Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 1 of 211
Found at i:4994 original size:1 final size:1
Alignment explanation
Indices: 4988--5014 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4978 TTTGCTTCCT
4988 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5015 GGACTTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6493 original size:86 final size:84
Alignment explanation
Indices: 6230--6526 Score: 285
Period size: 86 Copynumber: 3.4 Consensus size: 84
6220 GAAGACAAAG
* * * * **
6230 GATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTCCATCGGTTG-
* * * *
6295 GATAGAGCTGGTTGAAGACAAAA
64 CATGGAGC-AGTTGAAG-CAAGA
* * *
6318 GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
*
6382 AGTGGAGCTAGTTAAAG-AAGTA
65 A-TGGAGC-AGTTGAAGCAAG-A
*
6404 GATCTGGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
6469 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
6490 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAA
6527 GGATAGTAAT
Statistics
Matches: 175, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
85 7 0.04
86 98 0.56
87 33 0.19
88 35 0.20
89 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:6683 original size:46 final size:46
Alignment explanation
Indices: 6611--6866 Score: 201
Period size: 46 Copynumber: 5.8 Consensus size: 46
6601 GAAGATCACA
* * * *
6611 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
6657 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * * **
6702 T-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
** * * * * * *
6743 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
6785 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* *
6831 GCAGATCTTATCCCCCTGAGGTTACAGTGGAGCAGA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA
6867 TTGAAGCCAG
Statistics
Matches: 165, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
41 31 0.19
42 5 0.03
43 29 0.18
44 30 0.18
45 3 0.02
46 67 0.41
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
Found at i:6764 original size:44 final size:44
Alignment explanation
Indices: 6568--6906 Score: 194
Period size: 46 Copynumber: 7.8 Consensus size: 44
6558 TGGAGCGGAT
* * * *
6568 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATC--ACA
1 TAAA-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * *
6611 T-CAGGTCTTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAA
1 TAAAGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAA-AA
** * * *
6655 TTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA
1 -TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * *
6700 TATA-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAAAA
1 TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * *
6742 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CA
1 TAAA-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * * *
6785 T-CAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAA
1 TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAA-AA
** * * * **
6829 TTGCAGATCTTATCCCCCTGAGGTTACAGTGGAGCAGATTGAAGC
1 -TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * *
6874 CAGAGGTCTTATCTCCCTGATA-TTACAGTGGAG
1 TAAAGATCTTATCTCCCTGA-AGTTACAGTGGAG
6907 TAGACTTAAA
Statistics
Matches: 229, Mismatches: 51, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
40 2 0.01
41 58 0.25
42 8 0.03
43 33 0.14
44 58 0.25
45 3 0.01
46 66 0.29
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TAAAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAAA
Found at i:6789 original size:174 final size:170
Alignment explanation
Indices: 6489--6872 Score: 558
Period size: 174 Copynumber: 2.2 Consensus size: 170
6479 TTGAAGCCAG
* *
6489 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAGGATAGTAATCCTATCTCCTTGAGAT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAA-GATAGTAATCCTATCTCCCTGAGAT
6553 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
65 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
*
6618 TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
130 TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
6659 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGA-T
* * *
6722 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATC
* * ** *
6787 AGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
125 AGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* * *
6833 AGATCTTATCCCCCTGAGGTTACAGTGGAGCAGATTGAAG
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
6873 CCAGAGGTCT
Statistics
Matches: 193, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
168 1 0.01
169 30 0.16
170 40 0.21
171 2 0.01
174 120 0.62
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
Found at i:6838 original size:87 final size:87
Alignment explanation
Indices: 6573--6911 Score: 292
Period size: 87 Copynumber: 3.9 Consensus size: 87
6563 CGGATTAAAG
* * *
6573 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
* *
6638 TGGAACAGACCAAAGAATTTCA
66 TGGAGCAGACCAAAGAATTACA
* ** * ** *
6660 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTGA-AGTT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCG--CATCA-GGTCTTATCTCCCTGAGA-TT
* ** *
6723 ACAGTGGAGCGGA-TTAA-AA-TAAA
62 ACAGTGGAGCAGACCAAAGAATTACA
* * * *
6746 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACA
* * *
6811 GTGGAGTAGACCGAAGAATTGCA
65 GTGGAGCAGACCAAAGAATTACA
* * * * * * *
6834 GATCTTATCCCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGGTCTTATCTCCCTGATATTA
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCA-TC--AGGTCTTATCTCCCTGAGATTA
*
6899 CAGTGGAGTAGAC
63 CAGTGGAGCAGAC
6912 TTAAACCTAA
Statistics
Matches: 195, Mismatches: 44, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
85 27 0.14
86 5 0.03
87 96 0.49
88 7 0.04
89 28 0.14
90 32 0.16
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGACCAAAGAATTACA
Found at i:6887 original size:131 final size:128
Alignment explanation
Indices: 6657--6910 Score: 298
Period size: 131 Copynumber: 2.0 Consensus size: 128
6647 CCAAAGAATT
* *
6657 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGT
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCCCCCTGAAGT
* * *
6722 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA
66 TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATA-TTACAGTAGAGTAGATCGCA
* * * * *
6785 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATCCCCCTG
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATA-T--A-ATCCTATCCCCCTG
* ** * *
6849 AGGTTACAGTGGAGCAGATTGAAGCCAGAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGA
62 AAGTTACAGTGGAGCAGATT-AAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGA
6911 CTTAAACCTA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
127 1 0.01
128 39 0.37
130 1 0.01
131 57 0.54
132 7 0.07
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (128 bp):
TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCCCCCTGAAGT
TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGATCGCA
Found at i:7223 original size:15 final size:15
Alignment explanation
Indices: 7198--7230 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
7188 TACCCAATTA
7198 CAACACCCAATA-CC
1 CAACACCCAATAGCC
7212 CAACAGCCCAATAGCC
1 CAACA-CCCAATAGCC
7228 CAA
1 CAA
7231 AATCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.42, C:0.45, G:0.06, T:0.06
Consensus pattern (15 bp):
CAACACCCAATAGCC
Found at i:8420 original size:14 final size:14
Alignment explanation
Indices: 8399--8431 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8389 GCTCATTTAT
8399 TTAT-TTATTATTA
1 TTATATTATTATTA
*
8412 TTATATTATTATTT
1 TTATATTATTATTA
8426 TTATAT
1 TTATAT
8432 ATGTGCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:18236 original size:14 final size:14
Alignment explanation
Indices: 18217--18258 Score: 61
Period size: 12 Copynumber: 3.1 Consensus size: 14
18207 CAGCCCATGC
18217 ATATTAAATTTTTT
1 ATATTAAATTTTTT
18231 ATATT--ATTTTTT
1 ATATTAAATTTTTT
18243 ATATATAAATTTTTT
1 ATAT-TAAATTTTTT
18258 A
1 A
18259 AAAACCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 5 0.20
15 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTAAATTTTTT
Found at i:21791 original size:16 final size:16
Alignment explanation
Indices: 21770--21806 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
21760 CCCCTTTTAG
21770 TGTGGCATAGTAAATT
1 TGTGGCATAGTAAATT
21786 TGTGGCATAGTAAATT
1 TGTGGCATAGTAAATT
21802 TGTGG
1 TGTGG
21807 AACCTGAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38
Consensus pattern (16 bp):
TGTGGCATAGTAAATT
Found at i:54219 original size:29 final size:29
Alignment explanation
Indices: 54187--54246 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
