Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 177 of 186
Found at i:58686289 original size:9 final size:9
Alignment explanation
Indices: 58686263--58686305 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
58686253 AGTTTTGTAA
58686263 TTTTTGGAC
1 TTTTTGGAC
* *
58686272 TCTTCGGAC
1 TTTTTGGAC
58686281 TTTTTGGAC
1 TTTTTGGAC
58686290 TTTTTGGAC
1 TTTTTGGAC
58686299 TTTTTGG
1 TTTTTGG
58686306 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53
Consensus pattern (9 bp):
TTTTTGGAC
Found at i:58689297 original size:16 final size:15
Alignment explanation
Indices: 58689265--58689296 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58689255 AACATATAAT
*
58689265 AAGATTAATAAAAAA
1 AAGATTGATAAAAAA
58689280 AAGATTGATAAAAAA
1 AAGATTGATAAAAAA
58689295 AA
1 AA
58689297 ATATTGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (15 bp):
AAGATTGATAAAAAA
Found at i:58693134 original size:26 final size:26
Alignment explanation
Indices: 58693105--58693183 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
58693095 AATTGTAATA
*
58693105 AAAAAATAATATGAAATAAATTAAAG
1 AAAAAATAATATAAAATAAATTAAAG
* *
58693131 AAAATATAA-AAAAAAT-AATTAAA-
1 AAAAAATAATATAAAATAAATTAAAG
* *
58693154 ATAAAAAT-ATATTTAAATAAATTTAAG
1 A-AAAAATAATA-TAAAATAAATTAAAG
58693181 AAA
1 AAA
58693184 TCCAGGTTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
23 2 0.05
24 13 0.32
25 9 0.22
26 16 0.39
27 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAAAATAATATAAAATAAATTAAAG
Found at i:58693161 original size:15 final size:16
Alignment explanation
Indices: 58693141--58693174 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58693131 AAAATATAAA
58693141 AAAAATA-ATTAAAAT
1 AAAAATATATTAAAAT
*
58693156 AAAAATATATTTAAAT
1 AAAAATATATTAAAAT
58693172 AAA
1 AAA
58693175 TTTAAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATATATTAAAAT
Found at i:58693768 original size:21 final size:22
Alignment explanation
Indices: 58693733--58693773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58693723 AGTTGGAATG
*
58693733 AATAAAAATTCTATTATTAAAA
1 AATAAAAACTCTATTATTAAAA
*
58693755 AATAAAAACT-TATTTTTAA
1 AATAAAAACTCTATTATTAA
58693774 TGTCAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAAAACTCTATTATTAAAA
Found at i:58694132 original size:24 final size:25
Alignment explanation
Indices: 58694076--58694133 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
58694066 TTCATATATA
*
58694076 TATTTTTAAAAATATTATATTATTT
1 TATTTTTAAAAATATAATATTATTT
*
58694101 TA-ATTTAAAAAT-TAATATT-TTT
1 TATTTTTAAAAATATAATATTATTT
58694123 TATTTATTAAA
1 TATTT-TTAAA
58694134 TTTTATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.18
23 7 0.25
24 14 0.50
25 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTTTAAAAATATAATATTATTT
Found at i:58705836 original size:136 final size:136
Alignment explanation
Indices: 58705583--58705854 Score: 508
Period size: 136 Copynumber: 2.0 Consensus size: 136
58705573 TATTTGAGTT
* * *
58705583 GTTGGCAATTTGTTGAACTGGATGTTTGGATTATACTAAGATTGTGGATCGTATTTGGCCCATCA
1 GTTGACAAATTGTTGAACTGGATGTTTGGATTATACTAAGATTGTGGATCGTATCTGGCCCATCA
58705648 GTGAAGGTCATATCACTTGAGGAAACATATGTGGAGGATTGGATCAAATGGGATTATGCTTATCA
66 GTGAAGGTCATATCACTTGAGGAAACATATGTGGAGGATTGGATCAAATGGGATTATGCTTATCA
58705713 AATCCC
131 AATCCC
*
58705719 GTTGACAAATTGTTGAGCTGGATGTTTGGATTATACTAAGATTGTGGATCGTATCTGGCCCATCA
1 GTTGACAAATTGTTGAACTGGATGTTTGGATTATACTAAGATTGTGGATCGTATCTGGCCCATCA
58705784 GTGAAGGTCATATCACTTGAGGAAACATATGTGGAGGATTGGATCAAATGGGATTATGCTTATCA
66 GTGAAGGTCATATCACTTGAGGAAACATATGTGGAGGATTGGATCAAATGGGATTATGCTTATCA
58705849 AATCCC
131 AATCCC
58705855 TTAGATCAAG
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (136 bp):
GTTGACAAATTGTTGAACTGGATGTTTGGATTATACTAAGATTGTGGATCGTATCTGGCCCATCA
GTGAAGGTCATATCACTTGAGGAAACATATGTGGAGGATTGGATCAAATGGGATTATGCTTATCA
AATCCC
Found at i:58705901 original size:13 final size:13
Alignment explanation
Indices: 58705883--58705909 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58705873 ATTGGTCCGA
58705883 ATCACTGAAGAGT
1 ATCACTGAAGAGT
58705896 ATCACTGAAGAGT
1 ATCACTGAAGAGT
58705909 A
1 A
58705910 AACTGCCAAC
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:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (13 bp):
ATCACTGAAGAGT
Found at i:58706286 original size:21 final size:21
Alignment explanation
Indices: 58706262--58706317 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 21
58706252 ATGCATAGAG
*
58706262 GTACCTATACACCCCTAGAAT
1 GTACATATACACCCCTAGAAT
58706283 GTACTTATATATACACCCCTAGAAT
1 GTAC----ATATACACCCCTAGAAT
*
58706308 GTACTTATAC
1 GTACATATAC
58706318 TTTGCTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 9 0.31
25 20 0.69
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (21 bp):
GTACATATACACCCCTAGAAT
Found at i:58706295 original size:25 final size:25
Alignment explanation
Indices: 58706267--58706316 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
58706257 TAGAGGTACC
58706267 TATACACCCCTAGAATGTACTTATA
1 TATACACCCCTAGAATGTACTTATA
58706292 TATACACCCCTAGAATGTACTTATA
1 TATACACCCCTAGAATGTACTTATA
58706317 CTTTGCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (25 bp):
TATACACCCCTAGAATGTACTTATA
Found at i:58706733 original size:20 final size:21
Alignment explanation
Indices: 58706693--58706740 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
58706683 ATAAAAATCG
58706693 ATAGAATTGTTATTCTAGAAA
1 ATAGAATTGTTATTCTAGAAA
58706714 ATAGAATT-TATATT-TAGAAA
1 ATAGAATTGT-TATTCTAGAAA
58706734 ATA-AATT
1 ATAGAATT
58706741 CTCACTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (21 bp):
ATAGAATTGTTATTCTAGAAA
Found at i:58708073 original size:38 final size:38
Alignment explanation
Indices: 58708022--58708097 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
58708012 AAAGCAAGAA
58708022 TACAAAAAAAAGGTTGATTTCGATTTCTATTTTCGTGT
1 TACAAAAAAAAGGTTGATTTCGATTTCTATTTTCGTGT
58708060 TACAAAAAAAAGGTTGATTTCGATTTCTATTTTCGTGT
1 TACAAAAAAAAGGTTGATTTCGATTTCTATTTTCGTGT
58708098 CTTTTCGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (38 bp):
TACAAAAAAAAGGTTGATTTCGATTTCTATTTTCGTGT
Found at i:58709330 original size:24 final size:23
Alignment explanation
Indices: 58709276--58709330 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
58709266 TTTCAAATCG
*
58709276 TATTATTATTTACTTTAAGTTTA
1 TATTATTATTTACTTGAAGTTTA
* *
58709299 TATATATTATTTACTTGAGGCTTTT
1 TAT-TATTATTTACTTGAAG-TTTA
58709324 TATTATT
1 TATTATT
58709331 TATTCGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 18 0.67
25 6 0.22
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (23 bp):
TATTATTATTTACTTGAAGTTTA
Found at i:58713108 original size:19 final size:19
Alignment explanation
Indices: 58713084--58713131 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
58713074 ACGCCTCTTT
*
58713084 TTACA-TTCATTCATTTGCA
1 TTACATTTCA-TCATATGCA
58713103 TTACATTTCATCATATGCA
1 TTACATTTCATCATATGCA
*
58713122 TTAAATTTCA
1 TTACATTTCA
58713132 CGAAAAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (19 bp):
TTACATTTCATCATATGCA
Found at i:58721591 original size:45 final size:45
Alignment explanation
Indices: 58721350--58721812 Score: 199
Period size: 45 Copynumber: 10.2 Consensus size: 45
58721340 AATATTGTAG
* * * *
58721350 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGA-TCAAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-TTACCAA
* * ** *
58721395 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--AA-GGCTAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCAA
* * * * * *
58721437 ATCCTATAC-CTCTGAAGTTACAGTAGG-TCGGA-TCAAATCTACCATGGTAA
1 ATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAAT-TACC-----AA
* * *
58721487 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT-AAA--GCCATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCA--A
* *
58721531 A-CATTATCTCCCTGAAGATGCAGTGGAGCAGTTTGAAATTACCAA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCAA
* ** *
58721576 GTCTTATCTCCCTGAAGTTGCAGTGGAATAGACTGAAGA-TACCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATTACCAA
** * ** *
58721621 ATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATT-AAGGCTA-TAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATTACCAA
* * * * * *
58721665 ATCCTATACAT--CTGAAGTTGCAGTGG-GTCAG-GTCAAGTCACCATGGCGG
1 ATCTTAT-C-TCCCTGAAGTTGCAGTGGAG-CAGATTGAAATTACCA-----A
* *
58721714 ATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAATT-GCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCAA
* ** * *
58721758 ACCCCATCTCCCTGAAGATGCAGTGGAGCAGGTTGAAATTACCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCAA
*
58721803 GTCTTATCTC
1 ATCTTATCTC
58721813 TTTAAAGTTC
Statistics
Matches: 311, Mismatches: 68, Indels: 78
0.68 0.15 0.17
Matches are distributed among these distances:
41 1 0.00
42 26 0.08
43 9 0.03
44 95 0.31
45 108 0.35
46 4 0.01
47 6 0.02
48 1 0.00
49 27 0.09
50 33 0.11
51 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (45 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACCAA
Found at i:58721796 original size:227 final size:225
Alignment explanation
Indices: 58721351--58721812 Score: 637
Period size: 227 Copynumber: 2.0 Consensus size: 225
58721341 ATATTGTAGA
* * *
58721351 TCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGATAGCAAATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATCAAAGATACCAAATCTTATCTCTCTGAAGTTGC
*
58721416 AGTAGAGCAGATTAAGGCTAAATCCTATACCTCTGAAGTTACAGTAGGTCGGATCAAATCTACCA
66 AGTAGAGCAGATTAAGGCTAAATCCTATACATCTGAAGTTACAGTAGGTCGGATCAAATCTACCA
* * * **
58721481 TGGTAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCCATTAACATTATCTCCCTGA
131 TGGCAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCCA-TAACACCATCTCCCTGA
*
58721546 AGATGCAGTGGAGCAGTTTGAAATTACCAAG
195 AGATGCAGTGGAGCAGGTTGAAATTACCAAG
* * *
58721577 TCTTATCTCCCTGAAGTTGCAGTGGAATAGA-CTGAAGATACCAAATCTTATCTCTTTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATC-AAAGATACCAAATCTTATCTCTCTGAAGTTG
* * *
58721641 CAGTAGAGCAGATTAAGGCTATAAATCCTATACATCTGAAGTTGCAGTGGGTCAGG-TCAAGTC-
65 CAGTAGAGCAGATTAAGGC--TAAATCCTATACATCTGAAGTTACAGTAGGTC-GGATCAAATCT
** * *
58721704 ACCATGGCGGATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAATTG-CA-AACCCCATCT
127 ACCATGGCAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATT-AAA--GCCATAACACCATCT
58721767 CCCTGAAGATGCAGTGGAGCAGGTTGAAATTACCAAG
189 CCCTGAAGATGCAGTGGAGCAGGTTGAAATTACCAAG
58721804 TCTTATCTC
1 TCTTATCTC
58721813 TTTAAAGTTC
Statistics
Matches: 209, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
225 1 0.00
226 75 0.36
227 90 0.43
228 38 0.18
229 4 0.02
230 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (225 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGATCAAAGATACCAAATCTTATCTCTCTGAAGTTGC
AGTAGAGCAGATTAAGGCTAAATCCTATACATCTGAAGTTACAGTAGGTCGGATCAAATCTACCA
TGGCAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCCATAACACCATCTCCCTGAA
GATGCAGTGGAGCAGGTTGAAATTACCAAG
Found at i:58723470 original size:24 final size:23
Alignment explanation
Indices: 58723395--58723478 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
58723385 TTTGCTTCTG
58723395 TTTATT-TATTTAT-TTTTATTTT
1 TTTATTGT-TTTATATTTTATTTT
*
58723417 ATTT-TTGTTTT-TATTTTACTCTT
1 -TTTATTGTTTTATATTTTA-TTTT
**
58723440 TAAATTGTTTTATATTTTATTTAT
1 TTTATTGTTTTATATTTTATTT-T
*
58723464 TTTATTGTTTCATAT
1 TTTATTGTTTTATAT
58723479 ATATATCAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
21 1 0.02
22 11 0.23
23 16 0.33
24 20 0.42
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTATTGTTTTATATTTTATTTT
Found at i:58723711 original size:20 final size:21
Alignment explanation
Indices: 58723672--58723711 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
58723662 TATGTTATTT
*
58723672 TATTTTAAACTTTTACATATCA
1 TATTTTAAAC-TTCACATATCA
58723694 TATTTTAAA-TTCACATAT
1 TATTTTAAACTTCACATAT
58723712 TAAGTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTAAACTTCACATATCA
Found at i:58726176 original size:22 final size:23
Alignment explanation
Indices: 58726151--58726196 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
58726141 CAACCAAATC
58726151 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
58726173 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
58726196 A
1 A
58726197 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:58726202 original size:23 final size:23
Alignment explanation
Indices: 58726158--58726202 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
58726148 ATCAATTCAA
*
58726158 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
58726181 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
58726203 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:58733674 original size:20 final size:21
Alignment explanation
Indices: 58733636--58733676 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
58733626 TTCTTCACAA
*
58733636 AATTTTCTCTTCTTTTTCTCT
1 AATTTTCTCTTCTTCTTCTCT
*
58733657 AATTTT-TCTTGTTCTTCTCT
1 AATTTTCTCTTCTTCTTCTCT
58733677 GCAACTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (21 bp):
AATTTTCTCTTCTTCTTCTCT
Found at i:58749051 original size:14 final size:13
Alignment explanation
Indices: 58749031--58749062 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
58749021 AATATTTAAC
58749031 TTGTTCTTAATTA
1 TTGTTCTTAATTA
58749044 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
58749058 TTGTT
1 TTGTT
58749063 TTGATATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:58751430 original size:418 final size:418
Alignment explanation
Indices: 58750653--58751488 Score: 1645
Period size: 418 Copynumber: 2.0 Consensus size: 418
58750643 AACACAATTA
*
58750653 CATTAATACTTATTAACATACGAACTTACCTCGATCACAAAAACAACGGAATAGGATCGACTAAT
1 CATTAATACTTATTAACATACGAACTTACCTCGATCACAAAAACAACAGAATAGGATCGACTAAT
58750718 ACAATACTTTATTTTTCCCTCGATCTAGATCAGTACGTTGCTTTTCTTGATCTATATAATCAAAT
66 ACAATACTTTATTTTTCCCTCGATCTAGATCAGTACGTTGCTTTTCTTGATCTATATAATCAAAT
58750783 TTAACTCATTCAAAATACATTCTATTCAATTTAAATCAAAATTCATATTATATCAATTTTACACT
131 TTAACTCATTCAAAATACATTCTATTCAATTTAAATCAAAATTCATATTATATCAATTTTACACT
58750848 TTTACCCCTTATATTTTAACATCTTTACAATTTAGTCCCTAGCTCATAAAAATGCAAATTCATGC
196 TTTACCCCTTATATTTTAACATCTTTACAATTTAGTCCCTAGCTCATAAAAATGCAAATTCATGC
58750913 AATTGAGTCCACACCCATGCTAGCTGAATTTCATCTATGTTCATAGCAGCCCACACATTTCATTA
261 AATTGAGTCCACACCCATGCTAGCTGAATTTCATCTATGTTCATAGCAGCCCACACATTTCATTA
58750978 TTTCACACATTTCACCACTTAATTTTCATATTTCTCAATTTAATCCCTAATTGACAATTTTATAA
326 TTTCACACATTTCACCACTTAATTTTCATATTTCTCAATTTAATCCCTAATTGACAATTTTATAA
58751043 AAAATCACTTAACAAATGTTGTTTATCT
391 AAAATCACTTAACAAATGTTGTTTATCT
58751071 CATTAATACTTATTAACATACGAACTTACCTCGATCACAAAAACAACAGAATAGGATCGACTAAT
1 CATTAATACTTATTAACATACGAACTTACCTCGATCACAAAAACAACAGAATAGGATCGACTAAT
* *
58751136 ACAATACTTTATTTTTCCCTTGATCTAGATCTGTACGTTGCTTTTCTTGATCTATATAATCAAAT
66 ACAATACTTTATTTTTCCCTCGATCTAGATCAGTACGTTGCTTTTCTTGATCTATATAATCAAAT
58751201 TTAACTCATTCAAAATACATTCTATTCAATTTAAATCAAAATTCATATTATATCAATTTTACACT
131 TTAACTCATTCAAAATACATTCTATTCAATTTAAATCAAAATTCATATTATATCAATTTTACACT
58751266 TTTACCCCTTATATTTTAACATCTTTACAATTTAGTCCCTAGCTCATAAAAATGCAAATTCATGC
196 TTTACCCCTTATATTTTAACATCTTTACAATTTAGTCCCTAGCTCATAAAAATGCAAATTCATGC
58751331 AATTGAGTCCACACCCATGCTAGCTGAATTTCATCTATGTTCATAGCAGCCCACACATTTCATTA
261 AATTGAGTCCACACCCATGCTAGCTGAATTTCATCTATGTTCATAGCAGCCCACACATTTCATTA
58751396 TTTCACACATTTCACCACTTAATTTTCATATTTCTCAATTTAATCCCTAATTGACAATTTTATAA
326 TTTCACACATTTCACCACTTAATTTTCATATTTCTCAATTTAATCCCTAATTGACAATTTTATAA
58751461 AAAATCACTTAACAAATGTTGTTTATCT
391 AAAATCACTTAACAAATGTTGTTTATCT
58751489 AACAACAATC
Statistics
Matches: 415, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
418 415 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.38
Consensus pattern (418 bp):
CATTAATACTTATTAACATACGAACTTACCTCGATCACAAAAACAACAGAATAGGATCGACTAAT
ACAATACTTTATTTTTCCCTCGATCTAGATCAGTACGTTGCTTTTCTTGATCTATATAATCAAAT
TTAACTCATTCAAAATACATTCTATTCAATTTAAATCAAAATTCATATTATATCAATTTTACACT
TTTACCCCTTATATTTTAACATCTTTACAATTTAGTCCCTAGCTCATAAAAATGCAAATTCATGC
AATTGAGTCCACACCCATGCTAGCTGAATTTCATCTATGTTCATAGCAGCCCACACATTTCATTA
TTTCACACATTTCACCACTTAATTTTCATATTTCTCAATTTAATCCCTAATTGACAATTTTATAA
AAAATCACTTAACAAATGTTGTTTATCT
Found at i:58752368 original size:20 final size:21
Alignment explanation
Indices: 58752322--58752361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58752312 AGACTATAAG
58752322 TAAATTTCTCTTTTGGTCACT
1 TAAATTTCTCTTTTGGTCACT
* *
58752343 TAAATTTCTTTTTTTGTCA
1 TAAATTTCTCTTTTGGTCA
58752362 TTCAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (21 bp):
TAAATTTCTCTTTTGGTCACT
Found at i:58758219 original size:12 final size:12
Alignment explanation
Indices: 58758202--58758226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58758192 ACTTTATATT
58758202 TTTTATATACAA
1 TTTTATATACAA
58758214 TTTTATATACAA
1 TTTTATATACAA
58758226 T
1 T
58758227 ATAATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTATATACAA
Found at i:58760029 original size:2 final size:2
Alignment explanation
Indices: 58760022--58760080 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
58760012 CACAATCTAA
58760022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58760064 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
58760081 ATGGTTGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:58765488 original size:15 final size:15
Alignment explanation
Indices: 58765452--58765490 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
58765442 GCCTTAAATT
*
58765452 GTGAACCCCGGTTAA
1 GTGAACCCCAGTTAA
**
58765467 GCAAACCCCAGTTAA
1 GTGAACCCCAGTTAA
