Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 40 of 161
Found at i:12282331 original size:45 final size:45
Alignment explanation
Indices: 12282267--12282354 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
12282257 GTGAACCAAA
* *
12282267 CATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGGG
1 CATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGGG
*
12282312 CATCAATT-ATTAATAAGGTGGTTGCTATGTGTTGAATCCACCG
1 CATC-ATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
12282355 AGTATCTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (45 bp):
CATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGGG
Found at i:12282422 original size:23 final size:22
Alignment explanation
Indices: 12282396--12282442 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
12282386 GGAAATTGAC
12282396 TAAGTGT-AATTGAATAATGAATA
1 TAAGTGTGAATTGAAT--TGAATA
12282419 TAAGTGTGGAATTGAATTGAATA
1 TAAGTGT-GAATTGAATTGAATA
12282442 T
1 T
12282443 CGACTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (22 bp):
TAAGTGTGAATTGAATTGAATA
Found at i:12292826 original size:19 final size:19
Alignment explanation
Indices: 12292802--12292857 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
12292792 AATCATATCT
12292802 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
12292821 TCCAAGATTGCATAAATCATA
1 TCCAAGATTGCAT--ATCATA
*
12292842 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
12292858 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:12293248 original size:19 final size:19
Alignment explanation
Indices: 12293224--12293279 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
12293214 AATCATATCT
12293224 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
12293243 TCCAAGATTGCATAAATCATA
1 TCCAAGATTGCAT--ATCATA
*
12293264 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
12293280 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:12293700 original size:44 final size:44
Alignment explanation
Indices: 12293652--12294038 Score: 454
Period size: 44 Copynumber: 8.8 Consensus size: 44
12293642 ACCAGTATGG
* * * * * * *
12293652 GAAGATAAAATCTGCTACCTTTGATCTATTTCATGCCGATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
12293696 GAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * ***
12293738 GAAGACAAGATCTACTTTCTTCGATCTATTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATACAT
* * *
12293783 GAAGACAAAATCTGCTATCCTCGATCTACTTCACCCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
12293827 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
12293871 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
12293916 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
12293960 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATAAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
12294004 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACG
12294039 ACAACCCAGG
Statistics
Matches: 290, Mismatches: 49, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
42 38 0.13
44 180 0.62
45 72 0.25
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:12293853 original size:89 final size:88
Alignment explanation
Indices: 12293622--12294037 Score: 458
Period size: 89 Copynumber: 4.7 Consensus size: 88
12293612 ATAAGACTTG
* * *** * * * * * **
12293622 TATCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGCTACCTTTGATCTATTTCATG
1 TATCTTCGATCTACTTCACC-CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
*
12293687 CCGATACATGAAGACAAGATCTGC
65 CCAATACATGAAGACAAGATCTGC
* * * * *
12293711 TTTCTTCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTATTTCACCA
1 TATCTTCGATCTACTTCACCCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CA
* *** *
12293774 CCAGTATGGGAAGACAAAATCTGC
65 CCAATACATGAAGACAAGATCTGC
* *
12293798 TATCCTCGATCTACTTCACCCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACAC
1 TATCTTCGATCTACTTCACCCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACAC
12293863 CAATACATGAAGACAAGATCTGC
66 CAATACATGAAGACAAGATCTGC
* * * *** *
12293886 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
1 TATCTTCGATCTACTTCACC-CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
12293951 CCAATACATGAAGACAAGATCTGC
65 CCAATACATGAAGACAAGATCTGC
* * * * *
12293975 TATATTTGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTTCAC
1 TATCTTCGATCTACTTCACCCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
12294038 GACAACCCAG
Statistics
Matches: 272, Mismatches: 51, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
86 32 0.12
87 33 0.12
88 76 0.28
89 131 0.48
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (88 bp):
TATCTTCGATCTACTTCACCCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACAC
CAATACATGAAGACAAGATCTGC
Found at i:12293918 original size:133 final size:133
Alignment explanation
Indices: 12293624--12294035 Score: 650
Period size: 133 Copynumber: 3.1 Consensus size: 133
12293614 AAGACTTGTA
* * * *
12293624 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGCTA-CCTTTGATCTATTTCATGC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTGCTATCC-TCGATCTACTTCACGC
* * *
12293688 CGATACATGAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCAATACATGAAGACAAGATCT
65 CAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
*
12293751 ACTT
130 GCTT
* * *
12293755 TCTTCGATCTATTTCACCACCAGTATGGGAAGACAAAATCTGCTATCCTCGATCTACTTCACCCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTGCTATCCTCGATCTACTTCACGCC
*
12293820 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTG
66 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
12293885 CTT
131 CTT
* *
12293888 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTGCTATCCTCGATCTACTTCACGCC
* *
12293953 AATACATGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATAAATGAAGACAAGATCTG
66 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
12294018 CTT
131 CTT
12294021 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
12294036 ACGACAACCC
Statistics
Matches: 258, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
131 90 0.35
132 2 0.01
133 166 0.64
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (133 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTGCTATCCTCGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
CTT
Found at i:12294102 original size:88 final size:87
Alignment explanation
Indices: 12294004--12294585 Score: 804
Period size: 88 Copynumber: 6.6 Consensus size: 87
12293994 GCCAATAAAT
* * * * * * * *
12294004 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGACAACCCAGGGAGGCAAGACTGGTATCTTT
1 GAAGGCAAGATCTGCTATCTTC-AACTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
12294069 GATCTGCTTCACTGTCGGTACAG
65 GATCTGCTTCACTGTCGGTACAG
* * *
12294092 GAAGGTAAGATCTGTTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCCTC
1 GAAGGCAAGATCTGCTATCTTCAA-CTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
* *
12294157 GATCTGTTTCACTGTCGGTATAG
65 GATCTGCTTCACTGTCGGTACAG
*
12294180 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
1 GAAGGCAAGATCTGCTATCTTCAA-CTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
*
12294245 GATCTGCTTCACTGTCAGTACAG
65 GATCTGCTTCACTGTCGGTACAG
* *
12294268 GAAGGCAAGATCTGCTATCTTCAACTTGCTCCACTACGACCCAGGGAGGCAAGGCTGATATCTTC
1 GAAGGCAAGATCTGCTATCTTCAAC-TGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
*
12294333 GATCTGCTTCACTGTTGGTACAG
65 GATCTGCTTCACTGTCGGTACAG
* *
12294356 GAAGGCAAGATTTGCTATGTTCAACTTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
1 GAAGGCAAGATCTGCTATCTTCAAC-TGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
12294421 GATCTGCTTCACTGTCGGTACAG
65 GATCTGCTTCACTGTCGGTACAG
* * * * *
12294444 AAAGGCAAGATCTGCTATCTTCAACCTGGTCCACTACAACCCAAGGAGGCAAGGCCGGTATCTTT
1 GAAGGCAAGATCTGCTATCTTCAA-CTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
* * *
12294509 AATCTGCTTCACTGTCAGTACAA
65 GATCTGCTTCACTGTCGGTACAG
* * * * *
12294532 GAAGGCAAGATCTGCTATCTTCAACCTTCTCCGCTGCAAACCAGGAAGGCAAGG
1 GAAGGCAAGATCTGCTATCTTCAA-CTGCTCCACTACAACCCAGGGAGGCAAGG
12294586 TTTTGTGATT
Statistics
Matches: 443, Mismatches: 48, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
87 2 0.00
88 440 0.99
89 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (87 bp):
GAAGGCAAGATCTGCTATCTTCAACTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCG
ATCTGCTTCACTGTCGGTACAG
Found at i:12294161 original size:264 final size:264
Alignment explanation
Indices: 12293621--12294430 Score: 736
Period size: 264 Copynumber: 3.1 Consensus size: 264
12293611 GATAAGACTT
* * * * * *
12293621 GTATCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGCTACCTTTGATCTATTTCAT
1 GTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* *
12293686 GCCGATACATGAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCAATACATGAAGACAAGAT
66 GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
* * * ** * * * * *
12293749 CTACTTTCTTCGATCTATTTCACCACCA-GTATGGGAAGACAAAATCTGCTATCCTCGATCTACT
131 CTGCTTTCTTCGATCTACTTCACCACAACCCA-GGG-AGGCAAGA-CTGATATCTTCGATCTGCT
** ** * * ** * * * ** * * *
12293813 TCAC-CCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCAC-ACCAATACATGAAGA
193 TCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA-CAACCCAGGGAGG
*
12293876 CAAGATCTG
257 CAAG-GCTG
* *
12293885 CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
1 GTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
12293950 GCCAATACATGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATAAATGAAGACAAGAT
66 GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
* * *
12294015 CTGCTTTCTTCGATCTACTTCACGACAACCCAGGGAGGCAAGACTGGTATCTTTGATCTGCTTCA
131 CTGCTTTCTTCGATCTACTTCACCACAACCCAGGGAGGCAAGACTGATATCTTCGATCTGCTTCA
* *
12294080 CTGTCGGTACAGGAAGGTAAGATCTGTTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAG
196 CTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAG
12294145 GCTG
261 GCTG
* ** * *** * * * * * *
12294149 GTATCCTCGATCTGTTTCACTGTCGGTATAGGAAGGCAAGATCTGCTATCTTC-AACCAGCTCCA
1 GTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTA-CTTCA
** ** * * * * * * * * * *
12294213 CTACAACCCAGGGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
65 CGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
* * * * * * *
12294277 ATCTGCTATCTTC-AACTTGCTCCACTACGACCCAGGGAGGCAAGGCTGATATCTTCGATCTGCT
129 ATCTGCTTTCTTCGATC-TACTTCACCACAACCCAGGGAGGCAAGACTGATATCTTCGATCTGCT
* * * *
12294341 TCACTGTTGGTACAGGAAGGCAAGATTTGCTATGTTCAACTTGCTCCACTACAACCCAGGGAGGC
193 TCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGC
12294406 AAGGCTG
258 AAGGCTG
*
12294413 GTATCTTCGATCTGCTTC
1 GTATCTTCGATCTACTTC
12294431 ACTGTCGGTA
Statistics
Matches: 445, Mismatches: 93, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
263 24 0.05
264 322 0.72
265 49 0.11
266 49 0.11
267 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (264 bp):
GTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
CTGCTTTCTTCGATCTACTTCACCACAACCCAGGGAGGCAAGACTGATATCTTCGATCTGCTTCA
CTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAG
GCTG
Found at i:12294230 original size:44 final size:44
Alignment explanation
Indices: 12294009--12294584 Score: 228
Period size: 44 Copynumber: 13.1 Consensus size: 44
12293999 TAAATGAAGA
* * * * * *
12294009 CAAGATCTGCTTTCTTCGATCTACTTCACGACAACCCAGGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* ** * * * **** *
12294053 CAAGA-CTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
* *
12294097 TAAGATCTGTTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* * * * * * * * ***** *