54177 ATAACATGTT
54187 ATATGAGCGGATTGATATTTTAATTTGAA
1 ATATGAGCGGATTGATATTTTAATTTGAA
54216 ATATGAGCGGATTGATATTTTAATTTGAA
1 ATATGAGCGGATTGATATTTTAATTTGAA
54245 AT
1 AT
54247 TCTTTAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (29 bp):
ATATGAGCGGATTGATATTTTAATTTGAA
Found at i:60905 original size:56 final size:56
Alignment explanation
Indices: 60819--60932 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
60809 CCAAGGTATA
60819 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
1 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
60875 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
1 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
60931 TC
1 TC
60933 CATATAAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.54
Consensus pattern (56 bp):
TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
Found at i:69171 original size:21 final size:22
Alignment explanation
Indices: 69133--69173 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
69123 GTTTGCTTAT
69133 AATTTTTTTTTATCATTTTTAA
1 AATTTTTTTTTATCATTTTTAA
69155 AATTTTATTTTT-T-ATTTTT
1 AATTTT-TTTTTATCATTTTT
69174 GATTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
AATTTTTTTTTATCATTTTTAA
Found at i:70747 original size:18 final size:19
Alignment explanation
Indices: 70724--70759 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
70714 TATTTATTAT
70724 TCTC-TTTCCTTTCCCATC
1 TCTCTTTTCCTTTCCCATC
*
70742 TCTCTTTTTCTTTCCCAT
1 TCTCTTTTCCTTTCCCAT
70760 TCGAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTTTTCCTTTCCCATC
Found at i:77207 original size:17 final size:17
Alignment explanation
Indices: 77165--77209 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
77155 CTTATTTGAT
* *
77165 AATATTTTTATCTTAAA
1 AATATTTTTGTCCTAAA
*
77182 AGTACTTTTTGTCCTAAA
1 AATA-TTTTTGTCCTAAA
77200 AATATTTTTG
1 AATATTTTTG
77210 AGAAGCAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (17 bp):
AATATTTTTGTCCTAAA
Found at i:84787 original size:18 final size:18
Alignment explanation
Indices: 84764--84828 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
84754 AATTTTATCT
84764 ATTTATTTATAAAGACTA
1 ATTTATTTATAAAGACTA
84782 ATTTATTTATTTATTTAA-AC--
1 ATTTATTTA--TA---AAGACTA
84802 ATTT-TTTATAAAGACTA
1 ATTTATTTATAAAGACTA
84819 ATTTATTTAT
1 ATTTATTTAT
84829 TTTTTGAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
17 6 0.16
18 14 0.37
19 4 0.11
20 6 0.16
22 2 0.05
23 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTATTTATAAAGACTA
Found at i:92999 original size:14 final size:14
Alignment explanation
Indices: 92980--93007 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
92970 ATATTAACAT
92980 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
92994 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
93008 AACTGTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGTCAAAACTGAA
Found at i:101031 original size:27 final size:27
Alignment explanation
Indices: 101001--101056 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
100991 TACTAAAATG
101001 CTGCCAAGAGATTTCAATTATCCTACA
1 CTGCCAAGAGATTTCAATTATCCTACA
101028 CTGCCAAGAGATTTCAATTATCCTACA
1 CTGCCAAGAGATTTCAATTATCCTACA
101055 CT
1 CT
101057 CACTGCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (27 bp):
CTGCCAAGAGATTTCAATTATCCTACA
Found at i:122596 original size:2 final size:2
Alignment explanation
Indices: 122589--122633 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
122579 ACAAAGGAGG
122589 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
122630 GA GA
1 GA GA
122634 CGGGCGTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:123483 original size:20 final size:18
Alignment explanation
Indices: 123458--123505 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
123448 AAAACTTATT
123458 AATTTTAAAAATAGATTTAA
1 AATTTTAAAAAT-GATTT-A
* *
123478 AATTTTTAGAAATTATTTA
1 AA-TTTTAAAAATGATTTA
123497 AATTTTAAA
1 AATTTTAAA
123506 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 6 0.25
21 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
AATTTTAAAAATGATTTA
Found at i:125807 original size:28 final size:29
Alignment explanation
Indices: 125766--125835 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
125756 TTAATTTAAA
*
125766 ATTTTA-AAAGGCCTAAAT-AAAAAAATT
1 ATTTTAGAGAGGCCTAAATAAAAAAAATT
125793 ATTTTAGAGAGGCCTAAATAAAAAAAATT
1 ATTTTAGAGAGGCCTAAATAAAAAAAATT
125822 ATTTTAGAGAGGCC
1 ATTTTAGAGAGGCC
125836 GGGCCCGTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 6 0.15
28 11 0.28
29 23 0.57
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (29 bp):
ATTTTAGAGAGGCCTAAATAAAAAAAATT
Found at i:126210 original size:15 final size:16
Alignment explanation
Indices: 126190--126224 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
126180 AGCAAAAGAA
*
126190 AATTTTTAATTAA-TT
1 AATTTTTAAATAATTT
126205 AATTTTTAAATAATTT
1 AATTTTTAAATAATTT
126221 AATT
1 AATT
126225 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTTAAATAATTT
Found at i:140306 original size:18 final size:18
Alignment explanation
Indices: 140266--140314 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
140256 ATGGTGCTGG
140266 TGATGATGATGATGAAGA
1 TGATGATGATGATGAAGA
* **
140284 CGATGATGATGATGAATT
1 TGATGATGATGATGAAGA
*
140302 TGATGATGCTGAT
1 TGATGATGATGAT
140315 TCAGGAGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (18 bp):
TGATGATGATGATGAAGA
Found at i:156052 original size:34 final size:35
Alignment explanation
Indices: 156014--156080 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
156004 CAGTAAAATA
* *
156014 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAACGATTTACTGGAAAATATTTTAC
*
156048 TTTTCTGTAAAACGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAACGATTTACTGGAAAATATTTT
156081 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAACGATTTACTGGAAAATATTTTAC
Found at i:156066 original size:20 final size:20
Alignment explanation
Indices: 156029--156068 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
156019 CGTAAAATGA
* *
156029 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAACGATTTACT
*
156049 TTTCTGTAAAACGATTTACT
1 TTTCTGGAAAACGATTTACT
156069 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAACGATTTACT
Found at i:156705 original size:15 final size:16
Alignment explanation
Indices: 156681--156715 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
156671 ACTTAATAAT
*
156681 TAAAATATTTAATTA-
1 TAAAAAATTTAATTAC
156696 TAAAAAATTTAATTAC
1 TAAAAAATTTAATTAC
156712 TAAA
1 TAAA
156716 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAATTTAATTAC
Found at i:156736 original size:21 final size:22
Alignment explanation
Indices: 156697--156746 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
156687 ATTTAATTAT
156697 AAAAAATTTAATTACTAAAT-A
1 AAAAAATTTAATTACTAAATGA
*
156718 AAAAAATTTAA-TAGTTAAATGA
1 AAAAAATTTAATTA-CTAAATGA
*
156740 TAAAAAT
1 AAAAAAT
156747 AAAACAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAAATTTAATTACTAAATGA
Found at i:165592 original size:94 final size:93
Alignment explanation
Indices: 165422--165592 Score: 225
Period size: 94 Copynumber: 1.8 Consensus size: 93
165412 AAATCTTAGT
* * * * * *
165422 TTGATTTAGATGTAGTAAGGAGGTAAAGGTCGAGTTGGTGTTTGATCTAATGTTGGTAAATATGG
1 TTGATTTAAATGTAGCAAGGAGATAAAGGTCGAGTTGGTATATGATCTAATGTTGATAAATATGG
165487 TGGGAAATAACATTAAACTAGATTTTAC
66 TGGGAAATAACATTAAACTAGATTTTAC
* * ** *
165515 TTGATTTAAATGTAGCAATGAGATAAAGGTCGAGTCTGTTATATGATCTTGTGTTGATAGATATG
1 TTGATTTAAATGTAGCAAGGAGATAAAGGTCGAGT-TGGTATATGATCTAATGTTGATAAATATG
*
165580 GTGGGAAGTAACA
65 GTGGGAAATAACA
165593 ATAGACTGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
93 31 0.48
94 34 0.52
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (93 bp):
TTGATTTAAATGTAGCAAGGAGATAAAGGTCGAGTTGGTATATGATCTAATGTTGATAAATATGG
TGGGAAATAACATTAAACTAGATTTTAC
Found at i:174194 original size:18 final size:18
Alignment explanation
Indices: 174171--174207 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
174161 TAACACTATA
* *
174171 ATATATTATGTTATTTAT
1 ATATATTATATAATTTAT
174189 ATATATTATATAATTTAT
1 ATATATTATATAATTTAT
174207 A
1 A
174208 ACACAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATATTATATAATTTAT
Found at i:174299 original size:31 final size:31
Alignment explanation
Indices: 174257--174329 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
174247 TGTAAATATT
*
174257 AAAAAAT-ATATAAA-ATTATTAAATATT-G
1 AAAAAATAATATAAATATTATTAAAAATTCG
*
174285 AATTAAAATAATATAAATATTTTTAAAAATTCG
1 AA--AAAATAATATAAATATTATTAAAAATTCG
174318 AAAAAATAATAT
1 AAAAAATAATAT
174330 TTACAGACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 2 0.05