58765482 GTGAACCCC
1 GTGAACCCC
58765491 TATGTAAAAC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
GTGAACCCCAGTTAA
Found at i:58765614 original size:22 final size:22
Alignment explanation
Indices: 58765589--58765634 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
58765579 TGTGTTAGGT
* *
58765589 GAGCCATGTATTTATGTTATGC
1 GAGCCATGAATATATGTTATGC
58765611 GAGCCATGAATATATGTTATGC
1 GAGCCATGAATATATGTTATGC
58765633 GA
1 GA
58765635 ACCCTAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (22 bp):
GAGCCATGAATATATGTTATGC
Found at i:58765858 original size:58 final size:58
Alignment explanation
Indices: 58765768--58766087 Score: 260
Period size: 58 Copynumber: 5.6 Consensus size: 58
58765758 AACCTTAGGA
* *
58765768 CTAGGTACATGTGAGCCTATATGCGAACCTTAGGAACTTATGAGCCTTTATGCGAACC
1 CTAGGTACATGCGAGCCTATATGCGAACCTTAGGAACTTGTGAGCCTTTATGCGAACC
* * * *
58765826 CTAGGTACATGTGAGCCTATATGCGAACCTTAGAAACTTGCGAG-CTTGTATGCGAACA
1 CTAGGTACATGCGAGCCTATATGCGAACCTTAGGAACTTGTGAGCCTT-TATGCGAACC
* * * * * *
58765884 CTAGGTACACGCGAGCCTATATGCGAACCCTAGGAACTTGCGAGCCTGTATTCGAGCC
1 CTAGGTACATGCGAGCCTATATGCGAACCTTAGGAACTTGTGAGCCTTTATGCGAACC
* * * * *** *
58765942 CCATGTACATGCGAG-C--T-TGTGAAACTTAGGAA-TT-TGCAATTTTATATGCGAATC
1 CTAGGTACATGCGAGCCTATATGCGAACCTTAGGAACTTGTG-AGCCTT-TATGCGAACC
* * * * * * *
58765996 CTAGGAACCTACGAGCCTATATGCGAACAC-TAGGTACATGTGAGCCTATATGCAAACC
1 CTAGGTACATGCGAGCCTATATGCGAAC-CTTAGGAACTTGTGAGCCTTTATGCGAACC
* * * * *
58766054 CTAGGAACTTGTGAGCCTATATACGAACCCTAGG
1 CTAGGTACATGCGAGCCTATATGCGAACCTTAGG
58766088 TGCATGCAAG
Statistics
Matches: 205, Mismatches: 45, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
52 1 0.00
53 4 0.02
54 29 0.14
55 2 0.01
57 6 0.03
58 155 0.76
59 6 0.03
60 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (58 bp):
CTAGGTACATGCGAGCCTATATGCGAACCTTAGGAACTTGTGAGCCTTTATGCGAACC
Found at i:58766086 original size:87 final size:87
Alignment explanation
Indices: 58765767--58766106 Score: 267
Period size: 87 Copynumber: 4.0 Consensus size: 87
58765757 GAACCTTAGG
* * * ** * *
58765767 ACTAGGTACATGTGAGCCTATATGCGAACCTTAGGAACTTATGAGCCTTTATGCGAACCCTAGGT
1 ACTAGGTACATGCGAGCCTATATGCAAACCCTAGGAACTTGCGAGCCTATATGCGAACCCTAGGA
*
58765832 ACATGTGAGCCTATATGCGAAC
66 ACATGCGAGCCTATATGCGAAC
** * * * * * * **
58765854 -CTTAGAAACTTGCGAGCTTGTATGCGAACACTAGGTACACGCGAGCCTATATGCGAACCCTAGG
1 AC-TAGGTACATGCGAGCCTATATGCAAACCCTAGGAACTTGCGAGCCTATATGCGAACCCTAGG
* * * *
58765918 AACTTGCGAGCCTGTATTCGAGC
65 AACATGCGAGCCTATATGCGAAC
* * * * * * * *** *
58765941 CCCATGTACATGCGAG-CT-TGTG-AAA-CTTAGGAATTTGCAATTTTATATGCGAATCCTAGGA
1 ACTAGGTACATGCGAGCCTATATGCAAACCCTAGGAACTTGCGAGCCTATATGCGAACCCTAGGA
* *
58766002 ACCTACGAGCCTATATGCGAAC
66 ACATGCGAGCCTATATGCGAAC
* * * *
58766024 ACTAGGTACATGTGAGCCTATATGCAAACCCTAGGAACTTGTGAGCCTATATACGAACCCTAGGT
1 ACTAGGTACATGCGAGCCTATATGCAAACCCTAGGAACTTGCGAGCCTATATGCGAACCCTAGGA
* *
58766089 GCATGCAAGCCTATATGC
66 ACATGCGAGCCTATATGC
58766107 CATGCAAGCC
Statistics
Matches: 184, Mismatches: 63, Indels: 12
0.71 0.24 0.05
Matches are distributed among these distances:
83 54 0.29
84 4 0.02
85 6 0.03
86 5 0.03
87 114 0.62
88 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (87 bp):
ACTAGGTACATGCGAGCCTATATGCAAACCCTAGGAACTTGCGAGCCTATATGCGAACCCTAGGA
ACATGCGAGCCTATATGCGAAC
Found at i:58766099 original size:29 final size:29
Alignment explanation
Indices: 58765718--58766139 Score: 235
Period size: 29 Copynumber: 14.3 Consensus size: 29
58765708 GAACATTCAG
* **
58765718 GCCTATATGCGAACCCTAGGTAAATGCAA
1 GCCTATATGCGAACCCTAGGTACATGTGA
*
58765747 ACCTATATGCGAACCTTAGGACTAGGTACATGTGA
1 GCCTATATGCGAACC------CTAGGTACATGTGA
* * * *
58765782 GCCTATATGCGAACCTTAGGAACTTATGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
*
58765811 GCCTTTATGCGAACCCTAGGTACATGTGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* ** * *
58765840 GCCTATATGCGAACCTTAGAAACTTGCGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * * * *
58765869 GCTTGTATGCGAACACTAGGTACACGCGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * *
58765898 GCCTATATGCGAACCCTAGGAACTTGCGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * * * * *
58765927 GCCTGTATTCGAGCCCCATGTACATGCGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * * *
58765956 G-C--T-TGTGAAACTTAGG-A-ATTTGCAA
1 GCCTATATGCGAACCCTAGGTACATGTG--A
*** * * * **
58765981 TTTTATATGCGAATCCTAGGAACCTACGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
*
58766010 GCCTATATGCGAACACTAGGTACATGTGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * *
58766039 GCCTATATGCAAACCCTAGGAACTTGTGA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* * **
58766068 GCCTATATACGAACCCTAGGTGCATGCAA
1 GCCTATATGCGAACCCTAGGTACATGTGA
* *
58766097 GCCTATATGCCATGCAAGCCCTAAGAACATGTGA
1 GCCTATATG-C--G-AA-CCCTAGGTACATGTGA
58766131 GCCTATATG
1 GCCTATATG
58766140 ATCATGTGAA
Statistics
Matches: 290, Mismatches: 84, Indels: 33
0.71 0.21 0.08
Matches are distributed among these distances:
23 3 0.01
24 1 0.00
25 7 0.02
26 1 0.00
28 2 0.01
29 224 0.77
30 2 0.01
31 2 0.01
32 1 0.00
33 2 0.01
34 20 0.07
35 25 0.09
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (29 bp):
GCCTATATGCGAACCCTAGGTACATGTGA
Found at i:58770613 original size:11 final size:11
Alignment explanation
Indices: 58770597--58770630 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
58770587 AATATAGTGT
*
58770597 AAAGAAAAGGA
1 AAAGAAAAGAA
*
58770608 AAAGAAAATAA
1 AAAGAAAAGAA
58770619 AAAGAAAAGAA
1 AAAGAAAAGAA
58770630 A
1 A
58770631 TTGAAGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:58771155 original size:13 final size:15
Alignment explanation
Indices: 58771125--58771157 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
58771115 GTGAATGTAT
58771125 ATTAAATATTTATCA
1 ATTAAATATTTATCA
58771140 ATTAAA-ATTT-TCA
1 ATTAAATATTTATCA
58771153 ATTAA
1 ATTAA
58771158 TTAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATATTTATCA
Found at i:58772737 original size:21 final size:20
Alignment explanation
Indices: 58772699--58772737 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
58772689 GTTTTATAAG
*
58772699 TTTATATCTATTATAAATTT
1 TTTATATCTATTAAAAATTT
*
58772719 TTTATATTTTATTAAAAAT
1 TTTATA-TCTATTAAAAAT
58772738 GTCAAGTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATCTATTAAAAATTT
Found at i:58778564 original size:26 final size:26
Alignment explanation
Indices: 58778535--58778586 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
58778525 TGATATGTTT
58778535 GATTATATT-TAATGTTT-ATCAATTTA
1 GATTA-ATTATAAT-TTTGATCAATTTA
*
58778561 GATTAATTATAATTTTGATGAATTTA
1 GATTAATTATAATTTTGATCAATTTA
58778587 CTTAAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (26 bp):
GATTAATTATAATTTTGATCAATTTA
Found at i:58780762 original size:21 final size:20
Alignment explanation
Indices: 58780736--58780780 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
58780726 AAGCATATAA
* *
58780736 AAAATTTTATAAGGGAGTACC
1 AAAA-TTTATAAGAGAATACC
*
58780757 AAAATTTATGAGAGAATACC
1 AAAATTTATAAGAGAATACC
58780777 AAAA
1 AAAA
58780781 AAACACGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (20 bp):
AAAATTTATAAGAGAATACC
Found at i:58780862 original size:20 final size:21
Alignment explanation
Indices: 58780837--58780883 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
58780827 AGGGATTGTA
*
58780837 AAAAAATTGTGAGGAAATAC-
1 AAAAAATTATGAGGAAATACT
*
58780857 AAAAAATTATGAGGAATTACT
1 AAAAAATTATGAGGAAATACT
58780878 AAAAAA
1 AAAAAA
58780884 CTTGATGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (21 bp):
AAAAAATTATGAGGAAATACT
Found at i:58783000 original size:49 final size:50
Alignment explanation
Indices: 58782947--58783044 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
58782937 ATTTGTGGAG
58782947 TATGCCTCATATTTACG-AATTGACGTTTCAAGGAGGAAGAGCCAATGTT
1 TATGCCTCATATTTACGAAATTGACGTTTCAAGGAGGAAGAGCCAATGTT
** *
58782996 TATGCCTTGTATTTACGAAATTGACGTTTCAATGAGGAAGAGCCAATGT
1 TATGCCTCATATTTACGAAATTGACGTTTCAAGGAGGAAGAGCCAATGT
58783045 CTCGATGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 15 0.33
50 30 0.67
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (50 bp):
TATGCCTCATATTTACGAAATTGACGTTTCAAGGAGGAAGAGCCAATGTT
Found at i:58784200 original size:19 final size:20
Alignment explanation
Indices: 58784156--58784224 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
58784146 TGAGGGATTG
58784156 TCAAAAATTTTGAAGAAGTA
1 TCAAAAATTTTGAAGAAGTA
*
58784176 TCAAAAATTTTGAGGAAGTA
1 TCAAAAATTTTGAAGAAGTA
** * * *
58784196 GAAAAAATTGTGAAGGATTA
1 TCAAAAATTTTGAAGAAGTA
*
58784216 CCAAAAATT
1 TCAAAAATT
58784225 ATGAGGGAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (20 bp):
TCAAAAATTTTGAAGAAGTA
Found at i:58784202 original size:40 final size:41
Alignment explanation
