Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 40 of 310
Found at i:11449943 original size:11 final size:11
Alignment explanation
Indices: 11449927--11449951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11449917 TTCAGCTGAT
11449927 GAAAATGAAGA
1 GAAAATGAAGA
11449938 GAAAATGAAGA
1 GAAAATGAAGA
11449949 GAA
1 GAA
11449952 TTCTAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:11452928 original size:12 final size:12
Alignment explanation
Indices: 11452911--11452936 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11452901 ATAACAAAAC
11452911 ATAAATAAAAGA
1 ATAAATAAAAGA
11452923 ATAAATAAAAGA
1 ATAAATAAAAGA
11452935 AT
1 AT
11452937 TTAGGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (12 bp):
ATAAATAAAAGA
Found at i:11455882 original size:13 final size:14
Alignment explanation
Indices: 11455864--11455893 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11455854 TACTTTTAAA
11455864 TTTTTAGTTTTT-T
1 TTTTTAGTTTTTAT
11455877 TTTTTAGTTTTTAT
1 TTTTTAGTTTTTAT
11455891 TTT
1 TTT
11455894 AGCTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTTAGTTTTTAT
Found at i:11463489 original size:31 final size:31
Alignment explanation
Indices: 11463454--11463515 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11463444 TCTGGTGCAC
11463454 TTTATCGTGTTCAATTTTGGAATTTTTACTT
1 TTTATCGTGTTCAATTTTGGAATTTTTACTT
11463485 TTTATCGTGTTCAATTTTGGAATTTTTACTT
1 TTTATCGTGTTCAATTTTGGAATTTTTACTT
11463516 ACTTCCTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.13, T:0.58
Consensus pattern (31 bp):
TTTATCGTGTTCAATTTTGGAATTTTTACTT
Found at i:11472296 original size:14 final size:14
Alignment explanation
Indices: 11472277--11472306 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11472267 AGAATTTTAA
11472277 AATTAAAAAAATAT
1 AATTAAAAAAATAT
11472291 AATTAAAAAAATAT
1 AATTAAAAAAATAT
11472305 AA
1 AA
11472307 AGATTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATTAAAAAAATAT
Found at i:11475064 original size:15 final size:15
Alignment explanation
Indices: 11475037--11475075 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11475027 GAAAAAATAT
*
11475037 TAATAAGAATAATTA
1 TAATAAAAATAATTA
* *
11475052 TAGTAAAAATAATTT
1 TAATAAAAATAATTA
11475067 TAATAAAAA
1 TAATAAAAA
11475076 GAATAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
TAATAAAAATAATTA
Found at i:11476648 original size:44 final size:43
Alignment explanation
Indices: 11476599--11477022 Score: 194
Period size: 44 Copynumber: 9.6 Consensus size: 43
11476589 CAATTATTAG
11476599 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTGAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTATCTTGAA
* * * * * ** *
11476643 CCTGCTCCACTACAACTTTAGGGAGACAAGGTTGGTGGCTTAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTATCTTGAA
* * * * * **
11476687 TCTGCTCCATTGCCGA-TACATGGAGATAAAATTCGTCATCTTCTA
1 TCTGCTCCACTG-CAACTTCAGGGAGATAAGATT-GT-ATCTTGAA
* ** ** * * *
11476732 TCTGCTCCACTACTGCTT-AGGGAGATAAGATATACAATTTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-GTATCTTGAA
* * *
11476776 TTTGCTCCACTACAACTTCAAGGAGATAAGACTTGTATCTTGAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTATCTTGAA
* * * * ** *
11476820 CCTGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTATCTTGAA
* * * * * *
11476864 TCTGCTCCATTGCTGA-TACATGAAGATAAGATT-CACCGTCTTCG-A
1 TCTGCTCCACTGC-AACTTCAGGGAGATAAGATTGTA---TCTT-GAA
* **** * * * *
11476909 TCTACTCCACTATTGCTT-AGGGAGATAAGATATGCAATTTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-TATCTTGAA
* *
11476953 TCTGCTCCACTGCAATTTCAAGGAGATAAGACTTGTATCTTGAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTATCTTGAA
*
11476997 CCTGCTCCACTGCAACTTCAGGGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGA
11477023 CAAGGCTGAT
Statistics
Matches: 264, Mismatches: 96, Indels: 40
0.66 0.24 0.10
Matches are distributed among these distances:
43 4 0.02
44 198 0.75
45 59 0.22
46 2 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTATCTTGAA
Found at i:11476767 original size:177 final size:177
Alignment explanation
Indices: 11476468--11477126 Score: 978
Period size: 177 Copynumber: 3.7 Consensus size: 177
11476458 ATCTTCATTT
* * * * * * * *
11476468 TGCTCCATTGCAACTTCAGGGAAATAAGACTT-GTGGCTTAAATCTGTTTCATTGCCGCTACATG
1 TGCTCCACTGCAACTTTAGGGAGACAAG-GTTGGTGGCTTAAATCTGCTCCATTGCCGATACATG
* * * * *
11476532 GAGATAAGATTCGCCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAAATATACAATTATT
65 AAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATATACAATTTTT
*
11476597 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTGAACC
130 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTATCTTGAACC
* *
11476645 TGCTCCACTACAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGG
1 TGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGA
* ** * * *
11476710 AGATAAAATTCGTCATCTTCTATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAATTTTTA
66 AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATATACAATTTTTA
* *
11476775 GTTTGCTCCACTACAACTTCAAGGAGATAAGACTTGTATCTTGAACC
131 GTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTATCTTGAACC
*
11476822 TGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCTGATACATGA
1 TGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGA
* *
11476887 AGATAAGATTCACCGTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATATGCAATTTTTA
66 AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATATACAATTTTTA
*
11476952 GTCTGCTCCACTGCAATTTCAAGGAGATAAGACTTGTATCTTGAACC
131 GTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTATCTTGAACC
* * * *
11476999 TGCTCCACTGCAACTTCAGGGAGACAAGGCTGATGGCTTAAATCTGCTCCATTACCGATACATGA
1 TGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGA
* * * *
11477064 AGATAAGATTCACCGTTTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTT
66 AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATATACAATTTT
11477127 CTTCAATCCA
Statistics
Matches: 436, Mismatches: 45, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
176 2 0.00
177 434 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (177 bp):
TGCTCCACTGCAACTTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGA
AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATATACAATTTTTA
GTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTATCTTGAACC
Found at i:11477046 original size:44 final size:44
Alignment explanation
Indices: 11476953--11477049 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
11476943 CAATTTTTAG
* * *
11476953 TCTGCTCCACTGCAATTTCAAGGAGATAAGACTTGTATCTTGAA
1 TCTGCTCCACTGCAACTTCAAGGAGACAAGACTTGTATCTTAAA
* * *
11476997 CCTGCTCCACTGCAACTTCAGGGAGACAAGGC-TG-ATGGCTTAAA
1 TCTGCTCCACTGCAACTTCAAGGAGACAAGACTTGTAT--CTTAAA
11477041 TCTGCTCCA
1 TCTGCTCCA
11477050 TTACCGATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.05
43 2 0.05
44 40 0.91
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAAGGAGACAAGACTTGTATCTTAAA
Found at i:11477108 original size:88 final size:87
Alignment explanation
Indices: 11476836--11477110 Score: 188
Period size: 88 Copynumber: 3.1 Consensus size: 87
11476826 CCACTGCAAC
* * *
11476836 TTTAGGGAGACAAGGTTGGTGGCTTAAATCTGCTCCATTGCTGATACATGAAGATAAGATTCACC
1 TTTAGGGAGACAAGGATGATGGCTTAAATCTGCTCCATT-CCGATACATGAAGATAAGATTCACC
* * *
11476901 GTCTTCGATCTACTCCACTATTG
65 GTTTTCGATCTGCTCCACTACTG
* * * * * * * * * *
11476924 CTTAGGGAGATAA-GAT-AT-GCAATTTTTAGTCTGCTCCACTGCAATTTCAAGGAGATAAGACT
1 TTTAGGGAGACAAGGATGATGGC----TTAAATCTGCTCCATTCCGA-TACATGAAGATAAGA-T
* * **
11476986 T----GTATCTT-GAACCTGCTCCACTGCAAC
60 TCACCGT-T-TTCG-ATCTGCTCCACTAC-TG
* *
11477013 TTCAGGGAGACAAGGCTGATGGCTTAAATCTGCTCCATTACCGATACATGAAGATAAGATTCACC
1 TTTAGGGAGACAAGGATGATGGCTTAAATCTGCTCCATT-CCGATACATGAAGATAAGATTCACC
11477078 GTTTTCGATCTGCTCCACTACTG
65 GTTTTCGATCTGCTCCACTACTG
11477101 TTTAGGGAGA
1 TTTAGGGAGA
11477111 TAAGATCTAC
Statistics
Matches: 131, Mismatches: 37, Indels: 38
0.64 0.18 0.18
Matches are distributed among these distances:
85 2 0.02
86 3 0.02
87 5 0.04
88 58 0.44
89 51 0.39
90 6 0.05
91 4 0.03
92 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (87 bp):
TTTAGGGAGACAAGGATGATGGCTTAAATCTGCTCCATTCCGATACATGAAGATAAGATTCACCG
TTTTCGATCTGCTCCACTACTG
Found at i:11489124 original size:3 final size:3
Alignment explanation
Indices: 11489118--11489172 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
11489108 GGAAATAGAA
*
11489118 AAT AAT AAT AAT AAT AGATT AAT -AT GGAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-A-T AAT AAT -AAT AAT AAT AAT AAT AAT AAT
11489165 AA- AAT AAT
1 AAT AAT AAT
11489173 GGGGAAAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 4 0.09
5 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11489219 original size:15 final size:15
Alignment explanation
Indices: 11489192--11489230 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11489182 GGGAAAATAT
*
11489192 TAATAAGAATAATTA
1 TAATAAAAATAATTA
* *
11489207 TAGTAAAAATAATTT
1 TAATAAAAATAATTA
11489222 TAATAAAAA
1 TAATAAAAA
11489231 GAATAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
TAATAAAAATAATTA
Found at i:11491529 original size:18 final size:18
Alignment explanation
Indices: 11491508--11491547 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11491498 TAAAAAATTT
*
11491508 TATTTTAATTT-TTAAAAA
1 TATTTAAATTTATT-AAAA
11491526 TATTTAAATTTATTAAAA
1 TATTTAAATTTATTAAAA
11491544 TATT
1 TATT