30 5 0.13
31 17 0.45
32 11 0.29
33 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAATAATATAAATATTATTAAAAATTCG
Found at i:174639 original size:22 final size:22
Alignment explanation
Indices: 174611--174656 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
174601 CTTCCAACAC
*
174611 AAGTATGAAATGTTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
174633 AAGTATGAAATATTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
174655 AA
1 AA
174657 TTTCAAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (22 bp):
AAGTATGAAATATTTATGAGCA
Found at i:181991 original size:3 final size:3
Alignment explanation
Indices: 181983--182022 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
181973 TATATACTAT
181983 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
182023 AAGTGGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:182621 original size:31 final size:31
Alignment explanation
Indices: 182586--182644 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
182576 AATAGCACAA
182586 TGACTTAAAT-AAAATCTTTCGAATAGTTTAT
1 TGACTTAAATGAAAA-CTTTCGAATAGTTTAT
* *
182617 TGACTTGAATGAAAACTTTTGAATAGTT
1 TGACTTAAATGAAAACTTTCGAATAGTT
182645 CAATGATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCGAATAGTTTAT
Found at i:185605 original size:28 final size:27
Alignment explanation
Indices: 185566--185626 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
185556 TTTAGTGTAG
* * *
185566 AAAATATTAAATTAATT-TTATTTTATT
1 AAAAAATTAAATAAATTATT-TTTTATA
185593 AAAAAATTGAAATAAATTATTTTTTATA
1 AAAAAATT-AAATAAATTATTTTTTATA
185621 AAAAAA
1 AAAAAA
185627 ATATTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 20 0.69
29 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAAAATTAAATAAATTATTTTTTATA
Found at i:192789 original size:16 final size:16
Alignment explanation
Indices: 192768--192800 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
192758 TTTATATAAT
*
192768 TAAAAATTGAAGTTGG
1 TAAAAATAGAAGTTGG
192784 TAAAAATAGAAGTTGG
1 TAAAAATAGAAGTTGG
192800 T
1 T
192801 TGGGTTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (16 bp):
TAAAAATAGAAGTTGG
Found at i:193394 original size:4 final size:4
Alignment explanation
Indices: 193385--193410 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
193375 TTGATGATGA
193385 GCCT GCCT GCCT GCCT GCCT GCCT GC
1 GCCT GCCT GCCT GCCT GCCT GCCT GC
193411 TTACATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.27, T:0.23
Consensus pattern (4 bp):
GCCT
Found at i:198927 original size:16 final size:15
Alignment explanation
Indices: 198901--198930 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
198891 TTACTCACCC
198901 TGTTATCACTTTTCT
1 TGTTATCACTTTTCT
198916 TGTTACTCACTTTTC
1 TGTTA-TCACTTTTC
198931 AGTTCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (15 bp):
TGTTATCACTTTTCT
Found at i:202263 original size:22 final size:22
Alignment explanation
Indices: 202220--202260 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
202210 CGAATATAAT
202220 AAATATTTATTTTTTATTTTTA
1 AAATATTTATTTTTTATTTTTA
*
202242 AAATA-CT-TTTTTTATTTTT
1 AAATATTTATTTTTTATTTTT
202261 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 1 0.06
22 5 0.28
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
AAATATTTATTTTTTATTTTTA
Found at i:202280 original size:28 final size:27
Alignment explanation
Indices: 202217--202281 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
202207 GCCCGAATAT
*
202217 AATAAA-TATTTATTTTTTATTTTTAA
1 AATAAATTTTTTATTTTTTATTTTTAA
**
202243 AATACTTTTTTTATTTTTTTATTTTTAA
1 AATAAATTTTTTA-TTTTTTATTTTTAA
202271 AATAAATTTTT
1 AATAAATTTTT
202282 GGTGTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 4 0.12
27 5 0.16
28 23 0.72
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
AATAAATTTTTTATTTTTTATTTTTAA
Found at i:210354 original size:22 final size:22
Alignment explanation
Indices: 210329--210399 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
210319 TAAATGAAGG
210329 AGTAATTGTTGCGAGATTAAAA
1 AGTAATTGTTGCGAGATTAAAA
* ** * * **
210351 AGTAAGAATGTT-TTAAATGAAGG
1 AGT-A-ATTGTTGCGAGATTAAAA
210374 AGTAATTGTTGCGAGATTAAAA
1 AGTAATTGTTGCGAGATTAAAA
210396 AGTA
1 AGTA
210400 GTTAAATTTT
Statistics
Matches: 32, Mismatches: 14, Indels: 6
0.62 0.27 0.12
Matches are distributed among these distances:
21 5 0.16
22 13 0.41
23 9 0.28
24 5 0.16
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (22 bp):
AGTAATTGTTGCGAGATTAAAA
Found at i:210360 original size:45 final size:45
Alignment explanation
Indices: 210309--210399 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
210299 CATTGAGGAG
210309 AAGAATGTTTTAAATGAAGGAGTAATTGTTGCGAGATTAAAAAGT
1 AAGAATGTTTTAAATGAAGGAGTAATTGTTGCGAGATTAAAAAGT
210354 AAGAATGTTTTAAATGAAGGAGTAATTGTTGCGAGATTAAAAAGT
1 AAGAATGTTTTAAATGAAGGAGTAATTGTTGCGAGATTAAAAAGT
210399 A
1 A
210400 GTTAAATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (45 bp):
AAGAATGTTTTAAATGAAGGAGTAATTGTTGCGAGATTAAAAAGT
Found at i:219006 original size:21 final size:21
Alignment explanation
Indices: 218980--219020 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
218970 ATCTGCTCAA
* *
218980 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
219001 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
219021 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:227847 original size:13 final size:14
Alignment explanation
Indices: 227828--227869 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
227818 TTACAGAAAA
*
227828 GTAAAATATTTTTC
1 GTAAAATATTTTAC
227842 -TAAAATCATTTTAC
1 GTAAAAT-ATTTTAC
*
227856 GAAAAATATTTTAC
1 GTAAAATATTTTAC
227870 TGGCAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 6 0.25
14 13 0.54
15 5 0.21
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (14 bp):
GTAAAATATTTTAC
Found at i:227853 original size:34 final size:34
Alignment explanation
Indices: 227795--227860 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
227785 CAAACACCAG
227795 AAAATATTTTCCAATAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAATAAATCATTTTAC-GAAAAGT
* *
227830 AAAATATTTTTCTA-AAATCATTTTACGAAAA
1 AAAATATTTTCCAATAAATCATTTTACGAAAA
227861 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (34 bp):
AAAATATTTTCCAATAAATCATTTTACGAAAAGT
Found at i:228628 original size:15 final size:15
Alignment explanation
Indices: 228608--228650 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
228598 TGGCACCAAA
228608 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
228623 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
* *
228638 AGCGGAGGAGAAG
1 AGCTGAGAAGAAG
228651 AAGACGGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.40, T:0.05
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:234397 original size:322 final size:322
Alignment explanation
Indices: 233806--234778 Score: 1937
Period size: 322 Copynumber: 3.0 Consensus size: 322
233796 TATATTATGT
233806 TAATGTACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTT
1 TAATG-ACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTT
233871 ACTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTT
65 ACTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTT
233936 ATCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAG
130 ATCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAG
234001 AAATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTC
195 AAATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTC
234066 AATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
260 AATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
234129 TAATGACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTTA
1 TAATGACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTTA
234194 CTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTTA
66 CTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTTA
234259 TCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAGA
131 TCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAGA
234324 AATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTCA
196 AATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTCA
234389 ATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
261 ATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
234451 TAATGACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTTA
1 TAATGACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTTA
234516 CTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTTA
66 CTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTTA
234581 TCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAGA
131 TCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAGA
234646 AATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTCA
196 AATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTCA
234711 ATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
261 ATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
234773 TAATGA
1 TAATGA
234779 GGTAAAAATA
Statistics
Matches: 650, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
322 645 0.99
323 5 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (322 bp):
TAATGACAGAGACCAATTTTTAAGAGTAAAAATAGATTAAAAAAATTAATAAAATAACCAATTTA
CTATTTGATCTAATGTAAATTGGTAGAATTAGATTCATAAGTTGAAGGTTTAGGTTTGAGTTTTA
TCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATTGTACTCGTTATCCATTGAGCAAAGAGA
AATTAAAGATCAAAAATCAAACAACTCATAAAAATTAAACCCTAATTTTGAAATCAATCACTTCA
ATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAATTCCTTTCTAGAAGAGAAAGAAAA
Found at i:236157 original size:839 final size:824
Alignment explanation
Indices: 234554--236204 Score: 1846
Period size: 839 Copynumber: 2.0 Consensus size: 824
234544 TTAGATTCAT
* *
234554 AAGTTGAAGGTTTAGGTTTGAGTTTTATCATACTCGTTAAGCTTTACCACCAAACCAAAGCGATT
1 AAGTTGAAAGTTTAGGTTTGAGTTTTATCATACTCGTTAAGCTTTACCACCAAACCAAAGCCATT
* * * * * *
234619 GTACTCGTTATCCATTGAGCAAAGAGAAATTAAAGATCAAAAATCAAACAACTCATAAAAATTAA
66 ATACTCATTATCCATTAAGCAAAAAGAAATTAAAGATAAAAAATCAAACAACCCATAAAAATTAA
* * * * * * * * * * *
234684 ACCCTAATTTTGAAATCAATCACTTCAATTTTAAGTAAGAAGTGAAGACACGTGAAACCCTTAAA
131 ACCCCAAATCTGAAATCAATCACTTCAATATCAAGAAAAAAGTAAAAACAAGTGAAACCATTAAA
* *
234749 TTCCTTTCTAGAAGAGAAAGAAAATAATGAGGTAAAAATAATTATTTGATACAAAACAAAAAGGC
196 TTCCTTTCCAGAAGAGAAAGAAAATAAGGAGGTAAAAATAATTATTTGATACAAAACAAAAAGGC
* * * * *
234814 AAAGAGACCAATAAACAAACAAGAGAAAATACAGCTTTCATGAAATCAAATGATTAAAATTGGGG
261 AAAGAGACAAATAAACAAACAAGAAAAAATACAGCTTTCATAAAATCAAAGGATTAAAATTAGGG
* *
234879 AAAAAAAGAAAATAATACCTGAATTTCCCCTCTATTTTCTCTCTTTGATAGTTGGAACAAAACTT
326 AAAAAAAGAAAATAAAACCTGAATTTCCCCTCTATTTTCTCTCTTTCATAGTTGGAACAAAACTT
*
234944 CATCTTTTCAGGATTTGTTAACAATTGTATTGAATTTTTACATAAAGGGATTGTTCTAAAGAGAG
391 CATCTTTTCAGGATTTGTTAACAATTGCATTGAATTTTTACATAAAGGGATTGTTCTAAAGAGAG
* ** *
235009 AAAAATACAACAGAGAAAGATAAACAAAGAGGTTGAAAATAATTTTAATTATTGGTAACTGTCAC
456 AAAAATACAACAGAGAAAGACAAACAAAGAAATTAAAAATAATTTTAATTATTGGTAACTGTCAC
**
235074 TCAACTTGTCATTTAAACAACTCCAATAAAAACCCTAACTAGACATTAGAAGAAGAAGAGAAAAA
521 TCAACTTGGAATTTAAACAACTCCAATAAAAACCCTAACTAGACATTAGAAGAAGAAGAGAAAAA
*
235139 AAAAACCCTAACATAGACTCCAACGTGGCTAGTTAAATGCCGCGCCAATTTATCGTAACGTTTGT
586 AAAAA-CCTAACATAGACTCCAACGTGGCTAGTTAAATGCCACGCCAATTTATCGTAACGTTTGT
* * * * * *
235204 AACAGAAAATGGTTAGTAGGACCGATTTGTTGTTTTTTGAATGTTGATTGGCTGTTTTATCATTG
650 AACAGAAAATGGTTAATAGGACCAATTTGTTATTTTTTGAAAGTTGAGTGGCTATTTTATCATTG
* * *
235269 GAATCAAAATTAAACAACTGTTGGACATGAGGAGCGGAAGGGTCTTCTTCATT-TTCTAAAA-C-
715 AAATCAAAATTAAACAACTGTTGGACATGAGGAGCGAAAGAGTCTTCTTC-TTCTTCTAAAATCG
235331 GACCCTTCTTTCTTTTCCC-CTATTTTCTTCATAGAATTTGATTTTG
779 GACCCTTCTTTCTTTTCCCTC-ATTTTCTTCATAGAATTTGATTTTG
* * * *
235377 AAGTTGAAAGTTTGGGTTTGGGTTTTGTCATACTCGTTAAGCTTTACCACCAAA-CAAGGACCAT
1 AAGTTGAAAGTTTAGGTTTGAGTTTTATCATACTCGTTAAGCTTTACCACCAAACCAAAG-CCAT
*
235441 TATACTCATTATCCATTAAGCAAAAAGAAATTAAATATAAAAAATCAAACAACAACCCATAAAAA
65 TATACTCATTATCCATTAAGCAAAAAGAAATTAAAGATAAAAAATC--A-AACAACCCATAAAAA
* *
235506 TTAAACCCCAAATCTGAAAT-AAGTCGCTTTAATATCAAGAAAAAAGTCAAATAATCAAAAGATA
127 TTAAACCCCAAATCTGAAATCAA-TCACTTCAATATCAAGAAAAAAGT-AAA-AA-C--AAG---
** * *
235570 AATGAAACCATT-AATGTTTTTTCCA-AACGAGAAAGGAAATAAGGAGGTAAAAATAATTGTTTG
183 --TGAAACCATTAAAT-TCCTTTCCAGAA-GAGAAAGAAAATAAGGAGGTAAAAATAATTATTTG
* * * * *
235633 TTACAAAACAAATAA-GCAAAGAGACAAATAAGCAAAC-GGAAAAAATATAGCTTTCATAAAATT
244 ATACAAAACAAA-AAGGCAAAGAGACAAATAAACAAACAAGAAAAAATACAGCTTTCATAAAATC
*
235696 AAAGGATTAAAATTAGGGAAAAAAATAAAATAAAACCTGAATTTCCCCTCTATTTTCTCTCTTTC
308 AAAGGATTAAAATTAGGGAAAAAAAGAAAATAAAACCTGAATTTCCCCTCTATTTTCTCTCTTTC
* * * * * **
235761 ATCGTTGGAAGAAACCTTATCTTCGTCTTTTTAGGATTTGTTAACAATTGCATTGAGTTTTTGGA
373 ATAGTTGGAACAAA----A-CTTCATCTTTTCAGGATTTGTTAACAATTGCATTGAATTTTTACA
* * * *
235826 TGAAGGGATTGTTCTAAAGGGAGAAAAATATAACAGAGAAAGACAAACAAATAAATTAAAAATAA
433 TAAAGGGATTGTTCTAAAGAGAGAAAAATACAACAGAGAAAGACAAACAAAGAAATTAAAAATAA
*** * * ** *
235891 TTTTAAGTT-TTGGTAACTGTCACTCAACTTGGAATTTTTTTTC-CCTTCTTC-TTATACTATCC
498 TTTTAA-TTATTGGTAACTGTCACTCAACTTGGAA--TTTAAACAAC-TC--CAATA-AAAACCC
* *** *** ** ** * *** ** * *
235953 -AATTAGGGTTTTTTA-TCGGGGTTG-TTTAAATGA-C-AACATCGGCTCCAACGTGGCT-GTTT
556 TAACTAGACATTAGAAGAAGAAG-AGAAAAAAAAAACCTAACATAGACTCCAACGTGGCTAG-TT
* * * * * *
236012 AAATGCCATGTCAATTTGTCGTTACGTTTGTAACAGAAAATGGTTAATATGACTAATTTGTTATT
619 AAATGCCACGCCAATTTATCGTAACGTTTGTAACAGAAAATGGTTAATAGGACCAATTTGTTATT
* * * **
236077 TTTTGAAAGTTGAGTGTCTATTTTATTATTGAAATGAAAATTAAATGACTGTTGGACATGAGGAG
684 TTTTGAAAGTTGAGTGGCTATTTTATCATTGAAATCAAAATTAAACAACTGTTGGACATGAGGAG
*
236142 CGAAAGAGTCTTCTTCTTCTTCTAAAATCGGTCCCTTCTTTCTTTTCCCTCATTTTCTTCATA
749 CGAAAGAGTCTTCTTCTTCTTCTAAAATCGGACCCTTCTTTCTTTTCCCTCATTTTCTTCATA
236205 TTTTTTCTTT
Statistics
Matches: 680, Mismatches: 112, Indels: 54
0.80 0.13 0.06
Matches are distributed among these distances:
822 4 0.01
823 93 0.14
825 3 0.00
826 49 0.07
827 2 0.00
828 1 0.00
829 1 0.00
831 2 0.00
835 98 0.14
836 78 0.11
837 2 0.00
838 3 0.00
839 155 0.23
840 127 0.19
841 33 0.05
842 13 0.02
843 11 0.02
844 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (824 bp):
AAGTTGAAAGTTTAGGTTTGAGTTTTATCATACTCGTTAAGCTTTACCACCAAACCAAAGCCATT
ATACTCATTATCCATTAAGCAAAAAGAAATTAAAGATAAAAAATCAAACAACCCATAAAAATTAA
ACCCCAAATCTGAAATCAATCACTTCAATATCAAGAAAAAAGTAAAAACAAGTGAAACCATTAAA
TTCCTTTCCAGAAGAGAAAGAAAATAAGGAGGTAAAAATAATTATTTGATACAAAACAAAAAGGC
AAAGAGACAAATAAACAAACAAGAAAAAATACAGCTTTCATAAAATCAAAGGATTAAAATTAGGG
AAAAAAAGAAAATAAAACCTGAATTTCCCCTCTATTTTCTCTCTTTCATAGTTGGAACAAAACTT
CATCTTTTCAGGATTTGTTAACAATTGCATTGAATTTTTACATAAAGGGATTGTTCTAAAGAGAG
AAAAATACAACAGAGAAAGACAAACAAAGAAATTAAAAATAATTTTAATTATTGGTAACTGTCAC
TCAACTTGGAATTTAAACAACTCCAATAAAAACCCTAACTAGACATTAGAAGAAGAAGAGAAAAA
AAAAACCTAACATAGACTCCAACGTGGCTAGTTAAATGCCACGCCAATTTATCGTAACGTTTGTA
ACAGAAAATGGTTAATAGGACCAATTTGTTATTTTTTGAAAGTTGAGTGGCTATTTTATCATTGA
AATCAAAATTAAACAACTGTTGGACATGAGGAGCGAAAGAGTCTTCTTCTTCTTCTAAAATCGGA
CCCTTCTTTCTTTTCCCTCATTTTCTTCATAGAATTTGATTTTG
Found at i:238402 original size:26 final size:27
Alignment explanation
Indices: 238321--238403 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
238311 TTTTCTTCAT
*
238321 ATTTTTTAATAATATAAAGAACTATGA
1 ATTTTTTAATAACATAAAGAACTATGA
*
238348 ATTTTTTAATAACTTAAAATGAAGGACTATG-
1 ATTTTTTAATAACAT-AAA-G-A--ACTATGA
* *
238379 GTTTTTGAATAACATAAAGAACTAT
1 ATTTTTTAATAACATAAAGAACTAT
238404 AAGCTTTGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
26 5 0.11
27 13 0.28
28 4 0.09
29 2 0.04
30 4 0.09
31 12 0.26
32 6 0.13
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (27 bp):
ATTTTTTAATAACATAAAGAACTATGA
Found at i:244492 original size:19 final size:20
Alignment explanation
Indices: 244454--244494 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
244444 TATTTTATGA
**
244454 TACTATTATTTGTTTATTAT
1 TACTATTATTTGCATATTAT
244474 TACTATTA-TTGCATATTAT
1 TACTATTATTTGCATATTAT
244493 TA
1 TA
244495 TTAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (20 bp):
TACTATTATTTGCATATTAT
Found at i:244510 original size:19 final size:21
Alignment explanation
Indices: 244467--244512 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
244457 TATTATTTGT
*
244467 TTATTATTACTATTATTGCATA
1 TTATTATTAATATTATTGCA-A
244489 TTATTATTAATATTATT-C-A
1 TTATTATTAATATTATTGCAA
244508 TTATT
1 TTATT
244513 TTCATGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATTATTAATATTATTGCAA
Found at i:252751 original size:30 final size:28
Alignment explanation
Indices: 252693--252747 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
252683 CCCATGTTCA
*
252693 ATATTCTTTATTTTTGTTGAAAATAATT
1 ATATTCTTTATTTTTGGTGAAAATAATT
252721 ATATTCTAATTATTTTTGGT-AAAATAA
1 ATATTCT--TTATTTTTGGTGAAAATAA
252748 ATTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 7 0.29
30 10 0.42
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (28 bp):
ATATTCTTTATTTTTGGTGAAAATAATT
Found at i:253147 original size:33 final size:33
Alignment explanation
Indices: 253088--253158 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
253078 ATCCATATTA
*
253088 TATTTTAATTTTTTAAAAAATATTTATATTATAT
1 TATTTTAATTATTTAAAAAATATTTATATT-TAT
* *
253122 TATTTTAA-TATTTAATAAAA-GTTTATATTTTT
1 TATTTTAATTATTTAA-AAAATATTTATATTTAT
253154 TATTT
1 TATTT
253159 ATTGAAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 7 0.21
33 14 0.42
34 12 0.36
