Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 113 of 205
Found at i:33897225 original size:13 final size:13
Alignment explanation
Indices: 33897203--33897235 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33897193 AAACGTTTGT
33897203 TTAT-TAAACTAA
1 TTATCTAAACTAA
33897215 TTATCTAAACTAA
1 TTATCTAAACTAA
*
33897228 TTAACTAA
1 TTATCTAA
33897236 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:33900546 original size:32 final size:32
Alignment explanation
Indices: 33900506--33900574 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
33900496 AAATGACATG
33900506 GAATGAATTTTGTATTCAAATGATGAATTATT
1 GAATGAATTTTGTATTCAAATGATGAATTATT
33900538 GAATGAATTTTGTATTCAAATGATGAATTATT
1 GAATGAATTTTGTATTCAAATGATGAATTATT
33900570 GAATG
1 GAATG
33900575 TTGTGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (32 bp):
GAATGAATTTTGTATTCAAATGATGAATTATT
Found at i:33903091 original size:42 final size:43
Alignment explanation
Indices: 33903031--33903155 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 43
33903021 ATTTAGAACC
* *
33903031 ACACGAGTAGAGGACATGGGCGTGTACCTAGGCCATGTGAGTT
1 ACACGAGTAGAGGACATGGGCATGTACCCAGGCCATGTGAGTT
* * *
33903074 ACACGAGT-GAGGACATGGGCATGTGCCCAGGCTATGTGAGTC
1 ACACGAGTAGAGGACATGGGCATGTACCCAGGCCATGTGAGTT
** * * ** *
33903116 ATTCGGGTA-AGGACACGGGCATGTGTCCAGGTCATGTGAG
1 ACACGAGTAGAGGACATGGGCATGTACCCAGGCCATGTGAG
33903156 CCACGTGGGC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 61 0.88
43 8 0.12
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (43 bp):
ACACGAGTAGAGGACATGGGCATGTACCCAGGCCATGTGAGTT
Found at i:33903170 original size:42 final size:41
Alignment explanation
Indices: 33903083--33903195 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 41
33903073 TACACGAGTG
* * * *
33903083 AGGACATGGGCATGTGCCCAGG-CTATGTGAGTCATTCGGGTA
1 AGGACACGGGCATGTG-CCAGGTC-ATGTGAGCCAGTCGGGCA
33903125 AGGACACGGGCATGTGTCCAGGTCATGTGAGCCACGT-GGGCA
1 AGGACACGGGCATGTG-CCAGGTCATGTGAGCCA-GTCGGGCA
*
33903167 AGGACATC-GGCATGTGCTCAGGTCGTGTG
1 AGGACA-CGGGCATGTGC-CAGGTCATGTG
33903196 GCCTGTAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.02
42 57 0.93
43 3 0.05
ACGTcount: A:0.20, C:0.21, G:0.37, T:0.21
Consensus pattern (41 bp):
AGGACACGGGCATGTGCCAGGTCATGTGAGCCAGTCGGGCA
Found at i:33904623 original size:234 final size:236
Alignment explanation
Indices: 33904164--33904879 Score: 567
Period size: 234 Copynumber: 3.0 Consensus size: 236
33904154 AGTAGAAGTA
* * * * * * *
33904164 CTAACTTTCATATGTGTGGAAAGTATAAGGACTTAAAGCATATTCCAACAATATGATAATTAACA
1 CTAACTTTCAAATGTATGAAAAATATAAAGACTTAAAGCATATTCAAACAATATGATAATAAACA
* * **
33904229 ATAAAATATAATGTACTACTAGTATATATAACTATTATTATATTATAGACTATAATAAAATTTAT
66 ATAAAATATAATGTACTACTAGTATATATAAC-ATTATCATATTATAAACTATAATAAAAGATAT
* ** *
33904294 AGTATTACTTGACATGATAATGTTTAATCATTTATGTATATATTTAAACTTTTAAGATATTATAT
130 AGTATTACTCGACATGATAATGTTTAATCATTTACATATATATATAAACTTTTAAGATATTATAT
33904359 ACTATATGATATGATATAACATTATATAATATGGCAAGAGGG
195 ACTATATGATATGATATAACATTATATAATATGGCAAGAGGG
* * *
33904401 CTAAGTTTCAAATGTATGAAAAATATAAAGACTTAGAGCATATTTCAAAC-A-AT-ATAATAAAT
1 CTAACTTTCAAATGTATGAAAAATATAAAGACTTAAAGCATA-TTCAAACAATATGATAATAAAC
* * *
33904463 AATAATATATAATGTACTATTA-TCATATATAAC-TT-TCATATTATAAATTATAATAAAAGATA
65 AATAAAATATAATGTACTACTAGT-ATATATAACATTATCATATTATAAACTATAATAAAAGATA
* * * **
33904525 TAGTATTACTCGATATTATAATGTTTAATCCTTGATACATATATATATAAACTATTT-ATTTATT
129 TAGTATTACTCGACATGATAATGTTTAATCATT--TACATATATATATAAACT-TTTAAGATATT
* * * * *
33904589 ATATACTATTTGATATGATATAACATTTTATAATATAG-TAGTAAGG
191 ATATACTATATGATATGATATAACATTATATAATATGGCAAG-AGGG
* * * * *
33904635 CTAACTTTTAAATGTA-CAATAAGTAT-AGGATTTTAGAA-CATATTTCAACCAGTATAACAATA
1 CTAACTTTCAAATGTATGAA-AAATATAAAGA-CTTA-AAGCATA-TT----C---A-AACAAT-
* * * **
33904697 AATAATAATATATGATAATAATTAATATATAATATACTACTA-TGATATATAACTATTATTTTAT
53 -ATGATAATA-A--ACAAT-A--AA-ATATAATGTACTACTAGT-ATATATAAC-ATTATCATAT
* *** * * * * * ***
33904761 TGTAGTTTATAATAAAAGATATAGTAGTGC-CTGATATTATAATGTTTAATCATTGATGCATATA
108 TATAAACTATAATAAAAGATATAGTATTACTC-GACATGATAATGTTTAATCATTTACATATATA
* *
33904825 TATAAACTATTAATATATTATATACTATATGATATGATATAACATTATATAATAT
172 TATAAACTTTTAAGATATTATATACTATATGATATGATATAACATTATATAATAT
33904880 AGTAAGACTT
Statistics
Matches: 387, Mismatches: 58, Indels: 50
0.78 0.12 0.10
Matches are distributed among these distances:
232 51 0.13
233 9 0.02
234 88 0.23
235 40 0.10
236 2 0.01
237 36 0.09
238 7 0.02
241 1 0.00
242 3 0.01
243 1 0.00
246 2 0.01
247 6 0.02
248 1 0.00
250 5 0.01
251 1 0.00
253 1 0.00
254 26 0.07
255 54 0.14
256 3 0.01
257 50 0.13
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (236 bp):
CTAACTTTCAAATGTATGAAAAATATAAAGACTTAAAGCATATTCAAACAATATGATAATAAACA
ATAAAATATAATGTACTACTAGTATATATAACATTATCATATTATAAACTATAATAAAAGATATA
GTATTACTCGACATGATAATGTTTAATCATTTACATATATATATAAACTTTTAAGATATTATATA
CTATATGATATGATATAACATTATATAATATGGCAAGAGGG
Found at i:33904842 original size:17 final size:18
Alignment explanation
Indices: 33904820--33904880 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
33904810 TCATTGATGC
33904820 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
33904837 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
*
33904856 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
33904876 ATATA
1 ATATA
33904881 GTAAGACTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:33905735 original size:234 final size:231
Alignment explanation
Indices: 33905299--33906049 Score: 649
Period size: 255 Copynumber: 3.1 Consensus size: 231
33905289 GTGTGGAAAG
* * * * * * *
33905299 TATAAGGACTTAAAGCATA-TTCCAACAATATGATAATTAACAATAAAATATAATGTACTACTAG
1 TATAAAGACTTAGAGCATATTTCAAACAA-ATAATAATAAATAATAATATATAATGTACTACTA-