12294141 CAAG-GCTGGTATCCTCGATCTGTTTCACTGTCGGTATAGGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
*
12294185 CAAGATCTGCTATCTTCAACCAGCTCCACTACAACCCAGGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* * * * * * *** *
12294229 CAAG-GCTGGTATCTTCGATCTGCTTCACTGTCAGTACAGGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
* *
12294273 CAAGATCTGCTATCTTCAACTTGCTCCACTACGACCCAGGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* * * * * ****** *
12294317 CAAG-GCTGATATCTTCGATCTGCTTCACTGTTGGTACAGGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
* * *
12294361 CAAGATTTGCTATGTTCAACTTGCTCCACTACAACCCAGGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* * * * * * **** **
12294405 CAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGAAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
* *
12294449 CAAGATCTGCTATCTTCAACCTGGTCCACTACAACCCAAGGAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
* * * * * * * *** * *
12294493 CAAG-GCCGGTATCTTTAATCTGCTTCACTGTCAGTACAAGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACCCAGGGAGG
* * * * *
12294537 CAAGATCTGCTATCTTCAACCTTCTCCGCTGCAAACCAGGAAGG
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
12294581 CAAG
1 CAAG
12294585 GTTTTGTGAT
Statistics
Matches: 363, Mismatches: 157, Indels: 24
0.67 0.29 0.04
Matches are distributed among these distances:
43 110 0.30
44 145 0.40
45 108 0.30
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (44 bp):
CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGG
Found at i:12296671 original size:12 final size:12
Alignment explanation
Indices: 12296654--12296680 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12296644 CCCGTAGTAA
12296654 GTGCAAAAGAAT
1 GTGCAAAAGAAT
12296666 GTGCAAAAGAAT
1 GTGCAAAAGAAT
12296678 GTG
1 GTG
12296681 TGAATTTACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (12 bp):
GTGCAAAAGAAT
Found at i:12300691 original size:12 final size:12
Alignment explanation
Indices: 12300674--12300698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12300664 ATTAATAAAC
12300674 AAATAGAAAAAT
1 AAATAGAAAAAT
12300686 AAATAGAAAAAT
1 AAATAGAAAAAT
12300698 A
1 A
12300699 GAGTCCAAAT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATAGAAAAAT
Found at i:12301915 original size:21 final size:19
Alignment explanation
Indices: 12301864--12301915 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
12301854 CATATGTAAT
12301864 TATTATTATTTTATATATA
1 TATTATTATTTTATATATA
* *
12301883 TATGTATATATTTTCTATAATG
1 TAT-TAT-TATTTTATAT-ATA
12301905 TAATTATTATT
1 T-ATTATTATT
12301916 ATTTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 13 0.48
22 6 0.22
23 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TATTATTATTTTATATATA
Found at i:12301935 original size:45 final size:42
Alignment explanation
Indices: 12301845--12301935 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 42
12301835 TTTTTTATTT
* * *
12301845 TATAATTTTCATATGTAATTATTATTATTTTATATATATATG
1 TATAATTTTCATATGTAATTATTATTATTTTATATACACACG
*
12301887 TATATATTTTCTATAATGTAATTATTATTATTTTATGTACACACG
1 TATA-ATTTTC-AT-ATGTAATTATTATTATTTTATATACACACG
12301932 TATA
1 TATA
12301936 GATATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.10
43 6 0.14
44 2 0.05
45 30 0.71
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (42 bp):
TATAATTTTCATATGTAATTATTATTATTTTATATACACACG
Found at i:12303883 original size:19 final size:19
Alignment explanation
Indices: 12303859--12303914 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
12303849 AATCATATCT
*
12303859 TCCAAGAGTGCATATCATA
1 TCCAAGATTGCATATCATA
12303878 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
12303899 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
12303915 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:12303896 original size:21 final size:21
Alignment explanation
Indices: 12303870--12303913 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12303860 CCAAGAGTGC
12303870 ATATCATATCCAAGATTGCAT
1 ATATCATATCCAAGATTGCAT
*
12303891 ATATCATATCTAAGATTGCAT
1 ATATCATATCCAAGATTGCAT
12303912 AT
1 AT
12303914 CCTTGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATCATATCCAAGATTGCAT
Found at i:12304545 original size:20 final size:20
Alignment explanation
Indices: 12304520--12304604 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
12304510 TTAAAGGACA
12304520 TTTTTTATGCA-TTTTATAAT
1 TTTTTTATG-ATTTTTATAAT
*
12304540 TTTTTTATGATTTTTATAAA
1 TTTTTTATGATTTTTATAAT
* *** *
12304560 ATTTTCCGGTTTTTTAT-AT
1 TTTTTTATGATTTTTATAAT
12304579 TTTTTTACT-ATTTTTATATAT
1 TTTTTTA-TGATTTTTATA-AT
12304600 TTTTT
1 TTTTT
12304605 ATTAAAATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
19 13 0.27
20 29 0.59
21 7 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTATGATTTTTATAAT
Found at i:12304583 original size:11 final size:10
Alignment explanation
Indices: 12304569--12304604 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
12304559 AATTTTCCGG
12304569 TTTTTTATAT
1 TTTTTTATAT
12304579 TTTTTTACTAT
1 TTTTTTA-TAT
*
12304590 TTTTATATAT
1 TTTTTTATAT
12304600 TTTTT
1 TTTTT
12304605 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:12304917 original size:87 final size:84
Alignment explanation
Indices: 12304744--12304965 Score: 227
Period size: 87 Copynumber: 2.5 Consensus size: 84
12304734 TCAACTGTTA
* * * *
12304744 AAGTATTCAATTGAGTGCAAAAATAA-AAGGGTTTAATTGCCTTTTTTGAACAAGTCTAGGGCAT
1 AAGTATTCAATTGAGTG-AAAAAAAACAAGGG-TTAATTGCTTTTTTTGAAAAAATCTAGGGCAT
*
12304808 TTTTGATGCATTTCGACAGTTC
64 TTTTGATGCATTTC-AAAGTTC
*
12304830 AAGTATTCAATTGAGTGAAAAAAAAGCAAGGGCTTATTTGCTTTTTTTGAAAAAAAT-TGAGGGC
1 AAGTATTCAATTGAGTGAAAAAAAA-CAAGGG-TTAATTGCTTTTTTTG-AAAAAATCT-AGGGC
12304894 ATTTTT-ATGCAATTT-AAAGGTTC
62 ATTTTTGATGC-ATTTCAAA-GTTC
** *
12304917 AAGTACCCAATTGAGTATAAGAAAAAACAAGAGGTTAATTGCTTTTTTT
1 AAGTATTCAATTGAGT-GAA-AAAAAACAAG-GGTTAATTGCTTTTTTT
12304966 TTTAAAGTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
85 7 0.06
86 19 0.16
87 42 0.36
88 40 0.34
89 8 0.07
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (84 bp):
AAGTATTCAATTGAGTGAAAAAAAACAAGGGTTAATTGCTTTTTTTGAAAAAATCTAGGGCATTT
TTGATGCATTTCAAAGTTC
Found at i:12314764 original size:218 final size:218
Alignment explanation
Indices: 12314378--12314819 Score: 584
Period size: 218 Copynumber: 2.0 Consensus size: 218
12314368 AGTGACTGAC
* * * *
12314378 CAAATCAGGTAGAAGCAGAGACCTTTTAATGCAACTTTTTTTCCTTTTTGTGTTGGTTCCACATC
1 CAAATCAGGTAGAAGCAGAGACCCTTCAATG--ACTTTTTTTCCTTTTTGTATTGGTTCCACATA
* * *
12314443 TACTTTTTTTGTTCAGTATCTTAATGTAACTAATAACTAAATAATAACATTCTTACATTAATACT
64 TACTTTTTTTGCTCAGTATCTTAATGTAACGAATAACTAAATAATAACAGTCTTACATTAATACT
* * * *
12314508 AAAGTTCCAAATCTGGCACAACATGTTGTAGCCATCTGCAAGTTTCTTGTTTACATAGTTTTATC
129 AAAGTTCCAAAACTAGCACAACATCTTATAGCCATCTGCAAGTTTCTTGTTTACATAGTTTTATC
** * *
12314573 CTCTGGCTTTGGATCCACAACAAGA
194 AGCTCGCTTTGGATCCAAAACAAGA
* * *
12314598 CAAATCAGGTAGAAGCCGAGAACCCTTCAATG-CTTTTTATTCTTTTTTTTATTGGTTCCACATA
1 CAAATCAGGTAGAAGCAGAG-ACCCTTCAATGACTTTTT-TTCCTTTTTGTATTGGTTCCACATA
* * * * *
12314662 TCCTTTTGTTT-CTCAGTATCTTAATGT-ACGGATAACTAACTAATAATAGTCTTACATTAATAT
64 TACTTTT-TTTGCTCAGTATCTTAATGTAACGAATAACTAAATAATAACAGTCTTACATTAATAC
* *
12314725 TAAAGTTCCAAAACTAGCACAACTTCTTATAGTCATCTGCAAGTTTCTTGTTTACATAGTTTTAT
128 TAAAGTTCCAAAACTAGCACAACATCTTATAGCCATCTGCAAGTTTCTTGTTTACATAGTTTTAT
*
12314790 CAGGTCGCTTTGGATCCAAAACAAGA
193 CAGCTCGCTTTGGATCCAAAACAAGA
12314816 CAAA
1 CAAA
12314820 ATTTACTACA
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
218 120 0.62
219 42 0.22
220 22 0.11
221 9 0.05
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (218 bp):
CAAATCAGGTAGAAGCAGAGACCCTTCAATGACTTTTTTTCCTTTTTGTATTGGTTCCACATATA
CTTTTTTTGCTCAGTATCTTAATGTAACGAATAACTAAATAATAACAGTCTTACATTAATACTAA
AGTTCCAAAACTAGCACAACATCTTATAGCCATCTGCAAGTTTCTTGTTTACATAGTTTTATCAG
CTCGCTTTGGATCCAAAACAAGA
Found at i:12320080 original size:18 final size:19
Alignment explanation
Indices: 12320048--12320102 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
12320038 AATCTTCAAG
* *
12320048 GATATGTAATTTTAG-CAT
1 GATATGCAATCTTAGACAT
*
12320066 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGACAT
12320085 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
12320103 AGATATGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.42
19 3 0.10
21 15 0.48
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGACAT
Found at i:12320124 original size:23 final size:24
Alignment explanation
Indices: 12320067--12320125 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
12320057 TTTTAGCATG
12320067 ATATGCAATCTT---AGATATGAT
1 ATATGCAATCTTAGAAGATATGAT
12320088 ATATGCAATCTTAGAAGATATGAT
1 ATATGCAATCTTAGAAGATATGAT
* *
12320112 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
12320126 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (24 bp):
ATATGCAATCTTAGAAGATATGAT
Found at i:12330400 original size:42 final size:42
Alignment explanation
Indices: 12330324--12330473 Score: 239
Period size: 42 Copynumber: 3.5 Consensus size: 42
12330314 GTCGTTAACT
*
12330324 TTTA-CGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTTC
*
12330367 TTTAGCGGCGCTTAGGAAAAAACGCCGCAAAAGATCATGTTC
1 TTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTC
12330409 TTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTC
*
12330451 TTTAGCGGCGCTTTGGAAGAAAA
1 TTTAGCGGCGCTTAGGAA-AAAA
12330474 GGCTGTTGGA
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
42 85 0.84
43 8 0.08
44 8 0.08
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (42 bp):
TTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTC
Found at i:12332021 original size:42 final size:43
Alignment explanation
Indices: 12331974--12332065 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 43
12331964 ATACTCTAAC
*
12331974 AAACGCCTCTAAAAGTAATGTTCTATAGCGACGCTTG-TTCAA
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGACGCTTGTTTCAA
* * * *
12332016 AAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTGTTTCAC
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGACGCTTGTTTCAA
12332059 AAACGCC
1 AAACGCC
12332066 ACTGTTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAAGTAATGTTCTATAGCGACGCTTGTTTCAA
Found at i:12337831 original size:9 final size:9
Alignment explanation
Indices: 12337817--12338006 Score: 100
Period size: 9 Copynumber: 22.2 Consensus size: 9
12337807 TTTTTATGTA
12337817 TTATGTAAG
1 TTATGTAAG
12337826 TTATGT-A-
1 TTATGTAAG
12337833 TTATGTAAG
1 TTATGTAAG
12337842 -TACTGTAAG
1 TTA-TGTAAG
*
12337851 TAATGTAAG
1 TTATGTAAG
12337860 TTATGTAAG
1 TTATGTAAG
* * *
12337869 -AAAGTTA-
1 TTATGTAAG
12337876 TTATGTAAG
1 TTATGTAAG
*
12337885 TTGTGTATA-
1 TTATGTA-AG
*
12337894 ATAT-TAA-
1 TTATGTAAG
*
12337901 TTATGTGAG
1 TTATGTAAG
**
12337910 TCGTGT-A-
1 TTATGTAAG
*
12337917 TAATGTAAG
1 TTATGTAAG
*
12337926 TTAAG-AAGG
1 TTATGTAA-G
12337935 TTATGT-A-
1 TTATGTAAG
*
12337942 TAATGTAAG
1 TTATGTAAG
12337951 TTATGTAAG
1 TTATGTAAG
* * *
12337960 TAATTTAAT
1 TTATGTAAG
12337969 TTATGTAAG
1 TTATGTAAG
12337978 TTATGTAAG
1 TTATGTAAG
* *
12337987 TTATTTAAT
1 TTATGTAAG
*
12337996 TTATGTCAG
1 TTATGTAAG
12338005 TT
1 TT
12338007 TCTATATATG
Statistics
Matches: 133, Mismatches: 33, Indels: 30
0.68 0.17 0.15
Matches are distributed among these distances:
7 19 0.14
8 21 0.16
9 91 0.68
10 2 0.02
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:12337831 original size:16 final size:16
Alignment explanation
Indices: 12337810--12337866 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
12337800 TGATATATTT
12337810 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