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTTTAATTATTTAAAAAATATTTATATTTAT
Found at i:257400 original size:18 final size:16
Alignment explanation
Indices: 257368--257403 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
257358 ATGGGATGAG
257368 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
257384 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
257402 AA
1 AA
257404 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:279747 original size:19 final size:20
Alignment explanation
Indices: 279725--279763 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
279715 TAAGTTTTCT
*
279725 AAAATTTTAAATAT-ATTAA
1 AAAATGTTAAATATAATTAA
*
279744 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
279764 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATGTTAAATATAATTAA
Found at i:279771 original size:43 final size:40
Alignment explanation
Indices: 279724--279804 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 40
279714 TTAAGTTTTC
279724 TAAAATTTTAAATATATTAAAAAATGTTAAGTATAATTAATTT
1 TAAAATTTT-AATATATT-AAAAATGTTAA-TATAATTAATTT
* *
279767 TAAAATTTTAATATATTTAAAATGTTAATATACTTAAT
1 TAAAATTTTAATATATTAAAAATGTTAATATAATTAAT
279805 ATATATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 9 0.25
41 10 0.28
42 8 0.22
43 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (40 bp):
TAAAATTTTAATATATTAAAAATGTTAATATAATTAATTT
Found at i:279787 original size:17 final size:17
Alignment explanation
Indices: 279765--279803 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
279755 TATAATTAAT
*
279765 TTTAAAATTTTAATATA
1 TTTAAAATGTTAATATA
279782 TTTAAAATGTTAATATA
1 TTTAAAATGTTAATATA
*
279799 CTTAA
1 TTTAA
279804 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTAAAATGTTAATATA
Found at i:279918 original size:19 final size:17
Alignment explanation
Indices: 279870--279920 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
279860 AAAAAACTTA
*
279870 AAAAAATTGAATATATT
1 AAAAAATTAAATATATT
*
279887 AAAAAATTGAATATATT
1 AAAAAATTAAATATATT
279904 AAAAAATGTTAAATATA
1 AAAAAA--TTAAATATA
279921 ACCAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 23 0.74
19 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAAAAATTAAATATATT
Found at i:279919 original size:17 final size:17
Alignment explanation
Indices: 279870--279910 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
279860 AAAAAACTTA
279870 AAAAAATTGAATATATT
1 AAAAAATTGAATATATT
279887 AAAAAATTGAATATATT
1 AAAAAATTGAATATATT
279904 AAAAAAT
1 AAAAAAT
279911 GTTAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAAATTGAATATATT
Found at i:279933 original size:61 final size:63
Alignment explanation
Indices: 279867--279993 Score: 170
Period size: 62 Copynumber: 2.1 Consensus size: 63
279857 TTTAAAAAAC
* *
279867 TTAAAAAAATT-GAATATATTAAAAAATTGAATATA-TTAAAAAATGTTAAATATAACCAATT
1 TTAAAAAAATTAAAATATATTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATT
** * * *
279928 TT-AAAATTTTAAAATATTTTTAAAAATTAAATATATTTAAAAAATGTTAAGTATAACCAATT
1 TTAAAAAAATTAAAATATATTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATT
279990 TTAA
1 TTAA
279994 TATTTAATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 6 0.11
61 22 0.39
62 27 0.48
63 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (63 bp):
TTAAAAAAATTAAAATATATTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATT
Found at i:279952 original size:62 final size:62
Alignment explanation
Indices: 279885--280011 Score: 195
Period size: 62 Copynumber: 2.1 Consensus size: 62
279875 ATTGAATATA
*
279885 TTAAAAAATTGAATATA-TTAAAAAATGTTAAATATAACCAATTTTAAAATTTTAAAATATTT
1 TTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATTTTAAAA-TTTAAAATATTT
* * *
279947 TT-AAAAATTAAATATATTTAAAAAATGTTAAGTATAACCAATTTTAATATTTAATATATTT
1 TTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATTTTAAAATTTAAAATATTT
280008 TTAA
1 TTAA
280012 TAGGTAAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 26 0.44
62 33 0.56
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (62 bp):
TTAAAAAATTAAATATATTTAAAAAATGTTAAATATAACCAATTTTAAAATTTAAAATATTT
Found at i:279971 original size:19 final size:19
Alignment explanation
Indices: 279867--279971 Score: 56
Period size: 18 Copynumber: 5.4 Consensus size: 19
279857 TTTAAAAAAC
*
279867 TTAAAAAAATTGAATATA-
1 TTAAAAAAATTAAATATAT
*
279885 TT-AAAAAATTGAATATA-
1 TTAAAAAAATTAAATATAT
*
279902 TTAAAAAATGTTAAATATAACCAAT
1 TTAAAAAA-ATTAAATAT-----AT
* **
279927 TTTAAAATTTTAAA-ATAT
1 TTAAAAAAATTAAATATAT
**
279945 TTTTAAAAATTAAATATAT
1 TTAAAAAAATTAAATATAT
279964 TTAAAAAA
1 TTAAAAAA
279972 TGTTAAGTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
17 17 0.25
18 20 0.29
19 17 0.25
23 2 0.03
24 6 0.09
25 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAAAAATTAAATATAT
Found at i:280000 original size:61 final size:61
Alignment explanation
Indices: 279879--280011 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
279869 AAAAAAATTG
* * *
279879 AATATATTAAAAAATTGAATATATTAAAAAATGTTAAATATAACCAATTTTAAAATTTTAA
1 AATATTTTTAAAAATTAAATATATTAAAAAATGTTAAATATAACCAATTTTAAAATTTTAA
* *
279940 AATATTTTTAAAAATTAAATATATTTAAAAAATGTTAAGTATAACCAATTTTAATA-TTTAA
1 AATATTTTTAAAAATTAAATATA-TTAAAAAATGTTAAATATAACCAATTTTAAAATTTTAA
*
280001 TATATTTTTAA
1 AATATTTTTAA
280012 TAGGTAAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 35 0.54
62 30 0.46
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (61 bp):
AATATTTTTAAAAATTAAATATATTAAAAAATGTTAAATATAACCAATTTTAAAATTTTAA
Found at i:284411 original size:2 final size:2
Alignment explanation
Indices: 284404--284431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
284394 GTAAAAATTA
284404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
284432 CTTATTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:286109 original size:22 final size:22
Alignment explanation
Indices: 286079--286120 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
286069 CCTTTCAAAA
*
286079 AAACATAATAT-TATTTATGGT
1 AAACATAATATACATTTATGGT
286100 AAACAATAATATACATTTATG
1 AAAC-ATAATATACATTTATG
286121 TGAATGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (22 bp):
AAACATAATATACATTTATGGT
Found at i:292698 original size:20 final size:20
Alignment explanation
Indices: 292675--292713 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
292665 ATTAAAAATT
292675 TTGAACTAAA-ATGGTCTTAA
1 TTGAA-TAAATATGGTCTTAA
*
292695 TTGAATAAATATTGTCTTA
1 TTGAATAAATATGGTCTTA
292714 TAGGGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TTGAATAAATATGGTCTTAA
Found at i:293745 original size:59 final size:58
Alignment explanation
Indices: 293674--293865 Score: 145
Period size: 59 Copynumber: 3.3 Consensus size: 58
293664 AAATAATTTT
293674 TTAATAGCTTAGTGACCATTTTGTAACTTTTTGAAATTAATAACTAAAACGTAAGCTTA
1 TTAATAGCTTAGTGACCATTTTGTAACTTTTTGAAATTAATAACTAAAAC-TAAGCTTA
* * *** * * ** * ** ** *
293733 TTAATAGTTTAGTGACTAAAATGAAAAC-TATCAAATATTTTATGTCTAAAA-TAATTTTT
1 TTAATAGCTTAGTGACCATTTTG-TAACTTTTTGAA-A-TTAATAACTAAAACTAAGCTTA
* * * *
293792 TTAAGAGCTTAGTGACCATTTTGTAATTTTTTGAAATTAACAACTGAAACATAAGCTTA
1 TTAATAGCTTAGTGACCATTTTGTAACTTTTTGAAATTAATAACTAAAAC-TAAGCTTA
*
293851 TTAATAGTTTAGTGA
1 TTAATAGCTTAGTGA
293866 TACTGGGAGT
Statistics
Matches: 91, Mismatches: 36, Indels: 12
0.65 0.26 0.09
Matches are distributed among these distances:
57 8 0.09
58 3 0.03
59 66 0.73
60 4 0.04
61 10 0.11
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (58 bp):
TTAATAGCTTAGTGACCATTTTGTAACTTTTTGAAATTAATAACTAAAACTAAGCTTA
Found at i:293891 original size:118 final size:117
Alignment explanation
Indices: 293618--293865 Score: 415
Period size: 118 Copynumber: 2.1 Consensus size: 117
293608 AAAACGTTTG
* * * *
293618 AATAGTTTAGTGACTAAAATGAAAATTATCAAATATTTCAGGTCTAAAATAATTTTTTAATAGCT
1 AATAGTTTAGTGACTAAAATGAAAACTATCAAATATTTTATGTCTAAAATAATTTTTTAAGAGCT
* *
293683 TAGTGACCATTTTGTAACTTTTTGAAATTAATAACTAAAACGTAAGCTTATT
66 TAGTGACCATTTTGTAACTTTTTGAAATTAACAACTAAAACATAAGCTTATT
293735 AATAGTTTAGTGACTAAAATGAAAACTATCAAATATTTTATGTCTAAAATAATTTTTTTAAGAGC
1 AATAGTTTAGTGACTAAAATGAAAACTATCAAATATTTTATGTCTAAAATAA-TTTTTTAAGAGC
* *
293800 TTAGTGACCATTTTGTAATTTTTTGAAATTAACAACTGAAACATAAGCTTATT
65 TTAGTGACCATTTTGTAACTTTTTGAAATTAACAACTAAAACATAAGCTTATT
293853 AATAGTTTAGTGA
1 AATAGTTTAGTGA
293866 TACTGGGAGT
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
117 49 0.40
118 73 0.60
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (117 bp):
AATAGTTTAGTGACTAAAATGAAAACTATCAAATATTTTATGTCTAAAATAATTTTTTAAGAGCT
TAGTGACCATTTTGTAACTTTTTGAAATTAACAACTAAAACATAAGCTTATT
Found at i:297615 original size:26 final size:26
Alignment explanation
Indices: 297579--297628 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
