGA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:40035367 original size:153 final size:153
Alignment explanation
Indices: 40035045--40038571 Score: 4427
Period size: 153 Copynumber: 23.1 Consensus size: 153
40035035 AAGATGTATT
* * *
40035045 TTTGAGAACTTATAGCTTAACCCAATCGATTCATGCAACTAGCTAATCAATATAGCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * * * * * * *
40035110 TCCCCTAAATCTTAATTTGTTTCC-CTTTTATTAAAAAAATAAACCATCGCCAACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
40035174 TTAATGTGCTGCTAATATGCGTC
131 TTAATGTGCTGCTAATATGCGTC
* * * *
40035197 TTTGAGAACTTACAGCTTAACTCGATCGATACATGCAACTAGCTAATAAATGTAGCAATTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* *
40035262 TCCCCTTAATCTCAAAGTATTACCTCTTTTATTAAAAATATAAACCATCACCCACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* ** * *
40035327 TTAATGTACTATTAATATTCATC
131 TTAATGTGCTGCTAATATGCGTC
* * * * * *
40035350 TTTGAGAATTTATAGCTTAGCTCGATTGATTCATGCAACTAGCTAATAAATATTGCAATTGAACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * * ** *
40035415 TCCCTTTCATCTCAAATTATTTCCTCTTTTATTAAAAATATAAACCATTGCCAACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* * * *
40035480 TTAATGTGCCGTTAATATTCATC
131 TTAATGTGCTGCTAATATGCGTC
* * * * *
40035503 TTTGAGAACTTATAGCTTAAATCGATCGATTC-T-C-AGTTGCTTAATAAATA-AGCAATTGAAC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGC-TAATAAATATAGCAGTTGGAC
* * *
40035564 TTCCCCTTATTCTGAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCCAC-AAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
* * * *
40035628 ATTAACGTGCTTCTAGTATGCGTA
130 ATTAATGTGCTGCTAATATGCGTC
* * * *
40035652 TTTGAGAACTTATAGCTTAACTTGATCGATTCATGCAACTAACTAATAAATATAGTAATTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * * * * *
40035717 T-CCCTTAATCTCAAATTATTACCACTTTTATTAAAAATGTAAACTATC-GCAACAAAATTAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
*
40035780 TTAAAGTGCTGCTAATATGCGTC
131 TTAATGTGCTGCTAATATGCGTC
* ** * * * * *
40035803 TTTGAGAACTTATAACTTAACTTAATTGATTCATGCAAATAGCTAATAAATATTGCAATT-AATC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGA-C
* * * *
40035867 TTCCCCTTAATCTCAAATTATTTCCTCTTTTATTAAAAATATAAACTATCGCCAACAAAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
* * **
40035932 ATTAATGTGCTTCTAACATGCACC
130 ATTAATGTGCTGCTAATATGCGTC
* *
40035956 TCTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGTAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
*
40036021 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACTGACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
40036086 TTAATGTGCTGCTAATATGCGTC
131 TTAATGTGCTGCTAATATGCGTC
* *
40036109 TTTGAGAACTTATAGCTTAACTCAATCGATTCATGCAACTAGCTAATAAATATAACAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * *
40036174 TCCCCTTAATCTCAAAGTATTACCTCTTTCATTAAAAATATAAACCATCACCCACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* * *
40036239 TTAATGTACTACTAATATACGTC
131 TTAATGTGCTGCTAATATGCGTC
* * * * * *
40036262 TTTAAGAACTTATAGCTTAACTTGATCGATCCATACAACTAGTTAATAAATATATCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* *** *
40036327 TCCCCTTAATCTCAAATTATTTCCTCTTTTATTAAAAATATAAATTGTCGA-TGACAAAATCAAG
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATC-ACCGACAAAATCAAG
* * * *
40036391 AGTAATGTGTTGTTAATATGCATC
130 ATTAATGTGCTGCTAATATGCGTC
*
40036415 TTTGAGAACTTAAAGCTTAACTCGATCGATTCATGCAACTATAGCTAATAAATATAGCAGTTGGA
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAAC--TAGCTAATAAATATAGCAGTTGGA
*
40036480 CTTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCCACAAAATCAA
64 CTTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAA
* * *
40036545 GATTAATGTACTACTAATATGCGTA
129 GATTAATGTGCTGCTAATATGCGTC
* * *
40036570 TTTGAGAAAC-TATAGCTTAAATCGATCGATTCATGCATCTAGCTTATAAATATAGCAGTTGGAC
1 TTTGAG-AACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGAC
* *
40036634 TTCCCCTTAATCTCAATTTATTACCTCTTTTATTAAAAATATAAACCATCGA-CGATAAAAATCA
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATC-ACCGA-CAAAATCA
** *
40036698 AGATTAATGTGCTGCTTTTATGCATC
128 AGATTAATGTGCTGCTAATATGCGTC
* ** *
40036724 TTTGAGAACTTATAGCTTAACTCGAT-TAGTTCATGCATTTAGCTAATAAATATAGTAGTTGGAC
1 TTTGAGAACTTATAGCTTAACTCGATCGA-TTCATGCAACTAGCTAATAAATATAGCAGTTGGAC
* *
40036788 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATAAATAAATCATCGCCGACAAAATCA
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAAT--ATAAACCATCACCGACAAAATCA
* *
40036853 AGATTAAGGTGTTGCTAATATGCGTC
128 AGATTAATGTGCTGCTAATATGCGTC
* * * * *
40036879 TTTGAGAACCTATAGCTTAACTCGACCGATACATGTAGCTAGCTAATAAATATAGCAGTTGGAC-
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* *
40036943 TCCCCTTTAATCTCAAAGTATTACCTCTTTTATTAAAAATATAAACCATCACCCACAAAATCAAG
66 TCCCC-TTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
**
40037008 ATTAATGT--AACTAATATGCGTC
130 ATTAATGTGCTGCTAATATGCGTC
* *
40037030 TTTGAGAACTTATAGCTTAACTCAATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGGCT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* *
40037095 TCCCCTTAATCTCAAAGTATTACCTCTTTTATTAAAAATATAAACCATCACTGACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* *
40037160 TTAATGTGTTGCTAATATGCATC
131 TTAATGTGCTGCTAATATGCGTC
* * * * * *
40037183 TTTGAGCACTTATAGCTTAACTTGATTGATTCATGCAATTAGCTAAAAAAATATAGCAGTTGCAC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCT-AATAAATATAGCAGTTGGAC
* * * *
40037248 TTTCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAAAAATAAACCATCGCCAACAAAATCAA
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATT-AAAAATATAAACCATCACCGACAAAATCAA
* *
40037313 GATTAATGTGCTACTAATATGCATC
129 GATTAATGTGCTGCTAATATGCGTC
* * * * *
40037338 TTTGAGAACTTATAGCTTAACTCGATTGATACATGCAACTAACTAGTAAATATAGTAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
*
40037403 TCCCCTTAATCTCAAATTATTACCTCTTTTATT-AAAA-A-AAACCATCACCCACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* * * * *
40037465 TTAATGTACTACTAATGTTCCTC
131 TTAATGTGCTGCTAATATGCGTC
*
40037488 TTTGAGAAAC-TATAGCTTAACTCGATCGATTCATGCATCTAGCTAATAAATATAGCAGTTGGAC
1 TTTGAG-AACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGAC
* * *
40037552 TTCCCCTTAATCTCAATTTTTTACCTCTTTTATTAAAAATATAAACCATCAACGACAAAAATCAA
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGAC-AAAATCAA
* * **
40037617 AATTAGTGTGCTGCTAATATGAATC
129 GATTAATGTGCTGCTAATATGCGTC
* * *