12337826 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
12337842 -TACTGTAAGTAATGTAAG
1 TTA-TGT-A-TTATGTAAG
12337860 TTATGTA
1 TTATGTA
12337867 AGAAAGTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 2 0.06
16 19 0.53
17 2 0.06
18 11 0.31
19 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:12338123 original size:22 final size:21
Alignment explanation
Indices: 12338077--12338128 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
12338067 AGTGGTGTAT
* * *
12338077 TAAGTTATGGAAGTTATTATG
1 TAAGTTATGCAAGTTATAATA
12338098 TAAGTTATGCAAGATTATAATA
1 TAAGTTATGCAAG-TTATAATA
12338120 TAAGTTATG
1 TAAGTTATG
12338129 TATTATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (21 bp):
TAAGTTATGCAAGTTATAATA
Found at i:12338142 original size:8 final size:7
Alignment explanation
Indices: 12338124--12338161 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
12338114 ATAATATAAG
12338124 TTATGTA
1 TTATGTA
12338131 TTATGTTA
1 TTATG-TA
12338139 TTATGTA
1 TTATGTA
12338146 TTATGTA
1 TTATGTA
12338153 --ATGTA
1 TTATGTA
12338158 TTAT
1 TTAT
12338162 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:12338142 original size:27 final size:26
Alignment explanation
Indices: 12338109--12338181 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
12338099 AAGTTATGCA
*
12338109 AGATTATAATATAAGTTATGTATTATG
1 AGATTAT-ATATAAGTTATGTATTATC
** * * *
12338136 TTATTATGTATTATGTAATGTATTATC
1 AGATTATATA-TAAGTTATGTATTATC
12338163 AGATTATATATAAGTTATG
1 AGATTATATATAAGTTATG
12338182 AAAGTTATTA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (26 bp):
AGATTATATATAAGTTATGTATTATC
Found at i:12338198 original size:21 final size:22
Alignment explanation
Indices: 12338173--12338258 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 22
12338163 AGATTATATA
12338173 TAAGTTATGA-AAGTTATTATG
1 TAAGTTATGATAAGTTATTATG
* *
12338194 TAAGTTAT-ACAAGCTTA-TATA
1 TAAGTTATGATAAG-TTATTATG
*
12338215 TAAGTTATGTATTATGTTATTATG
1 TAAGTTATG-A-TAAGTTATTATG
*
12338239 T-A-TTATG-TAATTTATTATG
1 TAAGTTATGATAAGTTATTATG
12338258 T
1 T
12338259 TATTATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
19 11 0.21
20 1 0.02
21 22 0.42
22 8 0.15
23 5 0.09
24 6 0.11
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TAAGTTATGATAAGTTATTATG
Found at i:12338217 original size:42 final size:42
Alignment explanation
Indices: 12338166--12338309 Score: 119
Period size: 50 Copynumber: 3.2 Consensus size: 42
12338156 TATTATCAGA
12338166 TTATATATAAGTTATGAAAGTTATTATGTAAGTTATACAAGC
1 TTATATATAAGTTATGAAAGTTATTATGTAAGTTATACAAGC
* * * *
12338208 TTATATATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTATG-
1 TTATATATAAGTTATG-A--AAGTTATTATGTA--A-GT--TATA-CAAGC
* *
12338258 TTATTATATATACGTTATGGAAGTTATTATGTAAGTTATGCAAGC
1 TTA-TATATA-A-GTTATGAAAGTTATTATGTAAGTTATACAAGC
12338303 TTATATA
1 TTATATA
12338310 CCAATTATGC
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
42 16 0.20
43 1 0.01
44 6 0.08
45 17 0.22
47 3 0.04
48 3 0.04
50 18 0.23
51 8 0.10
52 1 0.01
53 6 0.08
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.47
Consensus pattern (42 bp):
TTATATATAAGTTATGAAAGTTATTATGTAAGTTATACAAGC
Found at i:12338237 original size:8 final size:7
Alignment explanation
Indices: 12338219--12338264 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
12338209 TATATATAAG
12338219 TTATGTA
1 TTATGTA
12338226 TTATGTTA
1 TTATG-TA
12338234 TTATGTA
1 TTATGTA
12338241 TTATGTA
1 TTATGTA
*
12338248 --ATTTA
1 TTATGTA
12338253 TTATGTTA
1 TTATG-TA
12338261 TTAT
1 TTAT
12338265 ATATACGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:12338238 original size:95 final size:95
Alignment explanation
Indices: 12338077--12338343 Score: 401
Period size: 95 Copynumber: 2.8 Consensus size: 95
12338067 AGTGGTGTAT
*
12338077 TAAGTTATGGAAGTTATTATGTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGTTATTA
1 TAAGTTATGGAAGTTATTATGTAAGTTATGCAAGCTTAT-ATATAAGTTATGTATTATGTTATTA
12338142 TGTATTATGTAATGTATTATCAGATTATATA
65 TGTATTATGTAATGTATTATCAGATTATATA
* *
12338173 TAAGTTATGAAAGTTATTATGTAAGTTATACAAGCTTATATATAAGTTATGTATTATGTTATTAT
1 TAAGTTATGGAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATGTATTATGTTATTAT
* ***
12338238 GTATTATGTAATTTATTATGTTATTATATA
66 GTATTATGTAATGTATTATCAGATTATATA
* * * *
12338268 TACGTTATGGAAGTTATTATGTAAGTTATGCAAGCTTATATACCAA-TTATGCATTGTGTTATTA
1 TAAGTTATGGAAGTTATTATGTAAGTTATGCAAGCTTATATA-TAAGTTATGTATTATGTTATTA
*
12338332 TGTATTAAGTAA
65 TGTATTATGTAA
12338344 GCAAATGATT
Statistics
Matches: 156, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
95 118 0.76
96 38 0.24
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (95 bp):
TAAGTTATGGAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATGTATTATGTTATTAT
GTATTATGTAATGTATTATCAGATTATATA
Found at i:12338239 original size:15 final size:15
Alignment explanation
Indices: 12338219--12338264 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
12338209 TATATATAAG
12338219 TTATGTATTATGTTA
1 TTATGTATTATGTTA
12338234 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
12338248 --ATTTATTATGTTA
1 TTATGTATTATGTTA
12338261 TTAT
1 TTAT
12338265 ATATACGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:12338580 original size:61 final size:61
Alignment explanation
Indices: 12338489--12338636 Score: 174
Period size: 61 Copynumber: 2.4 Consensus size: 61
12338479 AAAAATATAT
* * * *
12338489 AATTATTTACAAAACGTGTAAAATTGATACTTA-TAAA-TTTTATTAATAATAAATCTAGAAC
1 AATTATTTACAAAACTTATAAATTTAATAC-TACTAAATTTTTA-TAATAATAAATCTAGAAC
* * * * * *
12338550 ACTTTTTTAGAAAACTTATAAATTTAATACTACTAAATTTTTATACTAATAAATTTAGAAT
1 AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
12338611 AATTATTTACAAAACTTATAAATTTA
1 AATTATTTACAAAACTTATAAATTTA
12338637 GAAAACTTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
60 2 0.03
61 65 0.90
62 5 0.07
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (61 bp):
AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
Found at i:12338588 original size:15 final size:15
Alignment explanation
Indices: 12338567--12338606 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
12338557 TAGAAAACTT
12338567 ATAAATTTAATACTA
1 ATAAATTTAATACTA
* *
12338582 CTAAATTTTTATACTA
1 ATAAA-TTTAATACTA
12338598 ATAAATTTA
1 ATAAATTTA
12338607 GAATAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:12338641 original size:17 final size:17
Alignment explanation
Indices: 12338615--12338647 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12338605 TAGAATAATT
12338615 ATTTACAAAACTTATAA
1 ATTTACAAAACTTATAA
*
12338632 ATTTAGAAAACTTATA
1 ATTTACAAAACTTATA
12338648 TAGAAAATAA
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:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTACAAAACTTATAA
Found at i:12341106 original size:23 final size:24
Alignment explanation
Indices: 12341080--12341130 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12341070 TAATTTAAAT
12341080 ATTATCAA-TATTTAAAATTATT-A
1 ATTATCAATTATTT-AAATTATTCA
* *
12341103 ATTATTAATTATTTATATTATTCA
1 ATTATCAATTATTTAAATTATTCA
12341127 ATTA
1 ATTA
12341131 ATGTATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATCAATTATTTAAATTATTCA
Found at i:12341114 original size:14 final size:17
Alignment explanation
Indices: 12341095--12341130 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12341085 CAATATTTAA
12341095 AATTA-TTA-ATTATT-
1 AATTATTTATATTATTC
12341109 AATTATTTATATTATTC
1 AATTATTTATATTATTC
12341126 AATTA
1 AATTA
12341131 ATGTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 3 0.16
16 6 0.32
17 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATTTATATTATTC
Found at i:12342363 original size:228 final size:226
Alignment explanation
Indices: 12342026--12342569 Score: 732
Period size: 228 Copynumber: 2.4 Consensus size: 226
12342016 GCTTCTAGGA
* * *
12342026 AAGCGCTGCTAATAGTATACTTTAACGGCGTTTTTCAATAAGCGCCACTAATTCTAATATACATC
1 AAGCGCCGCTAATAGTATACTTTAGCGGCG-TTTTCTATAAGCGCCACTAATTCTAATATACATC
* * * *
12342091 AATACCAAACTCTGCGCTTTGGTGTGCGTATCTTGCGGCGCTTAAC-GTTAAGTGCCGCTAATAC
65 AATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAACTG-AAAGCGCCGCTAATAC
*
12342155 TGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGTTG
129 TGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTG
* *
12342220 AGTTTTGGTTAAGAAATATAGCGGCGCTTTATCAT
194 AGTTTTGGTTAAG-AATATAGCGGCGC-TTACCAC
* *
12342255 AAGCGCCGCTAATAGTATACTTTAGCGGCGTTTCCTATAAGCGCCACTAATTCTAATATACCTCA
1 AAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCTATAAGCGCCACTAATTCTAATATACATCA
12342320 ATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACTG
66 ATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACTG
* * * * *
12342385 TTATTTAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCGATACCAAAACGCTGCG
131 TTATGTAGCGGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTGAG
* * * *
12342450 TTTTGGTTAAGATTTTTGCGGCGCTTCCCAC
196 TTTTGGTTAAGAATATAGCGGCGCTTACCAC
* * * * * **
12342481 AATGCGCCGCTATTACT-TACTTTAGCGGCGTTTTATCATAATCGCCACTAATTATTGTATACAT
1 AA-GCGCCGCTAATAGTATACTTTAGCGGCGTTTTCT-ATAAGCGCCACTAATTCTAATATACAT
* **
12342545 CAATACAAAGACGATGCGTTTTGGT
64 CAATACCAA-ACTCTGCGTTTTGGT
12342570 CTTGAGATTT
Statistics
Matches: 278, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
226 23 0.08
227 52 0.19
228 174 0.63
229 29 0.10
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (226 bp):
AAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCTATAAGCGCCACTAATTCTAATATACATCA
ATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACTG
TTATGTAGCGGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTGAG
TTTTGGTTAAGAATATAGCGGCGCTTACCAC
Found at i:12342372 original size:113 final size:112
Alignment explanation
Indices: 12341990--12342647 Score: 482
Period size: 114 Copynumber: 5.8 Consensus size: 112
12341980 TTTAAACGCA
* * * * *
12341990 GCGTTTCGGTTAATATATCTTGCGGTGCTT--CTAGGAAAGCGCTGCTAATAGTATACTTTAACG
1 GCGTTTTGGTT-AGATATCTTGCGGCGCTTAACT--GAAAGCGCCGCTAATAGT-TACTTTAGCG
* * * *
12342053 GCGTTTTTCAATAAGCGCCACTAATTCTAATATACATCAATACCAAACTCT
62 GCGTTTTACTATAAGCGCCACTAATTATAGTATACATCAATACCAAACTCT
* * * * *
12342104 GCGCTTTGGTGT-GCGTATCTTGCGGCGCTTAAC-GTTAAGTGCCGCTAATACTGTTA-TGTAGC
1 GCGTTTTGGT-TAG-ATATCTTGCGGCGCTTAACTG-AAAGCGCCGCTAATA--GTTACTTTAGC
* * * *
12342166 GGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGT-T
61 GGCGTTTTACTATAAGCGCCACTAATTATAGTATACATCAATACC-AAAC-TCT
* * * * * *
12342219 GAGTTTTGGTTAAGAAATATAGCGGCGCTTTA-TCATAAGCGCCGCTAATAGTATACTTTAGCGG
1 GCGTTTTGGTT-AGATATCTTGCGGCGCTTAACTGA-AAGCGCCGCTAATAGT-TACTTTAGCGG
* * * *
12342283 CG-TTTCCTATAAGCGCCACTAATTCTAATATACCTCAATACCAAACTCT
63 CGTTTTACTATAAGCGCCACTAATTATAGTATACATCAATACCAAACTCT
12342332 GCGTTTTGGTGT-GCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACTGTTA-TTTAGCG
1 GCGTTTTGGT-TAG-ATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATA--GTTACTTTAGCG
* * * *
12342395 GCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCGATACCAAAACGCT
62 GCGTTTTACTATAAGCGCCACTAATTATAGTATACATCAATACC-AAACTCT
* ** ** * * *
12342447 GCGTTTTGGTTAAGAT-TTTTGCGGCGCTTCCCACAATGCGCCGCTATTACTTACTTTAGCGGCG
1 GCGTTTTGGTT-AGATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATAGTTACTTTAGCGGCG
* * * **
12342511 TTTTA-TCATAATCGCCACTAATTATTGTATACATCAATACAAAGACGAT
65 TTTTACT-ATAAGCGCCACTAATTATAGTATACATCAATACCAA-ACTCT
* * * * ** *
12342560 GCGTTTTGGTCTTGAGATTTTGCGGCGCATAACCAAAAACGCCGCTAATTATGTT-CTTTTA-CG
1 GCGTTTTGGT-TAGATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAA-TA-GTTAC-TTTAGCG
* *