297569 TCTATTTTTC
*
297579 AATAGTTTAATATCACATCAGTAAAA
1 AATAATTTAATATCACATCAGTAAAA
*
297605 AATAATTTAATATCATATCAGTAA
1 AATAATTTAATATCACATCAGTAA
297629 TTTCATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (26 bp):
AATAATTTAATATCACATCAGTAAAA
Found at i:310980 original size:24 final size:24
Alignment explanation
Indices: 310953--311001 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
310943 TATTTTTTTC
310953 ATATATTTTATATAAAATAAATAA
1 ATATATTTTATATAAAATAAATAA
310977 ATATATTTTATATAAAATAAATAA
1 ATATATTTTATATAAAATAAATAA
311001 A
1 A
311002 AATTCACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATATTTTATATAAAATAAATAA
Found at i:336008 original size:21 final size:19
Alignment explanation
Indices: 335971--336017 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
335961 AATAAACACC
335971 AAAAAA-ATTTTAGAAAATTT
1 AAAAAATATTTTAGAAAA--T
**
335991 AAAAAATATTTTTTAAAAT
1 AAAAAATATTTTAGAAAAT
336010 AAAAAATA
1 AAAAAATA
336018 AATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAAATATTTTAGAAAAT
Found at i:337286 original size:22 final size:22
Alignment explanation
Indices: 337261--337306 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
337251 TTTTGAGCAA
337261 TTTAA-TTT-TTTTCTTTTATTCT
1 TTTAACTTTCTTTT-TTTT-TTCT
337283 TTTAACTTTCTTTTTTTTTTCT
1 TTTAACTTTCTTTTTTTTTTCT
337305 TT
1 TT
337307 ATTTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTAACTTTCTTTTTTTTTTCT
Found at i:342624 original size:17 final size:17
Alignment explanation
Indices: 342591--342625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
342581 AAAGAAAACC
* *
342591 ATACAATAATTTTAATA
1 ATACAATAACTTAAATA
342608 ATACAATAACTTAAATA
1 ATACAATAACTTAAATA
342625 A
1 A
342626 AAACTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
ATACAATAACTTAAATA
Found at i:347805 original size:29 final size:29
Alignment explanation
Indices: 347773--347838 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
347763 ACCAAAAAAA
347773 GCCGTTTTTTTCAAAATTTACCGAAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
* * ** *
347802 GCCGATTTTTTGATTATTTACCGGAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
*
347831 GCCATTTT
1 GCCGTTTT
347839 CCGCGAAACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (29 bp):
GCCGTTTTTTTCAAAATTTACCGAAATGG
Found at i:356880 original size:9 final size:9
Alignment explanation
Indices: 356866--356921 Score: 94
Period size: 9 Copynumber: 6.2 Consensus size: 9
356856 TCGGGTATTT
*
356866 TTCGGTTAA
1 TTCGGGTAA
*
356875 TTCGGTTAA
1 TTCGGGTAA
356884 TTCGGGTAA
1 TTCGGGTAA
356893 TTCGGGTAA
1 TTCGGGTAA
356902 TTCGGGTAA
1 TTCGGGTAA
356911 TTCGGGTAA
1 TTCGGGTAA
356920 TT
1 TT
356922 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:362733 original size:7 final size:7
Alignment explanation
Indices: 362721--362749 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
362711 AATTTAAATT
362721 TAAAAAA
1 TAAAAAA
362728 TAAAAAA
1 TAAAAAA
362735 TAAAAAA
1 TAAAAAA
362742 TAAAAAA
1 TAAAAAA
362749 T
1 T
362750 TATAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:362932 original size:15 final size:16
Alignment explanation
Indices: 362912--362951 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
362902 TTATATAATA
362912 TATAAAATGTT-TTTT
1 TATAAAATGTTATTTT
*
362927 TATAAAATTTTAATTTT
1 TATAAAATGTT-ATTTT
362944 TATAAAAT
1 TATAAAAT
362952 TCTAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATAAAATGTTATTTT
Found at i:363176 original size:20 final size:19
Alignment explanation
Indices: 363119--363175 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
363109 TTTATAAAAA
*
363119 AATATTTTTA-AACATTTTT
1 AATAATTTTACAA-ATTTTT
363138 AATAATTTTACAAATTTTT
1 AATAATTTTACAAATTTTT
363157 AATAAATTTTAC-AATTTTT
1 AAT-AATTTTACAAATTTTT
363176 TTGTAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 25 0.71
20 10 0.29
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
AATAATTTTACAAATTTTT
Found at i:376921 original size:36 final size:36
Alignment explanation
Indices: 376871--376996 Score: 198
Period size: 36 Copynumber: 3.5 Consensus size: 36
376861 GACCGTTTAC
376871 AGTACTATTCACGTATACGGCACTATTCACGTATAT
1 AGTACTATTCACGTATACGGCACTATTCACGTATAT
* * * *
376907 GGTACTATTTACGTATACGACACTATTCACATATAT
1 AGTACTATTCACGTATACGGCACTATTCACGTATAT
*
376943 AGTACTATTCACGTATACGGCACTATTCACGTATAC
1 AGTACTATTCACGTATACGGCACTATTCACGTATAT
*
376979 AGTACTGTTCACGTATAC
1 AGTACTATTCACGTATAC
376997 AGTAGTTGGG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (36 bp):
AGTACTATTCACGTATACGGCACTATTCACGTATAT
Found at i:376990 original size:54 final size:54
Alignment explanation
Indices: 376868--377000 Score: 169
Period size: 54 Copynumber: 2.5 Consensus size: 54
376858 TACGACCGTT
* * * * *
376868 TACAGTACTATTCACGTATACGGCACTATTCACGTATATGGTACTATTTACGTA
1 TACAGTACTATTCACGTATACAGTACTATTCACGTATACGGCACTATTCACGTA
* * *
376922 TAC-GACACTATTCACATATATAGTACTATTCACGTATACGGCACTATTCACGTA
1 TACAG-TACTATTCACGTATACAGTACTATTCACGTATACGGCACTATTCACGTA
*
376976 TACAGTACTGTTCACGTATACAGTA
1 TACAGTACTATTCACGTATACAGTA
377001 GTTGGGATTG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.02
54 63 0.97
55 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (54 bp):
TACAGTACTATTCACGTATACAGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:376997 original size:18 final size:18
Alignment explanation
Indices: 376868--377000 Score: 151
Period size: 18 Copynumber: 7.4 Consensus size: 18
376858 TACGACCGTT
376868 TACAGTACTATTCACGTA
1 TACAGTACTATTCACGTA
* *
376886 TACGGCACTATTCACGTA
1 TACAGTACTATTCACGTA
** *
376904 TATGGTACTATTTACGTA
1 TACAGTACTATTCACGTA
* *
376922 TAC-GACACTATTCACATA
1 TACAG-TACTATTCACGTA
*
376940 TATAGTACTATTCACGTA
1 TACAGTACTATTCACGTA
* *
376958 TACGGCACTATTCACGTA
1 TACAGTACTATTCACGTA
*
376976 TACAGTACTGTTCACGTA
1 TACAGTACTATTCACGTA
376994 TACAGTA
1 TACAGTA
377001 GTTGGGATTG
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
17 1 0.01
18 93 0.98
19 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (18 bp):
TACAGTACTATTCACGTA
Found at i:385898 original size:25 final size:26
Alignment explanation
Indices: 385848--385899 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
385838 GTTGGTTTGC
385848 TGGGCTAGGCTTAATGGGTTTAAGTT
1 TGGGCTAGGCTTAATGGGTTTAAGTT
385874 TGGGCTAGG-TTAATAGGGTTT-AGTT
1 TGGGCTAGGCTTAAT-GGGTTTAAGTT
385899 T
1 T
385900 ACTGGGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.40
Consensus pattern (26 bp):
TGGGCTAGGCTTAATGGGTTTAAGTT
Found at i:418934 original size:26 final size:28
Alignment explanation
Indices: 418878--418938 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
418868 TGACTTAAAC
418878 CCAAAATGATACCAAAAAAAAAAAAAAAA
1 CCAAAATGATACC-AAAAAAAAAAAAAAA
* *
418907 CCAAAATGATA-C-AAACAAAAAAATAA
1 CCAAAATGATACCAAAAAAAAAAAAAAA
418933 CCAAAA
1 CCAAAA
418939 AATTTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 18 0.60
28 1 0.03
29 11 0.37
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.08
Consensus pattern (28 bp):
CCAAAATGATACCAAAAAAAAAAAAAAA
Found at i:428008 original size:18 final size:18
Alignment explanation
Indices: 427981--428015 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
427971 TGTCACATTA
*
427981 ATAAATAATTAAAAAATC
1 ATAAAAAATTAAAAAATC
427999 ATAAAAAATTAAAAAAT
1 ATAAAAAATTAAAAAAT
428016 AACATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTAAAAAATC
Found at i:428024 original size:18 final size:18
Alignment explanation
Indices: 427987--428025 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
427977 ATTAATAAAT
* *
427987 AATTAAAAAATCATAAAA
1 AATTAAAAAATAACAAAA
*
428005 AATTAAAAAATAACATAA
1 AATTAAAAAATAACAAAA
428023 AAT
1 AAT
428026 ACTCTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTAAAAAATAACAAAA
Found at i:435735 original size:12 final size:12
Alignment explanation
Indices: 435715--435748 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
435705 GGCCACACGT
* *
435715 CCGTTTCCTTGC
1 CCGTGTCCTAGC
435727 CCGTGTCCTAGC
1 CCGTGTCCTAGC
435739 CCGTGTCCTA
1 CCGTGTCCTA
435749 ACTAGTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.41, G:0.21, T:0.32
Consensus pattern (12 bp):
CCGTGTCCTAGC
Found at i:437941 original size:2 final size:2
Alignment explanation
Indices: 437891--437930 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
437881 GTATGTTCGA
* * *
437891 AT AT AA AT AT TT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
437931 TCAACATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:441792 original size:30 final size:30
Alignment explanation
Indices: 441753--441811 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