11491548 AATATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAAATTTATTAAAA
Found at i:11491750 original size:15 final size:15
Alignment explanation
Indices: 11491732--11491786 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
11491722 TATCAATATT
11491732 AATATTTTAATAATA
1 AATATTTTAATAATA
*
11491747 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
11491766 AATATATTAATAATA
1 AATATTTTAATAATA
11491781 AATATT
1 AATATT
11491787 CTGTAGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 15 0.47
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:11492276 original size:14 final size:14
Alignment explanation
Indices: 11492240--11492278 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11492230 CCAGGAAAGT
11492240 AAGTCATTTTCCAG
1 AAGTCATTTTCCAG
* * *
11492254 AAATTATTTTTCAG
1 AAGTCATTTTCCAG
11492268 AAGTCATTTTC
1 AAGTCATTTTC
11492279 AGTGAAACAA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (14 bp):
AAGTCATTTTCCAG
Found at i:11498331 original size:31 final size:31
Alignment explanation
Indices: 11498244--11498607 Score: 148
Period size: 31 Copynumber: 12.0 Consensus size: 31
11498234 TGATCTATGT
* *
11498244 AAATTA-A-ATTAAATAAAAATTTCATGTATA
1 AAATTACACATTAAATCAAAA-TTCATATATA
* * *
11498274 AAATTACACA--AAATTAAAATTTATATATG
1 AAATTACACATTAAATCAAAATTCATATATA
*
11498303 ACATTACACATTAAATCAAAATTCATATATA
1 AAATTACACATTAAATCAAAATTCATATATA
** * * **** *
11498334 ATTTTA-ATATT-TATCCCTTTTAACTATTATA
1 AAATTACACATTAAATCAAAATTCA-TA-TATA
* * *
11498365 AAATTACACA--AAATTAAAATTTATATATG
1 AAATTACACATTAAATCAAAATTCATATATA
*
11498394 ACATTACACATTAAATCAAAATTCATATATA
1 AAATTACACATTAAATCAAAATTCATATATA
** * * **** *
11498425 ATTTTA-ATATT-TATCCCTTTTAACTATTATA
1 AAATTACACATTAAATCAAAATTCA-TA-TATA
* * *
11498456 AAATTACACA--AAATTAAAATTTATATATG
1 AAATTACACATTAAATCAAAATTCATATATA
*
11498485 ACATTACACATTAAATCAAAATTCATATATA
1 AAATTACACATTAAATCAAAATTCATATATA
** * * **** *
11498516 ATTTTA-ATATT-TATCCCTTTTAACTATTATA
1 AAATTACACATTAAATCAAAATTCA-TA-TATA
* * *
11498547 AAATTACACA--AAATTAAAATTTATATATG
1 AAATTACACATTAAATCAAAATTCATATATA
*
11498576 ACATTACACATTAAATCAAAATTCATATATA
1 AAATTACACATTAAATCAAAATTCATATATA
11498607 A
1 A
11498608 TTTTAATATT
Statistics
Matches: 232, Mismatches: 80, Indels: 43
0.65 0.23 0.12
Matches are distributed among these distances:
29 70 0.30
30 38 0.16
31 117 0.50
32 7 0.03
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.39
Consensus pattern (31 bp):
AAATTACACATTAAATCAAAATTCATATATA
Found at i:11498425 original size:91 final size:91
Alignment explanation
Indices: 11498270--11498634 Score: 730
Period size: 91 Copynumber: 4.0 Consensus size: 91
11498260 AAATTTCATG
11498270 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
1 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
11498335 TTTTAATATTTATCCCTTTTAACTAT
66 TTTTAATATTTATCCCTTTTAACTAT
11498361 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
1 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
11498426 TTTTAATATTTATCCCTTTTAACTAT
66 TTTTAATATTTATCCCTTTTAACTAT
11498452 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
1 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
11498517 TTTTAATATTTATCCCTTTTAACTAT
66 TTTTAATATTTATCCCTTTTAACTAT
11498543 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
1 TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
11498608 TTTTAATATTTATCCCTTTTAACTAT
66 TTTTAATATTTATCCCTTTTAACTAT
11498634 T
1 T
11498635 TGTAAACGTA
Statistics
Matches: 274, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 274 1.00
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (91 bp):
TATAAAATTACACAAAATTAAAATTTATATATGACATTACACATTAAATCAAAATTCATATATAA
TTTTAATATTTATCCCTTTTAACTAT
Found at i:11499651 original size:18 final size:18
Alignment explanation
Indices: 11499628--11499687 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
11499618 AAAAGTTATG
11499628 ATAATTATATATTTATAA
1 ATAATTATATATTTATAA
*
11499646 ATAATTATA-ATTTAATAG
1 ATAATTATATATTT-ATAA
* * *
11499664 GTGA-TATATATTTAAAA
1 ATAATTATATATTTATAA
11499681 ATAATTA
1 ATAATTA
11499688 GAAAATTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATAATTATATATTTATAA
Found at i:11499766 original size:25 final size:25
Alignment explanation
Indices: 11499714--11499767 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11499704 AAATATACAA
*
11499714 AAAAAGTTGAGTTAATTTTATTTTT
1 AAAAAGTTGAGTTAATTTTATTTGT
11499739 AAAAAGTT-A-TTAATTTTATTGATGT
1 AAAAAGTTGAGTTAATTTTATT--TGT
11499764 AAAA
1 AAAA
11499768 TAGAGTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
24 1 0.04
25 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (25 bp):
AAAAAGTTGAGTTAATTTTATTTGT
Found at i:11500035 original size:27 final size:27
Alignment explanation
Indices: 11499984--11500036 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
11499974 CCTTAATTAC
*
11499984 TATAATTAAAAATAAAATATTTAAAAA
1 TATAATTAAAAATAAAATATGTAAAAA
* * *
11500011 TATAATTAAATATTAAATGTGTAAAA
1 TATAATTAAAAATAAAATATGTAAAA
11500037 TTACTTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
TATAATTAAAAATAAAATATGTAAAAA
Found at i:11500430 original size:13 final size:13
Alignment explanation
Indices: 11500412--11500436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11500402 TTGGTAATGC
11500412 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
11500425 TTTTGAAAAGTG
1 TTTTGAAAAGTG
11500437 TTGAGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:11500661 original size:18 final size:18
Alignment explanation
Indices: 11500626--11500664 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11500616 TTTAAGCAAT
*
11500626 AAATATTAATTATTTATA
1 AAATATTAATTATATATA
11500644 AAAT-TTAATTATAATATA
1 AAATATTAATTAT-ATATA
11500662 AAA
1 AAA
11500665 ACTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATTAATTATATATA
Found at i:11502351 original size:16 final size:15
Alignment explanation
Indices: 11502325--11502354 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11502315 CAACTCCGAA
11502325 CTCTTCTTTCTCTCT
1 CTCTTCTTTCTCTCT
11502340 CTCTTCCTTTCTCTC
1 CTCTT-CTTTCTCTC
11502355 CATTAAATAA
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:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
CTCTTCTTTCTCTCT
Found at i:11503287 original size:13 final size:13
Alignment explanation
Indices: 11503269--11503296 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11503259 GTTGCAACTA
11503269 GTGAATTGATATG
1 GTGAATTGATATG
11503282 GTGAATTGATATG
1 GTGAATTGATATG
11503295 GT
1 GT
11503297 TTTCTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (13 bp):
GTGAATTGATATG
Found at i:11506672 original size:23 final size:23
Alignment explanation
Indices: 11506645--11506695 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
11506635 AGGGTTGACG
11506645 TCACGCGATGAGGGGGTTCCTTA
1 TCACGCGATGAGGGGGTTCCTTA
* *
11506668 TCACGCGGTGAGGGGGTTCCTTG
1 TCACGCGATGAGGGGGTTCCTTA
11506691 TCACG
1 TCACG
11506696 ACACAACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.24, G:0.37, T:0.25
Consensus pattern (23 bp):
TCACGCGATGAGGGGGTTCCTTA
Found at i:11508427 original size:30 final size:31
Alignment explanation
Indices: 11508368--11508429 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
11508358 GGGGGTAGGA
* *
11508368 TGGGAGGAGAGCAAAAGTTATGGGGGGAAAG
1 TGGGAGGAGAGCAAAAGTTATAGGAGGAAAG
* *
11508399 TGGGAGG-GAGTAAAAGTTTTAGGAGGAAAG
1 TGGGAGGAGAGCAAAAGTTATAGGAGGAAAG
11508429 T
1 T
11508430 AAAGAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.35, C:0.02, G:0.45, T:0.18
Consensus pattern (31 bp):
TGGGAGGAGAGCAAAAGTTATAGGAGGAAAG
Found at i:11510874 original size:23 final size:24
Alignment explanation
Indices: 11510829--11510874 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
11510819 AAAGCTCGAT
* *
11510829 CATATTATATAAACAATCATTTAC
1 CATATTATATAAAAAACCATTTAC
*
11510853 CATA-TATATAAAAAACCCTTTA
1 CATATTATATAAAAAACCATTTA
11510875 ACAAATAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (24 bp):
CATATTATATAAAAAACCATTTAC
Found at i:11516517 original size:63 final size:63
Alignment explanation
Indices: 11516412--11516638 Score: 247
Period size: 63 Copynumber: 3.6 Consensus size: 63
11516402 CTAGACACAC
* * * *
11516412 GCCCGTGTGACCCTAATTCAAAAACAGTGAGATACACAGCCTGGACACATGTTCATGTCTCTA
1 GCCCGTGTGACCTTAATTCACAAACAGTGAGTTACACAGCCTGGACACACGTTCATGTCTCTA
* * * ** ** * *
11516475 GCCCATGTTACCTTAATTCACAAACAATGAGTTACATGGCCTGGAGGCACGTTCGTGTTTCTA
1 GCCCGTGTGACCTTAATTCACAAACAGTGAGTTACACAGCCTGGACACACGTTCATGTCTCTA
** ** * **
11516538 GCTTGTGTGACCTTAATTTTCAAACAGTGAGTTACACAGTCTGGACACACGCCCATGTCTCTA
1 GCCCGTGTGACCTTAATTCACAAACAGTGAGTTACACAGCCTGGACACACGTTCATGTCTCTA
* * *
11516601 GCCCGTGTGACCCTAATTCTCAAACAGTAAGTTACACA
1 GCCCGTGTGACCTTAATTCACAAACAGTGAGTTACACA
11516639 ACTTGCCACA
Statistics
Matches: 130, Mismatches: 34, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
63 130 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (63 bp):
GCCCGTGTGACCTTAATTCACAAACAGTGAGTTACACAGCCTGGACACACGTTCATGTCTCTA
Found at i:11521169 original size:47 final size:47
Alignment explanation
Indices: 11521106--11521369 Score: 415
Period size: 47 Copynumber: 5.6 Consensus size: 47
11521096 CCCTTCGGGA
* * *
11521106 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
11521153 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
11521200 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