40037642 TTTAAGAACTTATAGCTTAACTTGATCGATTCATGCATCTAGCTAATAAATATAGCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* ** * *
40037707 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAAAAATAAACCATTGCAGACAAAATCAAT
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATT-AAAAATATAAACCATCACCGACAAAATCAAG
* * * *
40037772 ATCAAGGTGTTGTTAATATGCGTC
130 ATTAATGTGCTGCTAATATGCGTC
* * * * *
40037796 TTTGAGAACTTATAACTTAACTCGA-CTGATACATGTAGCTAGCTAATAACTATAGCAGTTGGAC
1 TTTGAGAACTTATAGCTTAACTCGATC-GATTCATGCAACTAGCTAATAAATATAGCAGTTGGAC
* * * * *
40037860 TTCCCCTTAATCTCAAAGTATTACCTCTCTTATTAAAAATATAAACCATCGCGGTCAAAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
40037925 ATTAATGTGCTGCTAATATGCGTC
130 ATTAATGTGCTGCTAATATGCGTC
* * * *
40037949 TTTGAGAACTTACAGCTTAACTCGATTGATTCATGCAACTAGCTAATAAATATAGTAGTTGGATT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * *
40038014 TCCCCTTTATCTCAAATTTTTACCTCTTTTATTAAAAATATAAACCATCACCGAGAAAATCAAG-
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
40038078 TCTAATGTGCTGCTAATA-GTCGTC
131 T-TAATGTGCTGCTAATATG-CGTC
* * * * ** * *
40038102 TTTGAGAATTTATAGCTTAAATCGATCGATTCTTACAACTATTTAATAAATA-ATGCAATTGAAC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATA-GCAGTTGGAC
* * * *
40038166 TTCCCCTTAATATGAAATTATTACCTCTTTTGTTAAAAATATAAACCATCACCGTCAAAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
40038231 ATTAATGTGCTGCTAATATGCGTC
130 ATTAATGTGCTGCTAATATGCGTC
* * * *
40038255 TTTGAGAAATTATAACTTAACTCGATCGATTAATACAACTAGCTAATAAATATAGCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
* * *
40038320 T-CCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATCTAAACCATCACCGACAAATTCAATA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* * * ** *
40038384 TCAATGTGCTGCAAATGTTTGTA
131 TTAATGTGCTGCTAATATGCGTC
* * * * *
40038407 TTTGAGAACTTATAG-TATAACTCGATCCATTC-TG--ACTACCTAATAAGTATATCATTTGAAC
1 TTTGAGAACTTATAGCT-TAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTG---
* * ** * * *
40038468 CACTT-CCCTTAATATCAAATTACGA-CTTTTTTATTAAAAATATAAACTATCACCGGCAAAATC
62 GACTTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATC
* * *
40038531 AAGATTAATATGC-GACTAATATTCATC
127 AAGATTAATGTGCTG-CTAATATGCGTC
* *
40038558 TTTAAAAACTTATA
1 TTTGAGAACTTATA
40038572 ATTTAATTTA
Statistics
Matches: 2929, Mismatches: 396, Indels: 101
0.85 0.12 0.03
Matches are distributed among these distances:
149 74 0.03
150 195 0.07
151 351 0.12
152 268 0.09
153 1220 0.42
154 456 0.16
155 349 0.12
156 16 0.01
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (153 bp):
TTTGAGAACTTATAGCTTAACTCGATCGATTCATGCAACTAGCTAATAAATATAGCAGTTGGACT
TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
TTAATGTGCTGCTAATATGCGTC
Found at i:40039815 original size:3 final size:3
Alignment explanation
Indices: 40039809--40039870 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
40039799 ACCAGATCAG
* * * * * *
40039809 GAT GAT GAT GAT GAA GAT GAT GAT GAT GAC GAC GAT GAT GGT GCT GCT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
40039857 GCT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
40039871 GAACGATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:40043346 original size:135 final size:132
Alignment explanation
Indices: 40043183--40043448 Score: 396
Period size: 135 Copynumber: 2.0 Consensus size: 132
40043173 TTATTGAATT
40043183 CATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTAC
1 CATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTAC
*
40043248 GTGTGATTTTTTTTATCT-AAGCATT-TTTGTCGTTTATACGTTAATTTCTTATATAACATTTAC
66 GTGTGA-TTTTTTTATCTGAA-CATTATTT-TCGTTTATACCTTAATTTC-T-TATAACATTTAC
40043311 ATGTGAC
126 ATGTGAC
* *
40043318 CATTGAGTC-ACATCAATAATCAGT-TAACTTTTATCGTTTATATCTTCATTTATTATAACACTT
1 CATTGAGTCGA-ATCAATAATCA-TATAACTTTTATCGCTTATATCTTCATTTATCATAACACTT
**
40043381 GTGTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACATG
64 ACGTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACATG
40043446 TGA
129 TGA
40043449 TCTTTTTACC
Statistics
Matches: 122, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
132 18 0.15
133 1 0.01
134 34 0.28
135 68 0.56
136 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (132 bp):
CATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTAC
GTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACATGTG
AC
Found at i:40049040 original size:18 final size:18
Alignment explanation
Indices: 40049009--40049063 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
40048999 TCATCAGTCG
* *
40049009 CATCTTTTTTCTCATCTA
1 CATCTTCTTCCTCATCTA
* **
40049027 CATCTTCTTCCTCAGCCG
1 CATCTTCTTCCTCATCTA
*
40049045 CATATTCTTCCTCATCTA
1 CATCTTCTTCCTCATCTA
40049063 C
1 C
40049064 GCCTTCATTA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.16, C:0.36, G:0.04, T:0.44
Consensus pattern (18 bp):
CATCTTCTTCCTCATCTA
Found at i:40051620 original size:15 final size:15
Alignment explanation
Indices: 40051600--40051633 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40051590 ACCCTTTTTA
40051600 AAAAACCCAAAACCT
1 AAAAACCCAAAACCT
*
40051615 AAAAACCCAAAACTT
1 AAAAACCCAAAACCT
40051630 AAAA
1 AAAA
40051634 GTATTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.26, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAACCCAAAACCT
Found at i:40051642 original size:23 final size:23
Alignment explanation
Indices: 40051616--40051665 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
40051606 CCAAAACCTA
**
40051616 AAAACCCAAAACTTAAAAGTATT
1 AAAACCCAAAACTTAAAAACATT
**
40051639 AAAACCTTAAACTTAAAAACATT
1 AAAACCCAAAACTTAAAAACATT
40051662 AAAA
1 AAAA
40051666 ATCCTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAACCCAAAACTTAAAAACATT
Found at i:40071308 original size:43 final size:43
Alignment explanation
Indices: 40071261--40071416 Score: 156
Period size: 43 Copynumber: 3.6 Consensus size: 43
40071251 TCCGATATGT
*
40071261 GATTTCGTGTAAGACCACGTCTGGGACATTGGCCTCGATTTAA
1 GATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATTTAA
* * * * * *
40071304 GATTTACGTGTAAGATCATGTCTAGGACATCGGCATCG-TATAC
1 GATTT-CGTGTAAGACCACGTCTGGGACATTGGCATCGATTTAA
* * *
40071347 GATTTCGTGTAAGACC-CTGTCTGGGATAGTGGCATCGATATT-T
1 GATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTAA
* *
40071390 GATTACATGTAAGACCACGTCTGGGAC
1 GATTTCGTGTAAGACCACGTCTGGGAC
40071417 GCTGGCATTG
Statistics
Matches: 90, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