* ** * * *
33905363 TATATATAACTATTATTATATTATAGACTATAATAAAATTTATAGTATTACTTGACATGATAATG
64 TATATATAAC---T-TTATATTATAGATTATAATAAAAGATATAGTATTACTCGATATTATAATG
* * * *
33905428 TTTAATCATTTAT-GTATATATTTAAACT-TTTAAGATATTATATACTATATGATATGATATAAC
125 TTTAATCATTGATACTATATATATAAACTATTT-ATATATTATATACTATATGATATGATATAAC
* * * *
33905491 ATTATATAATATGGCAAGAGGGCTAAGTTTCAAATGTATGAAAAA
189 ATTATATAATATAG-AAGAAGGCTAACTTTCAAATGTA-CAAAAA
*
33905536 TATAAAGACTTAGAGCATATTTCAAAC-AAT-ATAATAAATAATAATATATAATGTACTATTATC
1 TATAAAGACTTAGAGCATATTTCAAACAAATAATAATAAATAATAATATATAATGTACTACTAT-
*
33905599 ATATATAACTTTCATATTATAAATTATAATAAAAGATATAGTATTACTCGATATTATAATGTTTA
65 ATATATAACTTT-ATATTATAGATTATAATAAAAGATATAGTATTACTCGATATTATAATGTTTA
* * * *
33905664 ATCCTTGATACATATATATATAAACTATTTATTTATTATATACTATTTGATATGATATAACATTT
129 ATCATTGATAC-TATATATATAAACTATTTATATATTATATACTATATGATATGATATAACATTA
* * *
33905729 TATAATATAGTAGTAAGGCTAACTTTTAAATGTACAATAAG
193 TATAATATAGAAG-AAGGCTAACTTTCAAATGTACAA-AAA
* * *
33905770 TAT-AGGATTTTAGAACATATTTCAACCAGTATAACAATAAATAATAATATATGATAATAATTAA
1 TATAAAGA-CTTAGAGCATATTT----C---A-AAC-----A-AATAATA-AT-A-AATAA-TAA
* * *
33905834 TATATAATATACTACTATGATATATAACTATTATTTTATTGTAGTTTATAATAAAAGATATAGTA
47 TATATAATGTACTACTAT-ATATATAACT-TTA---TATTATAGATTATAATAAAAGATATAGTA
* * * *
33905899 GTGC-CTGATATTATAATGTTTAATCATTGATGC-ATATATATAAACTATTAATATATTATATAC
107 TTACTC-GATATTATAATGTTTAATCATTGATACTATATATATAAACTATTTATATATTATATAC
* * *
33905962 TATATGATATGATATAACATTATATAATATAGTAAGATGACTAATTTTCAAACT-TACAAAAA
171 TATATGATATGATATAACATTATATAATATAG-AAGAAGGCTAACTTTCAAA-TGTACAAAAA
*
33906024 GTATAGAGACTCT-GAGCATATTTCAA
1 -TATAAAGACT-TAGAGCATATTTCAA
33906050 CCAGTATATA
Statistics
Matches: 419, Mismatches: 56, Indels: 68
0.77 0.10 0.13
Matches are distributed among these distances:
231 2 0.00
232 53 0.13
233 7 0.02
234 88 0.21
235 39 0.09
236 2 0.00
237 18 0.04
238 7 0.02
241 1 0.00
242 3 0.01
247 1 0.00
248 1 0.00
249 3 0.01
250 3 0.01
251 3 0.01
252 1 0.00
253 5 0.01
254 32 0.08
255 90 0.21
256 7 0.02
257 53 0.13
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (231 bp):
TATAAAGACTTAGAGCATATTTCAAACAAATAATAATAAATAATAATATATAATGTACTACTATA
TATATAACTTTATATTATAGATTATAATAAAAGATATAGTATTACTCGATATTATAATGTTTAAT
CATTGATACTATATATATAAACTATTTATATATTATATACTATATGATATGATATAACATTATAT
AATATAGAAGAAGGCTAACTTTCAAATGTACAAAAA
Found at i:33905954 original size:17 final size:18
Alignment explanation
Indices: 33905932--33905992 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
33905922 TCATTGATGC
33905932 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
33905949 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
*
33905968 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
33905988 ATATA
1 ATATA
33905993 GTAAGATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:33906028 original size:255 final size:249
Alignment explanation
Indices: 33905572--33906100 Score: 660
Period size: 255 Copynumber: 2.1 Consensus size: 249
33905562 CAATATAATA
*
33905572 AATAA-TAATATATAATGTACTATTATCATATATAACTTTCATATTATAAATTATAATAAAAGAT
1 AATAATTAATATATAATGTACTACTATCATATATAACTTTCATATTATAAATTATAATAAAAGAT
* * * *
33905636 ATAGTATTACTCGATATTATAATGTTTAATCCTTGATACATATATATATAAACTATTTATTTATT
66 ATAGTATGACTCGATATTATAATGTTTAATCATTGATACA-ATATATATAAACTATTAATATATT
* * *
33905701 ATATACTATTTGATATGATATAACATTTTATAATATAGTAGTAAGGCTAACTTTTAAATGTACAA
130 ATATACTATATGATATGATATAACATTATATAATATAGTAGTAAGACTAACTTTTAAATGTACAA
* * *
33905766 TAAGTATAG-GATTTTAGAACATATTTCAACCAGTATAACAATAAATAATAATATATGAT
195 AAAGTATAGAGACTCT-GAACATATTTCAACCAGTAT----ATAAATAATAATATATGAT
* * * **
33905825 AATAATTAATATATAATATACTACTATGATATATAACTATT-ATTTTATTGTAGTTTATAATAAA
1 AATAATTAATATATAATGTACTACTATCATATATAACT-TTCA---TATTATAAATTATAATAAA
* *
33905889 AGATATAGTAGTGCCT-GATATTATAATGTTTAATCATTGATGC-ATATATATAAACTATTAATA
62 AGATATAGTA-TGACTCGATATTATAATGTTTAATCATTGATACAATATATATAAACTATTAATA
*
33905952 TATTATATACTATATGATATGATATAACATTATATAATATAGTAAG-ATGACTAA-TTTTCAAAC
126 TATTATATACTATATGATATGATATAACATTATATAATATAGT-AGTAAGACTAACTTTT-AAA-
* *
33906015 T-TACAAAAAGTATAGAGACTCTGAGCATATTTCAACCAGTATATAACTAATAATATATGAT
188 TGTACAAAAAGTATAGAGACTCTGAACATATTTCAACCAGTATATAAATAATAATATATGAT
* * *
33906076 AAAAATGAATATATTATGTACTACT
1 AATAATTAATATATAATGTACTACT
33906101 CTAGTATTAT
Statistics
Matches: 241, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
251 39 0.16
253 5 0.02
254 34 0.14
255 102 0.42
256 7 0.03
257 51 0.21
258 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (249 bp):
AATAATTAATATATAATGTACTACTATCATATATAACTTTCATATTATAAATTATAATAAAAGAT
ATAGTATGACTCGATATTATAATGTTTAATCATTGATACAATATATATAAACTATTAATATATTA
TATACTATATGATATGATATAACATTATATAATATAGTAGTAAGACTAACTTTTAAATGTACAAA
AAGTATAGAGACTCTGAACATATTTCAACCAGTATATAAATAATAATATATGAT
Found at i:33906443 original size:23 final size:23
Alignment explanation
Indices: 33906416--33906463 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
33906406 TAATATTTAT
*
33906416 TTTTATATCATAAAAATTTAAAA
1 TTTTATATCATAAAAAATTAAAA
33906439 TTTTATATCATAAAAAATTAAAA
1 TTTTATATCATAAAAAATTAAAA
33906462 TT
1 TT
33906464 AAGTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTATATCATAAAAAATTAAAA
Found at i:33912766 original size:27 final size:29
Alignment explanation
Indices: 33912726--33912782 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
33912716 ACGGATGACT
*
33912726 CAACTCTTATTCAAAC-ACTTGTTTGAACA
1 CAACTCTTATTCAAACAACTT-TTTAAACA
33912755 CAAC-CTT-TTCAAACAACTTTTTAAACA
1 CAACTCTTATTCAAACAACTTTTTAAACA
33912782 C
1 C
33912783 CTATTTAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 15 0.58
28 7 0.27
29 4 0.15
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
CAACTCTTATTCAAACAACTTTTTAAACA