Indices: 58784134--58784243 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 41
58784124 TTTAAAAGCA
* * *
58784134 TACCAAATATTATGAGGG-ATTGTC-AAAAATTTTGAAGAAG
1 TACCAAAAATTATGAGGGAATAG-CAAAAAATTGTGAAGAAG
* * * *
58784174 TATCAAAAATTTTGA-GGAAGTAG-AAAAAATTGTGAAGGAT
1 TACCAAAAATTATGAGGGAA-TAGCAAAAAATTGTGAAGAAG
58784214 TACCAAAAATTATGAGGGAATAGCAAAAAA
1 TACCAAAAATTATGAGGGAATAGCAAAAAA
58784244 ACATGAGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.04
40 42 0.75
41 12 0.21
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.25
Consensus pattern (41 bp):
TACCAAAAATTATGAGGGAATAGCAAAAAATTGTGAAGAAG
Found at i:58784240 original size:20 final size:19
Alignment explanation
Indices: 58784137--58784242 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
58784127 AAAAGCATAC
* * *
58784137 CAAATATTATGAGGGATTG
1 CAAAAATTATGAGGAATAG
* * *
58784156 TCAAAAATTTTGAAGAAGTAT
1 -CAAAAATTATGAGGAA-TAG
*
58784177 CAAAAATTTTGAGGAAGTAG
1 CAAAAATTATGAGGAA-TAG
* * * *
58784197 AAAAAATTGTGAAGGATTAC
1 CAAAAATTATG-AGGAATAG
58784217 CAAAAATTATGAGGGAATAG
1 CAAAAATTATGA-GGAATAG
58784237 CAAAAA
1 CAAAAA
58784243 AACATGAGAA
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.01
20 61 0.91
21 5 0.07
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (19 bp):
CAAAAATTATGAGGAATAG
Found at i:58785022 original size:20 final size:21
Alignment explanation
Indices: 58785007--58785045 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58784997 CCATGACAGT
58785007 TTACC-AAAAATTATGAAGGA
1 TTACCAAAAAATTATGAAGGA
58785027 TTACCAAAAAATTATGAAG
1 TTACCAAAAAATTATGAAG
58785046 ATGTACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (21 bp):
TTACCAAAAAATTATGAAGGA
Found at i:58785036 original size:21 final size:20
Alignment explanation
Indices: 58785007--58785063 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
58784997 CCATGACAGT
58785007 TTACCAAAAATTATGAAGGA
1 TTACCAAAAATTATGAAGGA
58785027 TTACCAAAAAATTATGAA-GA
1 TTACC-AAAAATTATGAAGGA
* *
58785047 TGTACTAAAAACTATGA
1 T-TACCAAAAATTATGA
58785064 GAGATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (20 bp):
TTACCAAAAATTATGAAGGA
Found at i:58794566 original size:6 final size:6
Alignment explanation
Indices: 58794557--58794629 Score: 65
Period size: 6 Copynumber: 11.5 Consensus size: 6
58794547 GAAGACTAAG
* *
58794557 AAAATA AAAATAA AACAACTA AAAATA AAAATA AAAATAA AAAATA AACAGA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAAT-A AAAATA AAAATA
* * *
58794609 AAAATA AGAATG AAAAGA AAA
1 AAAATA AAAATA AAAATA AAA
58794630 GAAATAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 37 0.69
7 11 0.20
8 5 0.09
9 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:58794601 original size:19 final size:19
Alignment explanation
Indices: 58794557--58794615 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
58794547 GAAGACTAAG
58794557 AAAATAAAAATAAAACA-ACTA
1 AAAATAAAAATAAAA-ATA--A
58794578 AAAATAAAAATAAAAATAA
1 AAAATAAAAATAAAAATAA
* *
58794597 AAAATAAACAGAAAAATAA
1 AAAATAAAAATAAAAATAA
58794616 GAATGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 18 0.51
20 1 0.03
21 16 0.46
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAATAAAAATAAAAATAA
Found at i:58794611 original size:13 final size:13
Alignment explanation
Indices: 58794557--58794612 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
58794547 GAAGACTAAG
*
58794557 AAAATAAAAATAA
1 AAAATAAAAAGAA
*
58794570 AACAACTAAAAA-TA
1 AA-AA-TAAAAAGAA
*
58794584 AAAATAAAAATAA
1 AAAATAAAAAGAA
*
58794597 AAAATAAACAGAA
1 AAAATAAAAAGAA
58794610 AAA
1 AAA
58794613 TAAGAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 6 0.17
13 19 0.53
14 5 0.14
15 6 0.17
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAGAA
Found at i:58796109 original size:19 final size:19
Alignment explanation
Indices: 58796077--58796120 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
58796067 GTAATAAAAT
*
58796077 AAGAA-AATAATAAATGAA
1 AAGAATAATAATAAATAAA
* *
58796095 AATAATAATACTAAATAAA
1 AAGAATAATAATAAATAAA
58796114 AAGAATA
1 AAGAATA
58796121 TGAGTAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (19 bp):
AAGAATAATAATAAATAAA
Found at i:58796640 original size:13 final size:13
Alignment explanation
Indices: 58796617--58796659 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
58796607 AAAAGGGAGG
58796617 AAGAGAAAAAGAGA
1 AAGA-AAAAAGAGA
*
58796631 AAGAAAAAAGATA
1 AAGAAAAAAGAGA
*
58796644 AAGAAAAAAGGGA
1 AAGAAAAAAGAGA
58796657 AAG
1 AAG
58796660 GAGGAGGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAGAGA
Found at i:58804544 original size:37 final size:37
Alignment explanation
Indices: 58804503--58804678 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
58804493 TTTGAGTACT
58804503 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58804540 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58804577 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58804614 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
58804651 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
58804679 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:58804750 original size:45 final size:46
Alignment explanation
Indices: 58804641--58804764 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
58804631 GTGATAAGTG
* *
58804641 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
58804687 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
58804732 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
58804765 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:58812238 original size:37 final size:37
Alignment explanation
Indices: 58812197--58812372 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
58812187 TTTGAGTACT
58812197 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58812234 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58812271 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
58812308 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
58812345 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
58812373 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:58812444 original size:45 final size:46
Alignment explanation
Indices: 58812335--58812458 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
58812325 GTGATAAGTG
* *
58812335 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
58812381 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
58812426 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
58812459 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:58822581 original size:44 final size:45
Alignment explanation
Indices: 58822470--58822581 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
58822460 TTCTGGAAAT
* * *
58822470 GAGTAAGACCATAGCTGAAAGACGCTATGGTATCATGATTCAAAC
1 GAGTAAGACCATAGCTGAAAGATGCTATGGCATCACGATTCAAAC
**
58822515 GAGTAAGACTGTAGCT-ATAAGATGCTATGGCATCACGATTC-AAC
1 GAGTAAGACCATAGCTGA-AAGATGCTATGGCATCACGATTCAAAC
* **
58822559 GTGTAAGACCATAATTGAAAGAT
1 GAGTAAGACCATAGCTGAAAGAT
58822582 ATTATGACAA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
44 20 0.36
45 35 0.64
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGATGCTATGGCATCACGATTCAAAC
Found at i:58823018 original size:15 final size:15
Alignment explanation
Indices: 58822979--58823018 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
58822969 TAGCTATTCG
58822979 AAATGATTATATATA
1 AAATGATTATATATA
*
58822994 AAAAGA--ATATATA
1 AAATGATTATATATA
58823007 AAATGATTATAT
1 AAATGATTATAT
58823019 GAATCAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 12 0.57
15 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (15 bp):
AAATGATTATATATA
Found at i:58823992 original size:36 final size:36
Alignment explanation
Indices: 58823946--58824023 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
58823936 ATAAATTGTT
58823946 AATTG-AGGAAAATTATACTAATTGGGGAAGGACTA
1 AATTGTAGGAAAATTATACTAATTGGGGAAGGACTA
58823981 AATTGTAGGAAAATTATACTAATTGGGGAAGGACTA
1 AATTGTAGGAAAATTATACTAATTGGGGAAGGACTA
58824017 AATTGTA
1 AATTGTA
58824024 AAAACTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.12
36 37 0.88
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.28
Consensus pattern (36 bp):
AATTGTAGGAAAATTATACTAATTGGGGAAGGACTA
Found at i:58824480 original size:21 final size:21
Alignment explanation
Indices: 58824454--58824506 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
58824444 TTGTATTTAC
*
58824454 TTTCTGTTTAGCTC-TCATGAG
1 TTTCTGTTTAACTCAT-ATGAG
58824475 TTTCTG-TTAACTCATATGAG
1 TTTCTGTTTAACTCATATGAG
*
58824495 TTTCCGTTTAAC
1 TTTCTGTTTAAC
58824507 CCTAATGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (21 bp):
TTTCTGTTTAACTCATATGAG
Found at i:58824528 original size:42 final size:42
Alignment explanation
Indices: 58824481--58824561 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