12342623 GCGTTTTGCT-TGAAGCGCCGCTAAT
62 GCGTTTTACTAT-AAGCGCCACTAAT
12342648 GCCAGATATT
Statistics
Matches: 430, Mismatches: 79, Indels: 69
0.74 0.14 0.12
Matches are distributed among these distances:
112 8 0.02
113 115 0.27
114 200 0.47
115 94 0.22
116 13 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (112 bp):
GCGTTTTGGTTAGATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATAGTTACTTTAGCGGCGT
TTTACTATAAGCGCCACTAATTATAGTATACATCAATACCAAACTCT
Found at i:12342585 original size:228 final size:226
Alignment explanation
Indices: 12342026--12342647 Score: 718
Period size: 228 Copynumber: 2.7 Consensus size: 226
12342016 GCTTCTAGGA
* * *
12342026 AAGCGCTGCTAATAGTATACTTTAACGGCGTTTTTCAATAAGCGCCACTAATTCTAATATACATC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTTC-ATAAGCGCCACTAATTCTAATATACATC
* * * *
12342091 AATACCAAACTCTGCGCTTTGGTGTGCGTATCTTGCGGCGCTTAACGTTAAGTGCCGCTAATACT
65 AATACCAAACTCTGCGTTTTGGTGTGAG-ATCTTGCGGCGCTTAACG-AAAGCGCCGCTAATACT
* * *
12342156 GTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGTTGA
128 GTTATTTAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTGA
* *
12342221 GTTTTGGTTAAGAAATATAGCGGCGCTTTATCAT
193 GTTTTGGTTAAGAAATATAGCGGCGCTTTACCAC
* * *
12342255 AAGCGCCGCTAATAGTATACTTTAGCGGCG-TTTCCTATAAGCGCCACTAATTCTAATATACCTC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTTC-ATAAGCGCCACTAATTCTAATATACATC
*
12342319 AATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACT
65 AATACCAAACTCTGCGTTTTGGTGTG-AGATCTTGCGGCGCTTAAC-GAAAGCGCCGCTAATACT
* * *
12342384 GTTATTTAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCGATACCAAAACGCTGC
128 GTTATTTAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTGA
* * * *
12342449 GTTTTGGTTAAG-ATTTTTGCGGCGC-TTCCCAC
193 GTTTTGGTTAAGAAATATAGCGGCGCTTTACCAC
* * * **
12342481 AATGCGCCGCTATTACT-TACTTTAGCGGCGTTTTATCATAATCGCCACTAATTATTGTATACAT
1 AA-GCGCCGCTAATACTATACTTTAGCGGCGTTTT-TCATAAGCGCCACTAATTCTAATATACAT
* ** * * * * *
12342545 CAATACAAAGACGATGCGTTTTGGTCTTGAGATTTTGCGGCGCATAACCAAAAACGCCGCTAATT
64 CAATACCAA-ACTCTGCGTTTTGGT-GTGAGATCTTGCGGCGCTTAA-CGAAAGCGCCGCTAA-T
* * *
12342610 A-TGTTCTTTTA-CGGCGTTTTGCTTG-AAGCGCCGCTAAT
125 ACTGTT-ATTTAGCGGCGTTTT-ATTGTAAGCGCCACTAAT
12342648 GCCAGATATT
Statistics
Matches: 340, Mismatches: 42, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
226 19 0.06
227 55 0.16
228 225 0.66
229 41 0.12
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (226 bp):
AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTTCATAAGCGCCACTAATTCTAATATACATCA
ATACCAAACTCTGCGTTTTGGTGTGAGATCTTGCGGCGCTTAACGAAAGCGCCGCTAATACTGTT
ATTTAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTGAGTT
TTGGTTAAGAAATATAGCGGCGCTTTACCAC
Found at i:12346672 original size:15 final size:15
Alignment explanation
Indices: 12346652--12346683 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12346642 CATTCAACTA
*
12346652 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
12346667 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
12346682 TT
1 TT
12346684 TACATGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:12347916 original size:25 final size:24
Alignment explanation
Indices: 12347864--12347921 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
12347854 TGGCTCTCTT
* * * *
12347864 GAGCTTCCCGTTTATGGCTTGTAT
1 GAGCTTCCCGATAATGGCTCGTAA
12347888 GAGCTTCCCGATAATTGGCTCGTAA
1 GAGCTTCCCGATAA-TGGCTCGTAA
12347913 GAGCTTCCC
1 GAGCTTCCC
12347922 ATTACATGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATAATGGCTCGTAA
Found at i:12349274 original size:15 final size:15
Alignment explanation
Indices: 12349256--12349286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12349246 ATTATTTAGC
12349256 TTATTATTATTATTT
1 TTATTATTATTATTT
*
12349271 TTATTATTTTTATTT
1 TTATTATTATTATTT
12349286 T
1 T
12349287 CCCTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:12349555 original size:23 final size:23
Alignment explanation
Indices: 12349529--12349596 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
12349519 ATGTATATAA
12349529 ATATGCTTTCATACGCCTTTATT
1 ATATGCTTTCATACGCCTTTATT
* * * *
12349552 ATATACTTACATA----TATA-A
1 ATATGCTTTCATACGCCTTTATT
12349570 ATATGCTTTCATACGCCTTTATT
1 ATATGCTTTCATACGCCTTTATT
12349593 ATAT
1 ATAT
12349597 ATACACACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 11 0.34
19 3 0.09
22 3 0.09
23 15 0.47
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.46
Consensus pattern (23 bp):
ATATGCTTTCATACGCCTTTATT
Found at i:12349609 original size:41 final size:41
Alignment explanation
Indices: 12349523--12349621 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
12349513 AAATACATGT
* *
12349523 ATATAAATATGCTTTCATACGCCTTTATTATATACTTACAT
1 ATATAAATATGCTTTCATACGCCTTTATTATATACTCACAC
12349564 ATATAAATATGCTTTCATACGCCTTTATTATATA-TACACAC
1 ATATAAATATGCTTTCATACGCCTTTATTATATACT-CACAC
* *
12349605 ATATATATATACTTTCA
1 ATATAAATATGCTTTCA
12349622 AAAAATATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (41 bp):
ATATAAATATGCTTTCATACGCCTTTATTATATACTCACAC
Found at i:12349737 original size:21 final size:21
Alignment explanation
Indices: 12349713--12349752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12349703 ATACATATTT
* *
12349713 ATATATTCTTTATATTTTAAA
1 ATATATTATATATATTTTAAA
12349734 ATATATTATATATATTTTA
1 ATATATTATATATATTTTA
12349753 TAATTCACAT
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTATATATATTTTAAA
Found at i:12353214 original size:13 final size:13
Alignment explanation
Indices: 12353196--12353221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12353186 ACCCCAAATG
12353196 GCACAATGCGAAT
1 GCACAATGCGAAT
12353209 GCACAATGCGAAT
1 GCACAATGCGAAT
12353222 ATCATGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GCACAATGCGAAT
Found at i:12354558 original size:5 final size:5
Alignment explanation
Indices: 12354545--12354598 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
12354535 AGAATATTTC
* *
12354545 AAAAA AAAAG AAAAG AAAAG AAAAG -AAA- AAAAG AAGAAA AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG -AAAAG
12354595 AAAA
1 AAAA
12354599 AGGAGAGGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 6 0.14
5 27 0.64
6 9 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12354587 original size:24 final size:24
Alignment explanation
Indices: 12354547--12354599 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
12354537 AATATTTCAA
*
12354547 AAAAAAAGAAAAGAAAAG-AAAAG
1 AAAAAAAGAAAAAAAAAGAAAAAG
12354570 AAAAAAAGAAGAAAAAAAGAAAAAG
1 AAAAAAAGAA-AAAAAAAGAAAAAG
12354595 AAAAA
1 AAAAA
12354600 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 10 0.37
24 7 0.26
25 10 0.37
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAAAGAAAAAG
Found at i:12355916 original size:44 final size:43
Alignment explanation
Indices: 12355867--12356179 Score: 194
Period size: 44 Copynumber: 7.1 Consensus size: 43
12355857 GACAACAGAT
*
12355867 CTTGCCTTCCTGAATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTG-ATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * * *
12355911 CTTGCC-TCTCTCGGTTG-TGGTGCAGCTGGTTGAAGACA-ATAGAT
1 CTTGCCTTC-CT-GATTGACAGCGAAGCAGGTCGAAGACACA-A-AC
12355955 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTG-ATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * * *
12355999 CTTGCC-TCTCTCGGTTG-TGGTGCAGCTGGTTGAAGACA-ATAGAT
1 CTTGCCTTC-CT-GATTGACAGCGAAGCAGGTCGAAGACACA-A-AC
12356043 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTG-ATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * * *
12356087 CTTGCC-TCTCTCGGTTG-TGGTGCAGCTGGTTGAAGACA-ATAGAT
1 CTTGCCTTC-CT-GATTGACAGCGAAGCAGGTCGAAGACACA-A-AC
12356131 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTG-ATTGACAGCGAAGCAGGTCGAAGACACAAAC
12356175 CTTGC
1 CTTGC
12356180 TTCTCTCAGT
Statistics
Matches: 196, Mismatches: 49, Indels: 48
0.67 0.17 0.16
Matches are distributed among these distances:
42 3 0.02
43 56 0.29
44 77 0.39
45 57 0.29
46 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (43 bp):
CTTGCCTTCCTGATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:12356004 original size:88 final size:88
Alignment explanation
Indices: 12355855--12356419 Score: 682
Period size: 88 Copynumber: 6.5 Consensus size: 88
12355845 CAGATCAATA
* *
12355855 AAGACAACAGATCTTGCCTTCCTGAATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
12355920 CTCGGTTGTGGTGCAGCTGGTTG
66 CTCGGTTGTGGTGCAGCTGGTTG
*
12355943 AAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
12356008 CTCGGTTGTGGTGCAGCTGGTTG
66 CTCGGTTGTGGTGCAGCTGGTTG
*
12356031 AAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
12356096 CTCGGTTGTGGTGCAGCTGGTTG
66 CTCGGTTGTGGTGCAGCTGGTTG
* *
12356119 AAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCTTCT
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
* * *
12356184 CTCAGTTGTGATGGAGCTGGTTG
66 CTCGGTTGTGGTGCAGCTGGTTG
* * ** * * * * *
12356207 AAGACAAAAGGTCTTGCCTTCCTACATTAACAGTGAAGCA-GACCAA-AAACAAAGCCTTGCCTC
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTC
** * * *
12356270 -CATCGGTTGCAGTGGAGATGGTTA
65 TC-TCGGTTGTGGTGCAGCTGGTTG
* * * * * * *
12356294 AAGA-AGCAGGTCTTGCCTTCTTGCATTAACAACGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC
1 AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTC
** * *
12356356 -CATCGGTTGCAGTGGAGCTGGTTA
65 TC-TCGGTTGTGGTGCAGCTGGTTG
* *
12356380 AAGA-AGCAGATCTTGCC-TCCT-TACATTAACAGCGAAGCAG
1 AAGACAACAGATCTTGCCTTCCTGT--ATTGACAGCGAAGCAG
12356420 ACCAAAAACA
Statistics
Matches: 435, Mismatches: 37, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
85 3 0.01
86 105 0.24
87 36 0.08
88 291 0.67
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (88 bp):
AAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCT
CTCGGTTGTGGTGCAGCTGGTTG
Found at i:12356321 original size:86 final size:86
Alignment explanation
Indices: 12355853--12356485 Score: 449
Period size: 88 Copynumber: 7.3 Consensus size: 86
12355843 AACAGATCAA
* * * * *
12355853 TAAAGACAACAGATCTTGCCTTCCTGA-ATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGC
1 TAAAGA-AGCAGATCTTGCCTT-CTTACATTAACAGCGAAGCAGA-CCAA-AAACAAAGCCTTGC
** *
12355916 CTCTC-TCGGTTGTGGTGCAGCTGGT
62 CTC-CATCGGTTGCAGTGGAGCTGGT
* ** * ** * * * *
12355941 TGAAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCC
1 TAAAGA-AGCAGATCTTGCCTTCTTACATTAACAGCGAAGCA-GACCAA-AAACAAAGCCTTGCC
** *
12356005 TCTC-TCGGTTGTGGTGCAGCTGGT
63 TC-CATCGGTTGCAGTGGAGCTGGT
* ** * ** * * * *
12356029 TGAAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCC
1 TAAAGA-AGCAGATCTTGCCTTCTTACATTAACAGCGAAGCA-GACCAA-AAACAAAGCCTTGCC
** *
12356093 TCTC-TCGGTTGTGGTGCAGCTGGT
63 TC-CATCGGTTGCAGTGGAGCTGGT
* ** * ** * * * * *
12356117 TGAAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCT
1 TAAAGA-AGCAGATCTTGCCTTCTTACATTAACAGCGAAGCA-GACCAA-AAACAAAGCCTTGCC
* *
12356181 TCTC-TCAGTTG-TGATGGAGCTGGT
63 TC-CATCGGTTGCAG-TGGAGCTGGT
* ** * * *
12356205 TGAAGACAAAAGGTCTTGCCTTCCTACATTAACAGTGAAGCAGACCAAAAACAAAGCCTTGCCTC
1 TAAAGA-AGCAGATCTTGCCTTCTTACATTAACAGCGAAGCAGACCAAAAACAAAGCCTTGCCTC
*
12356270 CATCGGTTGCAGTGGAGATGGT
65 CATCGGTTGCAGTGGAGCTGGT
* * * * *
12356292 TAAAGAAGCAGGTCTTGCCTTCTTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCC
1 TAAAGAAGCAGATCTTGCCTTCTTACATTAACAGCGAAGCAGACCAAAAACAAAGCCTTGCCTCC
12356357 ATCGGTTGCAGTGGAGCTGGT
66 ATCGGTTGCAGTGGAGCTGGT
* * *
12356378 TAAAGAAGCAGATCTTGCCTCCTTACATTAACAGCGAAGCAGACCAAAAACAAAGTCTTGCCTTC
1 TAAAGAAGCAGATCTTGCCTTCTTACATTAACAGCGAAGCAGACCAAAAACAAAGCCTTGCCTCC
*
12356443 ATCGGTTGCAGTGGAGCTAGT
66 ATCGGTTGCAGTGGAGCTGGT