Found at i:33916321 original size:48 final size:48
Alignment explanation
Indices: 33916243--33916562 Score: 333
Period size: 48 Copynumber: 6.7 Consensus size: 48
33916233 TACGTGCACT
33916243 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCC
* * ** * *
33916291 AGTGTAAGACCATGTTTGGAACATTACATCG-GCA-ATGTAATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACA-AT-ATGAGAGCC
** * * *
33916339 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCA-CAATATGAGAGCC
* *
33916387 AGTGTAAGACCATGTCTAGGACATGGCATCGACCACACTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCC
* * * * *
33916435 AGTGTAAGACCATGTCAGGGACATGGCATCG-GCATTAAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCA-CAATATGAGAGCC
* * * * *
33916483 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCC
* * * *
33916531 AATGTAAGACCATGTTTGGAACACGGCATCGA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA
33916563 TAACTCACTC
Statistics
Matches: 222, Mismatches: 42, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
46 1 0.00
47 5 0.02
48 212 0.95
49 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCC
Found at i:33916490 original size:144 final size:144
Alignment explanation
Indices: 33916230--33916562 Score: 447
Period size: 144 Copynumber: 2.3 Consensus size: 144
33916220 GACATTTGGG
* * *
33916230 TGATACGTGCACTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACAATATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCACAATATGAGAGCCAGTG
** *
33916295 TAAGACCATGTTTGGAACATTACATCGGCAATGTAATGAGAGCCAGTGTAAGACCATGTCTGGGA
66 TAAGACCATGTCAGGAACATGACATCGGCAATGTAATGAGAGCCAGTGTAAGACCATGTCTGGGA
33916360 CATGGCATCGACAT
131 CATGGCATCGACAT
*
33916374 TGATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCACACTATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCACAATATGAGAGCCAGTG
* * *
33916439 TAAGACCATGTCAGGGACATGGCATCGGC-AT-TAAGATGAGAGCTAGTGTAAGACCATGTCTGG
66 TAAGACCATGTCAGGAACATGACATCGGCAATGT-A-ATGAGAGCCAGTGTAAGACCATGTCTGG
* *
33916502 GACATGGCATCGGCCT
129 GACATGGCATCGACAT
* * * * * * *
33916518 CGACATGTGAGCCAATGTAAGACCATGT-TTGGAACACGGCATCGA
1 TGATATGTGCGCTAGTGTAAGACCATGTCTAGG-ACATGGCATCGA
33916563 TAACTCACTC
Statistics
Matches: 167, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
142 1 0.01
143 6 0.04
144 160 0.96
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCACAATATGAGAGCCAGTG
TAAGACCATGTCAGGAACATGACATCGGCAATGTAATGAGAGCCAGTGTAAGACCATGTCTGGGA
CATGGCATCGACAT
Found at i:33919718 original size:31 final size:31
Alignment explanation
Indices: 33919675--33919738 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
33919665 CCTTTTCATA
33919675 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
33919706 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
33919737 TT
1 TT
33919739 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:33919981 original size:25 final size:26
Alignment explanation
Indices: 33919953--33920004 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
33919943 GCCTAGCCTC
33919953 TTTTAATAACTGGGGCA-AAGCCCTT
1 TTTTAATAACTGGGGCATAAGCCCTT
33919978 TTTTAATAACTGGGGCATAAGCCCTT
1 TTTTAATAACTGGGGCATAAGCCCTT
33920004 T
1 T
33920005 CGCACTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
TTTTAATAACTGGGGCATAAGCCCTT
Found at i:33920082 original size:20 final size:20
Alignment explanation
Indices: 33920059--33920121 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
33920049 GAACATCTCG
*
33920059 TGTGCATATCAGACATATCA
1 TGTGCATATCATACATATCA
*
33920079 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
33920099 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
33920119 TGT
1 TGT
33920122 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:33927412 original size:31 final size:31
Alignment explanation
Indices: 33927369--33927432 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
33927359 CCTTTTCATA
33927369 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
33927400 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
33927431 TT
1 TT
33927433 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:33927704 original size:48 final size:47
Alignment explanation
Indices: 33927644--33927768 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 47
33927634 GGCCTGGCCT
33927644 CTTTCAATAACTGCGGCA-AACCCCTTTTTTAATAACTGGGGCATAAGCC
1 CTTT-AATAACTGCGGCATAA-CCC-TTTTTAATAACTGGGGCATAAGCC
* * *
33927693 CTTTAATAACTGGGGCATAAGCCTTTTTAATGACTGGGGCATAAGCC
1 CTTTAATAACTGCGGCATAACCCTTTTTAATAACTGGGGCATAAGCC
* *
33927740 CTTTTAATAACTAG-AGCATAAGCCTTTTT
1 C-TTTAATAACT-GCGGCATAACCCTTTTT
33927769 GCACTTCCTC
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
47 24 0.35
48 38 0.55
49 7 0.10
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (47 bp):
CTTTAATAACTGCGGCATAACCCTTTTTAATAACTGGGGCATAAGCC
Found at i:33927728 original size:24 final size:24
Alignment explanation
Indices: 33927669--33927768 Score: 148
Period size: 24 Copynumber: 4.2 Consensus size: 24
33927659 GCAAACCCCT
33927669 TTTTTAATAACTGGGGCATAAGCC
1 TTTTTAATAACTGGGGCATAAGCC
*
33927693 -CTTTAATAACTGGGGCATAAGCC
1 TTTTTAATAACTGGGGCATAAGCC
*
33927716 TTTTTAATGACTGGGGCATAAGCC
1 TTTTTAATAACTGGGGCATAAGCC
* * *
33927740 CTTTTAATAACTAGAGCATAAGCC
1 TTTTTAATAACTGGGGCATAAGCC
33927764 TTTTT
1 TTTTT
33927769 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.33
24 45 0.67
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (24 bp):
TTTTTAATAACTGGGGCATAAGCC
Found at i:33927840 original size:9 final size:9
Alignment explanation
Indices: 33927826--33927882 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
33927816 ATCTCGTGTG
33927826 CATATCATA
1 CATATCATA
*
33927835 CATATCATGTG
1 CATATCA--TA
33927846 CATATCATA
1 CATATCATA
* *