11521247 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
11521294 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
11521343 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
11521370 TATTCAAATA
Statistics
Matches: 202, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
46 1 0.00
47 157 0.78
49 43 0.21
50 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:11523129 original size:56 final size:56
Alignment explanation
Indices: 11523062--11523181 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
11523052 TATTAGTTTA
11523062 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
11523118 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
11523174 TTGCCCAT
1 TTGCCCAT
11523182 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:11527219 original size:63 final size:63
Alignment explanation
Indices: 11527144--11527337 Score: 201
Period size: 63 Copynumber: 3.1 Consensus size: 63
11527134 CAAATTCCCA
* * * ** *
11527144 AAACAATAAGTTATACGGCCTAGACACACGCCTGTATCTCTGGCCCGTGTGACCCTAATTCAC
1 AAACAGTAAGTTACACGGCCTAGACACAAGCCCCTATCTCTAGCCCGTGTGACCCTAATTCAC
* * * * * *
11527207 AAACAGTGAGTTACACAGCTTAGAGACAAGCCCCTGTCTCTAGCCTGTGTGACCCTAATTCAC
1 AAACAGTAAGTTACACGGCCTAGACACAAGCCCCTATCTCTAGCCCGTGTGACCCTAATTCAC
* * * ** * *
11527270 AAACAGTAAGTTACACGGCCTAGACACATA-CCCATGTCTCCAGCCTATGTGACCCTAGTTCCC
1 AAACAGTAAGTTACACGGCCTAGACACA-AGCCCCTATCTCTAGCCCGTGTGACCCTAATTCAC
11527333 AAACA
1 AAACA
11527338 ATGCGTTACA
Statistics
Matches: 109, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
63 108 0.99
64 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (63 bp):
AAACAGTAAGTTACACGGCCTAGACACAAGCCCCTATCTCTAGCCCGTGTGACCCTAATTCAC
Found at i:11527346 original size:63 final size:64
Alignment explanation
Indices: 11527191--11527363 Score: 224
Period size: 63 Copynumber: 2.7 Consensus size: 64
11527181 CTCTGGCCCG
* * * *
11527191 TGTGACCCTAATTCACAAACAGTGAGTTACACAGCTTAGAGACA-AGCCCCTGTCTCTAGCCTG
1 TGTGACCCTAATTCACAAACAGTGAGTTACACAGCTTAGACACATAGCCCATGTCTCCAGCCTA
* * *
11527254 TGTGACCCTAATTCACAAACAGTAAGTTACACGGCCTAGACACATA-CCCATGTCTCCAGCCTA
1 TGTGACCCTAATTCACAAACAGTGAGTTACACAGCTTAGACACATAGCCCATGTCTCCAGCCTA
* * * * *
11527317 TGTGACCCTAGTTCCCAAACAATGCGTTACACAGTTTAGACACATAG
1 TGTGACCCTAATTCACAAACAGTGAGTTACACAGCTTAGACACATAG
11527364 TCATATGGTG
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
63 92 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (64 bp):
TGTGACCCTAATTCACAAACAGTGAGTTACACAGCTTAGACACATAGCCCATGTCTCCAGCCTA
Found at i:11538309 original size:27 final size:27
Alignment explanation
Indices: 11538261--11538365 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
11538251 GCGAGGCTGC
* *
11538261 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
11538288 CAGATATTGTGGCGGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
11538314 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
11538341 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
11538366 GACCCTTCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.12
27 57 0.84
28 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:11539988 original size:26 final size:26
Alignment explanation
Indices: 11539958--11540013 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
11539948 TGAAATTCCC
11539958 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
11539984 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACCCATT
11540010 ATCA
1 ATCA
11540014 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:11544299 original size:20 final size:21
Alignment explanation
Indices: 11544276--11544314 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11544266 CAATCTTTAT
11544276 AAAT-TTT-TTTTTGTTTTTGA
1 AAATCTTTGTTTTT-TTTTTGA
11544296 AAATCTTTGTTTTTTTTTT
1 AAATCTTTGTTTTTTTTTT
11544315 AAACCCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.72
Consensus pattern (21 bp):
AAATCTTTGTTTTTTTTTTGA
Found at i:11545322 original size:27 final size:27
Alignment explanation
Indices: 11545274--11545378 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
11545264 GCGAGGCTGC
* * *
11545274 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
*
11545301 CAGATATTGTGGCGGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
11545327 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
11545354 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
11545379 GACCCTTCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.12
27 57 0.85
28 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:11547005 original size:26 final size:26
Alignment explanation
Indices: 11546975--11547056 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
11546965 TGAAATTCCC
11546975 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
11547001 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
11547027 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACCCATT
11547053 ATCA
1 ATCA
11547057 ATTTATATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:11552123 original size:40 final size:40
Alignment explanation
Indices: 11552079--11552175 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
11552069 GTACAAATAA
* * * *
11552079 GGGCACTTATGTACATTTAAAAGTACCAAAGTCTAAGCAG
1 GGGCACGTATGTGCATTTAAAAGTACCAAAGTCCAAACAG
**
11552119 GGGCACGTATGTGCATTTAAGGGTACCAAAGTCCAAACAG
1 GGGCACGTATGTGCATTTAAAAGTACCAAAGTCCAAACAG
*
11552159 GGTCACGTATGTGCATT
1 GGGCACGTATGTGCATT
11552176 CAAGGTCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (40 bp):
GGGCACGTATGTGCATTTAAAAGTACCAAAGTCCAAACAG
Found at i:11556781 original size:19 final size:20
Alignment explanation
Indices: 11556757--11556794 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11556747 GGTACCACCA
11556757 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
11556776 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
11556795 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:11557090 original size:46 final size:45
Alignment explanation
Indices: 11557023--11557190 Score: 180
Period size: 46 Copynumber: 3.6 Consensus size: 45
11557013 CGCCCCTAAG
*
11557023 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCATAAA
* *
11557069 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCATAAA
* ** * *
11557116 CGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCATAAA
11557162 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
11557191 ATGCTCAACC
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 55 0.54
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCATAAA
Found at i:11557134 original size:93 final size:93
Alignment explanation
Indices: 11557024--11557194 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
11557014 GCCCCTAAGT
** *
11557024 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
11557089 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
11557117 GAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
11557182 CGAGTTCGGATGC
66 CGAGTTCGGATGC
11557195 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:11557646 original size:30 final size:30
Alignment explanation
Indices: 11557612--11557671 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11557602 ATCTAATACG
11557612 AACTTTTAAAAAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
** *
11557642 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
11557672 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAAATTACACTTTTGCCCCTA
Found at i:11562220 original size:47 final size:46
Alignment explanation
Indices: 11562150--11562243 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
11562140 TCTACCACAC
* *
11562150 CGCTGGCGCTCGGGTTTAACAAATCTCGAGTTCCCTACATTGGCTG
1 CGCTGGCACTCGGGTTTAACAAATCTCGAGTTCCCTACACTGGCTG
11562196 CNGCTGGCACTCGGGTTTAACAAATCTCGAGTTCCCTACACTGGCTG
1 C-GCTGGCACTCGGGTTTAACAAATCTCGAGTTCCCTACACTGGCTG
11562243 C
1 C
11562244 AGAAGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.02
47 44 0.98
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.27
Consensus pattern (46 bp):
CGCTGGCACTCGGGTTTAACAAATCTCGAGTTCCCTACACTGGCTG
Found at i:11564315 original size:47 final size:47
Alignment explanation
Indices: 11564246--11564411 Score: 314
Period size: 47 Copynumber: 3.5 Consensus size: 47
11564236 GCCCCTAAGT
* *
11564246 GAACTCGGACTCAACTCAACGAGTTGGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
11564293 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
11564340 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
11564387 GAACTCGGACTCAACTCAACGAGTT
1 GAACTCGGACTCAACTCAACGAGTT
11564412 CGAATGCTCA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 117 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATTTCAC
Found at i:11564872 original size:30 final size:30
Alignment explanation
Indices: 11564838--11564897 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11564828 ATCTAATACG
11564838 AACTTTTAAAAAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
** *
11564868 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
11564898 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAAATTACACTTTTGCCCCTA
Found at i:11565503 original size:68 final size:68
Alignment explanation
Indices: 11565428--11565562 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
11565418 CCTAATTTTT
11565428 TCCATGAACTTAAAATTAGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTT
1 TCCATGAACTTAAAATTAGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTT
11565493 CAG
66 CAG
*
11565496 TCCATGAACTTAAAATTGGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTT
1 TCCATGAACTTAAAATTAGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTT
11565561 CA
66 CA
11565563 TACTAAAAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (68 bp):
TCCATGAACTTAAAATTAGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTT
CAG
Found at i:11568291 original size:16 final size:18
Alignment explanation
Indices: 11568252--11568293 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
11568242 AAAGTTCTTA
11568252 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
11568269 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
11568286 A-ATTTATA
1 ATATTTATA
11568294 ACACATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:11569553 original size:23 final size:22
Alignment explanation
Indices: 11569522--11569570 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
11569512 CTTTTTCACC
*
11569522 TTTTTTCTTCTTC-TTTTCTTCTA
1 TTTTCTCTTCTTCATTTT-TT-TA
11569545 TTTTCTCTTCTTCATTTTTTTA
1 TTTTCTCTTCTTCATTTTTTTA
11569567 TTTT
1 TTTT
11569571 GATTTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTCTTCTTCATTTTTTTA
Found at i:11571604 original size:144 final size:144
Alignment explanation
Indices: 11571344--11571629 Score: 554
Period size: 144 Copynumber: 2.0 Consensus size: 144
11571334 ACATGTATAT
11571344 CAATAAGCTACCTAATTTTCATGTTCTATCAATTCCATTTAATCATGCAAATTACAGTTTGAAGA
1 CAATAAGCTACCTAATTTTCATGTTCTATCAATTCCATTTAATCATGCAAATTACAGTTTGAAGA
*
11571409 TCTTTCTAGAGTCTATTGACTCATTCGTATTCAGTTCGGCCACCAAGGCTCAATTCTAAATGGAT
66 TCTTTCTAGAGTCTATTGACTCATTCATATTCAGTTCGGCCACCAAGGCTCAATTCTAAATGGAT
11571474 CGCATAATCTTTAA
131 CGCATAATCTTTAA
11571488 CAATAAGCTACCTAATTTTCATGTTCTATCAATTCCATTTAATCATGCAAATTACAGTTTGAAGA
1 CAATAAGCTACCTAATTTTCATGTTCTATCAATTCCATTTAATCATGCAAATTACAGTTTGAAGA
*
11571553 TCTTTCTAGAGTCTATTGACTCATTCATATTCAGTTCGGCCACCAAGGCTCAATTCTAATTGGAT
66 TCTTTCTAGAGTCTATTGACTCATTCATATTCAGTTCGGCCACCAAGGCTCAATTCTAAATGGAT
11571618 CGCATAATCTTT
131 CGCATAATCTTT
11571630 TATATACTTT
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 140 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (144 bp):
CAATAAGCTACCTAATTTTCATGTTCTATCAATTCCATTTAATCATGCAAATTACAGTTTGAAGA
TCTTTCTAGAGTCTATTGACTCATTCATATTCAGTTCGGCCACCAAGGCTCAATTCTAAATGGAT
CGCATAATCTTTAA
Found at i:11571878 original size:19 final size:19
Alignment explanation
Indices: 11571856--11571893 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11571846 ACTGGTGCAA
* *
11571856 GAAGTGCATCTTGGCACAC
1 GAAGCGCATCTTCGCACAC
11571875 GAAGCGCATCTTCGCACAC
1 GAAGCGCATCTTCGCACAC
11571894 AAAATGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (19 bp):
GAAGCGCATCTTCGCACAC
Found at i:11571902 original size:19 final size:19
Alignment explanation
Indices: 11571860--11571902 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
11571850 GTGCAAGAAG
* * *
11571860 TGCATCTTGGCACACGAAG
1 TGCATCTTCGCACACAAAA
*
11571879 CGCATCTTCGCACACAAAA
1 TGCATCTTCGCACACAAAA
11571898 TGCAT
1 TGCAT
11571903 AAACCCGTAC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (19 bp):
TGCATCTTCGCACACAAAA
Found at i:11575855 original size:42 final size:43
Alignment explanation
Indices: 11575808--11575919 Score: 149
Period size: 41 Copynumber: 2.7 Consensus size: 43
11575798 TAACAGTGAT
* *
11575808 ATATCAGGCTTATTGCCTAGTAGGCTTTGATGCCGGTGTA-TG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCAGTGTATTG
* *
11575850 ATATCAAGCTTATTGCCTAGCAGGCTTT-ATGCTAGTGTATTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCAGTGTATTG
* *
11575892 A-ATCAGGTTTATTACCTAGCAGGCTTTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTG
11575920 TGTCGATGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 32 0.52
42 29 0.48
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (43 bp):
ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCAGTGTATTG
Found at i:11586880 original size:143 final size:143
Alignment explanation
Indices: 11586622--11587047 Score: 834
Period size: 143 Copynumber: 3.0 Consensus size: 143
11586612 CTGTTTGAAG
*
11586622 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACAAAACGGTGGTTCTTT
1 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
*
11586687 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAACAAAATCATTCCATTTGCTAG
66 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
11586752 AAGCCACATAAAC
131 AAGCCACATAAAC
11586765 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
1 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
11586830 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
66 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
11586895 AAGCCACATAAAC
131 AAGCCACATAAAC
11586908 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
1 AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
11586973 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
66 ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
11587038 AAGCCACATA
131 AAGCCACATA
11587048 GTAGATTCGT
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 281 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (143 bp):
AGTATAAAAATGTTGTCAATTCTACATACGAGGAATAATAATAGAAAACGAAACGGTGGTTCTTT
ATATCAGTTCAAGGATCTCAGCTCAGTGCTGTATCTATGTTTAGCAAAATCATTCCATTTGCTAG
AAGCCACATAAAC
Found at i:11588414 original size:27 final size:28
Alignment explanation
Indices: 11588346--11588419 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
11588336 GTCATTATCA
* * *
11588346 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATGAGATTCTTCCTAT
*
11588374 ACCCCATAAGTTATGAGATTTTTCCTAT
1 ACCCCATAAGTTATGAGATTCTTCCTAT
11588402 A-CCCATAAGTTATGAGAT
1 ACCCCATAAGTTATGAGAT
11588420 AAAAGGTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 17 0.40
28 25 0.60
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (28 bp):
ACCCCATAAGTTATGAGATTCTTCCTAT
Found at i:11594541 original size:20 final size:22
Alignment explanation
Indices: 11594513--11594558 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
11594503 TATCATTTTT
11594513 TAAAATTA-TAA-AAATATATA
1 TAAAATTATTAATAAATATATA
* *
11594533 TAAAGTTATTAATAAATATGTA
1 TAAAATTATTAATAAATATATA
11594555 TAAA
1 TAAA
11594559 TGAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 3 0.14
22 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAAATTATTAATAAATATATA
Found at i:11605781 original size:21 final size:21
Alignment explanation
Indices: 11605752--11605791 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11605742 AGCTCTTGGA
*
11605752 GCTTGTTTTAGTTTGTATAGT
1 GCTTGTTTTAGCTTGTATAGT
*
11605773 GCTTTTTTTAGCTTGTATA
1 GCTTGTTTTAGCTTGTATA
11605792 CCTTACTTTC
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:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (21 bp):
GCTTGTTTTAGCTTGTATAGT
Found at i:11612752 original size:49 final size:49
Alignment explanation
Indices: 11612675--11612802 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 49
11612665 TGTTGTGTGT
* * *
11612675 CAGTGTAAGACCTGTCTGGGACATGGCATTAACAC-CGATATATGAAAGC
1 CAGTATAAGACCTGTTTGGGACATGGCATCAAC-CTCGATATATGAAAGC
* *
11612724 CAGTATAAGA-CTTTTATGGGACATGGCATCAACCTCGATATATGAAAGT
1 CAGTATAAGACCTGTT-TGGGACATGGCATCAACCTCGATATATGAAAGC
* *
11612773 CAGTGTAAGACCTGTTTGGGACACGGCATC
1 CAGTATAAGACCTGTTTGGGACATGGCATC
11612803 GCCTTTAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 4 0.06
49 60 0.88
50 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (49 bp):
CAGTATAAGACCTGTTTGGGACATGGCATCAACCTCGATATATGAAAGC
Found at i:11612793 original size:142 final size:144
Alignment explanation
Indices: 11612588--11612847 Score: 318
Period size: 142 Copynumber: 1.8 Consensus size: 144
11612578 AGAGCTAGTG
* **
11612588 TAAGACATTTCTGGGACATGCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGAC
1 TAAGACATTTATGGGACATGCATCAACCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGAC
* * *
11612653 ATAGCGTCAG-CTTGT-TGTG-T-GTCAGTGTAAGACC-TGTCTGGGACATGGCATTAACACCGA
66 ACAGCATC-GCCTT-TATGTGTTAGCCAGTGTAAGACCATGTCTGGGACATGGCATTAACACCGA
11612713 TATATGAAAGCCAGTA
129 TATATGAAAGCCAGTA
* * * *
11612729 TAAGACTTTTATGGGACATGGCATCAACCTCGATATATGA-AAG-TCAGTGTAAGACCTGTTTGG
1 TAAGACATTTATGGGACAT-GCATCAACCTCGAGATAT-ACAAGCT-AGTGTAAGACCTATCTGG
*
11612792 GACACGGCATCGCCTTTAATGTGTTAGCCAGTGTAAGACCATGTCTGGGACATGGC
63 GACACAGCATCGCCTTT-ATGTGTTAGCCAGTGTAAGACCATGTCTGGGACATGGC
11612848 GTCGGCATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
141 20 0.20
142 45 0.45
143 5 0.05
144 1 0.01
145 13 0.13
146 15 0.15
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (144 bp):
TAAGACATTTATGGGACATGCATCAACCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGGAC
ACAGCATCGCCTTTATGTGTTAGCCAGTGTAAGACCATGTCTGGGACATGGCATTAACACCGATA
TATGAAAGCCAGTA
Found at i:11613671 original size:15 final size:13
Alignment explanation
Indices: 11613632--11613667 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
11613622 GGTAGACATA
11613632 TAGG-CGTGTGAC
1 TAGGCCGTGTGAC
11613644 TAGGCCGTGTGAC
1 TAGGCCGTGTGAC
11613657 TAGGCCGTGTG
1 TAGGCCGTGTG
11613668 TGACACACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.14, C:0.19, G:0.42, T:0.25
Consensus pattern (13 bp):
TAGGCCGTGTGAC
Found at i:11619875 original size:28 final size:28
Alignment explanation
Indices: 11619835--11619890 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11619825 ACACGGGCTA