441743 CGTATGGCCG
* *
441753 TGTGTCACACACGGTTGAGACACACGCCCT
1 TGTGCCACACACGATTGAGACACACGCCCT
*
441783 TGTGCCACACACGATTGAGACACATGCCC
1 TGTGCCACACACGATTGAGACACACGCCC
441812 GTGTATCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (30 bp):
TGTGCCACACACGATTGAGACACACGCCCT
Found at i:450119 original size:26 final size:26
Alignment explanation
Indices: 450083--450189 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 26
450073 GAAGTTCCGG
*
450083 AGAGCCATTAATCAGGAAGCTTACAA
1 AGAGCCTTTAATCAGGAAGCTTACAA
* * * *
450109 ATAGCCTTTAAT-TGGAAAGC-TCCAG
1 AGAGCCTTTAATCAGG-AAGCTTACAA
*
450134 AGAGCCATTT-ATCAGGAAGCTCACAA
1 AGAGCC-TTTAATCAGGAAGCTTACAA
*
450160 AGAGCCTTTAATTAGGAAGCTTA-AA
1 AGAGCCTTTAATCAGGAAGCTTACAA
450185 AGAGC
1 AGAGC
450190 TAAGGTGTGC
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
25 26 0.41
26 38 0.59
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (26 bp):
AGAGCCTTTAATCAGGAAGCTTACAA
Found at i:450180 original size:51 final size:50
Alignment explanation
Indices: 450072--450180 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 50
450062 AGCCATATCG
* * * *
450072 GGAAGTTCCGGAGAGCCATTAATCAGGAAGCTTACAAATAGCCTTTAATT
1 GGAAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATT
*
450122 GGAAAGCTCCAGAGAGCCATTTATCAGGAAGCTCACAAAGAGCCTTTAATT
1 GG-AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATT
450173 AGGAAGCT
1 -GGAAGCT
450181 TAAAAGAGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.04
51 48 0.92
52 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (50 bp):
GGAAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATT
Found at i:450660 original size:16 final size:15
Alignment explanation
Indices: 450636--450674 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
450626 AAATTTAACA
*
450636 TCAATTTAATACATT
1 TCAATTTAATACAAT
*
450651 TCATATTTAATTCAAT
1 TCA-ATTTAATACAAT
450667 TCAATTTA
1 TCAATTTA
450675 CATCCTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (15 bp):
TCAATTTAATACAAT
Found at i:456645 original size:20 final size:20
Alignment explanation
Indices: 456620--456665 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
456610 CACATACATG
456620 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
456640 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
456660 CCCCTG
1 CCCCTG
456666 AATTGCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.09, C:0.35, G:0.20, T:0.37
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:456730 original size:41 final size:40
Alignment explanation
Indices: 456641--456741 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 40
456631 ACTTCGGTAC
* * *
456641 CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTG
1 CCCTGTTTATACTTCGGTACCACTGAATTGCACATACATG
*
456681 CCCTTGTTTATACTTCGGTACCATTGAATTGCACATACATG
1 CCC-TGTTTATACTTCGGTACCACTGAATTGCACATACATG
* * *
456722 TTCCTGTTTAGACTTTGGTA
1 -CCCTGTTTATACTTCGGTA
456742 ATTATGAATC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.06
41 47 0.90
42 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (40 bp):
CCCTGTTTATACTTCGGTACCACTGAATTGCACATACATG
Found at i:463632 original size:24 final size:24
Alignment explanation
Indices: 463555--463633 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
463545 AAAGAACCTA
* *
463555 TAACGGGTAGCTCCGAAGAGCAGT
1 TAACGAGTAGCTCCGAAGAGCACT
* * *
463579 TAATGGGTAGCTCCGAAGAGCATT
1 TAACGAGTAGCTCCGAAGAGCACT
*
463603 TAACGAGTAGCTCCGAAGAGTACT
1 TAACGAGTAGCTCCGAAGAGCACT
463627 TAACGAG
1 TAACGAG
463634 AAGCACTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (24 bp):
TAACGAGTAGCTCCGAAGAGCACT
Found at i:469807 original size:33 final size:33
Alignment explanation
Indices: 469770--469948 Score: 96
Period size: 33 Copynumber: 5.4 Consensus size: 33
469760 TGACTCTGCC
** * *
469770 ATGGTCTTACATTCGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTCAAAATGCCATAACCCAGCT
**
469803 ATGGTCTTACCA-TCAAAATGCCATAGTCCAGCT
1 ATGGTCTTA-CATTCAAAATGCCATAACCCAGCT
* *** * *
469836 ATGGTCTTACATAT-AAACACTGTCATGGTCTA-AT
1 ATGGTCTTACAT-TCAAA-A-TGCCATAACCCAGCT
* * * * *
469870 CATGGTCTTACGTCCATAGTGCCATAACCCAGTT
1 -ATGGTCTTACATTCAAAATGCCATAACCCAGCT
* * *
469904 ATGGTCTTATCA-TCAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATTCAAAATGCCATAACCCAGCT
469937 ATGGTCTTACAT
1 ATGGTCTTACAT
469949 ATAAATACTG
Statistics
Matches: 109, Mismatches: 27, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
32 4 0.04
33 76 0.70
34 7 0.06
35 22 0.20
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACATTCAAAATGCCATAACCCAGCT
Found at i:469896 original size:101 final size:101
Alignment explanation
Indices: 469768--469983 Score: 333
Period size: 101 Copynumber: 2.1 Consensus size: 101
469758 CATGACTCTG
* * *
469768 CCATGGTCTTACATTCGTAGTGCCATAACCCAGTTATGGTCTTACCATCAAAATGCCATAGTCCA
1 CCATGGTCTTACATCCATAGTGCCATAACCCAGTTATGGTCTTACCATCAAAATGCCATAGCCCA
* * *
469833 GCTATGGTCTTACATATAAACACTGTCATGGTCTAA
66 ACTATGGTCTTACATATAAACACTGCCATGGTCCAA
* * * *
469869 TCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACATCCATAGTGCCATAACCCAGTTATGGTCTTACCATCAAAATGCCATAGCCCA
*
469934 ACTATGGTCTTACATATAAATACTGCCATGGTCCAA
66 ACTATGGTCTTACATATAAACACTGCCATGGTCCAA
469970 CCATGGTCTTACAT
1 CCATGGTCTTACAT
469984 TTGAATAATT
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
CCATGGTCTTACATCCATAGTGCCATAACCCAGTTATGGTCTTACCATCAAAATGCCATAGCCCA
ACTATGGTCTTACATATAAACACTGCCATGGTCCAA
Found at i:470681 original size:2 final size:2
Alignment explanation
Indices: 470674--470711 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
470664 TATTCTACTA
*
470674 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
470712 TTCACTTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:488052 original size:3 final size:3
Alignment explanation
Indices: 488035--488077 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
488025 CCCCAAATAG
*
488035 AAT AAG AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
488078 AAGAAAAGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:488500 original size:30 final size:30
Alignment explanation
Indices: 488465--488529 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
488455 TAACAAAAAA
488465 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
* *
488495 CTCTCAAATTTCTCCTTAGATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
488525 CTCTC
1 CTCTC
488530 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:490706 original size:24 final size:24
Alignment explanation
Indices: 490679--490734 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
490669 CATTTAATAA
* *
490679 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAAATTATTTTTATAT-TTTT
490703 AATAATAAATTATTTTTATATTTTT
1 AATAA-AAATTATTTTTATATTTTT
490728 AATAAAA
1 AATAAAA
490735 TAAAAGTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 19 0.68
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATAAAAATTATTTTTATATTTTT
Found at i:493939 original size:98 final size:96
Alignment explanation
Indices: 493818--493995 Score: 293
Period size: 98 Copynumber: 1.8 Consensus size: 96
493808 GAACTATTGT
* * *
493818 AGAAAAAGAGCATCCATGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCATGCTTGAAG
1 AGAAAAAGAACATCCACGTGAGAGCTTTTTT-AGTAATTTTGCTGACAATGCATCAT-CTTGAAG
493883 CGTTTTTGACACTATTTGTTCAGGAACTACTAC
64 CGTTTTTGACACTATTTGTTCAGGAACTACTAC
* *
493916 AGAAAAAGAACGTCCACGTGAGAGCTTTTTTAGTAATTTTGCTGACAATGCATCCTCTTGAAGCG
1 AGAAAAAGAACATCCACGTGAGAGCTTTTTTAGTAATTTTGCTGACAATGCATCATCTTGAAGCG
493981 TTTTTGACACTATTT
66 TTTTTGACACTATTT
493996 ATTTAGAACT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
96 24 0.32
97 23 0.31
98 28 0.37
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (96 bp):
AGAAAAAGAACATCCACGTGAGAGCTTTTTTAGTAATTTTGCTGACAATGCATCATCTTGAAGCG
TTTTTGACACTATTTGTTCAGGAACTACTAC
Found at i:494150 original size:34 final size:31
Alignment explanation
Indices: 494103--494209 Score: 115
Period size: 33 Copynumber: 3.3 Consensus size: 31
494093 CACAATATTA
*
494103 TTTAAAAAAACTAAACCTTAATTTAATTAATT
1 TTTAAAAATACTAAACC-TAATTTAATTAATT
* *
494135 TTCCTAAAAATACTAAAACCTAATTTTATTTATT
1 TT--TAAAAATACT-AAACCTAATTTAATTAATT
* *
494169 TATTTAAAATCCTAAACCCTAATTTAATTAATT
1 T-TTAAAAATACTAAA-CCTAATTTAATTAATT
494202 TTTAAAAA
1 TTTAAAAA
494210 AACACACTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
32 11 0.18
33 23 0.37
34 22 0.35
35 6 0.10
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTAAAAATACTAAACCTAATTTAATTAATT
Found at i:494184 original size:33 final size:32
Alignment explanation
Indices: 494141--494250 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 32
494131 AATTTTCCTA
*
494141 AAAATACTAAAACCTAATTTTATTTATTTATTT