33927855 CATGTCATGTG
1 CATATCA--TA
33927866 CATATCATA
1 CATATCATA
33927875 CATATCAT
1 CATATCAT
33927883 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:33927845 original size:20 final size:20
Alignment explanation
Indices: 33927822--33927884 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
33927812 GAACATCTCG
33927822 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
33927842 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
33927862 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
33927882 TGT
1 TGT
33927885 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:33927949 original size:25 final size:25
Alignment explanation
Indices: 33927921--33927968 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33927911 ATATATAAAC
* * *
33927921 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
33927946 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
33927969 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:33934505 original size:48 final size:48
Alignment explanation
Indices: 33934453--33934719 Score: 290
Period size: 48 Copynumber: 5.6 Consensus size: 48
33934443 TGCGCTAGTA
* * *
33934453 TAAGACCATGTATGGGACATGACATCGGCCATGATATGAGAGCCAGTT
1 TAAGACCATGTTTGGGACATGGCATCGGCCATGATATGAGAGCCAGTG
* *
33934501 TAAGACCATGTTTGGAACATGGCATCGGCAATG-TAATGAGAGCCAGTG
1 TAAGACCATGTTTGGGACATGGCATCGGCCATGAT-ATGAGAGCCAGTG
* * * * * *
33934549 TAAGGCCATGTCTGGGACATGGCATCGG-TATTGATATGTGCGCTAGTG
1 TAAGACCATGTTTGGGACATGGCATCGGCCA-TGATATGAGAGCCAGTG
* *
33934597 TAAGACCATGTTTGGGACATGGCATCGGCCA-CATTATGAGAGCTAGTG
1 TAAGACCATGTTTGGGACATGGCATCGGCCATGA-TATGAGAGCCAGTG
* * * * *
33934645 TAAGACCATGTCTGGGACATGGCATTGGTC-TCGACATGTGAGCCAGTG
1 TAAGACCATGTTTGGGACATGGCATCGGCCAT-GATATGAGAGCCAGTG
* *
33934693 TAAGACCATGTTTGGAACATGGAATCG
1 TAAGACCATGTTTGGGACATGGCATCG
33934720 ACAATTCACC
Statistics
Matches: 183, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.02
48 177 0.97
49 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
TAAGACCATGTTTGGGACATGGCATCGGCCATGATATGAGAGCCAGTG
Found at i:33934622 original size:96 final size:94
Alignment explanation
Indices: 33934453--33934725 Score: 350
Period size: 96 Copynumber: 2.9 Consensus size: 94
33934443 TGCGCTAGTA
* * * * *
33934453 TAAGACCATGTATGGGACATGACATCGGCCA-TGATATGAGAGCCAGTTTAAGACCATGTTTGGA
1 TAAGACCATGTCTGGGACATGGCATCGG-TATTGATATGTGAGCCAGTGTAAGACCATGTTTGGA
33934517 ACATGGCATCGGCAATGTAATGAGAGCCAGTG
65 ACATGGCATCGGCAAT-T-ATGAGAGCCAGTG
* * * *
33934549 TAAGGCCATGTCTGGGACATGGCATCGGTATTGATATGTGCGCTAGTGTAAGACCATGTTTGGGA
1 TAAGACCATGTCTGGGACATGGCATCGGTATTGATATGTGAGCCAGTGTAAGACCATGTTTGGAA
*
33934614 CATGGCATCGGCCACATTATGAGAGCTAGTG
66 CATGGCATCGG-CA-ATTATGAGAGCCAGTG
* * * *
33934645 TAAGACCATGTCTGGGACATGGCATTGGTCTCGACATGTGAGCCAGTGTAAGACCATGTTTGGAA
1 TAAGACCATGTCTGGGACATGGCATCGGTATTGATATGTGAGCCAGTGTAAGACCATGTTTGGAA
* *
33934710 CATGGAATCGACAATT
66 CATGGCATCGGCAATT
33934726 CACCCTCTTG
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
94 3 0.02
95 3 0.02
96 143 0.93
97 3 0.02
98 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (94 bp):
TAAGACCATGTCTGGGACATGGCATCGGTATTGATATGTGAGCCAGTGTAAGACCATGTTTGGAA
CATGGCATCGGCAATTATGAGAGCCAGTG
Found at i:33934696 original size:144 final size:143
Alignment explanation
Indices: 33934436--33934719 Score: 376
Period size: 144 Copynumber: 2.0 Consensus size: 143
33934426 GACATTTGGG
* *
33934436 TGATATGTGCGCTAGTATAAGACCATGTATGGGACATGACATCGGCCATGATATGAGAGCCAGTT
1 TGATATGTGCGCTAGTATAAGACCATGTATGGGACATGACATCGGCCATCATATGAGAGCCAGTG
* * *
33934501 TAAGACCATGTTTGGAACATGGCATCGGCAATGTAATGAGAGCCAGTGTAAGGCCATGTCTGGGA
66 TAAGACCATGTCTGGAACATGGCATCGGC-ATGTAATGAGAGCCAGTGTAAGACCATGTCTGGAA
*
33934566 CATGGCATCGGTAT
130 CATGGAATCGGTAT
* * * *
33934580 TGATATGTGCGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA-CATTATGAGAGCTAGT
1 TGATATGTGCGCTAGTATAAGACCATGTATGGGACATGACATCGGCCATCA-TATGAGAGCCAGT
* * * *
33934644 GTAAGACCATGTCTGGGACATGGCATTGGTC-TCG-ACATGTGAGCCAGTGTAAGACCATGTTTG
65 GTAAGACCATGTCTGGAACATGGCATCGG-CAT-GTA-ATGAGAGCCAGTGTAAGACCATGTCTG
33934707 GAACATGGAATCG
127 GAACATGGAATCG
33934720 ACAATTCACC
Statistics
Matches: 122, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
143 3 0.02
144 118 0.97
145 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (143 bp):
TGATATGTGCGCTAGTATAAGACCATGTATGGGACATGACATCGGCCATCATATGAGAGCCAGTG
TAAGACCATGTCTGGAACATGGCATCGGCATGTAATGAGAGCCAGTGTAAGACCATGTCTGGAAC
ATGGAATCGGTAT
Found at i:33935076 original size:143 final size:142
Alignment explanation
Indices: 33934818--33935103 Score: 527
Period size: 143 Copynumber: 2.0 Consensus size: 142
33934808 ATGGAATGAA
*
33934818 ATAATCATGTTGTGAGTGGTACAGGTTATTATTTGAAACTCATGAGATATGAGTCTAGTTATGTT
1 ATAATCATGTTGTGAGTGGTACAGGATATTATTTGAAACTCATGAGATATGAGTCTAGTTATGTT
*
33934883 GCCTTGATGGTAAAAATAACATGAGTAAGTACTAGCTATGAAATGATTTTTGGGATGATATTGTA
66 GCCTTGATGGTAAAAATAACATGAGTAAGTACTAGCTATGAAATGATTTTT-GGACGATATTGTA
33934948 ATCTTTGGCTTAT
130 ATCTTTGGCTTAT
*
33934961 ATAATCATGTTGTGAGTGGTACAGGATCTTATTTGAAACTCATGAGATATGAGTCTAGTTATGTT
1 ATAATCATGTTGTGAGTGGTACAGGATATTATTTGAAACTCATGAGATATGAGTCTAGTTATGTT
*
33935026 GCCTTGATGGTAAGAATAACATGAGTAAGTACTAGCTATGAAATGATTTTTGGACGATATTGTAA
66 GCCTTGATGGTAAAAATAACATGAGTAAGTACTAGCTATGAAATGATTTTTGGACGATATTGTAA
33935091 TCTTTGGCTTAT
131 TCTTTGGCTTAT
33935103 A
1 A
33935104 CTTGTGATAT
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
142 26 0.19
143 113 0.81
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (142 bp):
ATAATCATGTTGTGAGTGGTACAGGATATTATTTGAAACTCATGAGATATGAGTCTAGTTATGTT
GCCTTGATGGTAAAAATAACATGAGTAAGTACTAGCTATGAAATGATTTTTGGACGATATTGTAA
TCTTTGGCTTAT
Found at i:33936092 original size:21 final size:21
Alignment explanation