*
12356464 TAAAGAAGCAGATATTGCCTTC
1 TAAAGAAGCAGATCTTGCCTTC
12356486 CTAAGAACTA
Statistics
Matches: 495, Mismatches: 44, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
86 175 0.35
87 34 0.07
88 285 0.58
89 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (86 bp):
TAAAGAAGCAGATCTTGCCTTCTTACATTAACAGCGAAGCAGACCAAAAACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTGGT
Found at i:12356395 original size:43 final size:43
Alignment explanation
Indices: 12356348--12356483 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 43
12356338 AAAACAAAGC
12356348 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
* * * * * * *** *
12356391 CTTGCCTCCTTAC-ATTAACAGCGAAGCAGACCAAA-AA-CAAAGT
1 CTTGCCTCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGAAGCAGA-T
* *
12356434 CTTGCCTTCATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
*
12356477 ATTGCCT
1 CTTGCCT
12356484 TCCTAAGAAC
Statistics
Matches: 64, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
42 14 0.22
43 35 0.55
44 15 0.23
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (43 bp):
CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
Found at i:12357940 original size:3 final size:3
Alignment explanation
Indices: 12357932--12357963 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12357922 ATTATTTAGC
12357932 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12357964 TTCCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12358234 original size:23 final size:23
Alignment explanation
Indices: 12358208--12358275 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
12358198 ATGTATATAA
12358208 ATATGCTTTCATACGCCTTTATT
1 ATATGCTTTCATACGCCTTTATT
* * * *
12358231 ATATACTTACATA----TATA-A
1 ATATGCTTTCATACGCCTTTATT
12358249 ATATGCTTTCATACGCCTTTATT
1 ATATGCTTTCATACGCCTTTATT
12358272 ATAT
1 ATAT
12358276 ATACACACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 11 0.34
19 3 0.09
22 3 0.09
23 15 0.47
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.46
Consensus pattern (23 bp):
ATATGCTTTCATACGCCTTTATT
Found at i:12358288 original size:41 final size:41
Alignment explanation
Indices: 12358202--12358300 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
12358192 AAATACATGT
* *
12358202 ATATAAATATGCTTTCATACGCCTTTATTATATACTTACAT
1 ATATAAATATGCTTTCATACGCCTTTATTATATACTCACAC
12358243 ATATAAATATGCTTTCATACGCCTTTATTATATA-TACACAC
1 ATATAAATATGCTTTCATACGCCTTTATTATATACT-CACAC
* *
12358284 ATATATATATACTTTCA
1 ATATAAATATGCTTTCA
12358301 AAAAATATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (41 bp):
ATATAAATATGCTTTCATACGCCTTTATTATATACTCACAC
Found at i:12361008 original size:12 final size:13
Alignment explanation
Indices: 12360984--12361049 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 13
12360974 TAATATTATT
12360984 TTAATAGTTTAATA
1 TTAATA-TTTAATA
12360998 TTAA-ATTTAAT-
1 TTAATATTTAATA
12361009 TTAATATTT-ATA
1 TTAATATTTAATA
* *
12361021 TTAATA-GT-ATT
1 TTAATATTTAATA
12361032 TTAATAATTTAATA
1 TTAAT-ATTTAATA
12361046 TTAA
1 TTAA
12361050 AGTGATTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 14 0.33
12 17 0.40
13 2 0.05
14 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TTAATATTTAATA
Found at i:12361024 original size:17 final size:17
Alignment explanation
Indices: 12360991--12361047 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
12360981 ATTTTAATAG
*
12360991 TTTAATA-TTAAATTTAA
1 TTTAATATTTATA-TTAA
12361008 TTTAATATTTATATTAA
1 TTTAATATTTATATTAA
* *
12361025 --TAGTATTT-TAATAA
1 TTTAATATTTATATTAA
12361039 TTTAATATT
1 TTTAATATT
12361048 AAAGTGATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 6 0.18
17 11 0.33
18 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAATATTTATATTAA
Found at i:12361024 original size:23 final size:25
Alignment explanation
Indices: 12360983--12361050 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 25
12360973 ATAATATTAT
*
12360983 TTTAATAGTTTAATATTAAAT-TTAA
1 TTTAATA-TTTAATATTAAATAGTAA
*
12361008 TTTAATATTT-ATATT-AATAGTAT
1 TTTAATATTTAATATTAAATAGTAA
12361031 TTTAATAATTTAATATTAAA
1 TTTAAT-ATTTAATATTAAA
12361051 GTGATTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 3 0.08
23 13 0.35
24 7 0.19
25 12 0.32
26 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (25 bp):
TTTAATATTTAATATTAAATAGTAA
Found at i:12361038 original size:62 final size:64
Alignment explanation
Indices: 12360972--12361149 Score: 163
Period size: 62 Copynumber: 2.7 Consensus size: 64
12360962 TTATTCAAAA
* *
12360972 AATAATATTATTTTAATAGTTTAATATTAAATTTAATTTAATATTTATATT-A-AT-AGTATTTT
1 AATAATATTATTTTAATA-TTTAATATTAAATTTAATTTAATGTTTATATTAAGATAAATATTTT
* *
12361034 AATAAT-TTAATATTAAAGTGATTATCTGAATATTAAATTTAATTTAATGTTTATCTTGAAGATA
1 AATAATATT-AT-TTTAA-T-A-T-T-T-AATATTAAATTTAATTTAATGTTTATATT-AAGATA
12361098 AATATTTT
57 AATATTTT
* *
12361106 -ATTATATTA--ATAATATTTAATATTAAATTTAATTTAATGTTTAT
1 AATAATATTATTTTAATATTTAATATTAAATTTAATTTAATGTTTAT
12361150 CTTGTAGATT
Statistics
Matches: 96, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
61 2 0.02
62 34 0.35
63 5 0.05
64 2 0.02
65 3 0.03
66 2 0.02
67 2 0.02
68 29 0.30
70 1 0.01
71 7 0.07
72 9 0.09
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (64 bp):
AATAATATTATTTTAATATTTAATATTAAATTTAATTTAATGTTTATATTAAGATAAATATTTT
Found at i:12361920 original size:6 final size:6
Alignment explanation
Indices: 12361911--12362155 Score: 262
Period size: 6 Copynumber: 41.3 Consensus size: 6
12361901 ATTTCAATTT
* * * * *
12361911 TTCTTC TTCTTC TTCTTC TTATTT TTCTTC TTTTTC TTCTTT TTCTCC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * * * * * * * *
12361959 TTCTCC TTCTCC TTCTCC TCCTCC TCCTCC TCCTCC TCCTTC TCCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * *
12362007 -TCTT- TT-TTC TTCTTC TTTTTC TTCTTC TCCTTC TCCTTC TTCTTT
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
*
12362052 TTCTTC TTCTTC TTCTTT TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
*
12362100 TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
*
12362148 TCCTTC TT
1 TTCTTC TT
12362156 AACTTTATCA
Statistics
Matches: 212, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
4 2 0.01
5 6 0.03
6 204 0.96
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCTTC
Found at i:12361923 original size:9 final size:9
Alignment explanation
Indices: 12361911--12362155 Score: 262
Period size: 9 Copynumber: 27.6 Consensus size: 9
12361901 ATTTCAATTT
12361911 TTCTTCTTC
1 TTCTTCTTC
12361920 TTCTTCTTC
1 TTCTTCTTC
* *
12361929 TTATTTTTC
1 TTCTTCTTC
*
12361938 TTCTTTTTC
1 TTCTTCTTC
*
12361947 TTCTTTTTC
1 TTCTTCTTC
* *
12361956 TCCTTCTCC
1 TTCTTCTTC
*
12361965 TTCTCCTTC
1 TTCTTCTTC
* * *
12361974 TCCTCCTCC
1 TTCTTCTTC
* * *
12361983 TCCTCCTCC
1 TTCTTCTTC
* *
12361992 TCCTCCTTC
1 TTCTTCTTC
*
12362001 TCCTTC-TC
1 TTCTTCTTC
12362009 TT-TT-TTC
1 TTCTTCTTC
*
12362016 TTCTTCTTT
1 TTCTTCTTC
12362025 TTCTTCTTC
1 TTCTTCTTC
* *
12362034 TCCTTCTCC
1 TTCTTCTTC
*
12362043 TTCTTCTTT
1 TTCTTCTTC
12362052 TTCTTCTTC
1 TTCTTCTTC
*
12362061 TTCTTCTTT
1 TTCTTCTTC
12362070 TTCTTCTTC
1 TTCTTCTTC
12362079 TTCTTCTTC
1 TTCTTCTTC
12362088 TTCTTCTTC
1 TTCTTCTTC
12362097 TTCTTCTTC
1 TTCTTCTTC
*
12362106 TTTTTCTTC
1 TTCTTCTTC
12362115 TTCTTCTTC
1 TTCTTCTTC
12362124 TTCTTCTTC
1 TTCTTCTTC
12362133 TTCTTCTTC
1 TTCTTCTTC
*
12362142 TTCTTCTCC
1 TTCTTCTTC
12362151 TTCTT
1 TTCTT
12362156 AACTTTATCA
Statistics
Matches: 206, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
7 6 0.03
8 5 0.02
9 195 0.95
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:12362016 original size:15 final size:15
Alignment explanation
Indices: 12361997--12362155 Score: 121
Period size: 15 Copynumber: 10.8 Consensus size: 15
12361987 CCTCCTCCTC
12361997 CTTCTCCTTCTCTTTT
1 CTTCTCCTTCT-TTTT
*
12362013 -TTCTTCTTCTTTTT
1 CTTCTCCTTCTTTTT
* * * *
12362027 CTTCTTCTCCTTCTC
1 CTTCTCCTTCTTTTT
*
12362042 CTTCTTCTT-TTTCTT
1 CTTCTCCTTCTTT-TT
*
12362057 CTTCTTCTTCTTTTT
1 CTTCTCCTTCTTTTT
* *
12362072 CTTCTTCTTCTTCTT
1 CTTCTCCTTCTTTTT
* *
12362087 CTTCTTCTTCTTCTT
1 CTTCTCCTTCTTTTT
*
12362102 CTTCT--TT-TTCTT
1 CTTCTCCTTCTTTTT
* *
12362114 CTTCTTCTTCTTCTT
1 CTTCTCCTTCTTTTT
* *
12362129 CTTCTTCTTCTTCTT
1 CTTCTCCTTCTTTTT
12362144 CTTCTCCTTCTT
1 CTTCTCCTTCTT
12362156 AACTTTATCA
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.08
13 2 0.02
14 8 0.06
15 105 0.82
16 3 0.02
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTCCTTCTTTTT
Found at i:12362325 original size:34 final size:30
Alignment explanation
Indices: 12362263--12362321 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
12362253 GATTTGGACT
12362263 CTCGGTCTTTCTTTATTATTATTTACTTAG
1 CTCGGTCTTTCTTTATTATTATTTACTTAG
12362293 CTCGGTCTTTCTTTATTATTATTTACTTA
1 CTCGGTCTTTCTTTATTATTATTTACTTA
12362322 CTTAAGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (30 bp):
CTCGGTCTTTCTTTATTATTATTTACTTAG
Found at i:12370484 original size:45 final size:45
Alignment explanation
Indices: 12370420--12370506 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
12370410 CAGATACTCG
* *
12370420 GTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCA
* *
12370465 GTGGAATCAACATATAGCAACCACCTTACTAATTAATGATGT
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
12370507 TTGGTTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (45 bp):
GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:12370577 original size:51 final size:51
Alignment explanation
Indices: 12370517--12370700 Score: 196
Period size: 51 Copynumber: 3.6 Consensus size: 51
12370507 TTGGTTCATA
* *
12370517 TAGTAGCCTGCACATAGTACTATACATGTGA-CCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTAACCCA-TACCATCCGATACACG
* * * * * * * *
12370568 TAGTAGCCTGCACATAGTACTACACACGTAATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTAACCCATACCATCCGATACACG
**
12370619 TAGTAGCCTGCACATAGTACTACACATGCCACCCAT--CATTCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTAACCCATACCA-TCCGATACACG
* *
12370669 -AATAGCCTGCACATAGTACTACACACGTAACC
1 TAGTAGCCTGCACATAGTACTACACATGTAACC
12370701 ATCACTTTCA
Statistics
Matches: 108, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 29 0.27
50 8 0.07
51 69 0.64
52 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTAACCCATACCATCCGATACACG
Found at i:12370698 original size:100 final size:101
Alignment explanation
Indices: 12370516--12370698 Score: 282
Period size: 100 Copynumber: 1.8 Consensus size: 101
12370506 TTTGGTTCAT
* ** *
12370516 ATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGCCACCATTA-CATCCGATACACGTAATAGCCTGCAC
12370581 ATAGTACTACACACGTAATCGAAACTATCCGGTACGC
65 ATAGTACTACACACGTAATCGAAACTATCCGGTACGC
12370618 ATAGTAGCCTGCACATAGTACTACACATGCCACCCA-T-CATTCCGATACACG-AATAGCCTGCA
1 ATAGTAGCCTGCACATAGTACTACACATGCCA-CCATTACA-TCCGATACACGTAATAGCCTGCA
12370680 CATAGTACTACACACGTAA
64 CATAGTACTACACACGTAA
12370699 CCATCACTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
100 31 0.41
101 11 0.15
102 30 0.40
103 3 0.04
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.22
Consensus pattern (101 bp):
ATAGTAGCCTGCACATAGTACTACACATGCCACCATTACATCCGATACACGTAATAGCCTGCACA
TAGTACTACACACGTAATCGAAACTATCCGGTACGC
Found at i:12373842 original size:43 final size:41
Alignment explanation
Indices: 12373784--12373975 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 41
12373774 GTGATACTGA
* *
12373784 GAATCAGTACATAGCAACCCCTTTCACAATCAAAGATACGGTG
1 GAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATACGG-G
* * * * **
12373827 GAATCAGCACTTAGCAACCACGTTTATATTTAGTGATACGGG
1 GAATCAGCACTTAGCAACC-CCTTTACAATCAAAGATACGGG