58824471 TGAGTTTCTG
* * *
58824481 TTAACTCATATGAGTTTCCGTTTAACCCTAATGGATTTCCAT
1 TTAACTCATATGAGCTTCAGTTTAACCCTAATGCATTTCCAT
* * *
58824523 TTAACTCTTTTGAGCTTCAGTTTAACCCTTATGCATTTC
1 TTAACTCATATGAGCTTCAGTTTAACCCTAATGCATTTC
58824562 AGTTCAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.43
Consensus pattern (42 bp):
TTAACTCATATGAGCTTCAGTTTAACCCTAATGCATTTCCAT
Found at i:58824562 original size:21 final size:20
Alignment explanation
Indices: 58824489--58824565 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 20
58824479 TGTTAACTCA
*
58824489 TATGAGTTTCCGTTTAACCCT
1 TATGA-TTTCAGTTTAACCCT
* *
58824510 AATGGATTTCCA-TTTAACTCT
1 TAT-GATTT-CAGTTTAACCCT
* *
58824531 TTTGAGCTTCAGTTTAACCCT
1 TATGA-TTTCAGTTTAACCCT
58824552 TATGCATTTCAGTT
1 TATG-ATTTCAGTT
58824566 CAGCTCCTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
20 4 0.10
21 34 0.81
22 4 0.10
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TATGATTTCAGTTTAACCCT
Found at i:58824579 original size:42 final size:42
Alignment explanation
Indices: 58824483--58824595 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 42
58824473 AGTTTCTGTT
* * * * * *
58824483 AACTCATATGAGTTTCCGTTTAACCCTAATGGATTTCCATTT
1 AACTCCTATGAGCTTCAGTTTAACCCTTATGCATTTCCATTC
* *
58824525 AACTCTTTTGAGCTTCAGTTTAACCCTTATGCATTT-CAGTTC
1 AACTCCTATGAGCTTCAGTTTAACCCTTATGCATTTCCA-TTC
* *
58824567 AGCTCCTATGAGCTTCCA-TTCAACCCTTA
1 AACTCCTATGAGCTT-CAGTTTAACCCTTA
58824596 AGGGTTTTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 54 0.93
43 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.39
Consensus pattern (42 bp):
AACTCCTATGAGCTTCAGTTTAACCCTTATGCATTTCCATTC
Found at i:58825716 original size:73 final size:73
Alignment explanation
Indices: 58825637--58825785 Score: 235
Period size: 73 Copynumber: 2.0 Consensus size: 73
58825627 GAAATGAGAA
* * * * *
58825637 ATGTGAAATGTTAAATGAATAGATGTTGAATGAGTGATATATCTAATGTGTTTACTTGTATATGT
1 ATGTGAAATGTTAAATGAATAGATGTTGAATAAATGACATATCTAATGCGTTTACATGTATATGT
58825702 TTTATAAC
66 TTTATAAC
* *
58825710 ATGTGAAATGTTAAATGAATAGATGTTGAATAAATGGCATATCTATTGCGTTTACATGTATATGT
1 ATGTGAAATGTTAAATGAATAGATGTTGAATAAATGACATATCTAATGCGTTTACATGTATATGT
58825775 TTTATAAC
66 TTTATAAC
58825783 ATG
1 ATG
58825786 AAAAGGTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (73 bp):
ATGTGAAATGTTAAATGAATAGATGTTGAATAAATGACATATCTAATGCGTTTACATGTATATGT
TTTATAAC
Found at i:58828249 original size:3 final size:3
Alignment explanation
Indices: 58828243--58828285 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
58828233 AGAGAGAAGA
58828243 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
58828286 GGTCATCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58828954 original size:39 final size:39
Alignment explanation
Indices: 58828911--58828989 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
58828901 GATTAAAGAC
58828911 TTAATTGCTAAGAGTACAAAATTAGATAAGTGAAATAGA
1 TTAATTGCTAAGAGTACAAAATTAGATAAGTGAAATAGA
*
58828950 TTAATTGTTAAGAGTACAAAATTAGATAAGTGAAATAGA
1 TTAATTGCTAAGAGTACAAAATTAGATAAGTGAAATAGA
58828989 T
1 T
58828990 ATTAATACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (39 bp):
TTAATTGCTAAGAGTACAAAATTAGATAAGTGAAATAGA
Found at i:58837506 original size:16 final size:16
Alignment explanation
Indices: 58837485--58837517 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58837475 CTAGCATGGG
58837485 TTAATTT-TGAATTTCA
1 TTAATTTGTG-ATTTCA
58837501 TTAATTTGTGATTTCA
1 TTAATTTGTGATTTCA
58837517 T
1 T
58837518 GAAATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (16 bp):
TTAATTTGTGATTTCA
Found at i:58851336 original size:17 final size:18
Alignment explanation
Indices: 58851302--58851347 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
58851292 CCGTTATGTC
58851302 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
58851317 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
58851334 CGCGACCGCGACCG
1 CGCGACCGCGACCG
58851348 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:58851466 original size:46 final size:44
Alignment explanation
Indices: 58851373--58851466 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 44
58851363 ATTACAACAT
*
58851373 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
58851417 CATTCCATTCAACCAAACA-ATTA-AATTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA--AGAA-TAC-TATTACAGCTCTATTC
58851463 CATT
1 CATT
58851467 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 4 0.09
46 19 0.42
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:58851469 original size:16 final size:16
Alignment explanation
Indices: 58851448--58851503 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
58851438 TAAATTACTT
*
58851448 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
58851464 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
58851480 ATTACAGCCCTATTCA
1 ATTACAGCTCTATTCA
58851496 ATTACAGC
1 ATTACAGC
58851504 CAACCAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:58855533 original size:17 final size:19
Alignment explanation
Indices: 58855511--58855556 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
58855501 GACGTATAGA
58855511 AAGAAATAAAAAG-AGA-G
1 AAGAAATAAAAAGAAGAGG
*
58855528 AAGAAATAAATAGAAGAGG
1 AAGAAATAAAAAGAAGAGG
58855547 AA-AAATAAAA
1 AAGAAATAAAA
58855557 GCCGAAGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 10 0.40
19 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.09
Consensus pattern (19 bp):
AAGAAATAAAAAGAAGAGG
Found at i:58855538 original size:21 final size:19
Alignment explanation
Indices: 58855508--58855555 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
58855498 ACGGACGTAT
*
58855508 AGAAAGAAATAAAAAGAGAGA
1 AGAAATAAAT-AAAAGAG-GA
*
58855529 AGAAATAAATAGAAGAGGA
1 AGAAATAAATAAAAGAGGA
58855548 A-AAATAAA
1 AGAAATAAA
58855556 AGCCGAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 6 0.24
21 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
AGAAATAAATAAAAGAGGA
Found at i:58855875 original size:30 final size:31
Alignment explanation
Indices: 58855823--58855915 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 31
58855813 AGGTTTCAAT
* * *
58855823 TCAGTCACTAAAC-TT-TTAAAAAATGATAAA
1 TCAGTCACT-AACGTTATCAAAAAGTGACAAA
58855853 TCAGTCACTAACGTTATCAAAAAGTGACAAA
1 TCAGTCACTAACGTTATCAAAAAGTGACAAA
*
58855884 TCA---A-TAATGTTATCAAAAAGTGACAAA
1 TCAGTCACTAACGTTATCAAAAAGTGACAAA
58855911 TCAGT
1 TCAGT
58855916 TACCCACTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 25 0.45
28 1 0.02
29 3 0.05
30 11 0.20
31 15 0.27
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (31 bp):
TCAGTCACTAACGTTATCAAAAAGTGACAAA
Found at i:58856071 original size:3 final size:3
Alignment explanation
Indices: 58856065--58856213 Score: 291
Period size: 3 Copynumber: 50.0 Consensus size: 3
58856055 CCCTAACAAC
58856065 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
58856113 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
58856161 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
58856208 AGA AGA
1 AGA AGA
58856214 GACTGTAAAA
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 143 0.99
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:58857116 original size:17 final size:17
Alignment explanation
Indices: 58857094--58857126 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58857084 CTTTCTATTT
58857094 TTTTTCTCTTCTTCTTC
1 TTTTTCTCTTCTTCTTC
*
58857111 TTTTTCTTTTCTTCTT
1 TTTTTCTCTTCTTCTT
58857127 TTACTAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTCTTCTTCTTC
Found at i:58857677 original size:20 final size:20
Alignment explanation
Indices: 58857652--58857691 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
58857642 ATTATTTAAG
58857652 GATATTTTAGTCTTTTCATT
1 GATATTTTAGTCTTTTCATT
58857672 GATATTTTAGTCTTTTCATT
1 GATATTTTAGTCTTTTCATT
58857692 TCAACAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (20 bp):
GATATTTTAGTCTTTTCATT
Found at i:58877343 original size:13 final size:14
Alignment explanation
Indices: 58877305--58877336 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
58877295 ATGCTTGTGT
58877305 GAAAATTCTATGAG
1 GAAAATTCTATGAG
58877319 GAAAATTCTATGAG
1 GAAAATTCTATGAG
58877333 GAAA
1 GAAA
58877337 TTTTATGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (14 bp):
GAAAATTCTATGAG
Found at i:58878733 original size:42 final size:43
Alignment explanation
Indices: 58878674--58878778 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 43
58878664 TTCCGAACTT
* * * *
58878674 GTTGAGTGGTCCAAGTTCGTGAAATATGTG-GCATCCAAGCTC
1 GTTGAGTGGTTCGAGTTCATGAAAGATGTGAGCATCCAAGCTC
* ** * *
58878716 GTTGAGTGGTTCGAGTTCATTATGGATGTGAGCATCCGAGCTT
1 GTTGAGTGGTTCGAGTTCATGAAAGATGTGAGCATCCAAGCTC
*
58878759 GTTGAGTGATTCGAGTTCAT
1 GTTGAGTGGTTCGAGTTCAT