Indices: 33936058--33936097 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33936048 GGTAAGAAGA
* *
33936058 CACACGGGTATGTTGCCCTTC
1 CACACGGGCATGTTCCCCTTC
*
33936079 CACACGGGCGTGTTCCCCT
1 CACACGGGCATGTTCCCCT
33936098 ATCAGCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (21 bp):
CACACGGGCATGTTCCCCTTC
Found at i:33936683 original size:63 final size:62
Alignment explanation
Indices: 33936495--33936731 Score: 215
Period size: 63 Copynumber: 3.8 Consensus size: 62
33936485 TGGACACACT
* * * * ** * *
33936495 CCCATGTCCCTGGCCAATATGACCCTAAATCCAAAAGAATGAGTTACACA-ACTTGGACACACG
1 CCCATGT-CCTAGCCCATGTGACCCTAAATCCAAAATAATGAGTTACA-AGGGTTAGACACAAG
* * * * * *
33936558 CCCATGTCCCTAGCCCATGTGACCTTAAATTCAAAACAGTGAGTTACATGGGCTAGACACAAG
1 CCCATGT-CCTAGCCCATGTGACCCTAAATCCAAAATAATGAGTTACAAGGGTTAGACACAAG
* * * *
33936621 CCCATGTACCTAGTCCTTGTGACCCTAAATCTAAAATAATGAGTTACAAGGGTTAGAGACAAG
1 CCCATGT-CCTAGCCCATGTGACCCTAAATCCAAAATAATGAGTTACAAGGGTTAGACACAAG
* * * * *
33936684 CCAATGTCCTTAGCCCGTGTGACACAAAATCCAAAATAGTGAGTTACA
1 CCCATGTCC-TAGCCCATGTGACCCTAAATCCAAAATAATGAGTTACA
33936732 CGGCCTACCA
Statistics
Matches: 141, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
62 2 0.01
63 139 0.99
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (62 bp):
CCCATGTCCTAGCCCATGTGACCCTAAATCCAAAATAATGAGTTACAAGGGTTAGACACAAG
Found at i:33937295 original size:11 final size:12
Alignment explanation
Indices: 33937279--33937358 Score: 70
Period size: 11 Copynumber: 7.4 Consensus size: 12
33937269 GAAGCAAGCA
33937279 AAAAGAAA-AAG
1 AAAAGAAAGAAG
*
33937290 AAAAGAAAGATG
1 AAAAGAAAGAAG
33937302 -AAAG-AAGAA-
1 AAAAGAAAGAAG
*
33937311 AGAAGAAAGAAG
1 AAAAGAAAGAAG
*
33937323 -AAAGAAAGAAT
1 AAAAGAAAGAAG
33937334 AAAAG-AAG-AG
1 AAAAGAAAGAAG
33937344 AAAAG-AAGAA-
1 AAAAGAAAGAAG
33937354 AAAAG
1 AAAAG
33937359 TTAAAGAACA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
10 21 0.37
11 30 0.53
12 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
AAAAGAAAGAAG
Found at i:33937304 original size:7 final size:7
Alignment explanation
Indices: 33937281--33937354 Score: 68
Period size: 7 Copynumber: 10.9 Consensus size: 7
33937271 AGCAAGCAAA
33937281 AAGAAA-
1 AAGAAAG
33937287 AAG-AA-
1 AAGAAAG
33937292 AAGAAAG
1 AAGAAAG
*
33937299 ATGAAAG
1 AAGAAAG
33937306 AAGAAAG
1 AAGAAAG
33937313 AAGAAAG
1 AAGAAAG
33937320 AAGAAAG
1 AAGAAAG
*
33937327 AAAGAATAA
1 -AAGAA-AG
33937336 AAG-AAG
1 AAGAAAG
33937342 -AGAAAAG
1 AAG-AAAG
33937349 AAGAAA
1 AAGAAA
33937355 AAAGTTAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
5 7 0.12
6 6 0.11
7 33 0.58
8 10 0.18
9 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (7 bp):
AAGAAAG
Found at i:33937318 original size:21 final size:20
Alignment explanation
Indices: 33937280--33937358 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 20
33937270 AAGCAAGCAA
*
33937280 AAAGAAAAAGAAAAGAAAGATG
1 AAAGAAGAA-AAAAGAAAGA-G
*
33937302 AAAGAAGAAAGAAGAAAGAAG
1 AAAGAAGAAAAAAGAAAG-AG
33937323 AAAGAAAGAATAAAAG-AAGAG
1 AAAG-AAGAA-AAAAGAAAGAG
33937344 AAAAGAAGAAAAAAG
1 -AAAGAAGAAAAAAG
33937359 TTAAAGAACA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.10
21 20 0.40
22 21 0.42
23 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (20 bp):
AAAGAAGAAAAAAGAAAGAG
Found at i:33937350 original size:18 final size:17
Alignment explanation
Indices: 33937285--33937346 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
33937275 AGCAAAAAGA
*
33937285 AAAAGAAAAGAAAG-AT
1 AAAAGAAGAGAAAGAAT
* *
33937301 GAAAGAAGAAAGAAGAA-
1 AAAAGAAGAGA-AAGAAT
*
33937318 AGAAGAA-AGAAAGAAT
1 AAAAGAAGAGAAAGAAT
33937334 AAAAGAAGAGAAA
1 AAAAGAAGAGAAA
33937347 AGAAGAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
15 5 0.14
16 16 0.46
17 13 0.37
18 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAGAAAGAAT
Found at i:33937364 original size:26 final size:26
Alignment explanation
Indices: 33937309--33937366 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
33937299 ATGAAAGAAG
*
33937309 AAAGAAGAAAGAAGAAAGAAAGAATA
1 AAAGAAGAAAGAAGAAAGAAAAAATA
*
33937335 AAAGAAGAGAA-AAG-AAGAAAAAAGTT
1 AAAGAAGA-AAGAAGAAAGAAAAAA-TA
33937361 AAAGAA
1 AAAGAA
33937367 CATGGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.29
26 18 0.64
27 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.05
Consensus pattern (26 bp):
AAAGAAGAAAGAAGAAAGAAAAAATA
Found at i:33959185 original size:28 final size:28
Alignment explanation
Indices: 33959136--33959193 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
33959126 AACGCCCCAA
*
33959136 TTTTCGAGATTTTCGAGATTTCTGTGATT
1 TTTTCGAGATTTTAGAGATTTCTGTG-TT
33959165 TTTTACGA-ATTTTAGA-ATTTCTGTGTT
1 TTTT-CGAGATTTTAGAGATTTCTGTGTT
33959192 TT
1 TT
33959194 GACTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 9 0.33
29 11 0.41
30 3 0.11
ACGTcount: A:0.19, C:0.09, G:0.17, T:0.55
Consensus pattern (28 bp):
TTTTCGAGATTTTAGAGATTTCTGTGTT
Found at i:33961119 original size:27 final size:26
Alignment explanation
Indices: 33961052--33961162 Score: 134
Period size: 27 Copynumber: 4.1 Consensus size: 26
33961042 AGAAGCGTTT
*
33961052 TGGTGGC-CATGCCACAAATATCTATTTC
1 TGGTGGCTC-TGCCAC-AATATCT-GTTC
*
33961080 TGGTGGCTATGCCACAAATATCTGTTC
1 TGGTGGCTCTGCCAC-AATATCTGTTC
33961107 TGGTGGCTCTGCCACAATATCTGTATC
1 TGGTGGCTCTGCCACAATATCTGT-TC
* *
33961134 TGGTGACTCTGTCACAATATCTGTTC
1 TGGTGGCTCTGCCACAATATCTGTTC
33961160 TGG
1 TGG
33961163 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
26 14 0.18
27 41 0.54
28 21 0.28
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (26 bp):
TGGTGGCTCTGCCACAATATCTGTTC
Found at i:33989944 original size:27 final size:27
Alignment explanation
Indices: 33989906--33990018 Score: 158
Period size: 27 Copynumber: 4.2 Consensus size: 27