* * *
12373869 GAATCAGCACATAGCAACCCCTTTCACAGTCAAATATACGGTG
1 GAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATACGG-G
* * * *
12373912 GAATCAGCACTTAGCAACCATCTTTAGAATCAATA-ATCCAGG
1 GAATCAGCACTTAGCAACC-CCTTTACAATCAA-AGATACGGG
12373954 GAATCAGCACTTAGCAACCCCT
1 GAATCAGCACTTAGCAACCCCT
12373976 CGAGGAATTT
Statistics
Matches: 121, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
41 6 0.05
42 49 0.40
43 57 0.47
44 9 0.07
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
GAATCAGCACTTAGCAACCCCTTTACAATCAAAGATACGGG
Found at i:12373881 original size:85 final size:84
Alignment explanation
Indices: 12373738--12373975 Score: 298
Period size: 85 Copynumber: 2.8 Consensus size: 84
12373728 ATCCGTTACT
* * * * * * *
12373738 CGGTGGATTCAACACTTAGCGACCACCTTAAATTCAGTGATACTGAGAATCAGTACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACTTTAAATTCAGTGATACAGGGAATCAGCACATAGCAACC
12373803 CCTTTCACAATCAAAGATA
66 CCTTTCACAATCAAAGATA
* * *
12373822 CGGTGGAATCAGCACTTAGCAACCACGTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCAC-TTTAAATTCAGTGATACAGGGAATCAGCACATAGCAAC
* *
12373887 CCCTTTCACAGTCAAATATA
65 CCCTTTCACAATCAAAGATA
* * * *
12373907 CGGTGGAATCAGCACTTAGCAACCATCTTTAGAA-TCAATAATCCAGGGAATCAGCACTTAGCAA
1 CGGTGGAATCAGCACTTAGCAACCA-CTTTA-AATTCAGTGATACAGGGAATCAGCACATAGCAA
12373971 CCCCT
64 CCCCT
12373976 CGAGGAATTT
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
84 23 0.17
85 108 0.81
86 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACTTTAAATTCAGTGATACAGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGATA
Found at i:12379051 original size:67 final size:70
Alignment explanation
Indices: 12378876--12379180 Score: 214
Period size: 70 Copynumber: 4.4 Consensus size: 70
12378866 CATCGAAAAT
* ** * ** * * * *
12378876 CCAAACAGTTAGCGAGAGTTAAAAGCTCCCAGTTGTCA-TCTTTTGGCTCACAAGTTTAATACCG
1 CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAACTATCATTC-TAAGGCTCACAGGCTCAATACTG
*
12378940 C-ATCC
65 CAAGCC
* * * * * *
12378945 CCTAAATATTTAGTGAGAGTTAAAAACTC-CTAGA-TATCATTCTAAGGCTCATAGGTTC-A-A-
1 CC-AAACAGTTAGCGAGAGTTAAAAGCTCTC-A-ACTATCATTCTAAGGCTCACAGGCTCAATAC
12379005 TGC-AGCC
63 TGCAAGCC
* * * *
12379012 CGCAAACAGTTAGCGAGAGTTAAAAGTTCTCAGCTATCATTCTAAGACTCGCAGGCTCAATACTG
1 C-CAAACAGTTAGCGAGAGTTAAAAGCTCTCAACTATCATTCTAAGGCTCACAGGCTCAATACTG
12379077 CAAGCC
65 CAAGCC
* * * * * * *
12379083 CCAAATAGTTAGCGAGAGTTAAAAGCTCTTAACGATCATTCTATGGCTCGCATGCTCAATACCG-
1 CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAACTATCATTCTAAGGCTCACAGGCTCAATACTGC
*
12379147 TAGTCC
66 AAG-CC
* *
12379153 CCTAACAATTAGCGAGAGTTAAAAGCTC
1 CCAAACAGTTAGCGAGAGTTAAAAGCTC
12379181 CTAGCTGTCA
Statistics
Matches: 188, Mismatches: 36, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
67 48 0.26
68 4 0.02
69 7 0.04
70 122 0.65
71 7 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (70 bp):
CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAACTATCATTCTAAGGCTCACAGGCTCAATACTGC
AAGCC
Found at i:12379105 original size:70 final size:70
Alignment explanation
Indices: 12379007--12379324 Score: 277
Period size: 70 Copynumber: 4.5 Consensus size: 70
12378997 AGGTTCAATG
* * *
12379007 CAGCCCGCAAACAGTTAGCGAGAGTTAAAAG-TTCTCAGCTATCATTCTAAGACTCGCAGGCTCA
1 CAGCCC-CAAATAGTTAGCGAGAGTTAAAAGCTCCT-AGCTATCATTCTAAGGCTCGCAGGCTCA
12379071 ATACTGCA
64 ATACT-CA
* * * * *
12379079 -AGCCCCAAATAGTTAGCGAGAGTTAAAAGCTCTTAACGATCATTCTATGGCTCGCATGCTCAAT
1 CAGCCCCAAATAGTTAGCGAGAGTTAAAAGCTCCTAGCTATCATTCTAAGGCTCGCAGGCTCAAT
*
12379143 AC-CG
66 ACTCA
* * * * * * * * *
12379147 TAGTCCCCTAACAATTAGCGAGAGTTAAAAGCTCCTAGCTGTCATTCTAATGCTTGTAGGTTCAA
1 CAG-CCCCAAATAGTTAGCGAGAGTTAAAAGCTCCTAGCTATCATTCTAAGGCTCGCAGGCTCAA
12379212 TA-TCA
65 TACTCA
* * ** * * * *
12379217 TAGCCATCAAATAGTTAGAAAGAGTTAAAAGCTCCTAGCTCTTATTTTAAGGCTCGCAGGTTCAA
1 CAGCC-CCAAATAGTTAGCGAGAGTTAAAAGCTCCTAGCTATCATTCTAAGGCTCGCAGGCTCAA
12379282 TAC-CA
65 TACTCA
* * **
12379287 CACCACCCAAATAGTTAACGAGAGCCAAAAGCTCCTAG
1 CAGC-CCCAAATAGTTAGCGAGAGTTAAAAGCTCCTAG
12379325 TTGTTTTTTT
Statistics
Matches: 196, Mismatches: 43, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
68 1 0.01
69 4 0.02
70 183 0.93
71 8 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (70 bp):
CAGCCCCAAATAGTTAGCGAGAGTTAAAAGCTCCTAGCTATCATTCTAAGGCTCGCAGGCTCAAT
ACTCA
Found at i:12379273 original size:140 final size:140
Alignment explanation
Indices: 12379016--12379285 Score: 314
Period size: 140 Copynumber: 1.9 Consensus size: 140
12379006 GCAGCCCGCA
* *
12379016 AACAGTTAGCGAGAGTTAAAAGTTCTCAGCTATCATTCTAAGACTCGCAGGCTCAATACTGCAAG
1 AACAATTAGCGAGAGTTAAAAGTCCTCAGCTATCATTCTAAGACTCGCAGGCTCAATACTGCAAG
** * * *
12379081 CCCCAAATAGTTAGCGAGAGTTAAAAGCTCTTAACGATCATTCTATGGCTCGCATGCTCAATACC
66 CCCCAAATAGTTAGAAAGAGTTAAAAGCTCCTAACGATCATTCTAAGGCTCGCAGGCTCAATACC
12379146 GTAGTCCCCT
131 GTAGTCCCCT
* * * *
12379156 AACAATTAGCGAGAGTTAAAAGCTCCT-AGCTGTCATTCTAATG-CTTGTAGGTTCAATA-T-CA
1 AACAATTAGCGAGAGTTAAAAG-TCCTCAGCTATCATTCTAA-GACTCGCAGGCTCAATACTGCA
* * ** * * *
12379217 TAGCCATCAAATAGTTAGAAAGAGTTAAAAGCTCCTAGCTCTTATTTTAAGGCTCGCAGGTTCAA
64 -AGCC-CCAAATAGTTAGAAAGAGTTAAAAGCTCCTAACGATCATTCTAAGGCTCGCAGGCTCAA
12379282 TACC
127 TACC
12379286 ACACCACCCA
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
138 2 0.02
139 5 0.05
140 97 0.90
141 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (140 bp):
AACAATTAGCGAGAGTTAAAAGTCCTCAGCTATCATTCTAAGACTCGCAGGCTCAATACTGCAAG
CCCCAAATAGTTAGAAAGAGTTAAAAGCTCCTAACGATCATTCTAAGGCTCGCAGGCTCAATACC
GTAGTCCCCT
Found at i:12379319 original size:210 final size:206
Alignment explanation
Indices: 12378933--12379320 Score: 451
Period size: 210 Copynumber: 1.9 Consensus size: 206
12378923 TCACAAGTTT
*
12378933 AATACCGCATCCCCTAAATATTTAGTGAGAGTTAAAAACTCCTAGATATCATTCTAAGGCTCATA
1 AATACCGCATCCCCTAAATATTTAGCGAGAGTTAAAAACTCCTAGATATCATTCTAAGGCTCATA
* ** *
12378998 GGTTCAATGCAGCCCGCAAACAGTTAGCGAGAGTTAAAAGTTCTCAGCTATCATTCTAAGACTCG
66 GGTTCAATGCAGCCAGCAAACAGTTAGAAAGAGTTAAAAGTCCTCAGCTATCATTCTAAGACTCG
* * **
12379063 CAGGCTCAATACTGCAAGCCCCAAATAGTTAGCGAGAGTTAAAAGCTCTTAACGATCATTCTATG
131 CAGGCTCAATAC-GCAACCCCCAAATAGTTAACGAGAGCCAAAAGCTCTTAACGATCATTCTATG
12379128 GCTCGCATGCTC
195 GCTCGCATGCTC
* * * * * **
12379140 AATACCGTAGTCCCCTAACA-A-TTAGCGAGAGTTAAAAGCTCCTAGCTGTCATTCTAATGCTTG
1 AATACCGCA-TCCCCTAA-ATATTTAGCGAGAGTTAAAAACTCCTAGATATCATTCTAAGGCTCA
* * * * * *
12379203 TAGGTTCAATATCATAGCCATCAAATAGTTAGAAAGAGTTAAAAGCTCCT-AGCTCTTATTTTAA
64 TAGGTTCAAT-GC--AGCCAGCAAACAGTTAGAAAGAGTTAAAAG-TCCTCAGCTATCATTCTAA
* *
12379267 GGCTCGCAGGTTCAATAC-CACACCACCCAAATAGTTAACGAGAGCCAAAAGCTC
125 GACTCGCAGGCTCAATACGCA-ACC-CCCAAATAGTTAACGAGAGCCAAAAGCTC
12379321 CTAGTTGTTT
Statistics
Matches: 149, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
207 53 0.36
208 12 0.08
209 3 0.02
210 78 0.52
211 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (206 bp):
AATACCGCATCCCCTAAATATTTAGCGAGAGTTAAAAACTCCTAGATATCATTCTAAGGCTCATA
GGTTCAATGCAGCCAGCAAACAGTTAGAAAGAGTTAAAAGTCCTCAGCTATCATTCTAAGACTCG
CAGGCTCAATACGCAACCCCCAAATAGTTAACGAGAGCCAAAAGCTCTTAACGATCATTCTATGG
CTCGCATGCTC
Found at i:12379452 original size:58 final size:58
Alignment explanation
Indices: 12379379--12379543 Score: 186
Period size: 58 Copynumber: 2.8 Consensus size: 58
12379369 TCTCGAATTT
* * * * * *
12379379 ACATTCCCAGCTGAGTATCTCAGAAAATATGCCTAAGTTCAAAATAGCTCGAGGATTC
1 ACATTCTCAGCTGAGTATATCAGAAAATATGCCTAACTTCAAAACAACTCAAGGATTC
* * *
12379437 ACATTCTCAGCTGAGTGTTTCAGAAAATATGCCTAACTTCAAAACAACTCAAGGATTT
1 ACATTCTCAGCTGAGTATATCAGAAAATATGCCTAACTTCAAAACAACTCAAGGATTC
* * * * * * *
12379495 ATATTCTCTGTTGATTATATCAGAAAATAAGCCTAAATTTAAAACAACT
1 ACATTCTCAGCTGAGTATATCAGAAAATATGCCTAACTTCAAAACAACT
12379544 TGCGGATTCA
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 90 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (58 bp):
ACATTCTCAGCTGAGTATATCAGAAAATATGCCTAACTTCAAAACAACTCAAGGATTC
Found at i:12383121 original size:47 final size:49
Alignment explanation
Indices: 12383034--12383145 Score: 156
Period size: 50 Copynumber: 2.2 Consensus size: 49
12383024 AAAATTCTAT
* *
12383034 CTTCACGTCTCTACCCTGCTGCTATTATTTTTTTGGCAACTGTTTTGTTG-
1 CTTCACGTCTCTACCCTGCTGC--TTATTTTTTCGGCAACTGCTTTGTTGC
12383084 CTTCACGTCTCTACCCTGCTGC-TATTTTTTCGGCAACTGCTTTGTTGCC
1 CTTCACGTCTCTACCCTGCTGCTTATTTTTTCGGCAACTGCTTTGTTG-C
12383133 TCTTCACGTCTCT
1 -CTTCACGTCTCT
12383146 TTGCAACCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
47 23 0.40
50 34 0.60
ACGTcount: A:0.11, C:0.29, G:0.15, T:0.45
Consensus pattern (49 bp):
CTTCACGTCTCTACCCTGCTGCTTATTTTTTCGGCAACTGCTTTGTTGC
Found at i:12383256 original size:60 final size:60
Alignment explanation
Indices: 12383131--12383279 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 60
12383121 TGCTTTGTTG
* * * ** *
12383131 CCTCTTCACGTCTCTTTGCAACCCCTACTGCTATTACTTTTTTTGGCAACCTTGTTGCTG
1 CCTCTTCACATCTCTCTGCAACCCCTACTGCTATTACTTTTTTTGACAACCTACTTGCTA
*
12383191 CCTCTTCACATCTCTCTGCAACCCCTGCTGCTATTA-TTTTTTTCGACAA-CTACTTAGCTA
1 CCTCTTCACATCTCTCTGCAACCCCTACTGCTATTACTTTTTTT-GACAACCTACTT-GCTA
* * *
12383251 TCTCTTCACATTTCTCTGTAACCCCTACT
1 CCTCTTCACATCTCTCTGCAACCCCTACT
12383280 AATTTGCTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 11 0.14
60 65 0.86
ACGTcount: A:0.17, C:0.34, G:0.09, T:0.40
Consensus pattern (60 bp):
CCTCTTCACATCTCTCTGCAACCCCTACTGCTATTACTTTTTTTGACAACCTACTTGCTA
Found at i:12383552 original size:60 final size:61
Alignment explanation
Indices: 12383450--12383580 Score: 201
Period size: 60 Copynumber: 2.2 Consensus size: 61
12383440 CACGTCTCTG
* * ** *
12383450 CCTTGCTGCTATTATTTTTTTTTGGCAACTGCTTTGTTGCCTCTTCACGTCTCTTTGCAAC
1 CCTTGCTGCTATTATTTTTTTCTGGCAACTACTTTACTGCCTCTTCACGTCTCTCTGCAAC
*
12383511 CCTTGCTGCTATTA-TTTTTTCTGGCAACTACTTTACTGCCTCTTCACGTCTCTCTGTAAC
1 CCTTGCTGCTATTATTTTTTTCTGGCAACTACTTTACTGCCTCTTCACGTCTCTCTGCAAC
12383571 CCTTGCTGCT
1 CCTTGCTGCT
12383581 TTGCTTTGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 50 0.78
61 14 0.22
ACGTcount: A:0.12, C:0.29, G:0.14, T:0.45
Consensus pattern (61 bp):
CCTTGCTGCTATTATTTTTTTCTGGCAACTACTTTACTGCCTCTTCACGTCTCTCTGCAAC
Found at i:12389923 original size:15 final size:15
Alignment explanation
Indices: 12389905--12389937 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12389895 TGAAAATGAA
12389905 TAATA-TTATCATAAT
1 TAATATTTATCA-AAT
12389920 TAATATTTATCAAAT
1 TAATATTTATCAAAT
12389935 TAA
1 TAA
12389938 AATTGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTTATCAAAT
Found at i:12400412 original size:12 final size:11
Alignment explanation
Indices: 12400388--12400460 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 11
12400378 AAGTTTATAG
12400388 TTTTA-AATTT
1 TTTTATAATTT
12400398 TTTTATAACTTT
1 TTTTATAA-TTT
12400410 TTTTATAAATTT
1 TTTTAT-AATTT
12400422 TGTTTATAA---
1 T-TTTATAATTT
*
12400431 TTTTATGATTT
1 TTTTATAATTT
12400442 TTTTAATAATTT
1 TTTT-ATAATTT
*
12400454 TTATATA
1 TTTTATA
12400461 TTAAAAGGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
8 6 0.12
9 1 0.02
10 5 0.10
11 9 0.17
12 24 0.46
13 7 0.13
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:12400455 original size:21 final size:22
Alignment explanation
Indices: 12400391--12400458 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
12400381 TTTATAGTTT
12400391 TAAATTTT-TTTATAACTTTTTTTA
1 TAAATTTTGTTTATAA---TTTTTA
12400415 TAAATTTTGTTTATAA-TTTTA
1 TAAATTTTGTTTATAATTTTTA
*
12400436 T-GATTTT-TTTAATAATTTTTA
1 TAAATTTTGTTT-ATAATTTTTA
12400457 TA
1 TA
12400459 TATTAAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.08
20 9 0.23
21 12 0.31