58878779 TGTGGATGCG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
42 23 0.44
43 29 0.56
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (43 bp):
GTTGAGTGGTTCGAGTTCATGAAAGATGTGAGCATCCAAGCTC
Found at i:58878765 original size:43 final size:42
Alignment explanation
Indices: 58878699--58878786 Score: 131
Period size: 43 Copynumber: 2.1 Consensus size: 42
58878689 TTCGTGAAAT
*
58878699 ATGTGGCATCCAAGCTCGTTGAGTGGTTCGAGTTCATTATGG
1 ATGTGGCATCCAAGCTCGTTGAGTGATTCGAGTTCATTATGG
* * *
58878741 ATGTGAGCATCCGAGCTTGTTGAGTGATTCGAGTTCATTGTGG
1 ATGTG-GCATCCAAGCTCGTTGAGTGATTCGAGTTCATTATGG
58878784 ATG
1 ATG
58878787 CGAGGCTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.34
Consensus pattern (42 bp):
ATGTGGCATCCAAGCTCGTTGAGTGATTCGAGTTCATTATGG
Found at i:58888552 original size:24 final size:25
Alignment explanation
Indices: 58888509--58888571 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
58888499 TTCTCCTAAA
* *
58888509 TTTCAATTTAATTTAATTATT-TATT
1 TTTCAAATT-ATTGAATTATTATATT
58888534 TTTCAAATTATTGAATTATTAATATT
1 TTTCAAATTATTGAATTATT-ATATT
58888560 TTATGCAAATTA
1 TT-T-CAAATTA
58888572 AATTTTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 10 0.31
25 8 0.25
26 6 0.19
27 1 0.03
28 7 0.22
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTCAAATTATTGAATTATTATATT
Found at i:58892095 original size:20 final size:22
Alignment explanation
Indices: 58892066--58892106 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
58892056 GTTTATAAGC
*
58892066 AATTAGATG-TACTTA-ATATT
1 AATTAAATGTTACTTATATATT
58892086 AATTAAATGTTACTTATATAT
1 AATTAAATGTTACTTATATAT
58892107 GCTGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (22 bp):
AATTAAATGTTACTTATATATT
Found at i:58898721 original size:20 final size:19
Alignment explanation
Indices: 58898696--58898753 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
58898686 ACCAATACAC
58898696 AAATTGAAAATATATAATAA
1 AAATTGAAAATATA-AATAA
** *
58898716 AAATTGATTATATTAAAATTA
1 AAATTGAAAATA-T-AAATAA
58898737 AAATT-AAAATATAAATA
1 AAATTGAAAATATAAATA
58898754 TAATTAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 4 0.13
19 1 0.03
20 14 0.47
21 10 0.33
22 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAATTGAAAATATAAATAA
Found at i:58898761 original size:23 final size:23
Alignment explanation
Indices: 58898732--58898777 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
58898722 ATTATATTAA
* *
58898732 AATTAAAATTAAAATATAAATAT
1 AATTAAAAATAAAAAATAAATAT
*
58898755 AATTAAAAATAAAAAATATATAT
1 AATTAAAAATAAAAAATAAATAT
58898778 TTATTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTAAAAATAAAAAATAAATAT
Found at i:58900679 original size:13 final size:13
Alignment explanation
Indices: 58900640--58900690 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
58900630 AGTTTGGCAA
* *
58900640 TGCTTTTGACAAT
1 TGCTTTTGAAAAG
* *
58900653 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
58900666 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
58900679 TGCTTTTGAAAA
1 TGCTTTTGAAAA
58900691 ATTTGGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:58909111 original size:14 final size:15
Alignment explanation
Indices: 58909083--58909129 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
58909073 AATATATATT
*
58909083 TATTAATAATAAATTA
1 TATT-ATAATTAATTA
58909099 TATTA-AATTAATT-
1 TATTATAATTAATTA
58909112 TATTATAATTATATTA
1 TATTATAATTA-ATTA
58909128 TA
1 TA
58909130 AGATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.44
15 4 0.15
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATAATTAATTA
Found at i:58909291 original size:20 final size:20
Alignment explanation
Indices: 58909230--58909281 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
58909220 ATATAAGTAT
*
58909230 TTAATTATTAATGGATATTTA
1 TTAATTA-TAATAGATATTTA
58909251 TTAATTATAATAGATATTTA
1 TTAATTATAATAGATATTTA
58909271 TTAATTA-AATA
1 TTAATTATAATA
58909282 ATTATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 4 0.13
20 19 0.63
21 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TTAATTATAATAGATATTTA
Found at i:58911224 original size:46 final size:46
Alignment explanation
Indices: 58911157--58911292 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
58911147 GCTCTTTGAA
* *
58911157 ATGAAATGTATAAAACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
58911203 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
58911249 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
58911293 TCAAAGATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:58912861 original size:222 final size:216
Alignment explanation
Indices: 58912425--58912862 Score: 592
Period size: 222 Copynumber: 2.0 Consensus size: 216
58912415 TGGTGAATTG
* * **
58912425 GGTATACGACTTTTGCAGTTTGTAACGTCATTCATAATAGTGGAATTTATAGCCCAAGAAATGGG
1 GGTATACGACTTGTGCAGTATGTAACGTCATTCATAATAGTGGAATCCATAGCCCAAGAAATGGG
* * * *
58912490 TAAATGATATCCTCTCATTAGCATTACATGGTTGATGAAAAGTAAATATGGCCACTGGTCGTTTG
66 T--ATGATATCCTCTCATTAGCATTACATGGTTGATGAAAAGTAAACATGGCCACGGGTCGCTCG
* * *
58912555 TTTATGTGTTGAATTACTCTTTGATAGTAATTGACTTTTCATGAAGGAAGATGTACTAGATATCA
129 TTTATGTGTTGAATTACTATTTAATAGTAATTGACTTTTCATGAAGGAAGATGTACTAGATATAA
58912620 TGAGATAAAATAAGATCATATTT
194 TGAGATAAAATAAGATCATATTT
*
58912643 GGTATACGACTTGTGCAGTATGTAGCGTCATTCATAATAGTGGAATCCATAGCCCAAGAAATGGG
1 GGTATACGACTTGTGCAGTATGTAACGTCATTCATAATAGTGGAATCCATAGCCCAAGAAATGGG
* * *
58912708 T-T-ATATCTTCTTATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCACGGGTCGCTCGTT
66 TATGATATCCTCTCATTAGCATTACATGGTTGATGAAAAGTAAACATGGCCACGGGTCGCTCGTT
* * *
58912771 TATGTGATGAATGACCTGATTATTATTTAATAGTAATTGACTTTTCATGAAGGAAGATGTATTGG
131 TATGTG-T---TGA----ATTACTATTTAATAGTAATTGACTTTTCATGAAGGAAGATGTACTAG
* *
58912836 TTATAATGAGATAAAATAGGATCATAT
188 ATATAATGAGATAAAATAAGATCATAT
58912863 AGGGAGAACG
Statistics
Matches: 192, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
214 60 0.31
215 2 0.01
218 64 0.33
222 66 0.34
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (216 bp):
GGTATACGACTTGTGCAGTATGTAACGTCATTCATAATAGTGGAATCCATAGCCCAAGAAATGGG
TATGATATCCTCTCATTAGCATTACATGGTTGATGAAAAGTAAACATGGCCACGGGTCGCTCGTT
TATGTGTTGAATTACTATTTAATAGTAATTGACTTTTCATGAAGGAAGATGTACTAGATATAATG
AGATAAAATAAGATCATATTT
Found at i:58915045 original size:25 final size:23
Alignment explanation
Indices: 58915002--58915073 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 23
58914992 TTAATATTTT
58915002 TATATACAATA-AAATATAAATAA
1 TATATACAATATAAA-ATAAATAA
58915025 TATATACACCATATAAAATAATATAA
1 TATATACA--ATATAAAATAA-ATAA
* *
58915051 TAATATATAATATAATA-AAATAA
1 T-ATATACAATATAAAATAAATAA
58915074 ATGGATTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
23 12 0.29
24 2 0.05
25 14 0.33
26 8 0.19
27 6 0.14
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
TATATACAATATAAAATAAATAA
Found at i:58915054 original size:8 final size:8
Alignment explanation
Indices: 58915041--58915073 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
58915031 CACCATATAA
58915041 AATAATAT
1 AATAATAT
58915049 AATAATAT
1 AATAATAT
58915057 -ATAATAT
1 AATAATAT
*
58915064 AATAAAAT
1 AATAATAT
58915072 AA
1 AA
58915074 ATGGATTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATAT
Found at i:58915058 original size:20 final size:20
Alignment explanation
Indices: 58915009--58915074 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
58914999 TTTTATATAC
58915009 AATAAAATAT-AAATAATAT
1 AATAAAATATAAAATAATAT
*
58915028 -ATACACCATATAAAATAATAT
1 AATA-A-AATATAAAATAATAT
* * *
58915049 AATAATATATAATATAATAA
1 AATAAAATATAAAATAATAT
58915069 AATAAA
1 AATAAA
58915075 TGGATTTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 21 0.55
21 10 0.26
22 3 0.08
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAAAATATAAAATAATAT
Found at i:58915185 original size:28 final size:28
Alignment explanation
Indices: 58915125--58915185 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
58915115 ATATAACTTT
** *
58915125 TAATATAAAATAATAATGAGTATTAATA
1 TAATATAAAATAATAATGACAATAAATA
*
58915153 TAATATAAAATAATAATATACAATAAATA
1 TAATATAAAATAATAAT-GACAATAAATA
58915182 -AATA
1 TAATA
58915186 ATAATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (28 bp):
TAATATAAAATAATAATGACAATAAATA
Found at i:58915186 original size:21 final size:22
Alignment explanation
Indices: 58915132--58915207 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
58915122 TTTTAATATA
* *
58915132 AAAT-AATAATGAGTATTAATAT
1 AAATAAATAAT-AATATTAAAAT
*
58915154 AATATAAAATAATAATA-TACAAT
1 AA-AT-AAATAATAATATTAAAAT
58915177 AAATAAATAATAATATTTAAAAT
1 AAATAAATAATAATA-TTAAAAT
58915200 AAATAAAT
1 AAATAAAT
58915208 TTAAAAGTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
21 11 0.24
22 4 0.09
23 21 0.47
24 3 0.07
25 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (22 bp):