*
11619835 GGACACGGGTGTGTG-ATGGCCGTGTGAG
1 GGACACAGGTGTGTGTA-GGCCGTGTGAG
11619863 GGACACAGGTGTGTGTCAGGCCGTGTGA
1 GGACACAGGTGTGTGT-AGGCCGTGTGA
11619891 AAACTCCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 10 0.40
30 1 0.04
ACGTcount: A:0.16, C:0.16, G:0.46, T:0.21
Consensus pattern (28 bp):
GGACACAGGTGTGTGTAGGCCGTGTGAG
Found at i:11620031 original size:21 final size:20
Alignment explanation
Indices: 11620007--11620046 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11619997 ATGTTCAAGT
*
11620007 TCCACACGGGCGTGTTGCCCA
1 TCCACACGAGCGTG-TGCCCA
*
11620028 TCCACATGAGCGTGTGCCC
1 TCCACACGAGCGTGTGCCC
11620047 TGTTTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (20 bp):
TCCACACGAGCGTGTGCCCA
Found at i:11622026 original size:34 final size:33
Alignment explanation
Indices: 11621987--11622068 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
11621977 AAATGCTAAT
* *
11621987 AAAAGAAAATGAGAGAAT-ATGAAATGAAATTGA
1 AAAAGAAAAAGAGAGAATAATGAAA-AAAATTGA
*
11622020 GAAAAGAAAAAAAGA-AATGAATGAAAAAAATTGA
1 -AAAAGAAAAAGAGAGAAT-AATGAAAAAAATTGA
11622054 AAAAGAAAAAGAGAG
1 AAAAGAAAAAGAGAG
11622069 TGAGAGAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 16 0.39
34 19 0.46
35 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (33 bp):
AAAAGAAAAAGAGAGAATAATGAAAAAAATTGA
Found at i:11622088 original size:21 final size:20
Alignment explanation
Indices: 11622055--11622094 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11622045 AAAAATTGAA
11622055 AAAGAAAAAGAGAGTGAGAG
1 AAAGAAAAAGAGAGTGAGAG
* *
11622075 AAAGCAAAACGAGATTGAGA
1 AAAG-AAAAAGAGAGTGAGA
11622095 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.05, G:0.30, T:0.07
Consensus pattern (20 bp):
AAAGAAAAAGAGAGTGAGAG
Found at i:11622145 original size:18 final size:17
Alignment explanation
Indices: 11622080--11622158 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
11622070 GAGAGAAAGC
*
11622080 AAAACGAGATTGAGATTG
1 AAAA-GAGATTGAGAATG
11622098 AAAA-AGAATGTGAGAATG
1 AAAAGAG-AT-TGAGAATG
* *
11622116 AAAAGAAAATTGAAAATG
1 AAAAG-AGATTGAGAATG
*
11622134 AGAAAGAGATTGGAGAAAG
1 A-AAAGAGATT-GAGAATG
11622153 AAAAGA
1 AAAAGA
11622159 AAGAGAGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.04
17 2 0.04
18 32 0.65
19 12 0.24
20 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.27, T:0.15
Consensus pattern (17 bp):
AAAAGAGATTGAGAATG
Found at i:11622156 original size:37 final size:37
Alignment explanation
Indices: 11622046--11622160 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 37
11622036 ATGAATGAAA
* *
11622046 AAAATTGAAAAAGAAAAAGAGAGTGAGAGAAAGCAAAACG
1 AAAATTGAAAATG-AAAAGAGAATGAGAGAAAG-AAAA-G
* * * * *
11622086 -AGATTGAGATTGAAAA-AGAATGTGAGAATGAAAAG
1 AAAATTGAAAATGAAAAGAGAATGAGAGAAAGAAAAG
*
11622121 AAAATTGAAAATGAGAAAGAGATTG-GAGAAAGAAAAG
1 AAAATTGAAAATGA-AAAGAGAATGAGAGAAAGAAAAG
11622158 AAA
1 AAA
11622161 GAGAGCAAGA
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
35 1 0.02
36 14 0.23
37 28 0.47
38 9 0.15
39 8 0.13
ACGTcount: A:0.59, C:0.02, G:0.26, T:0.13
Consensus pattern (37 bp):
AAAATTGAAAATGAAAAGAGAATGAGAGAAAGAAAAG
Found at i:11626758 original size:27 final size:26
Alignment explanation
Indices: 11626728--11626803 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 26
11626718 AACTTCCAAA
11626728 AAATTATTACGGTGTAGGAATTGGAGG
1 AAATT-TTACGGTGTAGGAATTGGAGG
*
11626755 AAATTCGTACGGTGTAGGAATTGGAGG
1 AAATT-TTACGGTGTAGGAATTGGAGG
11626782 AAATTTGTACGGTGTAGGAATT
1 AAATTT-TACGGTGTAGGAATT
11626804 TCCAAATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (26 bp):
AAATTTTACGGTGTAGGAATTGGAGG
Found at i:11629768 original size:18 final size:18
Alignment explanation
Indices: 11629749--11629798 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
11629739 TAAATGATAT
11629749 TTTTATTAA-TAATAATA
1 TTTTATTAAGTAATAATA
* *
11629766 TTTTAATAAGTACTAATA
1 TTTTATTAAGTAATAATA
*
11629784 TTTTATTAATTAATA
1 TTTTATTAAGTAATA
11629799 TTATAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTATTAAGTAATAATA
Found at i:11643514 original size:42 final size:44
Alignment explanation
Indices: 11643456--11643583 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 44
11643446 TAATTAAACA
* *
11643456 TCGATGCCACTGTCCCAGATAGGGTCTTACACG-AAA-CCGAA-
1 TCGATGCCAATGTCCCAGATAGGGTCTTACACGTAAAGCAGAAG
* *
11643497 TACGATGCCAATGTCCCAGACATGGTCTTACACGTAAAGCAGAAG
1 T-CGATGCCAATGTCCCAGATAGGGTCTTACACGTAAAGCAGAAG
* * * *
11643542 TTGATGCCAACGTCTCAGAT-GTGGTCTTACACGTAAAACAGA
1 TCGATGCCAATGTCCCAGATAG-GGTCTTACACGTAAAGCAGA
11643584 TATCGAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.40
43 3 0.04
44 38 0.53
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (44 bp):
TCGATGCCAATGTCCCAGATAGGGTCTTACACGTAAAGCAGAAG
Found at i:11652184 original size:29 final size:29
Alignment explanation
Indices: 11652114--11652173 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
11652104 ACCATGAGAA
*
11652114 ACATTGCCACTCAGTCTCGAATTTTGCAC
1 ACATTGCCACTCGGTCTCGAATTTTGCAC
11652143 ACATTGCCACTCGGTCTCGAATTTTGCAC
1 ACATTGCCACTCGGTCTCGAATTTTGCAC
11652172 AC
1 AC
11652174 TTTCTTACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (29 bp):
ACATTGCCACTCGGTCTCGAATTTTGCAC
Found at i:11653391 original size:28 final size:29
Alignment explanation
Indices: 11653318--11653405 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
11653308 AGCATGGCTG
* * *
11653318 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGACATAGCCA
* *
11653345 CCAGATACAGATATTTTGTGGCA-ATGCCA
1 CCAGATACAGATAATTTGTGACATA-GCCA
11653374 CCAGA-ACAGATAATTTGTGACATAGCCA
1 CCAGATACAGATAATTTGTGACATAGCCA
11653402 CCAG
1 CCAG
11653406 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 11 0.22
28 25 0.49
29 15 0.29
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGACATAGCCA
Found at i:11657690 original size:43 final size:42
Alignment explanation
Indices: 11657643--11657740 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
11657633 CCCAAATGTA
*
11657643 GTCTTACATGTAATCAAACATCGATGCC-ACTGTCCCAGACAGG
1 GTCTTACACGTAATCAAACAT-GATGCCGA-TGTCCCAGACAGG
* * * *
11657686 GTCTTACACGAAATCAGATATGATGCCGATGTCCCAGACATG
1 GTCTTACACGTAATCAAACATGATGCCGATGTCCCAGACAGG
11657728 GTCTTACACGTAA
1 GTCTTACACGTAA
11657741 AATAGAAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
GTCTTACACGTAATCAAACATGATGCCGATGTCCCAGACAGG
Found at i:11657767 original size:44 final size:41
Alignment explanation
Indices: 11657665--11657780 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 41
11657655 ATCAAACATC
*
11657665 GATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAGATAT
1 GATGCCAC-GTCCCAGACATGGTCTTACACGAAATCAGATAT
*
11657707 GATGCCGATGTCCCAGACATGGTCTTACACGTAAAAT-AGA-AGTT
1 GATGCC-ACGTCCCAGACATGGTCTTACACG--AAATCAGATA--T
*
11657751 GATGCCAACGTCCCAGACGTGGTCTTACAC
1 GATGCC-ACGTCCCAGACATGGTCTTACAC
11657781 ACAAAACAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 28 0.44
43 4 0.06
44 32 0.50
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
GATGCCACGTCCCAGACATGGTCTTACACGAAATCAGATAT
Found at i:11662262 original size:138 final size:138
Alignment explanation
Indices: 11661914--11662307 Score: 408
Period size: 131 Copynumber: 2.9 Consensus size: 138
11661904 ACACTCCAAC
* * * * * *
11661914 TGATATTCTAAAAGCTCTAAAGGTTAAGCTCGAAGCTCCAACACAACTAGCGAACCTATG-TTCC
1 TGATATTCTAAGAGCTCAAAAGGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGTTTCC
* * *
11661978 TAGCTGATGTTATAAAAGTTTGTCAGTTTATGATCGCAACCTCCAAAAATAGCTAGCGGACTTAT
66 -AACTGATGTTATAAAGGTTTGTCAATTTATGATCGCAACCTCCAAAAATAGCTAGCGGACTTAT
*
11662043 GCTCCCAGT
130 GCTCCCAGG
*** * * * * * * *
11662052 TG--A---T--GAGCTTGCAGGGTTAAGCTCGCAACTCTAATATAGCTAGCAGACCTACGTTCCC
1 TGATATTCTAAGAGCTCAAAAGGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGTTTCC
* * * * * *
11662110 AACTGATGTGATAAAGGTTTGTTAATTTATGATTGCAACCTTCGAAAATAGCTAGTGGACTTATG
66 AACTGATGTTATAAAGGTTTGTCAATTTATGATCGCAACCTCCAAAAATAGCTAGCGGACTTATG
* *
11662175 CTGCTAGG
131 CTCCCAGG
* *
11662183 TGATATTCTAAGAGCTCAAAAGGTTAAGCTCGCAGCTCCGACACAGCCAGCGGACCTACGTTTCC
1 TGATATTCTAAGAGCTCAAAAGGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGTTTCC
* ** * *
11662248 ATCTGATGTTATAAAGGTTTACCGATTTATGATCGCAACATCCAAAAATAGCTAGCGGAC
66 AACTGATGTTATAAAGGTTTGTCAATTTATGATCGCAACCTCCAAAAATAGCTAGCGGAC
11662308 CAACGTTCTC
Statistics
Matches: 198, Mismatches: 50, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
131 98 0.49
132 3 0.02
133 2 0.01
136 2 0.01
138 93 0.47
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (138 bp):
TGATATTCTAAGAGCTCAAAAGGTTAAGCTCGCAGCTCCAACACAGCTAGCGGACCTACGTTTCC
AACTGATGTTATAAAGGTTTGTCAATTTATGATCGCAACCTCCAAAAATAGCTAGCGGACTTATG
CTCCCAGG
Found at i:11662616 original size:15 final size:16
Alignment explanation
Indices: 11662587--11662617 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11662577 CACTAATAAC
11662587 TAAACTTCAAAATTTT
1 TAAACTTCAAAATTTT
11662603 TAAACTTC-AAATTTT
1 TAAACTTCAAAATTTT
11662618 CTTATTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAACTTCAAAATTTT
Found at i:11683897 original size:43 final size:43
Alignment explanation
Indices: 11683832--11683950 Score: 202
Period size: 43 Copynumber: 2.8 Consensus size: 43
11683822 TACATGAATT
* *
11683832 GCATCCATTATGAACTCGGACCTCTCAACGAGCCCTGATACTC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
* *