42 25 0.28
43 36 0.40
44 29 0.32
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATTTAA
Found at i:40074275 original size:18 final size:18
Alignment explanation
Indices: 40074252--40074290 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
40074242 AATGCAGAGT
40074252 GATAGTTTTGAAAATTTC
1 GATAGTTTTGAAAATTTC
40074270 GATAGTTTTGAAAATTTC
1 GATAGTTTTGAAAATTTC
40074288 GAT
1 GAT
40074291 CCCTCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (18 bp):
GATAGTTTTGAAAATTTC
Found at i:40075075 original size:36 final size:34
Alignment explanation
Indices: 40075034--40075194 Score: 169
Period size: 36 Copynumber: 4.4 Consensus size: 34
40075024 ATCCACGGTT
* *
40075034 TTATGTTAGTTATGATATGATATATATTTGTGTAA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A
40075069 GTTATGTAAGTTATGTAAGTTATTGTATGATATATATTTATGTA
1 -TTATGTAAGTTA--T--G--A---TATGATATATATTTATGTA
* *
40075113 TTATGTAAGTTATGATCTGGTATATATTTATGTGA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A
40075148 GTTATGTAAGTTATGATATGATATATATTTATGTA
1 -TTATGTAAGTTATGATATGATATATATTTATGTA
40075183 TTATGTAAGTTA
1 TTATGTAAGTTA
40075195 AGTTATATAA
Statistics
Matches: 108, Mismatches: 6, Indels: 24
0.78 0.04 0.17
Matches are distributed among these distances:
34 28 0.26
35 2 0.02
36 42 0.39
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 12 0.11
44 1 0.01
45 17 0.16
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.50
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:40075076 original size:9 final size:9
Alignment explanation
Indices: 40075064--40075162 Score: 62
Period size: 9 Copynumber: 11.2 Consensus size: 9
40075054 TATATATTTG
40075064 TGTAAGTTA
1 TGTAAGTTA
40075073 TGTAAGTTA
1 TGTAAGTTA
40075082 TGTAAGTTA
1 TGTAAGTTA
* *
40075091 TTGTATGATA
1 -TGTAAGTTA
* *
40075101 TAT-ATTTA
1 TGTAAGTTA
40075109 TGT-A-TTA
1 TGTAAGTTA
40075116 TGTAAGTTA
1 TGTAAGTTA
** *
40075125 TGATCTGGTA
1 TG-TAAGTTA
* *
40075135 TAT-ATTTA
1 TGTAAGTTA
*
40075143 TGTGAGTTA
1 TGTAAGTTA
40075152 TGTAAGTTA
1 TGTAAGTTA
40075161 TG
1 TG
40075163 ATATGATATA
Statistics
Matches: 68, Mismatches: 17, Indels: 10
0.72 0.18 0.11
Matches are distributed among these distances:
7 6 0.09
8 10 0.15
9 40 0.59
10 12 0.18
ACGTcount: A:0.30, C:0.01, G:0.20, T:0.48
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:40075090 original size:45 final size:43
Alignment explanation
Indices: 40075034--40075126 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 43
40075024 ATCCACGGTT
* *
40075034 TTATGTTAGTTA-TGATATGATATATATTTGTGTAAGTTATGTAAG
1 TTATGTAAGTTATTG-TATGATATATATTTATGT-A-TTATGTAAG
40075079 TTATGTAAGTTATTGTATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATTGTATGATATATATTTATGTATTATGTAAG
40075122 TTATG
1 TTATG
40075127 ATCTGGTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 14 0.31
44 1 0.02
45 28 0.62
46 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (43 bp):
TTATGTAAGTTATTGTATGATATATATTTATGTATTATGTAAG
Found at i:40075119 original size:34 final size:36
Alignment explanation
Indices: 40075070--40075194 Score: 179
Period size: 34 Copynumber: 3.6 Consensus size: 36
40075060 TTTGTGTAAG
40075070 TTATGTAAGTTATGTAAGTTATTG-TATGATATATAT
1 TTATGTAAGTTATGTAAGTTA-TGATATGATATATAT
* *
40075106 TTATGT-A-TTATGTAAGTTATGATCTGGTATATAT
1 TTATGTAAGTTATGTAAGTTATGATATGATATATAT
*
40075140 TTATGTGAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGTAAGTTATGATATGATATATAT
40075176 TTATGT-A-TTATGTAAGTTA
1 TTATGTAAGTTATGTAAGTTA
40075195 AGTTATATAA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
33 2 0.02
34 40 0.49
35 3 0.04
36 37 0.45
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.50
Consensus pattern (36 bp):
TTATGTAAGTTATGTAAGTTATGATATGATATATAT
Found at i:40075317 original size:13 final size:13
Alignment explanation
Indices: 40075299--40075325 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40075289 TGATTATCAT
40075299 CTTTAAATTTTAA
1 CTTTAAATTTTAA
40075312 CTTTAAATTTTAA
1 CTTTAAATTTTAA
40075325 C
1 C
40075326 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:40075862 original size:20 final size:20
Alignment explanation
Indices: 40075837--40075879 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
40075827 AAGTTATCTT
40075837 AAATTTTAAAATAAAAACAA
1 AAATTTTAAAATAAAAACAA
* *
40075857 AAA-TTTAGAATAAAAACTA
1 AAATTTTAAAATAAAAACAA
40075876 AAAT
1 AAAT
40075880 AAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATTTTAAAATAAAAACAA
Found at i:40075887 original size:19 final size:19
Alignment explanation
Indices: 40075846--40075891 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40075836 TAAATTTTAA
**
40075846 AATAAAAACAAAAATTTAG
1 AATAAAAACAAAAATAAAG
* *
40075865 AATAAAAACTAAAATAAAT
1 AATAAAAACAAAAATAAAG
40075884 AATAAAAA
1 AATAAAAA
40075892 TTGGATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (19 bp):
AATAAAAACAAAAATAAAG
Found at i:40076345 original size:72 final size:72
Alignment explanation
Indices: 40076257--40076488 Score: 243
Period size: 72 Copynumber: 3.2 Consensus size: 72
40076247 TGTATAACAG
* * *
40076257 AATAAATGGTTCTACTTAATATCAAAACTCAATAAGTTGAACTAAACTAACCTTTTTAAAAATTC
1 AATAAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTC
*
40076322 ATAATTG
66 ATAATTA
* * ** ** * * *
40076329 AACAAATGTTTTTACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGC-TTCTGAAAATGT
1 AATAAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAAT-T
*
40076393 -ATAACTA
65 CATAATTA
** * * **
40076400 AATAAATGGTTTCGCTTAATAACAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAACAC
1 AATAAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTC
40076465 ATAATTA
66 ATAATTA
* *
40076472 AATAAACGATTTTACTT
1 AATAAATGGTTTTACTT
40076489 GATAATTAAT
Statistics
Matches: 123, Mismatches: 34, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
71 54 0.44
72 69 0.56
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (72 bp):
AATAAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTC
ATAATTA
Found at i:40079583 original size:27 final size:27
Alignment explanation
Indices: 40079533--40079608 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
40079523 CAGAGGAGTG
* * * *
40079533 TCGACGGTGATGCAGCAAAGGGGACAG
1 TCGACAGTAATGCAGCAGAGGGGACAA
* *
40079560 TTGACAGTAATGCAGCAGATGGGACAA
1 TCGACAGTAATGCAGCAGAGGGGACAA
* *
40079587 TCGACGGTGATGCAGCAGAGGG
1 TCGACAGTAATGCAGCAGAGGG