33989896 GAGGAAGCAT
33989906 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
*
33989933 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
*
33989961 TCTGGTGGCTCTACCACAATATCTGTA
1 TCTGGTGGCTCTGCCACAATATCTGTA
* *
33989988 TCTGGTGACTCTGTCACAATATCTGT-
1 TCTGGTGGCTCTGCCACAATATCTGTA
33990014 TCTGG
1 TCTGG
33990019 CAGCCATGCT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 16 0.20
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAATATCTGTA
Found at i:33990012 original size:54 final size:54
Alignment explanation
Indices: 33989905--33990018 Score: 169
Period size: 55 Copynumber: 2.1 Consensus size: 54
33989895 GGAGGAAGCA
* *
33989905 TTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG
1 TTCTGGTGGCTCTACCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTG
*
33989959 TTTCTGGTGGCTCTACCAC-AATATCTGTATCTGGTGACTCTGTCAC-AATATCTG
1 -TTCTGGTGGCTCTACCACAAATATCTG-ATCTGGTGACTCTGCCACAAATATCTG
33990013 TTCTGG
1 TTCTGG
33990019 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 6 0.11
54 16 0.29
55 33 0.60
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (54 bp):
TTCTGGTGGCTCTACCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTG
Found at i:33990876 original size:412 final size:412
Alignment explanation
Indices: 33990112--33990936 Score: 1623
Period size: 412 Copynumber: 2.0 Consensus size: 412
33990102 GTATACGGAT
33990112 GAATATGGGTTGGGTTTTTTGCATACATGATATATCTGTTTTGTTTCTGTTATAGGCCTATAGGC
1 GAATATGGGTTGGGTTTTTTGCATACATGATATATCTGTTTTGTTTCTGTTATAGGCCTATAGGC
*
33990177 TTCATTCTGAATTCTGTATAGGGCTAAGGCCCAACTTAATCTGTTTCTGTGGTTTGAACTGATCT
66 TTCATTCTGAATTCTGTATAGGGCTAAGGCCCAACTTAATCTGTTTCTCTGGTTTGAACTGATCT
*
33990242 GGACTATGGTTATTTTACACATTGAGTCTTCCAAACTCACCCCTTAATTTTATCCGTGCAGGTAA
131 GGACTATGGTTATTTTACACATTGAGTCTTCCAAACTCACCCCTGAATTTTATCCGTGCAGGTAA
33990307 CCCCCAACCATAGTGGACTTGGAGCTGAGAGGGATTCGGAGTGGCTACATGTTTTGCTTGCTCAA
196 CCCCCAACCATAGTGGACTTGGAGCTGAGAGGGATTCGGAGTGGCTACATGTTTTGCTTGCTCAA
33990372 TTTTCTTCTTATGACTGGATTAGTTTCATTTACTTTAATTGCTTTGGGTTTTAAGTTGTAATAAG
261 TTTTCTTCTTATGACTGGATTAGTTTCATTTACTTTAATTGCTTTGGGTTTTAAGTTGTAATAAG
33990437 GCCGCTTTAATTATTTTTAATTGCTGTAGTATAATTATTAGCTTAGGCATGATATGGATTTAAAT
326 GCCGCTTTAATTATTTTTAATTGCTGTAGTATAATTATTAGCTTAGGCATGATATGGATTTAAAT
33990502 GTTTGAAATTGAATAGCTCTAG
391 GTTTGAAATTGAATAGCTCTAG
33990524 GAATATGGGTTGGGTTTTTTGCATACATGATATATCTGTTTTGTTTCTGTTATAGGCCTATAGGC
1 GAATATGGGTTGGGTTTTTTGCATACATGATATATCTGTTTTGTTTCTGTTATAGGCCTATAGGC
33990589 TTCATTCTGAATTCTGTATAGGGCTAAGGCCCAACTTAATCTGTTTCTCTGGTTTGAACTGATCT
66 TTCATTCTGAATTCTGTATAGGGCTAAGGCCCAACTTAATCTGTTTCTCTGGTTTGAACTGATCT
*
33990654 GGACTATGGTTATTTTACACATTGAGTCTTCCAAACTCACCCCTGAATTTTGTCCGTGCAGGTAA
131 GGACTATGGTTATTTTACACATTGAGTCTTCCAAACTCACCCCTGAATTTTATCCGTGCAGGTAA
33990719 CCCCCAACCATAGTGGACTTGGAGCTGAGAGGGATTCGGAGTGGCTACATGTTTTGCTTGCTCAA
196 CCCCCAACCATAGTGGACTTGGAGCTGAGAGGGATTCGGAGTGGCTACATGTTTTGCTTGCTCAA
33990784 TTTTCTTCTTATGACTGGATTAGTTTCATTTACTTTAATTGCTTTGGGTTTTAAGTTGTAATAAG
261 TTTTCTTCTTATGACTGGATTAGTTTCATTTACTTTAATTGCTTTGGGTTTTAAGTTGTAATAAG
33990849 GCCGCTTTAATTATTTTTAATTGCTGTAGTATAATTATTAGCTTAGGCATGATATGGATTTAAAT
326 GCCGCTTTAATTATTTTTAATTGCTGTAGTATAATTATTAGCTTAGGCATGATATGGATTTAAAT
33990914 GTTTGAAATTGAATAGCTCTAG
391 GTTTGAAATTGAATAGCTCTAG
33990936 G
1 G
33990937 GTGCGTTTTT
Statistics
Matches: 410, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
412 410 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (412 bp):
GAATATGGGTTGGGTTTTTTGCATACATGATATATCTGTTTTGTTTCTGTTATAGGCCTATAGGC
TTCATTCTGAATTCTGTATAGGGCTAAGGCCCAACTTAATCTGTTTCTCTGGTTTGAACTGATCT
GGACTATGGTTATTTTACACATTGAGTCTTCCAAACTCACCCCTGAATTTTATCCGTGCAGGTAA
CCCCCAACCATAGTGGACTTGGAGCTGAGAGGGATTCGGAGTGGCTACATGTTTTGCTTGCTCAA
TTTTCTTCTTATGACTGGATTAGTTTCATTTACTTTAATTGCTTTGGGTTTTAAGTTGTAATAAG
GCCGCTTTAATTATTTTTAATTGCTGTAGTATAATTATTAGCTTAGGCATGATATGGATTTAAAT
GTTTGAAATTGAATAGCTCTAG
Found at i:33991413 original size:353 final size:353
Alignment explanation
Indices: 33990756--33991469 Score: 1396
Period size: 353 Copynumber: 2.0 Consensus size: 353
33990746 AGAGGGATTC
33990756 GGAGTGG--CTACATGTTTTGCTTGCTCAATTTTCTTCTTATGACTGGATTAGTTTCATTTACTT
1 GGAGTGGATCTACATGTTTTGCTTGCTCAATTTTCTTCTTATGACTGGATTAGTTTCATTTACTT
33990819 TAATTGCTTTGGGTTTTAAGTTGTAATAAGGCCGCTTTAATTATTTTTAATTGCTGTAGTATAAT
66 TAATTGCTTTGGGTTTTAAGTTGTAATAAGGCCGCTTTAATTATTTTTAATTGCTGTAGTATAAT
33990884 TATTAGCTTAGGCATGATATGGATTTAAATGTTTGAAATTGAATAGCTCTAGGGTGCGTTTTTAA
131 TATTAGCTTAGGCATGATATGGATTTAAATGTTTGAAATTGAATAGCTCTAGGGTGCGTTTTTAA
33990949 AAGAGATTACCTGATTTCAAAATATCATGAAACAAGACAAAGCTTCCGAAATGAAAACGTTTTCA
196 AAGAGATTACCTGATTTCAAAATATCATGAAACAAGACAAAGCTTCCGAAATGAAAACGTTTTCA
*
33991014 AAAATTAATAGGTGTTTTCAAAGGCTTAAAATGAAATGGCTTTTCCTTAACAATCATTCAGTTAA
261 AAAATTAATAGGTGTTTTCAAAGGCTTAAAATGAAATGGCTTTTCCTGAACAATCATTCAGTTAA
33991079 AGTGTGGCAATGGTTGTGTGCATGTCTA
326 AGTGTGGCAATGGTTGTGTGCATGTCTA
33991107 GGAGTGGATCTACATGTTTTGCTTGCTCAATTTTCTTCTTATGACTGGATTAGTTTCATTTACTT
1 GGAGTGGATCTACATGTTTTGCTTGCTCAATTTTCTTCTTATGACTGGATTAGTTTCATTTACTT
33991172 TAATTGCTTTGGGTTTTAAGTTGTAATAAGGCCGCTTTAATTATTTTTAATTGCTGTAGTATAAT
66 TAATTGCTTTGGGTTTTAAGTTGTAATAAGGCCGCTTTAATTATTTTTAATTGCTGTAGTATAAT
33991237 TATTAGCTTAGGCATGATATGGATTTAAATGTTTGAAATTGAATAGCTCTAGGGTGCGTTTTTAA
131 TATTAGCTTAGGCATGATATGGATTTAAATGTTTGAAATTGAATAGCTCTAGGGTGCGTTTTTAA
33991302 AAGAGATTACCTGATTTCAAAATATCATGAAACAAGACAAAGCTTCCGAAATGAAAACGTTTTCA
196 AAGAGATTACCTGATTTCAAAATATCATGAAACAAGACAAAGCTTCCGAAATGAAAACGTTTTCA
*
33991367 AAAATTAATAGGTGTTTTCAAAGGCTTAAAATGAAATGGTTTTTCCTGAACAATCATTCAGTTAA
261 AAAATTAATAGGTGTTTTCAAAGGCTTAAAATGAAATGGCTTTTCCTGAACAATCATTCAGTTAA
33991432 AGTGTGGCAATGGTTGTGTGCATGTCTA