AAATAAATAATAATATTAAAAT
Found at i:58915199 original size:15 final size:15
Alignment explanation
Indices: 58915181--58915213 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
58915171 TACAATAAAT
58915181 AAAT-AATAATATTTA
1 AAATAAATAA-ATTTA
58915196 AAATAAATAAATTTA
1 AAATAAATAAATTTA
58915211 AAA
1 AAA
58915214 GTGTAAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAATAAATTTA
Found at i:58915945 original size:7 final size:7
Alignment explanation
Indices: 58915933--58915977 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
58915923 AACAGGTAAG
58915933 AAAAATA
1 AAAAATA
58915940 AAAAATA
1 AAAAATA
*
58915947 TAAAAA-G
1 -AAAAATA
58915954 AAAAATA
1 AAAAATA
58915961 AAAAATA
1 AAAAATA
58915968 TAAAAATA
1 -AAAAATA
58915976 AA
1 AA
58915978 GAAACGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.15
7 16 0.48
8 12 0.36
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:58915956 original size:21 final size:21
Alignment explanation
Indices: 58915930--58915973 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
58915920 GCAAACAGGT
58915930 AAGAAAAATAAAAAATATAAA
1 AAGAAAAATAAAAAATATAAA
58915951 AAGAAAAATAAAAAATATAAA
1 AAGAAAAATAAAAAATATAAA
58915972 AA
1 AA
58915974 TAAAGAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (21 bp):
AAGAAAAATAAAAAATATAAA
Found at i:58915957 original size:15 final size:14
Alignment explanation
Indices: 58915933--58915977 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
58915923 AACAGGTAAG
58915933 AAAAATAAAAAATA
1 AAAAATAAAAAATA
*
58915947 TAAAAA-GAAAAATA
1 -AAAAATAAAAAATA
58915961 AAAAATATAAAAATA
1 AAAAATA-AAAAATA
58915976 AA
1 AA
58915978 GAAACGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 14 0.54
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:58926829 original size:14 final size:14
Alignment explanation
Indices: 58926778--58926841 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
58926768 TTATATAATT
58926778 TATATATTTTAAAA
1 TATATATTTTAAAA
*
58926792 -ATAAAATTTTAGAAA
1 TAT-ATATTTTA-AAA
* * *
58926807 TTTAT-TTTTTAAT
1 TATATATTTTAAAA
58926820 TATATATTTTAAAA
1 TATATATTTTAAAA
58926834 TATATATT
1 TATATATT
58926842 CAGAATACGT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
13 8 0.21
14 25 0.66
15 4 0.11
16 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATATTTTAAAA
Found at i:58936952 original size:18 final size:17
Alignment explanation
Indices: 58936924--58936957 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
58936914 ATTTAGTCAT
58936924 AATTTTTAAAAAATAAC
1 AATTTTTAAAAAATAAC
58936941 AATTTTTAAAAAATAAC
1 AATTTTTAAAAAATAAC
58936958 TCTCAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTTTTAAAAAATAAC
Found at i:58955805 original size:13 final size:13
Alignment explanation
Indices: 58955784--58955816 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58955774 TTTATTTAAA
*
58955784 TTAGTTAATTAGT
1 TTAGATAATTAGT
58955797 TTAGATAATTAGT
1 TTAGATAATTAGT
58955810 TTA-ATAA
1 TTAGATAA
58955817 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:58961137 original size:22 final size:22
Alignment explanation
Indices: 58961123--58961197 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 22
58961113 TTTTTAATTA
58961123 TTTATTCTTATTTTTATTTTAT
1 TTTATTCTTATTTTTATTTTAT
* *
58961145 TTTATTTTTATTTTTATTTTTCT
1 TTTATTCTTATTTTTA-TTTTAT
* * *
58961168 TTTGATTTTTATTTTCATTTCAAT
1 TTT-ATTCTTATTTTTATTT-TAT
58961192 TTTATT
1 TTTATT
58961198 ATTTTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.33
23 14 0.31
24 16 0.36
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTATTCTTATTTTTATTTTAT
Found at i:58961139 original size:6 final size:6
Alignment explanation
Indices: 58961113--58961187 Score: 82
Period size: 6 Copynumber: 12.5 Consensus size: 6
58961103 TCCTCCTATT
*
58961113 TTTTTAA TTATTTA TTCTTA TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA
1 TTTTT-A TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
58961161 TTTTTC TTTTGA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
58961188 CAATTTTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
5 10 0.17
6 41 0.69
7 5 0.08
8 3 0.05
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:58961139 original size:16 final size:15
Alignment explanation
Indices: 58961120--58961157 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
58961110 ATTTTTTTAA
58961120 TTATTTATTCTTATTT
1 TTATTTATT-TTATTT
58961136 TTATTTTATTTTATTT
1 TTA-TTTATTTTATTT
58961152 TTATTT
1 TTATTT
58961158 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:58961144 original size:5 final size:5
Alignment explanation
Indices: 58961123--58961207 Score: 57
Period size: 6 Copynumber: 15.6 Consensus size: 5
58961113 TTTTTAATTA
*
58961123 TTTAT TCTTATT TTTAT TTTAT TTTATT TTTATT TTTATT TTTCT TTTGATT
1 TTTAT T-TTA-T TTTAT TTTAT TTTA-T TTTA-T TTTA-T TTTAT TTT-A-T
*
58961175 TTTAT TTTCAT TTCAAT TTTA- -TTAT TTTAT TTT
1 TTTAT TTT-AT TT-TAT TTTAT TTTAT TTTAT TTT
58961208 GAAAGACATA
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
3 3 0.04
5 27 0.40
6 31 0.46
7 6 0.09
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:58961193 original size:18 final size:18
Alignment explanation
Indices: 58961114--58961207 Score: 72
Period size: 18 Copynumber: 5.2 Consensus size: 18
58961104 CCTCCTATTT
58961114 TTTTAATTATTTATTCTT-A
1 TTTTAATT-TTTATT-TTCA
*
58961133 TTTTTA-TTTTATTTT-A
1 TTTTAATTTTTATTTTCA
*
58961149 TTTTTATTTTTATTTTTC-
1 TTTTAATTTTTA-TTTTCA
*
58961167 TTTTGATTTTTATTTTCA
1 TTTTAATTTTTATTTTCA
*
58961185 TTTCAATTTTATTATTTT-A
1 TTTTAA-TTT-TTATTTTCA
58961204 TTTT
1 TTTT
58961208 GAAAGACATA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.14
17 16 0.25
18 20 0.31
19 12 0.19
20 7 0.11
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (18 bp):
TTTTAATTTTTATTTTCA
Found at i:58964127 original size:13 final size:13
Alignment explanation
Indices: 58964111--58964143 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58964101 TTTAATTAAA
*
58964111 TTAGTTAATTAGT
1 TTAGATAATTAGT
58964124 TTAGATAATTAGT
1 TTAGATAATTAGT
58964137 TTA-ATAA
1 TTAGATAA
58964144 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:58967206 original size:38 final size:38
Alignment explanation
Indices: 58967162--58967257 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
58967152 TTCGAATTAT
* * ***
58967162 GTGTTATTCAAGCTTAGTGCCTAGCTGGATTCGTGGTG
1 GTGTTATTCAAGCTTAATGCCTAGCAGGATTCGTGCCA
* * *
58967200 GTGTTATTCAGGCTTAATGCCTAGCAGGCTTTGTGCCA
1 GTGTTATTCAAGCTTAATGCCTAGCAGGATTCGTGCCA
58967238 GTGTTATTCAAGCTTAATGC
1 GTGTTATTCAAGCTTAATGC
58967258 TGGTGTTATT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (38 bp):
GTGTTATTCAAGCTTAATGCCTAGCAGGATTCGTGCCA
Found at i:58967263 original size:22 final size:22
Alignment explanation
Indices: 58967238--58967279 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
58967228 CTTTGTGCCA
58967238 GTGTTATTCAAGCTTAATGCTG
1 GTGTTATTCAAGCTTAATGCTG
58967260 GTGTTATTCAAGCTTAATGC
1 GTGTTATTCAAGCTTAATGC
58967280 CTAGCAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (22 bp):
GTGTTATTCAAGCTTAATGCTG
Found at i:58967288 original size:38 final size:38
Alignment explanation
Indices: 58967246--58967321 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
58967236 CAGTGTTATT
* *
58967246 CAAGCTTAATGCTGGTGTTATTCAAGCTTAATGCCTAG
1 CAAGCTTAATGCCGATGTTATTCAAGCTTAATGCCTAG
** * *
58967284 CAAGCTTTGTGCCGATGTTATTCAGGCTTAGTGCCTAG
1 CAAGCTTAATGCCGATGTTATTCAAGCTTAATGCCTAG
58967322 TAGGCCTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (38 bp):
CAAGCTTAATGCCGATGTTATTCAAGCTTAATGCCTAG
Found at i:58967291 original size:60 final size:60
Alignment explanation
Indices: 58967198--58967313 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
58967188 GGATTCGTGG
* *
58967198 TGGTGTTATTCAGGCTTAATGCCTAGCAGGCTTTGTGCC-AGTGTTATTCAAGCTTAATGC
1 TGGTGTTATTCAAGCTTAATGCCTAGCAAGCTTTGTGCCGA-TGTTATTCAAGCTTAATGC
*
58967258 TGGTGTTATTCAAGCTTAATGCCTAGCAAGCTTTGTGCCGATGTTATTCAGGCTTA
1 TGGTGTTATTCAAGCTTAATGCCTAGCAAGCTTTGTGCCGATGTTATTCAAGCTTA
58967314 GTGCCTAGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (60 bp):
TGGTGTTATTCAAGCTTAATGCCTAGCAAGCTTTGTGCCGATGTTATTCAAGCTTAATGC
Found at i:58967339 original size:98 final size:98
Alignment explanation
Indices: 58967162--58967343 Score: 247
Period size: 98 Copynumber: 1.9 Consensus size: 98
58967152 TTCGAATTAT
* ** ** *
58967162 GTGTTATTCAAGCTTAGTGCCTAGCTGGATTCGTGGTGGTGTTATTCAGGCTTAATGCCTAGCAG
1 GTGTTATTCAAGCTTAATGCCTAGCAAGATTCGTGCCGATGTTATTCAGGCTTAATGCCTAGCAG
* *
58967227 GCTTTGTGCCAGTGTTATTCAAGCTTAATGCTG
66 GCCTAGTGCCAGTGTTATTCAAGCTTAATGCTG
* * * *
58967260 GTGTTATTCAAGCTTAATGCCTAGCAAGCTTTGTGCCGATGTTATTCAGGCTTAGTGCCTAGTAG
1 GTGTTATTCAAGCTTAATGCCTAGCAAGATTCGTGCCGATGTTATTCAGGCTTAATGCCTAGCAG
*