40079609 TCGGGGAAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.38, T:0.14
Consensus pattern (27 bp):
TCGACAGTAATGCAGCAGAGGGGACAA
Found at i:40092545 original size:9 final size:9
Alignment explanation
Indices: 40092531--40092559 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
40092521 TAAACAATTC
40092531 AATAATATA
1 AATAATATA
40092540 AATAATATA
1 AATAATATA
40092549 AATAATATA
1 AATAATATA
40092558 AA
1 AA
40092560 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:40092853 original size:30 final size:31
Alignment explanation
Indices: 40092814--40092873 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
40092804 GAAGGTGGGA
*
40092814 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
40092845 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
40092874 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:40093184 original size:9 final size:9
Alignment explanation
Indices: 40093167--40093199 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40093157 TCGAGTTGAT
*
40093167 TCGAATAAC
1 TCGATTAAC
40093176 TCGATTAAC
1 TCGATTAAC
40093185 TCGATTAAC
1 TCGATTAAC
40093194 TCGATT
1 TCGATT
40093200 CGTTTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:40095408 original size:22 final size:21
Alignment explanation
Indices: 40095381--40095449 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
40095371 AAATTGTTGC
* *
40095381 ATTTGTTTTGATATTGTTCTTG
1 ATTTGTTCTGAAATTGTT-TTG
40095403 ATTTGTTCTGAAATTGTTTTG
1 ATTTGTTCTGAAATTGTTTTG
40095424 A-TTGTCTGCTGGAAATTGTTTTG
1 ATTTGT-T-CT-GAAATTGTTTTG
40095447 ATT
1 ATT
40095450 GTCTGCTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.10
21 5 0.12
22 18 0.44
23 13 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (21 bp):
ATTTGTTCTGAAATTGTTTTG
Found at i:40095440 original size:23 final size:23
Alignment explanation
Indices: 40095412--40095464 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
40095402 GATTTGTTCT
40095412 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
40095435 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
40095458 GAAATTG
1 GAAATTG
40095465 AATTTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (23 bp):
GAAATTGTTTTGATTGTCTGCTG
Found at i:40096622 original size:25 final size:25
Alignment explanation
Indices: 40096588--40096789 Score: 188
Period size: 25 Copynumber: 8.2 Consensus size: 25
40096578 TACATCAATA
*
40096588 ATTAAAATAAGGACTTTAATATTTC
1 ATTAAAATAAGGACTTTAATATTTT
* * *
40096613 ATTAAAATAATGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
40096636 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
40096661 ATTAAAATAAGGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
40096684 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* * *
40096709 ATTAAAATAAGTAC--TAATCAATAT
1 ATTAAAATAAGGACTTTAAT-ATTTT
40096733 -TTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
40096757 ATTAAAAATCAAGAAATTTAATATTTT
1 ATT-AAAAT-AAGGACTTTAATATTTT
*
40096784 AATAAA
1 ATTAAA
40096790 GAAATTTAAA
Statistics
Matches: 144, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
23 53 0.37
24 10 0.07
25 56 0.39
26 8 0.06
27 17 0.12
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTAAAATAAGGACTTTAATATTTT
Found at i:40096636 original size:48 final size:47
Alignment explanation
Indices: 40096581--40096763 Score: 321
Period size: 48 Copynumber: 3.8 Consensus size: 47
40096571 AAATAATTAC
*
40096581 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAATGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAA-GACTA
40096629 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAA-GACTA
40096677 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGTACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAG-ACTA
*
40096725 ATCAATATTTAAAATAAGGACTTTAATATTTTATTAAAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAA
40096764 ATCAAGAAAT
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
47 1 0.01
48 130 0.99
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (47 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGACTA
Found at i:40100235 original size:24 final size:25
Alignment explanation
Indices: 40100202--40100249 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
40100192 TTATGAAATT
*
40100202 TAATATTAATTA-TTAAATTATATG
1 TAATAATAATTATTTAAATTATATG
40100226 TAATAATAATTATTTTAAATTATA
1 TAATAATAATTA-TTTAAATTATA
40100250 CAAATTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATAATAATTATTTAAATTATATG
Found at i:40100428 original size:120 final size:120
Alignment explanation
Indices: 40100290--40100822 Score: 1030
Period size: 120 Copynumber: 4.4 Consensus size: 120
40100280 AATTATTTTA
* * *
40100290 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
40100355 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40100410 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
40100475 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40100530 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
40100595 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTGTTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40100650 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
40100715 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40100770 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40100823 TAAATATGAT
Statistics
Matches: 408, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 408 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:40100450 original size:15 final size:15
Alignment explanation
Indices: 40100415--40100466 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40100405 TTAAGAATTT
*
40100415 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40100429 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40100443 TATTTAATAATAAT-
1 TATTTAATTATAATA
40100457 TATGTTAATT
1 TAT-TTAATT
40100467 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40100570 original size:15 final size:15
Alignment explanation
Indices: 40100535--40100586 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40100525 TTAAGAATTT
*
40100535 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40100549 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40100563 TATTTAATAATAAT-
1 TATTTAATTATAATA
40100577 TATGTTAATT
1 TAT-TTAATT
40100587 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40100690 original size:15 final size:15