1 AAAATCCTAAAACCTAATTTTATTTATTT-TTT
* * *
494174 AAAATCCTAAACCCTAA-TTTAATTAATTTTT
1 AAAATCCTAAAACCTAATTTTATTTATTTTTT
494205 AAAA----AAACACACTAAATTTTAATTTATTTTTT
1 AAAATCCTAAA-AC-CT-AATTTT-ATTTATTTTTT
494237 AAAATTCCTAAAAC
1 AAAA-TCCTAAAAC
494251 TCAAAACCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
27 3 0.05
28 1 0.02
29 2 0.03
30 2 0.03
31 10 0.17
32 22 0.37
33 15 0.25
36 2 0.03
37 3 0.05
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATCCTAAAACCTAATTTTATTTATTTTTT
Found at i:494196 original size:67 final size:64
Alignment explanation
Indices: 494113--494248 Score: 170
Period size: 67 Copynumber: 2.1 Consensus size: 64
494103 TTTAAAAAAA
* *
494113 CTAAACCTTAATTTAATTAATTTTCCTAAAAATACTAAAACCT-AATTTT-ATTTATTTATTTAA
1 CTAAACCCTAATTTAATTAATTTT--TAAAAAAAC--AAA-CTAAATTTTAATTTATTT-TTTAA
494176 AA-TC
60 AATTC
*
494180 CTAAACCCTAATTTAATTAATTTTTAAAAAAACACACTAAATTTTAATTTATTTTTTAAAATTC
1 CTAAACCCTAATTTAATTAATTTTTAAAAAAACAAACTAAATTTTAATTTATTTTTTAAAATTC
494244 CTAAA
1 CTAAA
494249 ACTCAAAACC
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
62 2 0.03
63 15 0.24
64 15 0.24
65 8 0.13
67 23 0.37
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (64 bp):
CTAAACCCTAATTTAATTAATTTTTAAAAAAACAAACTAAATTTTAATTTATTTTTTAAAATTC
Found at i:494277 original size:21 final size:20
Alignment explanation
Indices: 494252--494324 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
494242 TCCTAAAACT
494252 CAAAACCCTAAATTATTTTAA
1 CAAAACCCTAAATT-TTTTAA
* * ***
494273 CAAAACTCTAAACTCTACAAA
1 CAAAACCCTAAA-TTTTTTAA
**
494294 CCTAACCCTAAATTTTTTAA
1 CAAAACCCTAAATTTTTTAA
*
494314 CAAAATCCTAA
1 CAAAACCCTAA
494325 CCCTAAAAAC
Statistics
Matches: 36, Mismatches: 15, Indels: 3
0.67 0.28 0.06
Matches are distributed among these distances:
20 12 0.33
21 23 0.64
22 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAAACCCTAAATTTTTTAA
Found at i:494895 original size:3 final size:3
Alignment explanation
Indices: 494887--494960 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
494877 CGAGCGAGAC
* * ** * *
494887 GAA GAA GAA GAA GAT GAC GTT GAA GAT GAA GAA GAA GAA GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
494935 GAA GAG GAA GAG GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
494961 GCCGAGGCTT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.55, C:0.01, G:0.38, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:503544 original size:20 final size:20
Alignment explanation
Indices: 503520--503566 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
503510 AAATTAGTAT
*
503520 CTTTTTATAATATTTTTTTAA
1 CTTTTTAT-ATATTATTTTAA
503541 -TTTTTATATATTATTTTAA
1 CTTTTTATATATTATTTTAA
503560 CTTTTTA
1 CTTTTTA
503567 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
CTTTTTATATATTATTTTAA
Found at i:503596 original size:23 final size:21
Alignment explanation
Indices: 503562--503627 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
503552 TATTTTAACT
* *
503562 TTTTAAAATTTAAAATTATATA
1 TTTTAAATTTTAAAA-AATATA
*
503584 TTTTAGAATTTTATAAAAATTTA
1 TTTTA-AATTTTA-AAAAATATA
503607 TTTTAAACTTTTAAAAAATAT
1 TTTTAAA-TTTTAAAAAATAT
503628 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 14 0.38
23 20 0.54
24 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTAAATTTTAAAAAATATA
Found at i:503630 original size:23 final size:24
Alignment explanation
Indices: 503572--503630 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
503562 TTTTAAAATT
*
503572 TAAAATTATATATTTTAGAATTTTA
1 TAAAAATAT-TATTTTAGAATTTTA
503597 TAAAAAT-TTATTTTA-AACTTTTA
1 TAAAAATATTATTTTAGAA-TTTTA
503620 -AAAAATATTAT
1 TAAAAATATTAT
503631 ATATATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 8 0.26
23 16 0.52
24 1 0.03
25 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAAAATATTATTTTAGAATTTTA
Found at i:503803 original size:19 final size:20
Alignment explanation
Indices: 503779--503816 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
503769 TTAAATATTA
503779 TAATATTTAT-TTTTAAATC
1 TAATATTTATATTTTAAATC
*
503798 TAATATTTTTATTTTAAAT
1 TAATATTTATATTTTAAAT
503817 GAACTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATATTTATATTTTAAATC
Found at i:511801 original size:23 final size:23
Alignment explanation
Indices: 511774--511820 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
511764 TGTTCCACCT
*
511774 TTGTGTTGCGGAAGGTCCATGCA
1 TTGTGTTGCAGAAGGTCCATGCA
511797 TTGTGTTGCAGAAGGTCCATGCA
1 TTGTGTTGCAGAAGGTCCATGCA
511820 T
1 T
511821 AGTCTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (23 bp):
TTGTGTTGCAGAAGGTCCATGCA
Found at i:523235 original size:23 final size:24
Alignment explanation
Indices: 523204--523252 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
523194 ACACATTTAA
523204 TTTAA-TTTTCA-ATATATTATATT
1 TTTAATTTTTCACATATATTA-ATT
* *
523227 TTTACTTTTTCACTTATATTAATT
1 TTTAATTTTTCACATATATTAATT
523251 TT
1 TT
523253 GAAAAGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 7 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATTTTTCACATATATTAATT
Found at i:527924 original size:29 final size:30
Alignment explanation
Indices: 527890--527948 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
527880 TTATAGGGAG
527890 TGGATCAA-GTTAGTCACTATATTATTAAA
1 TGGATCAATGTTAGTCACTATATTATTAAA
* *
527919 TGGATCAATTTTAGTCCCTATATTATTAAA
1 TGGATCAATGTTAGTCACTATATTATTAAA
527949 AAGAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
TGGATCAATGTTAGTCACTATATTATTAAA
Found at i:536209 original size:21 final size:20
Alignment explanation
Indices: 536185--536223 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
536175 ATTATATGAT
*
536185 GTAATTTACAATACATCTATA
1 GTAATATACAATAC-TCTATA
*
536206 GTAATATATAATACTCTA
1 GTAATATACAATACTCTA
536224 ATGTAAACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
GTAATATACAATACTCTATA
Found at i:538370 original size:25 final size:25
Alignment explanation
Indices: 538336--538383 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
538326 TTTTATCAAA
538336 TATAAGTACCACATTAGAAAAAAAC
1 TATAAGTACCACATTAGAAAAAAAC
538361 TATAAGTACCACATTAGAAAAAA
1 TATAAGTACCACATTAGAAAAAA
538384 GTGTCAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (25 bp):
TATAAGTACCACATTAGAAAAAAAC
Found at i:548161 original size:17 final size:18
Alignment explanation
Indices: 548116--548161 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
548106 TTTAATGAAT
*
548116 ATATTTTTTTTACATAAA
1 ATATTTTTTATACATAAA
*
548134 AT-TATTTTTATAC-TCAA
1 ATAT-TTTTTATACATAAA
548151 ATATTTTTTAT
1 ATATTTTTTAT
548162 CAAAACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTTTTTATACATAAA
Found at i:554576 original size:31 final size:31
Alignment explanation
Indices: 554540--554613 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
554530 TGAAAAAAAA
*
554540 TCAAGTACCAAAGCGGATATTGAATCCAAAC
1 TCAAGTACCAAAGCGGACATTGAATCCAAAC
* ** * *
554571 TCAAGTATCAAATTGGACATTTAATCTAAAC
1 TCAAGTACCAAAGCGGACATTGAATCCAAAC
554602 TCATA-TACCAAA
1 TCA-AGTACCAAA
554614 TAATATATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (31 bp):
TCAAGTACCAAAGCGGACATTGAATCCAAAC
Found at i:558904 original size:52 final size:52
Alignment explanation
Indices: 558826--558929 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
558816 AAAATAAGAA
* * *
558826 TAAAAATTTTTCTTTATCAATGTATAAAAAAATTATTCGATTTAAAGCGAAC
1 TAAAAAATTTTCTTTATCAATGTATAAAAAAATTATTCAATTTAAAACGAAC
*
558878 TAAAAAATTTTCTTTATCAATGTATAAAATAATTATTCAATTTAAAACGAAC
1 TAAAAAATTTTCTTTATCAATGTATAAAAAAATTATTCAATTTAAAACGAAC
558930 AGAAAGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (52 bp):
TAAAAAATTTTCTTTATCAATGTATAAAAAAATTATTCAATTTAAAACGAAC
Found at i:558905 original size:24 final size:24
Alignment explanation
Indices: 558825--558911 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 24
558815 AAAAATAAGA
*
558825 ATAAAAATTTTTCTTTATCAATGT
1 ATAAAAAATTTTCTTTATCAATGT
* *
558849 ATAAAAAAATTATTCGATTTA--AAGCGA
1 AT-AAAAAATT-TTC--TTTATCAA-TGT
558876 ACTAAAAAATTTTCTTTATCAATGT
1 A-TAAAAAATTTTCTTTATCAATGT
558901 ATAAAATAATT
1 ATAAAA-AATT
558912 ATTCAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
24 11 0.22
25 13 0.27
26 10 0.20
27 10 0.20
28 5 0.10
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (24 bp):
ATAAAAAATTTTCTTTATCAATGT
Found at i:568682 original size:20 final size:21
Alignment explanation
Indices: 568659--568697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
568649 AGGACATCGG
568659 TTTGCC-AGTTCAACCAGTCA
1 TTTGCCTAGTTCAACCAGTCA
*
568679 TTTGCCTTGTTCAACCAGT
1 TTTGCCTAGTTCAACCAGT
568698 TATTACCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTGCCTAGTTCAACCAGTCA
Done.