24 8 0.21
25 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (22 bp):
TAAATTTTGTTTATAATTTTTA
Found at i:12402920 original size:25 final size:25
Alignment explanation
Indices: 12402868--12402922 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
12402858 AGCTCTTATA
*
12402868 AGCTTCTCGATATTCAGCTCGCATG
1 AGCTTCTCGATATTCAGCTCGCAAG
* * *
12402893 AGCTTCTCGTTATTCAGCTTGGAAG
1 AGCTTCTCGATATTCAGCTCGCAAG
12402918 AGCTT
1 AGCTT
12402923 ACTGTTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (25 bp):
AGCTTCTCGATATTCAGCTCGCAAG
Found at i:12408752 original size:15 final size:15
Alignment explanation
Indices: 12408732--12408777 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12408722 ATTTGCTTAT
12408732 ATTTATTTATTTTAA
1 ATTTATTTATTTTAA
*
12408747 ATTTA-TTATTTTTTA
1 ATTTATTTA-TTTTAA
*
12408762 AGTT-TTTATTTTAA
1 ATTTATTTATTTTAA
12408776 AT
1 AT
12408778 AAAATTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTTATTTATTTTAA
Found at i:12418243 original size:18 final size:18
Alignment explanation
Indices: 12418220--12418256 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12418210 ACTCTGTCTC
12418220 TTCTTCGCC-TCCTCCGCT
1 TTCTTCGCCAT-CTCCGCT
12418238 TTCTTCGCCATCTCCGCT
1 TTCTTCGCCATCTCCGCT
12418256 T
1 T
12418257 GCTCCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.03, C:0.46, G:0.11, T:0.41
Consensus pattern (18 bp):
TTCTTCGCCATCTCCGCT
Found at i:12420248 original size:31 final size:32
Alignment explanation
Indices: 12420190--12420250 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
12420180 GTCAATTGTA
12420190 ATTTTTTTCCTATAAATACCAGATCTTTCTTC
1 ATTTTTTTCCTATAAATACCAGATCTTTCTTC
12420222 ATTTTTTTCACT-TAAAT-CCA-AGTCTTTCT
1 ATTTTTTTC-CTATAAATACCAGA-TCTTTCT
12420251 ATTTTCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.04
31 10 0.37
32 14 0.52
33 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTTTTTTCCTATAAATACCAGATCTTTCTTC
Found at i:12424738 original size:20 final size:20
Alignment explanation
Indices: 12424713--12424767 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
12424703 ACGAGTTAAA
* *
12424713 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
12424733 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
12424753 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
12424768 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:12425140 original size:51 final size:51
Alignment explanation
Indices: 12425081--12425182 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
12425071 ACAAATAAGT
12425081 ATGTCATTTTAGAGTATTATCATATTCCCCCTACTTAGCCCATGTTTGCCC
1 ATGTCATTTTAGAGTATTATCATATTCCCCCTACTTAGCCCATGTTTGCCC
12425132 ATGTCATTTTAGAGTATTATCATATTCCCCCTACTTAGCCCATGTTTGCCC
1 ATGTCATTTTAGAGTATTATCATATTCCCCCTACTTAGCCCATGTTTGCCC
12425183 TCAAGTATGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (51 bp):
ATGTCATTTTAGAGTATTATCATATTCCCCCTACTTAGCCCATGTTTGCCC
Found at i:12425471 original size:15 final size:15
Alignment explanation
Indices: 12425453--12425482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12425443 TTTTCCTTCG
*
12425453 TTTTTTTATTTTTTA
1 TTTTATTATTTTTTA
12425468 TTTTATTATTTTTTA
1 TTTTATTATTTTTTA
12425483 ATTCTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTATTTTTTA
Found at i:12426981 original size:24 final size:24
Alignment explanation
Indices: 12426954--12427016 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
12426944 AAACAATGGC
*
12426954 TGGAGATGAAGATGTAG-ACGAGGG
1 TGGAGATGAAGATG-AGTACAAGGG
*
12426978 TGGAAATGAAGATGAGTACAAGGG
1 TGGAGATGAAGATGAGTACAAGGG
* *
12427002 TCGAGGTGAAGATGA
1 TGGAGATGAAGATGA
12427017 AGAAGATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.37, C:0.05, G:0.41, T:0.17
Consensus pattern (24 bp):
TGGAGATGAAGATGAGTACAAGGG
Found at i:12433650 original size:152 final size:152
Alignment explanation
Indices: 12433425--12433716 Score: 530
Period size: 152 Copynumber: 1.9 Consensus size: 152
12433415 ATTGTTGATG
*
12433425 AGTAAGGATATTGAAAGGTGTAAGAAAAGTAGAGTGTGAGTGAAAGGCCCTACATAGGGGTTGCA
1 AGTAAGGATATTGAAACGTGTAAGAAAAGTAGAGTGTGAGTGAAAGGCCCTACATAGGGGTTGCA
* *
12433490 TGTAGTTGAAACGTTAGTAAACTATCTATTACTGAAGATTCTAATAGAAATTTCATGATCTTGTA
66 TGTAGTTGAAACATTAGTAAACTATCTATTAATGAAGATTCTAATAGAAATTTCATGATCTTGTA
12433555 CGCAGTTACTATCTATTAATGA
131 CGCAGTTACTATCTATTAATGA
*
12433577 AGTAAGGATATTGAAACGTGTAAGAAAAGTAGAGTGTGAGTGAAAGGCCCTGCATAGGGGTTGCA
1 AGTAAGGATATTGAAACGTGTAAGAAAAGTAGAGTGTGAGTGAAAGGCCCTACATAGGGGTTGCA
**
12433642 TGTAGTTGAAACATTAGTAAACTATCTATTAATGAAGATTCTAATAGAAATTTTGTGATCTTGTA
66 TGTAGTTGAAACATTAGTAAACTATCTATTAATGAAGATTCTAATAGAAATTTCATGATCTTGTA
12433707 CGCAGTTACT
131 CGCAGTTACT
12433717 GCTACTGGAT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 134 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (152 bp):
AGTAAGGATATTGAAACGTGTAAGAAAAGTAGAGTGTGAGTGAAAGGCCCTACATAGGGGTTGCA
TGTAGTTGAAACATTAGTAAACTATCTATTAATGAAGATTCTAATAGAAATTTCATGATCTTGTA
CGCAGTTACTATCTATTAATGA
Found at i:12434392 original size:25 final size:25
Alignment explanation
Indices: 12434364--12434426 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
12434354 GTGATGAGTC
12434364 ACTTGTAAAGCCTTTGTGGCAATTT
1 ACTTGTAAAGCCTTTGTGGCAATTT
** *
12434389 ACTTGGGAAGCCTTTGTGGCAGTTT
1 ACTTGTAAAGCCTTTGTGGCAATTT
*
12434414 ACCTGTAAAGCCT
1 ACTTGTAAAGCCT
12434427 ATATGACGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (25 bp):
ACTTGTAAAGCCTTTGTGGCAATTT
Found at i:12436671 original size:24 final size:24
Alignment explanation
Indices: 12436634--12436688 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
12436624 GACACACGGT
* * *
12436634 CGTGTGGCAGCCCGTGTCTCAGGC
1 CGTGTGACAACCCGTGTCCCAGGC
12436658 CGTGTGACAACCCGTGTCCCAGGC
1 CGTGTGACAACCCGTGTCCCAGGC
12436682 CGTGTGA
1 CGTGTGA
12436689 TCCATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.33, G:0.35, T:0.20
Consensus pattern (24 bp):
CGTGTGACAACCCGTGTCCCAGGC
Found at i:12440691 original size:16 final size:17
Alignment explanation
Indices: 12440662--12440695 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
12440652 CAATTCGGTC
12440662 CAAAATTCATACTTTTG
1 CAAAATTCATACTTTTG
12440679 CAAAATT-ATACTTTTG
1 CAAAATTCATACTTTTG
12440695 C
1 C
12440696 CCTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
CAAAATTCATACTTTTG
Found at i:12444695 original size:3 final size:3
Alignment explanation
Indices: 12444687--12444752 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
12444677 ATTATTTAGT
* * *
12444687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTG TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
12444735 TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
12444753 ATTTTATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12444759 original size:9 final size:10
Alignment explanation
Indices: 12444687--12444760 Score: 61
Period size: 9 Copynumber: 7.8 Consensus size: 10
12444677 ATTATTTAGT
12444687 TTATTATT-A
1 TTATTATTAA
12444696 TTATTATT-A
1 TTATTATTAA
12444705 TTATTATT-A
1 TTATTATTAA
*
12444714 TTATTATTAGTG
1 TTATTATTA--A
*
12444726 TTATTA-TCA
1 TTATTATTAA
12444735 TTATTATT-A
1 TTATTATTAA
*
12444744 CTATTATTAA
1 TTATTATTAA
12444754 TT-TTATT
1 TTATTATT
12444761 TTCCTTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
9 45 0.82
10 3 0.05
11 1 0.02
12 6 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
TTATTATTAA
Found at i:12445020 original size:29 final size:30
Alignment explanation
Indices: 12444961--12445020 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
12444951 TTTACGAATA
* * *
12444961 TATATACATACTTACATGTTTTTAGAAACTT
1 TATATACATAC-TACATGTATATACAAACTT
*
12444992 TATATACATAC-ACATGTATATACACACTT
1 TATATACATACTACATGTATATACAAACTT
12445021 ACATAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
TATATACATACTACATGTATATACAAACTT
Found at i:12446236 original size:18 final size:18
Alignment explanation
Indices: 12446201--12446239 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12446191 TAATTATGTG
*
12446201 AATTCAAATTTCAAAATA
1 AATTCAAATTCCAAAATA
12446219 AATT-AAATTCCAATAATA
1 AATTCAAATTCCAA-AATA
12446237 AAT
1 AAT
12446240 ATTGGAATAG
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:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTCAAATTCCAAAATA
Found at i:12465332 original size:51 final size:50
Alignment explanation
Indices: 12465254--12465440 Score: 239
Period size: 51 Copynumber: 3.7 Consensus size: 50
12465244 CATGTGAACT
* * * * *
12465254 CATGTGTAGTACTATGTGTAGGATACTATGAGTATAAGATATTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATATTT-TGGTCA
*
12465305 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATAGCTTTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATA-TTTTGGTCA
* * * * *
12465356 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGATATTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGAT-ATTTTGGTCA
*
12465407 CATGTGTAGTACTAAGTGTAGGCTACTATGTGTA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTA
12465441 CCGGATAGCA
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
51 115 0.97
52 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATATTTTGGTCA
Found at i:12465432 original size:102 final size:102
Alignment explanation
Indices: 12465256--12465458 Score: 282
Period size: 102 Copynumber: 2.0 Consensus size: 102
12465246 TGTGAACTCA
* * * *
12465256 TGTGTAGTACTATGTGTAGGATACTATGAGTATAAGATATTTATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGCAGGATACTACGAGTACAAGATATATATGGTCACATGTGTAGTACTAAG
* * *
12465321 TGCAGGCTACTATGTGTATCAGATAGCTTTGGTCACG
66 TGCAGGCTACTATGTGTACCAGATAGCATTGATCACG
* * *
12465358 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGATAT-TGGTCACATGTGTAGTACTAA
1 TGTGTAGTACTATGTGCAGGATACTACGAGTACAAGAT-ATATATGGTCACATGTGTAGTACTAA
* *
12465422 GTGTAGGCTACTATGTGTACCGGATAGCATTGATCAC
65 GTGCAGGCTACTATGTGTACCAGATAGCATTGATCAC
12465459 AAGGGTGGTG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 85 0.97
103 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (102 bp):
TGTGTAGTACTATGTGCAGGATACTACGAGTACAAGATATATATGGTCACATGTGTAGTACTAAG
TGCAGGCTACTATGTGTACCAGATAGCATTGATCACG
Found at i:12473472 original size:29 final size:29
Alignment explanation
Indices: 12473439--12473497 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12473429 GTATGTATAA
12473439 TCACATACAAAAAGTTGTTATCAGCAGTT
1 TCACATACAAAAAGTTGTTATCAGCAGTT
12473468 TCACATACAAAAAGTTGTTATCAGCAGTT
1 TCACATACAAAAAGTTGTTATCAGCAGTT
12473497 T
1 T
12473498 TCTCACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (29 bp):
TCACATACAAAAAGTTGTTATCAGCAGTT
Found at i:12474734 original size:93 final size:93
Alignment explanation
Indices: 12474575--12474750 Score: 325
Period size: 93 Copynumber: 1.9 Consensus size: 93
12474565 AGCGAAACCG
12474575 GATTCAGGATACATGCATTCATTTTCTGGTGTAGCAGAACTTATCGAATGAGTCGAGTTGCTTAT
1 GATTCAGGATACATGCATTCATTTTCTGGTGTAGCAGAACTTATCGAATGAGTCGAGTTGCTTAT
12474640 AACTTCAGTCAAAGAAATCGTGAAATCA
66 AACTTCAGTCAAAGAAATCGTGAAATCA
* *
12474668 GATTCAGGATTCATGCATTCATTTTCTGGTGTAGCAGAACTTATTGAATGAGTCGAGTTGCTTAT
1 GATTCAGGATACATGCATTCATTTTCTGGTGTAGCAGAACTTATCGAATGAGTCGAGTTGCTTAT
*
12474733 AACTTCTGTCAAAGAAAT
66 AACTTCAGTCAAAGAAAT
12474751 TACTGATTCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (93 bp):
GATTCAGGATACATGCATTCATTTTCTGGTGTAGCAGAACTTATCGAATGAGTCGAGTTGCTTAT
AACTTCAGTCAAAGAAATCGTGAAATCA
Found at i:12477997 original size:132 final size:132
Alignment explanation
Indices: 12477760--12478023 Score: 519
Period size: 132 Copynumber: 2.0 Consensus size: 132
12477750 GATGGAGAAG