Alignment explanation
Indices: 40100655--40100706 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40100645 TTAAGAATTT
*
40100655 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40100669 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40100683 TATTTAATAATAAT-
1 TATTTAATTATAATA
40100697 TATGTTAATT
1 TAT-TTAATT
40100707 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40100805 original size:16 final size:16
Alignment explanation
Indices: 40100784--40100825 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40100774 TTATTAAATT
*
40100784 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40100800 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40100815 AT-TATGTTTAA
1 ATATAT-TTTAA
40100826 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40100810 original size:15 final size:15
Alignment explanation
Indices: 40100775--40100816 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40100765 TTAAGAATTT
*
40100775 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40100789 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40100803 TATTTAATAATAAT
1 TATTTAATTATAAT
40100817 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40101545 original size:38 final size:37
Alignment explanation
Indices: 40101484--40101559 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
40101474 AATTTGAACT
* *
40101484 TTTAAATTTTTTTATAATTTTTATTAGTGTTTTAAAA
1 TTTAAATTTTTTTATAATTTTTATAAGTATTTTAAAA
* *
40101521 TTTAAATTTTTTTA-ATTTTCTTTATAATTATTTTAAAA
1 TTTAAATTTTTTTATA-ATT-TTTATAAGTATTTTAAAA
40101559 T
1 T
40101560 AAATCTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 1 0.03
37 16 0.48
38 16 0.48
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (37 bp):
TTTAAATTTTTTTATAATTTTTATAAGTATTTTAAAA
Found at i:40102279 original size:17 final size:17
Alignment explanation
Indices: 40102257--40102320 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
40102247 AATCTTAGAG
40102257 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
40102274 TTCTAATTGTGT-CTAAGAG
1 TTCTAATTGTATAC--AG-C
*
40102293 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
40102310 TTTTAATTGTA
1 TTCTAATTGTA
40102321 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:40102600 original size:47 final size:48
Alignment explanation
Indices: 40102524--40102617 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
40102514 TGAGGGAATT
40102524 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
* *
40102572 CTGTTGAATCCTTT-TCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTT
40102618 ATGCAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 30 0.68
48 14 0.32
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
Found at i:40107417 original size:17 final size:17
Alignment explanation
Indices: 40107395--40107458 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
40107385 AATCTTAGAG
40107395 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
40107412 TTCTAATTGTGT-CTAAGAG
1 TTCTAATTGTATAC--AG-C
*
40107431 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
40107448 TTTTAATTGTA
1 TTCTAATTGTA
40107459 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:40107740 original size:47 final size:48
Alignment explanation
Indices: 40107662--40107755 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
40107652 TGAGGGAATT
*
40107662 CTGTTGAATCCTTTATTATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
*
40107710 CTGTTGAATCCTTT-TCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTT
40107756 AAGCAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 30 0.68
48 14 0.32
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
Found at i:40110545 original size:121 final size:122
Alignment explanation
Indices: 40110245--40110590 Score: 550
Period size: 123 Copynumber: 2.8 Consensus size: 122
40110235 TTATTTCGAG
* *
40110245 TTGACGTTTGTGAGCAAATAGTATAAAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
40110310 AAATCGCGCCCTCGTGGACGCGGTTTGGCTACAGTAGGTCATGTAATAAATAATTGTT
66 AAATCGCGCCCTCGTGGACGCGGTTTTGCTACAGTAGGTCATGTAAGAAAT-ATTGTT
* *
40110368 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * * *
40110433 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAAT-TTTTT
66 AAATCGCGCCCTCGTGGACGCGGTTTTGCTACAGTAGGTCATGTAAGAAATATTGTT
*
40110489 TTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
40110554 AAATCGCACCTTCTTGGACGCGGTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGGTTTTGCTACAGTAG
40110591 CAAGTTTGGG
Statistics
Matches: 204, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 97 0.48
123 107 0.52
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (122 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGGTTTTGCTACAGTAGGTCATGTAAGAAATATTGTT
Found at i:40113714 original size:10 final size:10
Alignment explanation
Indices: 40113699--40113723 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40113689 CAAATCTAAC
40113699 ATTATGTAAA
1 ATTATGTAAA
40113709 ATTATGTAAA
1 ATTATGTAAA
40113719 ATTAT
1 ATTAT
40113724 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:40113768 original size:55 final size:55
Alignment explanation
Indices: 40113707--40113832 Score: 252
Period size: 55 Copynumber: 2.3 Consensus size: 55
40113697 ACATTATGTA
40113707 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
40113762 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
40113817 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
40113833 GGTTAGGGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:40113958 original size:117 final size:116
Alignment explanation
Indices: 40113827--40114052 Score: 416
Period size: 117 Copynumber: 1.9 Consensus size: 116
40113817 AAATTATGTA
*
40113827 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTTAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
* *
40113892 GTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
66 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGG-TTAGGGTTTTTAATT
40113944 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
40114009 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTT
66 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTT
40114053 AGGGTTTTGA
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 8 0.08
117 98 0.92
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (116 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATT
Found at i:40114066 original size:117 final size:116
Alignment explanation
Indices: 40113827--40114098 Score: 400
Period size: 117 Copynumber: 2.4 Consensus size: 116
40113817 AAATTATGTA
*
40113827 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTTAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
* * *
40113892 GTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
66 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTTAGGGTTGTT-ATT
40113944 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
40114009 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGG-TTAGGGTTAGGGTT-TT
66 ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTTAGGGTT---GTTATT
*
40114061 GAATTA----A---TTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
40114099 TTTAATTAAA
Statistics
Matches: 147, Mismatches: 5, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
110 31 0.21
113 1 0.01
116 8 0.05
117 105 0.71
119 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (116 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
ATTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTTAGGGTTGTTATT
Found at i:40114075 original size:29 final size:29
Alignment explanation
Indices: 40113827--40114052 Score: 416
Period size: 29 Copynumber: 7.8 Consensus size: 29
40113817 AAATTATGTA
40113827 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
40113856 AAATTAGGTTAGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
40113885 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
40113914 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
40113944 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
40113973 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
40114002 AAATTAGATTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
40114031 AAATTAGATTAGGGTTAGGGTT
1 AAATTAGGTTAGGGTTAGGGTT
40114053 AGGGTTTTGA
Statistics
Matches: 193, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 164 0.85
30 29 0.15
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:40114087 original size:18 final size:18
Alignment explanation
Indices: 40114051--40114120 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 18
40114041 AGGGTTAGGG
*
40114051 TTAGGGTTTTGAATT-AA
1 TTAGGGTTTTTAATTAAA
40114068 TTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATT-AA--A
40114089 GGTTAGGGTTTTTAATTAAA
1 --TTAGGGTTTTTAATTAAA
40114109 TTAGGGTTTTTA
1 TTAGGGTTTTTA
40114121 TTGCATCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
17 14 0.30
18 12 0.26
19 1 0.02
20 1 0.02
21 1 0.02
22 2 0.04
23 15 0.33
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:40114199 original size:36 final size:36
Alignment explanation
Indices: 40114159--40114273 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
40114149 ATATCAAATA
*
40114159 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
40114195 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
40114230 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
40114266 ACATCAAA
1 ATATCAAA
40114274 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:40114225 original size:25 final size:25
Alignment explanation
Indices: 40114191--40114301 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
40114181 TTTCTATGCC
*
40114191 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
40114216 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
40114237 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
40114262 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
40114287 TATTACATCAAATAA
1 TATTACATCAAATAA
40114302 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:40114226 original size:71 final size:71
Alignment explanation
Indices: 40114119--40114303 Score: 325
Period size: 71 Copynumber: 2.6 Consensus size: 71
40114109 TTAGGGTTTT
* *
40114119 TATTGCATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
40114184 CTATGCC
65 CTATGCC
*
40114191 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
40114256 TATGCG
66 TATGCC
40114262 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
40114304 AATTTAAATA
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 96 0.89
72 12 0.11
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:40114745 original size:18 final size:18
Alignment explanation
Indices: 40114701--40114746 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
40114691 GATTCGGAAA
* *
40114701 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
40114719 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
40114737 AGGAAACATA
1 AGGATACATA
40114747 CCTGGTATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:40115401 original size:7 final size:7
Alignment explanation
Indices: 40115391--40115415 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40115381 TTATATACAT
40115391 AATACTA
1 AATACTA
40115398 AATACTA
1 AATACTA
40115405 AATACTA
1 AATACTA
40115412 AATA
1 AATA
40115416 TCAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:40116516 original size:10 final size:10
Alignment explanation
Indices: 40116497--40116548 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
40116487 GCCATTGATG
*
40116497 AAAATATAAA
1 AAAATTTAAA
40116507 AAAATTTAAA
1 AAAATTTAAA
* *
40116517 ATTATTTTAAA
1 A-AAATTTAAA
*
40116528 AAAATATAAAA
1 AAAAT-TTAAA
40116539 AAAATTTAAA
1 AAAATTTAAA
40116549 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:40116532 original size:31 final size:31
Alignment explanation
Indices: 40116497--40116561 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
40116487 GCCATTGATG
40116497 AAAATAT-AAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTT-AAATTATTTTAAA
40116528 AAAATATAAAAAAAATTTAAATTATTTTAAA
1 AAAATATAAAAAAAATTTAAATTATTTTAAA
40116559 AAA
1 AAA
40116562 TGAAATTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTTAAATTATTTTAAA
Found at i:40116618 original size:51 final size:51
Alignment explanation
Indices: 40116563--40116684 Score: 183
Period size: 51 Copynumber: 2.4 Consensus size: 51
40116553 TTTAAAAAAT
* *
40116563 GAAATTGAGGGGAAATTGAAATTAAATATGAATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGAATTTGAGAGAATTTTGAAAG
**
40116614 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGAAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGAATTTGAGAGAATTTTGAAAG
40116665 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