11683875 GCATCCATAATAAACTCAGACCTCTCAACGAGCCTTGATACTC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
11683918 GCATCCATAATAAACTCGGACCTCTCAACGAGC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGC
11683951 TTAGATGCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (43 bp):
GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
Found at i:11687937 original size:9 final size:9
Alignment explanation
Indices: 11687923--11687979 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
11687913 TTTAGTAAAC
11687923 ATGATATGT
1 ATGATATGT
*
11687932 ATGATATGCAC
1 ATGATATG--T
*
11687943 ATGACATGT
1 ATGATATGT
*
11687952 ATGATATGCAC
1 ATGATATG--T
11687963 ATGATATGT
1 ATGATATGT
11687972 ATGATATG
1 ATGATATG
11687980 CACATGATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:11687946 original size:20 final size:20
Alignment explanation
Indices: 11687921--11687987 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
11687911 ATTTTAGTAA
11687921 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
11687941 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
11687961 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
11687981 ACATGAT
1 ACATGAT
11687988 GTATTCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:11687968 original size:11 final size:11
Alignment explanation
Indices: 11687932--11687987 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
11687922 CATGATATGT
11687932 ATGATATGCAC
1 ATGATATGCAC
* *
11687943 ATGACATG--T
1 ATGATATGCAC
11687952 ATGATATGCAC
1 ATGATATGCAC
*
11687963 ATGATATG--T
1 ATGATATGCAC
11687972 ATGATATGCAC
1 ATGATATGCAC
11687983 ATGAT
1 ATGAT
11687988 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:11688063 original size:24 final size:24
Alignment explanation
Indices: 11688036--11688250 Score: 312
Period size: 24 Copynumber: 9.0 Consensus size: 24
11688026 GGAGGAAGTG
11688036 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
11688060 T-AAAGGGCTTATGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
11688083 CAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* * *
11688107 CAAAAGGGCTTACGCCCCAGGTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
11688131 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
11688154 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
11688179 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
11688203 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
11688226 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
11688251 ATGATAAAGC
Statistics
Matches: 174, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
23 60 0.34
24 83 0.48
25 31 0.18
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:11688106 original size:47 final size:48
Alignment explanation
Indices: 11688036--11688252 Score: 302
Period size: 47 Copynumber: 4.5 Consensus size: 48
11688026 GGAGGAAGTG
*
11688036 TAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATATAAAGGGCTTATGCCCCAGTTAT
* * *
11688083 CAAAAGGGCTTATGCCCCAGTTATCA-AAAGGGCTTACGCCCCAGGTAT
1 TAAAAGGGCTTATGCCCCAGTTAT-ATAAAGGGCTTATGCCCCAGTTAT
11688131 T-AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT-ATAAAGGGCTTATGCCCCAGTTAT
11688179 TAAAAGGGCTTATGCCCCAGTTAT-TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATAT-AAAGGGCTTATGCCCCAGTTAT
*
11688226 TAAAAGAGGC-TAGGCCTCCAGTTATAT
1 TAAAAG-GGCTTATGCC-CCAGTTATAT
11688253 GATAAAGCAG
Statistics
Matches: 153, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
47 70 0.46
48 60 0.39
49 23 0.15
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (48 bp):
TAAAAGGGCTTATGCCCCAGTTATATAAAGGGCTTATGCCCCAGTTAT
Found at i:11688479 original size:31 final size:31
Alignment explanation
Indices: 11688444--11688507 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
11688434 CGTTTACAGT
11688444 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
11688475 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
11688506 AA
1 AA
11688508 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:11700417 original size:43 final size:43
Alignment explanation
Indices: 11700352--11700470 Score: 202
Period size: 43 Copynumber: 2.8 Consensus size: 43
11700342 TACATGAATT
* *
11700352 GCATCCATTATGAACTCGGACCTCTCAACGAGCCCTGATACTC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
* *
11700395 GCATCCATAATAAACTCAGACCTCTCAACGAGCCTTGATACTC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
11700438 GCATCCATAATAAACTCGGACCTCTCAACGAGC
1 GCATCCATAATAAACTCGGACCTCTCAACGAGC
11700471 TTAGATGCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (43 bp):
GCATCCATAATAAACTCGGACCTCTCAACGAGCCCTGATACTC
Found at i:11705929 original size:38 final size:38
Alignment explanation
Indices: 11705878--11705951 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
11705868 TCCCTAAAGA
11705878 GAATGTAACAATATGTAATGAATTTGAAAGCTATAAGG
1 GAATGTAACAATATGTAATGAATTTGAAAGCTATAAGG
11705916 GAATGTAACAATATGTAATGAATTTGAAAGCTATAA
1 GAATGTAACAATATGTAATGAATTTGAAAGCTATAA
11705952 TCTTTAACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (38 bp):
GAATGTAACAATATGTAATGAATTTGAAAGCTATAAGG
Found at i:11705938 original size:19 final size:19
Alignment explanation
Indices: 11705878--11705938 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
11705868 TCCCTAAAGA
11705878 GAATGTAACAATATGTAAT
1 GAATGTAACAATATGTAAT
* * ** * *
11705897 GAATTTGA-AAGCTATAAGG
1 GAATGTAACAATATGTAA-T
11705916 GAATGTAACAATATGTAAT
1 GAATGTAACAATATGTAAT
11705935 GAAT
1 GAAT
11705939 TTGAAAGCTA
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.30
Consensus pattern (19 bp):
GAATGTAACAATATGTAAT
Found at i:11709902 original size:10 final size:10
Alignment explanation
Indices: 11709875--11709930 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
11709865 TTAAATTCTC
11709875 AAAGATAAAT
1 AAAGATAAAT
11709885 ATAA-ATAAAT
1 A-AAGATAAAT
*
11709895 AAAGATAATT
1 AAAGATAAAT
11709905 AAAGATAAAT
1 AAAGATAAAT
* *
11709915 AAGGACAAAT
1 AAAGATAAAT
11709925 AAAGAT
1 AAAGAT
11709931 GAAAGCTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 2 0.05
10 34 0.89
11 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:11716565 original size:20 final size:20
Alignment explanation
Indices: 11716539--11716593 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
11716529 GATCCATAAT
*
11716539 AGGGGCACCAAAGTGCAGAC
1 AGGGGCACCAAAGTGCAAAC
* *
11716559 TGGGGCA-CATATGTGCAAAC
1 AGGGGCACCA-AAGTGCAAAC
*
11716579 AGGGGCACCATAGTG
1 AGGGGCACCAAAGTG
11716594 TGAATAGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.31, C:0.22, G:0.35, T:0.13
Consensus pattern (20 bp):
AGGGGCACCAAAGTGCAAAC
Found at i:11716602 original size:20 final size:20
Alignment explanation
Indices: 11716536--11716607 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
11716526 ATAGATCCAT
* *
11716536 AATAGGGGCACCAAAGTGCAG
1 AATAGGGGCACCATAGTG-TG
*
11716557 ACT-GGGGCA-CATA-TGTG
1 AATAGGGGCACCATAGTGTG
*
11716574 CAAACAGGGGCACCATAGTGTG
1 --AATAGGGGCACCATAGTGTG
*
11716596 AATAGGGACACC
1 AATAGGGGCACC
11716608 GAAGAGTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
17 1 0.03
18 2 0.05
19 4 0.10
20 22 0.56
21 6 0.15
22 4 0.10
ACGTcount: A:0.33, C:0.21, G:0.32, T:0.14
Consensus pattern (20 bp):
AATAGGGGCACCATAGTGTG
Found at i:11717751 original size:22 final size:22
Alignment explanation
Indices: 11717712--11717777 Score: 96
Period size: 22 Copynumber: 2.9 Consensus size: 22
11717702 AGAAGAAAAC
*
11717712 CTTTTGTTTTCTTATTTTATTAA
1 CTTTTATTTT-TTATTTTATTAA
11717735 CTTTTATTTTTTATTTTATTAA
1 CTTTTATTTTTTATTTTATTAA
11717757 CTTTTATTTTTTTTATTTTAT
1 CTTTTA--TTTTTTATTTTAT
11717778 CTTTTAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 18 0.45
23 9 0.22
24 13 0.32
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (22 bp):
CTTTTATTTTTTATTTTATTAA
Found at i:11722976 original size:32 final size:32
Alignment explanation
Indices: 11722940--11723007 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
11722930 GATTTGTCTT
11722940 AAATTAGTTATTTATCCAAACAAAGCAATTAC
1 AAATTAGTTATTTATCCAAACAAAGCAATTAC
* *
11722972 AAATTAGTTATTTATCCCAATAAAGCAATTAC
1 AAATTAGTTATTTATCCAAACAAAGCAATTAC
11723004 AAAT
1 AAAT
11723008 GTTAGCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (32 bp):
AAATTAGTTATTTATCCAAACAAAGCAATTAC
Found at i:11726962 original size:25 final size:25
Alignment explanation
Indices: 11726859--11726963 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
11726849 CACTATTAAA
*
11726859 CAGAGAGCACTAAAGTTC-TAT-AT
1 CAGAGAGCACTAAAGTGCTTATAAT
* *
11726882 -AGAGATCA-TAAATGTGCTAATAAT
1 CAGAGAGCACTAAA-GTGCTTATAAT
* * * *
11726906 CGGAGAACAATAACGTGCTTATAAT
1 CAGAGAGCACTAAAGTGCTTATAAT
*
11726931 CAAAGAGCACTAAAGTGCTTATAAT
1 CAGAGAGCACTAAAGTGCTTATAAT
*
11726956 CGGAGAGC
1 CAGAGAGC
11726964 GCATAAGATC
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
21 4 0.06
22 10 0.16
23 2 0.03
24 2 0.03
25 42 0.67
26 3 0.05
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (25 bp):
CAGAGAGCACTAAAGTGCTTATAAT
Found at i:11742833 original size:16 final size:15
Alignment explanation
Indices: 11742812--11742857 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
11742802 ATCCTCCTTT
11742812 TTTTTATTTAGTCTTA
1 TTTTTATTTA-TCTTA
*
11742828 TTTTTATTTTATTTTA
1 TTTTTA-TTTATCTTA
*
11742844 TTTTTATTTTTCTT
1 TTTTTATTTATCTT
11742858 TTGATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.23
16 16 0.62
17 4 0.15
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTATTTATCTTA
Found at i:11742839 original size:5 final size:5
Alignment explanation
Indices: 11742829--11742896 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
11742819 TTAGTCTTAT
* *
11742829 TTTTA TTTTA TTTTA TTTTTA TTTTTC TTTTGA TTTTTA TTTTCA TTTCAA
1 TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTT-A -TTTTA TTTT-A TTT-TA
11742880 TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
11742897 CCAAGACAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
3 3 0.06
5 26 0.50
6 19 0.37
7 4 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:11742841 original size:11 final size:11
Alignment explanation
Indices: 11742825--11742896 Score: 65
Period size: 12 Copynumber: 6.2 Consensus size: 11
11742815 TTATTTAGTC
11742825 TTATTTTTATT
1 TTATTTTTATT
11742836 TTA-TTTTATTT
1 TTATTTTTA-TT
*
11742847 TTATTTTTCTT
1 TTATTTTTATT
11742858 TTGATTTTTATT
1 TT-ATTTTTATT
**
11742870 TTCATTTCAATT
1 TT-ATTTTTATT
11742882 TTATTATTTTATT
1 TTA-T-TTTTATT
11742895 TT
1 TT
11742897 CCAAGACAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 5 0.10
11 13 0.27
12 24 0.49
13 7 0.14
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:11742866 original size:7 final size:6
Alignment explanation
Indices: 11742825--11742876 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
11742815 TTATTTAGTC
* *
11742825 TTATTT TTA-TT TTA-TT TTATTT TTATTT TTCTTT TGATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
11742871 TCATTT
1 TTATTT
11742877 CAATTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 10 0.25
6 30 0.75
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:11746467 original size:13 final size:14
Alignment explanation
Indices: 11746444--11746476 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11746434 TACAAATAAC
*
11746444 AGAATCAGATATGT
1 AGAATCAGATATAT
11746458 AGAA-CAGATATAT
1 AGAATCAGATATAT
11746471 AGAATC
1 AGAATC
11746477 CTACCCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (14 bp):
AGAATCAGATATAT
Found at i:11748254 original size:22 final size:21
Alignment explanation
Indices: 11748228--11748272 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11748218 TTTACACCAA
*
11748228 GTTGTGGGTAAAACCACTCATT
1 GTTGTGGAT-AAACCACTCATT
*
11748250 GTTGTGGATGAACCACTCATT
1 GTTGTGGATAAACCACTCATT
11748271 GT
1 GT
11748273 AGATAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (21 bp):
GTTGTGGATAAACCACTCATT
Found at i:11748936 original size:29 final size:29
Alignment explanation
Indices: 11748906--11749012 Score: 105
Period size: 28 Copynumber: 3.8 Consensus size: 29
11748896 AATTCTAGGT
*
11748906 AAAATTGTAAAATATGAAAAACATGAGGT
1 AAAATTGTAAAATATGAAAAACATGAGGG
*
11748935 AAAATTGTAAAA-ACT-AAAAA-ATAAGGG
1 AAAATTGTAAAATA-TGAAAAACATGAGGG
* * *
11748962 GAAATTGTAAAATTTGAAAAATA-GAGGG
1 AAAATTGTAAAATATGAAAAACATGAGGG
* * *
11748990 ACAATTGTAAAATCTAAAAAACA
1 AAAATTGTAAAATATGAAAAACA
11749013 GGGGTCACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
27 17 0.27
28 33 0.52
29 14 0.22
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAATTGTAAAATATGAAAAACATGAGGG
Found at i:11748953 original size:56 final size:54
Alignment explanation
Indices: 11748906--11749009 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 54
11748896 AATTCTAGGT
*
11748906 AAAATTGTAAAATATGAAAAACATGAGGTAAAATTGTAAAAACTAAAAAATAAGGG
1 AAAATTGTAAAATATGAAAAACA-GAGGGAAAATTGTAAAAACT-AAAAATAAGGG
* * * * *
11748962 GAAATTGTAAAATTTGAAAAATAGAGGGACAATTGTAAAATCTAAAAA
1 AAAATTGTAAAATATGAAAAACAGAGGGAAAATTGTAAAAACTAAAAA
11749010 ACAGGGGTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 5 0.12
55 17 0.40
56 20 0.48
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (54 bp):
AAAATTGTAAAATATGAAAAACAGAGGGAAAATTGTAAAAACTAAAAATAAGGG
Found at i:11748966 original size:27 final size:27
Alignment explanation
Indices: 11748907--11749010 Score: 104
Period size: 27 Copynumber: 3.7 Consensus size: 27
11748897 ATTCTAGGTA
* *
11748907 AAATTGTAAAATATGAAAAACAT-GAGGTA
1 AAATTGTAAAATCT-AAAAA-ATAGAGG-G
*
11748936 AAATTGTAAAAACTAAAAAATA-AGGGG
1 AAATTGTAAAATCTAAAAAATAGA-GGG
* *
11748963 AAATTGTAAAATTTGAAAAATAGAGGG
1 AAATTGTAAAATCTAAAAAATAGAGGG
11748990 ACAATTGTAAAATCTAAAAAA
1 A-AATTGTAAAATCTAAAAAA
11749011 CAGGGGTCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
27 26 0.41
28 25 0.40
29 12 0.19
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (27 bp):
AAATTGTAAAATCTAAAAAATAGAGGG
Found at i:11750183 original size:21 final size:21
Alignment explanation
Indices: 11750154--11750195 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11750144 TAATTATTAC
* *
11750154 ATAATTTATAGTATTTGAAAT
1 ATAACTTATAATATTTGAAAT
11750175 ATAACTTATAATATTTGAAAT
1 ATAACTTATAATATTTGAAAT
11750196 TTTGAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAACTTATAATATTTGAAAT
Found at i:11751145 original size:17 final size:18
Alignment explanation
Indices: 11751123--11751158 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
11751113 AAAAAATATA
11751123 TAATTTTTTTAT-ATTTT
1 TAATTTTTTTATGATTTT
11751140 TAATTTTTTTATGATTTT
1 TAATTTTTTTATGATTTT
11751158 T
1 T
11751159 TAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TAATTTTTTTATGATTTT
Found at i:11751651 original size:30 final size:30
Alignment explanation
Indices: 11751615--11751674 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
11751605 AATATTTCGT
11751615 TTTTTTGGCTTAGCTTAAAATTTC-ATATTA
1 TTTTTTGGCTTAGCTTAAAA-TTCAATATTA
11751645 TTTTTTGGCTTAGCTTAAAATTCAATATTA
1 TTTTTTGGCTTAGCTTAAAATTCAATATTA
11751675 AAATCAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTTTTGGCTTAGCTTAAAATTCAATATTA
Found at i:11752114 original size:6 final size:6
Alignment explanation
Indices: 11752103--11752127 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11752093 TCATTTTCCT
11752103 TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA T
11752128 AGTGTTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:11760042 original size:79 final size:81
Alignment explanation
Indices: 11759906--11760090 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
11759896 TTGAATGATG
* *
11759906 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
11759970 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
11759985 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
11760047 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
11760065 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11760091 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:11760104 original size:40 final size:40
Alignment explanation
Indices: 11759907--11760090 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
11759897 TGAATGATGT
* * * *
11759907 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
11759947 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
11759987 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
11760025 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
11760066 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
11760091 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:11760112 original size:79 final size:79
Alignment explanation
Indices: 11759959--11760123 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
11759949 GGACTAAGAT
* * **
11759959 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
11760024 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
11760038 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
11760101 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
11760117 CCGAAGG
1 CCGAAGG
11760124 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:11766966 original size:20 final size:20
Alignment explanation
Indices: 11766938--11766985 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
11766928 GACAATCCCA
* *
11766938 TAAACTACAATTCCTTAGAT
1 TAAAATACAATACCTTAGAT
11766958 TAAAATAC-ATACCTTAGAT
1 TAAAATACAATACCTTAGAT
11766977 TAAAATACA
1 TAAAATACA
11766986 TACTTCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAATACAATACCTTAGAT
Found at i:11766974 original size:19 final size:19
Alignment explanation
Indices: 11766950--11766988 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11766940 AACTACAATT
11766950 CCTTAGATTAAAATACATA
1 CCTTAGATTAAAATACATA
11766969 CCTTAGATTAAAATACATA
1 CCTTAGATTAAAATACATA
11766988 C
1 C
11766989 TTCATGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (19 bp):
CCTTAGATTAAAATACATA
Found at i:11768028 original size:37 final size:37
Alignment explanation
Indices: 11767963--11768077 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
11767953 ACCTTTAGCT
* * *
11767963 CGGACGAAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
*
11768000 CGGGCAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
* * *
11768037 CGGACATACTCTCCACACGTAGTCATCGGGTCTCACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
11768074 CGGA
1 CGGA
11768078 ATATATTTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (37 bp):
CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:11768353 original size:94 final size:94
Alignment explanation
Indices: 11768240--11768566 Score: 555
Period size: 94 Copynumber: 3.5 Consensus size: 94
11768230 TTTCACACTA
* * *
11768240 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
11768305 ACATATGCATGCTCACATTCATCACATTG
66 ACATATGCATGCTCACATTCATCACATTG
11768334 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
*