12477760 CAATGAAAGATATAGGCAAGAGAAGCATGTTAAGTATCTCCTTAGGTGCACATGTAACACCCCTA
1 CAATGAAAGATATAGGCAAGAGAAGCATGTTAAGTATCTCCTTAGGTGCACATGTAACACCCCTA
12477825 ACCCATATCCGTCACTAGAACAAGGTTATGGAGCATTACTAGAATTTACAGATCAGATATAGACA
66 ACCCATATCCGTCACTAGAACAAGGTTATGGAGCATTACTAGAATTTACAGATCAGATATAGACA
12477890 TT
131 TT
12477892 CAATGAAAGATATAGGCAAGAGAAGCATGTTAAGTATCTCCTTAGGTGCACATGTAACACCCCTA
1 CAATGAAAGATATAGGCAAGAGAAGCATGTTAAGTATCTCCTTAGGTGCACATGTAACACCCCTA
*
12477957 ACCCATATCTGTCACTAGAACAAGGTTATGGAGCATTACTAGAATTTACAGATCAGATATAGACA
66 ACCCATATCCGTCACTAGAACAAGGTTATGGAGCATTACTAGAATTTACAGATCAGATATAGACA
12478022 TT
131 TT
12478024 TAATATCATT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (132 bp):
CAATGAAAGATATAGGCAAGAGAAGCATGTTAAGTATCTCCTTAGGTGCACATGTAACACCCCTA
ACCCATATCCGTCACTAGAACAAGGTTATGGAGCATTACTAGAATTTACAGATCAGATATAGACA
TT
Found at i:12479870 original size:25 final size:25
Alignment explanation
Indices: 12479838--12479901 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
12479828 GAAGAGCTAT
12479838 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
12479863 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
12479888 TAACGGGAAGCTCG
1 TAACGGGAAGCTCG
12479902 AGAGGGCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACCATA
Found at i:12481393 original size:21 final size:21
Alignment explanation
Indices: 12481351--12481393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12481341 TTTTTTCTCA
* *
12481351 AATAAAATTGTCTCTTGTATC
1 AATAAAATTGTCTCATGCATC
*
12481372 AATAAAATTGTGTCATGCATC
1 AATAAAATTGTCTCATGCATC
12481393 A
1 A
12481394 TCCAATCAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
AATAAAATTGTCTCATGCATC
Found at i:12482344 original size:19 final size:18
Alignment explanation
Indices: 12482303--12482347 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12482293 AATTTAGACA
* *
12482303 GTTTTTTGATAGTCTGCT
1 GTTTTTTGATAATCTGCC
12482321 GTTTTTTGATAATCTGCC
1 GTTTTTTGATAATCTGCC
12482339 GTTTTTTGA
1 GTTTTTTGA
12482348 AAGAGTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (18 bp):
GTTTTTTGATAATCTGCC
Found at i:12482596 original size:107 final size:107
Alignment explanation
Indices: 12482408--12482868 Score: 798
Period size: 107 Copynumber: 4.3 Consensus size: 107
12482398 TTAGTTTCTC
12482408 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
1 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
* *
12482473 TTCTGGAAATTATTTTGATAGTCTGCTGGAAATTGTTCCTGA
66 TTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGA
* *
12482515 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTACATTTGTTTAGATATTGTTCTTGATTTG
1 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
* *
12482580 TTCTGGCAATTGTTTTGATAGTCTGCTAGAAATTGTTCTTGA
66 TTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGA
*
12482622 TTTGTTAGTGAGTAGAAGATGAAATTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
1 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
* *
12482687 TTCTGGAAATTGTTTTGATAGTCTGTTGGAAACTGTTCTTGA
66 TTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGA
* *
12482729 TTTGTTTGTGAG-AGGAAGATGAAGCTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTT
1 TTTGTTAGTGAGTA-GAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTT
*
12482793 GTTCTGGAAATTGTTTTGATAGTCTGCTGGAGATTGTTCTTGA
65 GTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGA
12482836 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATT
1 TTTGTTAGTGAGTAGAAGATGAAACTGGAAATT
12482869 ACAAGTATAG
Statistics
Matches: 331, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
106 1 0.00
107 329 0.99
108 1 0.00
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (107 bp):
TTTGTTAGTGAGTAGAAGATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTG
TTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGA
Found at i:12482687 original size:22 final size:22
Alignment explanation
Indices: 12482647--12482705 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
12482637 AAGATGAAAT
12482647 TGGAAATTG--TTGCATTTGTT-
1 TGGAAATTGTTTTG-ATTTGTTC
* *
12482667 TTGATATTGTTCTTGATTTGTTC
1 TGGAAATTGTT-TTGATTTGTTC
12482690 TGGAAATTGTTTTGAT
1 TGGAAATTGTTTTGAT
12482706 AGTCTGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 7 0.23
22 12 0.39
23 12 0.39
ACGTcount: A:0.19, C:0.05, G:0.22, T:0.54
Consensus pattern (22 bp):
TGGAAATTGTTTTGATTTGTTC
Found at i:12482794 original size:22 final size:22
Alignment explanation
Indices: 12482753--12482841 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 22
12482743 GAAGATGAAG
12482753 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
12482774 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
12482796 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
*
12482818 GCTGGAGATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
12482842 AGTGAGTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.23
23 23 0.43
24 5 0.09
25 3 0.06
ACGTcount: A:0.17, C:0.08, G:0.24, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:12486952 original size:47 final size:47
Alignment explanation
Indices: 12486899--12487043 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
12486889 TCATATAAGA
*
12486899 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
12486946 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * *
12486990 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
12487037 ATATTTA
1 ATATTTA
12487044 ATAATAATTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 32 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:12486996 original size:91 final size:91
Alignment explanation
Indices: 12486884--12487099 Score: 369
Period size: 91 Copynumber: 2.4 Consensus size: 91
12486874 ATGATTTTAG
*
12486884 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
12486949 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* *
12486975 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12487040 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* * *
12487066 CAAATTCATATAAGAAAATTTATTAGTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
12487100 ATTTTAAATT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:12487030 original size:101 final size:92
Alignment explanation
Indices: 12486976--12487167 Score: 194
Period size: 101 Copynumber: 2.0 Consensus size: 92
12486966 TAAATTATAT
12486976 AAATTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGA--AATTATATATTATTATTAAATT
1 AAATTCATATAAGAAAATTTATTAGT-AAGAATTATT-TGATTAATTATATA-TATTATTAAATT
*
12487037 ATATTTAATAATAATTATTTTAAATTATAC
63 ATATTTAATAATAATTATTTTAAATTATAT
* * *
12487067 AAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTA-TTT-GA-TTAATT--AT-ATATA--TT-AT
* *
12487132 TAAAATATATTTAATAATAATTATTTCAAATTATAT
57 TAAATTATATTTAATAATAATTATTTTAAATTATAT
12487168 TTTATAGTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
91 30 0.37
92 2 0.02
93 3 0.04
96 3 0.04
98 4 0.05
99 3 0.04
100 2 0.02
101 35 0.43
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (92 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTATTTGATTAATTATATATATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATAT
Found at i:12487057 original size:47 final size:47
Alignment explanation
Indices: 12486915--12487058 Score: 140
Period size: 47 Copynumber: 3.1 Consensus size: 47
12486905 ATTATTAAGA
* *
12486915 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
* * **
12486962 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-AATT
*
12487006 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
12487053 ATTTTA
1 ATTTTA
12487059 AATTATACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
43 6 0.08
44 20 0.27
45 8 0.11
46 8 0.11
47 26 0.35
48 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
Found at i:12487185 original size:59 final size:58
Alignment explanation
Indices: 12487117--12487401 Score: 191
Period size: 61 Copynumber: 4.8 Consensus size: 58
12487107 ATTTTATTAA
12487117 ATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTTATAGT
* * ** * * * * * * * *
12487176 ATCATATATTATGATTTTAGTAAATTCTTATAAGAA-TATTGATTATTAAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATT-TAATAATAATTATTTA-AATT-A-TATTTTA-TAGT
*
12487237 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTTATAGT
* * ** * * * * * * * *
12487296 ATCATATATTATGATTTGAGTAAATTCATATAAGAA-TATTGATTATTAAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTA-AATT-A-TATTTTA-TAGT
*
12487357 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAA
12487402 ATATGATTAA
Statistics
Matches: 162, Mismatches: 49, Indels: 28
0.68 0.21 0.12
Matches are distributed among these distances:
58 5 0.03
59 59 0.36
60 29 0.18
61 61 0.38
62 8 0.05
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTTTATAGT
Found at i:12487236 original size:120 final size:120
Alignment explanation
Indices: 12487106--12487401 Score: 549
Period size: 120 Copynumber: 2.5 Consensus size: 120
12487096 AATTATTTTA
*
12487106 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
12487170 TATAGTATCATATATTATGATTTTAGTAAATTCTTATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
12487226 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
12487291 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
12487346 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
12487402 ATATGATTAA
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
120 170 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:12487255 original size:18 final size:17
Alignment explanation
Indices: 12487227--12487261 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12487217 ATTATTAAGA
*
12487227 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12487244 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12487262 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12487375 original size:18 final size:17
Alignment explanation
Indices: 12487347--12487381 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12487337 ATTATTAAGA
*
12487347 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12487364 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12487382 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12487641 original size:16 final size:16
Alignment explanation
Indices: 12487620--12487652 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12487610 TTGATTTGCT
12487620 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
12487636 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
12487652 A
1 A
12487653 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:12502327 original size:54 final size:54
Alignment explanation
Indices: 12502269--12502373 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
12502259 TTGGAGTTGG
12502269 GCATATTTGGAGAGGGTTGAATAAAAGAAATGAAAGTAGATGGATGTGAGTTTC
1 GCATATTTGGAGAGGGTTGAATAAAAGAAATGAAAGTAGATGGATGTGAGTTTC
12502323 GCATATTTGGAGAGGGTTGAATAAAAGAAATGAAAGTAGATGGATGTGAGT
1 GCATATTTGGAGAGGGTTGAATAAAAGAAATGAAAGTAGATGGATGTGAGT
12502374 GACGTAAGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (54 bp):
GCATATTTGGAGAGGGTTGAATAAAAGAAATGAAAGTAGATGGATGTGAGTTTC
Found at i:12502509 original size:12 final size:12
Alignment explanation
Indices: 12502492--12502538 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
12502482 AAGATGAAAG
12502492 CTTGATGAAAAA
1 CTTGATGAAAAA
12502504 CTTGATGAAAAACA
1 CTTGATG-AAAA-A
*
12502518 CTTGATGAAAGA
1 CTTGATGAAAAA
12502530 CTTGATGAA
1 CTTGATGAA
12502539 TAAATGAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.53
13 7 0.22
14 8 0.25
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (12 bp):
CTTGATGAAAAA
Done.