40116685 GAGGAAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 52 0.80
52 13 0.20
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGAATTTGAGAGAATTTTGAAAG
Found at i:40117019 original size:29 final size:29
Alignment explanation
Indices: 40116971--40117026 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40116961 AAAATGGATC
*
40116971 ATTTCGGTAAATAATCAAAAAATCGGCCT
1 ATTTCGGTAAATAATCAAAAAAACGGCCT
** *
40117000 ATTTCGGTAAATTTTGAAAAAAACGGC
1 ATTTCGGTAAATAATCAAAAAAACGGC
40117027 TTCTATTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (29 bp):
ATTTCGGTAAATAATCAAAAAAACGGCCT
Found at i:40119482 original size:11 final size:11
Alignment explanation
Indices: 40119466--40119491 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40119456 ATTTTTTTAA
40119466 TTTTAAAATAC
1 TTTTAAAATAC
40119477 TTTTAAAATAC
1 TTTTAAAATAC
40119488 TTTT
1 TTTT
40119492 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40119528 original size:22 final size:23
Alignment explanation
Indices: 40119500--40119547 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
40119490 TTTTTAAAAA
*
40119500 TTTTTTAA-TTTTAAAATAATTT
1 TTTTTTAATTTTTAAAATAAATT
40119522 TTTTTTAATTTTTAAAATAAATT
1 TTTTTTAATTTTTAAAATAAATT
40119545 TTT
1 TTT
40119548 GATATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTAATTTTTAAAATAAATT
Found at i:40119559 original size:24 final size:23
Alignment explanation
Indices: 40119497--40119562 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
40119487 CTTTTTTTAA
40119497 AAATTTTT--TAA-TTTTAAAAT
1 AAATTTTTGATAATTTTTAAAAT
* **
40119517 AATTTTTTTTTAATTTTTAAAAT
1 AAATTTTTGATAATTTTTAAAAT
*
40119540 AAATTTTTGATATTTATTTAAAA
1 AAATTTTTGATAATT-TTTAAAA
40119563 AACGAGCCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.19
22 3 0.08
23 20 0.54
24 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AAATTTTTGATAATTTTTAAAAT
Found at i:40121370 original size:85 final size:85
Alignment explanation
Indices: 40121227--40121400 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 85
40121217 TTGCACTCCT
40121227 GGTTTATCTTTGTTCTCACATTTTGTACATGCTTGCAGTGGCTTAAGATATATTTTTCCTATCTG
1 GGTTTATCTTTGTTCTCACATTTTGTACATGCTTGCAGTGGCTTAAGATATATTTTTCCTATCTG
40121292 CTGATTTCTTTATATTTTGC
66 CTGATTTCTTTATATTTTGC
* *
40121312 GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGCTTAATATATATTTTTCCTATCTG
1 GGTTTATCTTTGTTCTCACATTTTGTACATGCTTGCAGTGGCTTAAGATATATTTTTCCTATCTG
40121377 CTGATTTCTTTATATTTTGC
66 CTGATTTCTTTATATTTTGC
40121397 GGTT
1 GGTT
40121401 CCCTATGGTC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (85 bp):
GGTTTATCTTTGTTCTCACATTTTGTACATGCTTGCAGTGGCTTAAGATATATTTTTCCTATCTG
CTGATTTCTTTATATTTTGC
Found at i:40123278 original size:7 final size:7
Alignment explanation
Indices: 40123266--40123297 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40123256 AGATTATGAT
40123266 GGGCATA
1 GGGCATA
40123273 GGGCATA
1 GGGCATA
40123280 GGGCATA
1 GGGCATA
40123287 GGGCATA
1 GGGCATA
40123294 GGGC
1 GGGC
40123298 TGACAGACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.47, T:0.12
Consensus pattern (7 bp):
GGGCATA
Found at i:40123703 original size:9 final size:9
Alignment explanation
Indices: 40123689--40123907 Score: 89
Period size: 9 Copynumber: 23.9 Consensus size: 9
40123679 ATATTTTTTC
40123689 TATAAAAAT
1 TATAAAAAT
40123698 TATAAAAA-
1 TATAAAAAT
*
40123706 AATAAAAA-
1 TATAAAAAT
40123714 -ATAAAAA-
1 TATAAAAAT
*
40123721 TATTAAAAGAA
1 TA-TAAAA-AT
*
40123732 TATGAAAAT
1 TATAAAAAT
* *
40123741 TGATATAAAC
1 T-ATAAAAAT
40123751 T-T-AAAAT
1 TATAAAAAT
40123758 TATAAAAA-
1 TATAAAAAT
*
40123766 CATAAAAAT
1 TATAAAAAT
*
40123775 TCTAATAAAT
1 TATAA-AAAT
40123785 TATAAAAAT
1 TATAAAAAT
40123794 TAT--AAAT
1 TATAAAAAT
40123801 TAGT-AAAAT
1 TA-TAAAAAT
*
40123810 ATATTTAAAAT
1 -TA-TAAAAAT
*
40123821 TTTATAAAAT
1 TATA-AAAAT
*
40123831 CGTATTAAAATT
1 --TA-TAAAAAT
40123843 CTATAAAAAT
1 -TATAAAAAT
* *
40123853 CATAAAAAA
1 TATAAAAAT
** *
40123862 TATTTAAAG
1 TATAAAAAT
*
40123871 TATTAAAAT
1 TATAAAAAT
*
40123880 TAATATAAATT
1 T-ATA-AAAAT
40123891 TATAAAAAT
1 TATAAAAAT
40123900 TATAAAAA
1 TATAAAAA
40123908 AAATCATAAA
Statistics
Matches: 161, Mismatches: 30, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
7 17 0.11
8 18 0.11
9 66 0.41
10 39 0.24
11 14 0.09
12 5 0.03
13 2 0.01
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
TATAAAAAT
Found at i:40123712 original size:17 final size:17
Alignment explanation
Indices: 40123709--40123799 Score: 51
Period size: 17 Copynumber: 5.1 Consensus size: 17
40123699 ATAAAAAAAT
40123709 AAAAAATAAAAA-TATTA
1 AAAAAATAAAAATTA-TA
*
40123726 AAAGAATATGAAAATTGAT-
1 AAA-AA-ATAAAAATT-ATA
* * *
40123745 ATAAACTTAAAATTATA
1 AAAAAATAAAAATTATA
* *
40123762 AAAACATAAAAATTCTA
1 AAAAAATAAAAATTATA
*
40123779 ATAAATTATAAAAATTATA
1 A-AAA-AATAAAAATTATA
40123798 AA
1 AA
40123800 TTAGTAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
16 2 0.04
17 23 0.41
18 8 0.14
19 20 0.36
20 2 0.04
21 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAATAAAAATTATA
Found at i:40123830 original size:21 final size:21
Alignment explanation
Indices: 40123804--40123856 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40123794 TATAAATTAG
*
40123804 TAAAAT-ATATTTAAAATTTTA
1 TAAAATCATA-TTAAAATTCTA
*
40123825 TAAAATCGTATTAAAATTCTA
1 TAAAATCATATTAAAATTCTA
40123846 TAAAAATCATA
1 T-AAAATCATA
40123857 AAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAATCATATTAAAATTCTA
Found at i:40125528 original size:29 final size:29
Alignment explanation
Indices: 40125493--40125558 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
40125483 TTTTTCTCAT
*
40125493 CCAATTATCAAAAG-TTATAAAATGGTCAC
1 CCAATTAT-AAAAGCTTACAAAATGGTCAC
* * *
40125522 CTAATTATGAAAGCTTACAAAATGGTTAC
1 CCAATTATAAAAGCTTACAAAATGGTCAC
40125551 CCAATTAT
1 CCAATTAT
40125559 TTAAATTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (29 bp):
CCAATTATAAAAGCTTACAAAATGGTCAC
Found at i:40127282 original size:20 final size:22
Alignment explanation
Indices: 40127242--40127282 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40127232 TCAGCAACCT
40127242 TTCTTCATTTGTTGGCTCTCTCA
1 TTCTTCATTTGTT-GCTCTCTCA
40127265 TTCTTCATTT-TT-CTCTCT
1 TTCTTCATTTGTTGCTCTCT
40127283 AAAATAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.59
Consensus pattern (22 bp):
TTCTTCATTTGTTGCTCTCTCA
Found at i:40130372 original size:84 final size:84