11768399 ACATGTGCATGCTCACATTCATCACATTG
66 ACATATGCATGCTCACATTCATCACATTG
* *
11768428 GCCATTCGACCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCAGCCTTATCAC
1 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
*
11768493 ACATATGCATGCTCACATTCATTACATTG
66 ACATATGCATGCTCACATTCATCACATTG
** * *
11768522 GCCATTCGGCCTTATCACATATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACAT
11768567 AAAATCCTAA
Statistics
Matches: 220, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 220 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (94 bp):
GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTGGCCATTCGGCCTTATCAC
ACATATGCATGCTCACATTCATCACATTG
Found at i:11768446 original size:22 final size:22
Alignment explanation
Indices: 11768374--11768447 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
11768364 TCATATTCAC
*
11768374 CACATTGGCCATTCGGCCTTAT
1 CACATTGGCCATTCGACCTTAT
* *
11768396 CACACATGTG-CATGCTC-ACATTCAT
1 CACA-TTG-GCCAT--TCGACCTT-AT
11768421 CACATTGGCCATTCGACCTTAT
1 CACATTGGCCATTCGACCTTAT
11768443 CACAT
1 CACAT
11768448 ATATACATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
22 13 0.32
23 10 0.25
24 9 0.22
25 8 0.20
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (22 bp):
CACATTGGCCATTCGACCTTAT
Found at i:11768556 original size:47 final size:47
Alignment explanation
Indices: 11768240--11768566 Score: 447
Period size: 47 Copynumber: 7.0 Consensus size: 47
11768230 TTTCACACTA
* * * *
11768240 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
11768287 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * *
11768334 GCCATTCGGCCTTATCACATATATACATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * *
11768381 GCCATTCGGCCTTATCACACATGTGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * * *
11768428 GCCATTCGACCTTATCACATATATACATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * * *
11768475 GCCATTCAGCCTTATCACACATATGCATGCTCACATTCATTACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* **
11768522 GCCATTCGGCCTTATCACATATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
11768567 AAAATCCTAA
Statistics
Matches: 241, Mismatches: 39, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 241 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:11771873 original size:7 final size:7
Alignment explanation
Indices: 11771861--11771890 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
11771851 TTTTTTCATC
11771861 ATCACAT
1 ATCACAT
*
11771868 ATCACAA
1 ATCACAT
11771875 ATCACAT
1 ATCACAT
11771882 ATCACAT
1 ATCACAT
11771889 AT
1 AT
11771891 TGATGGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
ATCACAT
Found at i:11775273 original size:47 final size:47
Alignment explanation
Indices: 11775197--11775450 Score: 332
Period size: 47 Copynumber: 5.4 Consensus size: 47
11775187 ATCACAATAA
*
11775197 TGCAGATAAACTGCCACTTAATAATATTGTGGACAAGCCA-CAGCTTT
1 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCA-CTTT
* *
11775244 TGCAAATAAACTGCCACTTAAAAAAATTGTGGACAAGCCACCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
* *
11775291 TGCAAATAAACTGCCACTTTATAATATGGTGGACAAGCTC-CCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGC-CACCACTTT
* * *
11775338 TGCAAATAAACTGCCATTTAATAAAATTGTGGACAAGTCACCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
* * * * * *
11775385 TGCAGATAAACTGTCACTTTATAATATTCTAGACAAGCTACCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
* *
11775432 TGTAGATAAACTGCCACTT
1 TGCAAATAAACTGCCACTT
11775451 CTTCCTCCAT
Statistics
Matches: 181, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
46 1 0.01
47 177 0.98
48 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (47 bp):
TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
Found at i:11775364 original size:94 final size:94
Alignment explanation
Indices: 11775197--11775450 Score: 375
Period size: 94 Copynumber: 2.7 Consensus size: 94
11775187 ATCACAATAA
* *
11775197 TGCAGATAAACTGCCACTTAATAATATTGTGGACAAGC-CACAGCTTTTGCAAATAAACTGCCAC
1 TGCAGATAAACTGCCACTTTATAATATTGTGGACAAGCTCCCA-CTTTTGCAAATAAACTGCCAC
11775261 TTAAAAAAATTGTGGACAAGCCACCACTTT
65 TTAAAAAAATTGTGGACAAGCCACCACTTT
* * *
11775291 TGCAAATAAACTGCCACTTTATAATATGGTGGACAAGCTCCCACTTTTGCAAATAAACTGCCATT
1 TGCAGATAAACTGCCACTTTATAATATTGTGGACAAGCTCCCACTTTTGCAAATAAACTGCCACT
* *
11775356 TAATAAAATTGTGGACAAGTCACCACTTT
66 TAAAAAAATTGTGGACAAGCCACCACTTT
* * * * * *
11775385 TGCAGATAAACTGTCACTTTATAATATTCTAGACAAGCTACCACTTTTGTAGATAAACTGCCACT
1 TGCAGATAAACTGCCACTTTATAATATTGTGGACAAGCTCCCACTTTTGCAAATAAACTGCCACT
11775450 T
66 T
11775451 CTTCCTCCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
94 140 0.98
95 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (94 bp):
TGCAGATAAACTGCCACTTTATAATATTGTGGACAAGCTCCCACTTTTGCAAATAAACTGCCACT
TAAAAAAATTGTGGACAAGCCACCACTTT
Found at i:11779925 original size:47 final size:47
Alignment explanation
Indices: 11779850--11779996 Score: 181
Period size: 47 Copynumber: 3.1 Consensus size: 47
11779840 AGTAATGCAA
* * *
11779850 ATAAACTACCACTTAAT-AATAATATGGACAAATCACCACTTTT-TCAG
1 ATAAACTACCACTTAATAAAT-TTGTGGACAAACCACCACTTTTGT-AG
*
11779897 ATAAACTACCACTTAATAAATTTGTGGACAAGCCACCACTTTTGTAG
1 ATAAACTACCACTTAATAAATTTGTGGACAAACCACCACTTTTGTAG
* * * * *
11779944 ATAAACTACCACTTTATAAAATTGTGAACAAGCTACCACTTTTGTAG
1 ATAAACTACCACTTAATAAATTTGTGGACAAACCACCACTTTTGTAG
11779991 ATAAAC
1 ATAAAC
11779997 CACTTCTTCC
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 86 0.96
48 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (47 bp):
ATAAACTACCACTTAATAAATTTGTGGACAAACCACCACTTTTGTAG
Found at i:11791728 original size:4 final size:4
Alignment explanation
Indices: 11791719--11791750 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
11791709 TCATGACAAT
11791719 ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA
1 ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA
11791751 TTTAGTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATCA
Found at i:11793811 original size:309 final size:309
Alignment explanation
Indices: 11793255--11794178 Score: 1809
Period size: 309 Copynumber: 3.0 Consensus size: 309
11793245 ATGGTGCGAG
11793255 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCC--AAAAAAACAATACCT
1 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
*
11793318 CATTTATTTCCTAAAAACGCATAGATAATAT-AAAAAATTAGAGCATGACCACTTTCTCTCTTAA
66 CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
11793382 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
131 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
11793447 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
196 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
11793512 ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
261 ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
11793561 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
1 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
11793626 CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
66 CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
11793691 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
131 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
11793756 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
196 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
11793821 ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
261 ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
11793870 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
1 AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
11793935 CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
66 CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
11794000 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
131 TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
11794065 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
196 TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
*
11794130 ATGCCAATCATTTCTTATAACATTAGAAATGTTCTAGTCTTACTACGAA
261 ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
11794179 CATTACAAGA
Statistics
Matches: 613, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
306 48 0.08
308 46 0.08
309 519 0.85
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (309 bp):
AGAAGGGATTTGATTGGGTTTCAAGGAGCGTTTCACTAGCACTTATCCAAAAAAAAACAATACCT
CATTTATTTCCTAAAAACGCATAGATAATATAAAAAAATTAGAGCATGACCACTTTCTCTCTTGA
TTCTCAAACCCGATTCTACTAGCCCCCTATTTTTGGGATGTTACAGATATAATACATGAAAATTT
TATCACATAAATGTTATGTCAAATCATGACTTCTTGTAACTTGGGTAGCGATGATGCATTACTAG
ATGCCAATCATTTCTTGTAACATTAGAAATGTTCTAGTCTTACTACGAA
Found at i:11803571 original size:19 final size:20
Alignment explanation
Indices: 11803534--11803579 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
11803524 TATAAATTAT
* *
11803534 TTAATCATGTTTTTTCTTAA
1 TTAATCATGATTTTACTTAA
11803554 TTAATCAT-ATTTTACTTAA
1 TTAATCATGATTTTACTTAA
11803573 TTAATCA
1 TTAATCA
11803580 AAATATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATCATGATTTTACTTAA
Found at i:11808148 original size:12 final size:12
Alignment explanation
Indices: 11808128--11808160 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11808118 AAAACCCTCC
11808128 ACCCC-ACCCGT
1 ACCCCTACCCGT
*
11808139 ACCCGTACCCGT
1 ACCCCTACCCGT
11808151 ACCCCTACCC
1 ACCCCTACCC
11808161 TCTCCTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.18, C:0.61, G:0.09, T:0.12
Consensus pattern (12 bp):
ACCCCTACCCGT
Done.