326 AGTGTGGCAATGGTTGTGTGCATGTCTA
33991460 GGAGTGGATC
1 GGAGTGGATC
33991470 CGTGGAGAGC
Statistics
Matches: 359, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
351 7 0.02
353 352 0.98
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (353 bp):
GGAGTGGATCTACATGTTTTGCTTGCTCAATTTTCTTCTTATGACTGGATTAGTTTCATTTACTT
TAATTGCTTTGGGTTTTAAGTTGTAATAAGGCCGCTTTAATTATTTTTAATTGCTGTAGTATAAT
TATTAGCTTAGGCATGATATGGATTTAAATGTTTGAAATTGAATAGCTCTAGGGTGCGTTTTTAA
AAGAGATTACCTGATTTCAAAATATCATGAAACAAGACAAAGCTTCCGAAATGAAAACGTTTTCA
AAAATTAATAGGTGTTTTCAAAGGCTTAAAATGAAATGGCTTTTCCTGAACAATCATTCAGTTAA
AGTGTGGCAATGGTTGTGTGCATGTCTA
Found at i:34001061 original size:40 final size:39
Alignment explanation
Indices: 34000963--34001225 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
34000953 TCCTCGTTCA
* * * *
34000963 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
34001002 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
34001041 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
34001081 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
34001121 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
34001161 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
34001202 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34001226 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:34001185 original size:120 final size:119
Alignment explanation
Indices: 34000963--34001225 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
34000953 TCCTCGTTCA
* * *
34000963 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
34001028 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
34001081 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
34001146 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
34001202 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
34001226 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:34001234 original size:41 final size:41
Alignment explanation
Indices: 34001157--34001234 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34001147 TTTGTATCTC
* * *
34001157 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34001198 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34001235 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34008985 original size:39 final size:40
Alignment explanation
Indices: 34008940--34009108 Score: 189
Period size: 40 Copynumber: 4.2 Consensus size: 40
34008930 GCTCCTCGTT
* * * *
34008940 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
34008980 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
34009019 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * ** *
34009059 CAAAGGCCTTCGGGGCTTAACCCAGAATTT-GTATTTTGCA
1 CAAATGCCTTCGGGACTTAACCC-GGATTTAGTAACTCGCA
34009099 CAAATGCCTT
1 CAAATGCCTT
34009109 TTGATCTTAG
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 34 0.31
40 72 0.65
41 5 0.05
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:34009109 original size:80 final size:79
Alignment explanation
Indices: 34008940--34009088 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 79
34008930 GCTCCTCGTT
* * * * *
34008940 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGAA
34009005 TTTAATAACTCGCA
66 TTTAATAACTCGCA
* * * * *
34009019 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCAG
1 CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCC-G
34009084 AATTT
64 AATTT
34009089 GTATTTTGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 34 0.59
80 19 0.33
81 5 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGAA
TTTAATAACTCGCA
Found at i:34021646 original size:35 final size:35
Alignment explanation
Indices: 34021596--34021670 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
34021586 GTTCTAGGAT
34021596 AATA-AAAACTCAAAAATTACAAGAAAAGAAATTA
1 AATAGAAAACTCAAAAATTACAAGAAAAGAAATTA
* *
34021630 AATAGAAAACTCAAAAATTATAAGAATAGAAATTA
1 AATAGAAAACTCAAAAATTACAAGAAAAGAAATTA
34021665 AATAGA
1 AATAGA
34021671 CTTACCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 4 0.11
35 34 0.89
ACGTcount: A:0.65, C:0.07, G:0.08, T:0.20
Consensus pattern (35 bp):
AATAGAAAACTCAAAAATTACAAGAAAAGAAATTA
Found at i:34021804 original size:8 final size:8
Alignment explanation
Indices: 34021793--34021823 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
34021783 GTTTAATATA
34021793 ATAATAAT
1 ATAATAAT
34021801 ATAATAAT
1 ATAATAAT
*
34021809 ATAATAGT
1 ATAATAAT
34021817 ATAATAA
1 ATAATAA
34021824 GTTTTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:34024416 original size:27 final size:25
Alignment explanation
Indices: 34024385--34024443 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
34024375 ATAAAAATCA
*
34024385 ATTTTCGAGCATAAGGGTAAAATGGTC
1 ATTTTCG-GC-TAAGGGCAAAATGGTC
*
34024412 ATTTTGTCGTCTAAGGGCAAAATGGTC
1 A-TTT-TCGGCTAAGGGCAAAATGGTC
34024439 ATTTT
1 ATTTT
34024444 ACCAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 17 0.61
28 4 0.14
29 3 0.11
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (25 bp):
ATTTTCGGCTAAGGGCAAAATGGTC
Found at i:34024895 original size:47 final size:47
Alignment explanation
Indices: 34024796--34024961 Score: 148
Period size: 47 Copynumber: 3.5 Consensus size: 47
34024786 TGTGAGAGCT
* * *
34024796 AGTGTAAGACCATGTCTGGGACATGGCATC-GAC-GTTG-AGATGAGTAC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTGATGAAG-TAAGT-C
34024843 GAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGATGAAGTAAGTC
1 -AGTGTAAGACCATGTCTGGGACATGCATCGGCCT-GATGAAGTAAGTC
* * * * *
34024891 AGTGTAAGA-CATGTTTGGGACATGCGTTGG-CTG-TGAGGCGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTGATGAAG-TA-AGTC
34024937 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
34024962 GCTTTGACTT
Statistics