58967325 GCCTAGTGCTAGTGTTATT
66 GCCTAGTGCCAGTGTTATT
58967344 TAAGTTTAGC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
98 71 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (98 bp):
GTGTTATTCAAGCTTAATGCCTAGCAAGATTCGTGCCGATGTTATTCAGGCTTAATGCCTAGCAG
GCCTAGTGCCAGTGTTATTCAAGCTTAATGCTG
Found at i:58967341 original size:38 final size:38
Alignment explanation
Indices: 58967246--58967361 Score: 90
Period size: 38 Copynumber: 3.1 Consensus size: 38
58967236 CAGTGTTATT
* * *
58967246 CAAGCTTAATGCTGGTGTTATTCAAGCTTAATGCCTAG
1 CAAGCCTAGTGCTAGTGTTATTCAAGCTTAATGCCTAG
* * * * *
58967284 CAAGCTTTGTGC-CGATGTTATTCAGGCTTAGTGCCTAG
1 CAAGCCTAGTGCTAG-TGTTATTCAAGCTTAATGCCTAG
* * * * **
58967322 TAGGCCTAGTGCTAGTGTTATTTAAGTTTAGCGCCTAG
1 CAAGCCTAGTGCTAGTGTTATTCAAGCTTAATGCCTAG
58967360 CA
1 CA
58967362 GGATTTGTGC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
37 1 0.02
38 59 0.97
39 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (38 bp):
CAAGCCTAGTGCTAGTGTTATTCAAGCTTAATGCCTAG
Found at i:58973375 original size:13 final size:13
Alignment explanation
Indices: 58973357--58973383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58973347 AAAGTAATCG
58973357 CACACGGGCGTGT
1 CACACGGGCGTGT
58973370 CACACGGGCGTGT
1 CACACGGGCGTGT
58973383 C
1 C
58973384 CCTGTCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:58978017 original size:21 final size:22
Alignment explanation
Indices: 58977979--58978026 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
58977969 ATAATTTTCA
* * *
58977979 TTTTCTTTCATGTTCAAGTTTT
1 TTTTATTTCATGTACAAGATTT
58978001 TTTTATTTCAT-TACAAGATTT
1 TTTTATTTCATGTACAAGATTT
*
58978022 CTTTA
1 TTTTA
58978027 CTCCATTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTTATTTCATGTACAAGATTT
Found at i:58978191 original size:73 final size:73
Alignment explanation
Indices: 58978068--58978205 Score: 249
Period size: 73 Copynumber: 1.9 Consensus size: 73
58978058 ATGGTTAGGA
* * *
58978068 TAGGTGGAATACTCATGCTTTTTTCAAATATTCTAACTCAATCCTTATACTTTTCAAATGCTTCT
1 TAGGTGGAATACTCATGCCTTCTTCAAATATTCTAACTCAATCCTCATACTTTTCAAATGCTTCT
58978133 AGTCAGGT
66 AGTCAGGT
58978141 TAGGTGGAATACTCATGCCTTCTTCAAATATTCTAACTCAATCCTCATACTTTTCAAATGCTTCT
1 TAGGTGGAATACTCATGCCTTCTTCAAATATTCTAACTCAATCCTCATACTTTTCAAATGCTTCT
58978206 TATTATTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (73 bp):
TAGGTGGAATACTCATGCCTTCTTCAAATATTCTAACTCAATCCTCATACTTTTCAAATGCTTCT
AGTCAGGT
Found at i:58986772 original size:31 final size:31
Alignment explanation
Indices: 58986728--58986801 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
58986718 GTCCCAAGTC
*
58986728 ACACAGGCGTGTGAGTCCACACGGCCCATCT
1 ACACGGGCGTGTGAGTCCACACGGCCCATCT
* *
58986759 ACACGGGTGTGTGAGTCCACACGGCCCTTCT
1 ACACGGGCGTGTGAGTCCACACGGCCCATCT
58986790 ACACGGGCGTGT
1 ACACGGGCGTGT
58986802 AACACTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.19, C:0.32, G:0.30, T:0.19
Consensus pattern (31 bp):
ACACGGGCGTGTGAGTCCACACGGCCCATCT
Found at i:58987992 original size:48 final size:47
Alignment explanation
Indices: 58987862--58988032 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 47
58987852 ACATCTTGTA
* *
58987862 GCCGATGCATGTCCTAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTACATCTCAAG
* *
58987908 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTACATCTCAAG
* * * *
58987954 GCCGATGCTATGTCCCAAATATGGTCTTACACTGGCTCTTATAATGT---G
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACTGGCTC-TA-CATCTCAAG
58988002 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
58988033 AGCACACAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 58 0.54
47 23 0.21
48 22 0.21
49 1 0.01
51 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTACATCTCAAG
Found at i:58993250 original size:40 final size:39
Alignment explanation
Indices: 58993219--58993428 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
58993209 GGACTAAGAT
* *
58993219 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
58993259 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
58993299 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
58993339 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
58993379 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
58993418 CCGAAGGCATT
1 CCGAAGGCATT
58993429 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:58993382 original size:120 final size:120
Alignment explanation
Indices: 58993166--58993428 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
58993156 TTGAATGCTG
* *
58993166 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
58993230 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
58993286 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
58993349 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
58993405 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
58993429 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:58993448 original size:79 final size:80
Alignment explanation
Indices: 58993167--58993463 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
58993157 TGAATGCTGT
* ** * * * **
58993167 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
58993230 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
58993247 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
58993311 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
58993327 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
58993391 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
58993406 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
58993464 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:58998109 original size:92 final size:94
Alignment explanation
Indices: 58997993--58998162 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
58997983 ATCTATGATG
* * **
58997993 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACACAT-CTCGTAG-CTGATGCATGTCCCAGAC
1 ATGCCATGTCCCAGACATGATCTTACACTAGCACACATAAT-GT-GTCCAATGCATGTCCCAGAC
58998054 ATGTCTTACACTAGCACTCGTCTCAATGCCA
64 ATGTCTTACACTAGCACTCGTCTCAATGCCA
* * *
58998085 ATGCCATGTTCCAGACATGATCTTACACTAGCTCTCATAATGTGTCCAATGCATGTCCCAGACAT
1 ATGCCATGTCCCAGACATGATCTTACACTAGCACACATAATGTGTCCAATGCATGTCCCAGACAT
58998150 GTCTTACACTAGC
66 GTCTTACACTAGC
58998163 TCACAATAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
92 27 0.40
93 2 0.03
94 37 0.55
95 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (94 bp):
ATGCCATGTCCCAGACATGATCTTACACTAGCACACATAATGTGTCCAATGCATGTCCCAGACAT
GTCTTACACTAGCACTCGTCTCAATGCCA
Found at i:58998134 original size:48 final size:44
Alignment explanation
Indices: 58998039--58998164 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 44
58998029 CTCGTAGCTG
58998039 ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCCA
1 ATGCATGTCCCAGACATGTCTTACACTAG--CTCGTCTCAATGCCA
*
58998085 ATGCCATGTTCCAGACATGATCTTACACTAGCTC-TCAT-AATGTGTCCA
1 ATG-CATGTCCCAGACATG-TCTTACACTAGCTCGTC-TCAA--TG-CCA
58998133 ATGCATGTCCCAGACATGTCTTACACTAGCTC
1 ATGCATGTCCCAGACATGTCTTACACTAGCTC
58998165 ACAATAGCTC
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
45 4 0.06
46 21 0.29
47 30 0.42
48 17 0.24
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (44 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCGTCTCAATGCCA
Found at i:59014571 original size:46 final size:46
Alignment explanation
Indices: 59014513--59014729 Score: 335
Period size: 46 Copynumber: 4.7 Consensus size: 46
59014503 TTTCTGTCAT
* * * *
59014513 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
*
59014559 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATACCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
* * *
59014605 GCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
* * *
59014651 GCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAAATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
59014697 GTTGCCATGGTATCTTTCAACCATGGTCTTATA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATA
59014730 TCAAGTTGCC
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 160 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAG
Found at i:59014622 original size:25 final size:24
Alignment explanation
Indices: 59014594--59014673 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 24
59014584 GTCTTATACA
59014594 TTTCATACCAGGCTGCCATGGTATC
1 TTTCA-ACCAGGCTGCCATGGTATC
*
59014619 TTTCAACCATGG-T--C-T--TACAC
1 TTTCAACCA-GGCTGCCATGGTA-TC
59014639 ATTTCATACCAGGCTGCCATGGTATC
1 -TTTCA-ACCAGGCTGCCATGGTATC
59014665 TTTCAACCA
1 TTTCAACCA
59014674 TGGTCTTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 21
0.65 0.03 0.32
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 8 0.19
22 6 0.14
24 10 0.23
25 13 0.30
26 1 0.02
27 2 0.05
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.33
Consensus pattern (24 bp):
TTTCAACCAGGCTGCCATGGTATC
Done.