Alignment explanation
Indices: 40130231--40130401 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 84
40130221 TGGGAAGAAT
*
40130231 GCAATATATGTCAAAGTCTGGAATTGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
1 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
40130296 TGCAAACCAGTTCTTTCAG
66 TGCAAACCAGTTCTTTCAG
40130315 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
1 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
40130380 TGCAAACCAGTTCTTTCAG
66 TGCAAACCAGTTCTTTCAG
40130399 GCA
1 GCA
40130402 TGGGGATGAT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (84 bp):
GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
TGCAAACCAGTTCTTTCAG
Found at i:40133238 original size:10 final size:9
Alignment explanation
Indices: 40133224--40133327 Score: 81
Period size: 9 Copynumber: 11.4 Consensus size: 9
40133214 ACATGTGGCA
40133224 AAAAATTAT
1 AAAAATTAT
40133233 AAAAA--AT
1 AAAAATTAT
*
40133240 AAAAATAAAT
1 AAAAAT-TAT
*
40133250 AAAATTTAT
1 AAAAATTAT
40133259 AAAAATTATT
1 AAAAATTA-T
**
40133269 AAATTTTAAT
1 AAAAATT-AT
40133279 AAAAA-TATT
1 AAAAATTA-T
40133288 AAAAATTAT
1 AAAAATTAT
**
40133297 AAAAATCGT
1 AAAAATTAT
40133306 AAAAA-TATT
1 AAAAATTA-T
40133315 AAAAATTAT
1 AAAAATTAT
40133324 AAAA
1 AAAA
40133328 TTGTATTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
7 7 0.09
8 1 0.01
9 45 0.60
10 21 0.28
11 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40133262 original size:19 final size:18
Alignment explanation
Indices: 40133238--40133302 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
40133228 ATTATAAAAA
*
40133238 ATAAAAATAAATAAAATTT
1 ATAAAAAT-ATTAAAATTT
*
40133257 ATAAAAATTATTAAATTTT
1 ATAAAAA-TATTAAAATTT
*
40133276 AATAAAAATATTAAAAATT
1 -ATAAAAATATTAAAATTT
40133295 ATAAAAAT
1 ATAAAAAT
40133303 CGTAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.20
19 24 0.60
20 8 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATATTAAAATTT
Found at i:40133326 original size:18 final size:18
Alignment explanation
Indices: 40133238--40133329 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 18
40133228 ATTATAAAAA
* *
40133238 ATAAAAATAAATAAAATTT
1 ATAAAAAT-ATTAAAAATT
**
40133257 ATAAAAATTATTAAATTTT
1 ATAAAAA-TATTAAAAATT
40133276 AATAAAAATATTAAAAATT
1 -ATAAAAATATTAAAAATT
**
40133295 ATAAAAATCGTAAAAA-T
1 ATAAAAATATTAAAAATT
*
40133312 ATTAAAA-ATTATAAAATT
1 ATAAAAATATTA-AAAATT
40133330 GTATTAATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
16 2 0.03
17 11 0.18
18 15 0.25
19 24 0.40
20 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
ATAAAAATATTAAAAATT
Found at i:40133876 original size:31 final size:32
Alignment explanation
Indices: 40133838--40133900 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
40133828 TGGCAAATTA
40133838 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
40133869 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
40133901 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:40140018 original size:31 final size:32
Alignment explanation
Indices: 40139980--40140042 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
40139970 AGGCAAATTA
40139980 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
40140011 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
40140043 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:40140502 original size:17 final size:19
Alignment explanation
Indices: 40140480--40140514 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
40140470 TTTGGTACGA
40140480 TAATTTTA-ATTT-TTTAC
1 TAATTTTATATTTCTTTAC
40140497 TAATTTTATATTTCTTTA
1 TAATTTTATATTTCTTTA
40140515 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATTTTATATTTCTTTAC
Found at i:40140553 original size:48 final size:47
Alignment explanation
Indices: 40140498--40140629 Score: 142
Period size: 48 Copynumber: 2.7 Consensus size: 47
40140488 ATTTTTTACT
40140498 AATTTTATATTTCTTTATATTTTTTATAATTTTCTTAC-AACTTTATAA
1 AATTTTATATTT-TTTATATTTTTTATAATTTT-TTACGAACTTTATAA
* * **
40140546 AATTTTATATATTTCTATATATTTTATAATTTTTTACGATTTTTATAA
1 AATTTTATAT-TTTTTATATTTTTTATAATTTTTTACGAACTTTATAA
* * *
40140594 AATTTTACAATTTTTT-TAATTTTTAATAATATTTTA
1 AATTTTA-TATTTTTTAT-ATTTTTTATAATTTTTTA
40140630 ACATTTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
47 5 0.07
48 62 0.87
49 4 0.06
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (47 bp):
AATTTTATATTTTTTATATTTTTTATAATTTTTTACGAACTTTATAA
Found at i:40140580 original size:29 final size:27
Alignment explanation
Indices: 40140486--40140640 Score: 91
Period size: 29 Copynumber: 5.4 Consensus size: 27
40140476 ACGATAATTT
*
40140486 TAATTTTTTACTAATTTTATATTTCTTTA
1 TAATTTTTTA-TAATTTTATATAT-TTTA
* * *
40140515 T-ATTTTTTATAATTTTCTTACAACTTTA
1 TAATTTTTTATAATTTT-ATA-TATTTTA
**
40140543 TAAAATTTTATATATTTCTATATATTTTA
1 TAATTTTTTATA-ATTT-TATATATTTTA
* * *
40140572 TAATTTTTTACGATTTTTATAAAATTTTA
1 TAATTTTTTA-TAATTTTAT-ATATTTTA
*
40140601 CAATTTTTT-TAATTTTTAATAATATTTTA
1 TAATTTTTTATAA-TTTT-AT-ATATTTTA
40140630 -ACATTTTTTAT
1 TA-ATTTTTTAT
40140641 TAAAATTTAA
Statistics
Matches: 97, Mismatches: 18, Indels: 21
0.71 0.13 0.15
Matches are distributed among these distances:
27 8 0.08
28 23 0.24
29 57 0.59
30 8 0.08
31 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (27 bp):
TAATTTTTTATAATTTTATATATTTTA
Found at i:40140589 original size:19 final size:19
Alignment explanation
Indices: 40140567--40140639 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
40140557 TTTCTATATA
*
40140567 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACAAT
**
40140586 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
* * *
40140605 TTTTTTAATTTTTAATAAT
1 TTTTATAATTTTTTACAAT
40140624 ATTTTA-ACATTTTTTA
1 -TTTTATA-ATTTTTTA
40140640 TTAAAATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
19 31 0.74
20 11 0.26
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:40141090 original size:14 final size:14
Alignment explanation
Indices: 40141055--40141101 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
40141045 TATGATTATG
*
40141055 TTTAAA-TTTAGAG
1 TTTAAATTTTAGAA
*
40141068 TTTAGAATTTTGGAA
1 TTTA-AATTTTAGAA
40141083 TTTAAATTTTAGAA
1 TTTAAATTTTAGAA
40141097 CTTTA
1 -TTTA
40141102 TGATTTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 13 0.46
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (14 bp):
TTTAAATTTTAGAA
Done.