Matches: 102, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 20 0.20
47 57 0.56
48 10 0.10
49 7 0.07
50 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCTGATGAAGTAAGTC
Found at i:34029956 original size:13 final size:13
Alignment explanation
Indices: 34029938--34029965 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34029928 ACAAAATTGG
34029938 AAAGATGAAAAAT
1 AAAGATGAAAAAT
34029951 AAAGATGAAAAAT
1 AAAGATGAAAAAT
34029964 AA
1 AA
34029966 TAAAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:34033933 original size:13 final size:12
Alignment explanation
Indices: 34033903--34033950 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
34033893 ATAGAGGAAG
34033903 AAGAGAAAGAAAA
1 AAGAGAAA-AAAA
34033916 AAGA-AAAAAAA
1 AAGAGAAAAAAA
*
34033927 GAGAGAAAAAAA
1 AAGAGAAAAAAA
*
34033939 TAAAAGAAAAAA
1 -AAGAGAAAAAA
34033951 TGAATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 7 0.23
12 10 0.33
13 13 0.43
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
AAGAGAAAAAAA
Found at i:34033948 original size:22 final size:22
Alignment explanation
Indices: 34033903--34033948 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
34033893 ATAGAGGAAG
34033903 AAGAGAAAGAAAAAAGAAAAAA
1 AAGAGAAAGAAAAAAGAAAAAA
* *
34033925 AAGAGAGA-AAAAAATAAAAGAA
1 AAGAGAAAGAAAAAAGAAAA-AA
34033947 AA
1 AA
34033949 AATGAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAGAGAAAGAAAAAAGAAAAAA
Found at i:34044413 original size:39 final size:39
Alignment explanation
Indices: 34044249--34044431 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
34044239 TTGAATGCTG
* * * * * * *
34044249 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
34044289 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
34044329 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
34044369 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
34044408 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
34044432 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:34044451 original size:79 final size:80
Alignment explanation
Indices: 34044285--34044466 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
34044275 GCTAAGTGAA
* * * *
34044285 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
34044349 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
34044365 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
34044429 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
34044444 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
34044467 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:34044576 original size:34 final size:34
Alignment explanation
Indices: 34044531--34044598 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
34044521 AACATCCCAA
*
34044531 TATGGGGATATGTTACGTATGTGTTGAATTTAAT
1 TATGGGAATATGTTACGTATGTGTTGAATTTAAT
34044565 TATGGGAATATGTTACGTATGTGTTGAATTTAAT
1 TATGGGAATATGTTACGTATGTGTTGAATTTAAT
34044599 CGAGCCCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (34 bp):
TATGGGAATATGTTACGTATGTGTTGAATTTAAT
Found at i:34052234 original size:40 final size:40
Alignment explanation
Indices: 34052135--34052359 Score: 222
Period size: 40 Copynumber: 5.7 Consensus size: 40
34052125 TTGAATGCTG
* * * * *
34052135 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
34052175 TCCGGATTAAGAT-CAGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * **
34052215 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* **
34052255 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
34052295 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
34052334 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
34052360 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
39 34 0.22
40 115 0.73
41 8 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34056970 original size:22 final size:25
Alignment explanation
Indices: 34056924--34056971 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
34056914 TTTATTTGAT
34056924 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAACAAATTAA
34056949 AATAT-TTTTGA-ATAA-AAATTAA
1 AATATGTTTTGATATAACAAATTAA
34056971 A
1 A
34056972 GTTGAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 6 0.26
25 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (25 bp):
AATATGTTTTGATATAACAAATTAA
Found at i:34057103 original size:20 final size:19
Alignment explanation
Indices: 34057078--34057135 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 19
34057068 CCTTTAAATT
34057078 AAGTTAAAATGGTTTCAATC-
1 AAGTTAAAAT--TTTCAATCA
34057098 AAGTTAGAAATTTTCAATCA
1 AAGTTA-AAATTTTCAATCA
34057118 AAGTTAAACTATTTTCAA
1 AAGTTAAA--ATTTTCAA
34057136 AACAAGTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.29
20 12 0.35
21 12 0.35
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (19 bp):
AAGTTAAAATTTTCAATCA
Found at i:34059374 original size:21 final size:20
Alignment explanation
Indices: 34059310--34059380 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
34059300 CGTGATTTTG
*
34059310 TATCGATACCATTTTAAAAT
1 TATCGATACCATTTAAAAAT
* *
34059330 TATCAATA-TATTTATAAAAT
1 TATCGATACCATTTA-AAAAT
*
34059350 TATCGATACCATCTTAAAAAA
1 TATCGATACCAT-TTAAAAAT
34059371 TATCGATACC
1 TATCGATACC
34059381 TATCGGGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 4 0.10
20 19 0.45
21 16 0.38
22 3 0.07
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (20 bp):
TATCGATACCATTTAAAAAT
Found at i:34061625 original size:20 final size:19
Alignment explanation
Indices: 34061600--34061657 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
34061590 TCAACCTTTA
34061600 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
* *
34061620 AATCAAGTTAGAATTTTTC
1 AATCAAGTTAAAATGTTTC
*
34061639 AATCAAAGTTAAATTGTTT
1 AATC-AAGTTAAAATGTTT
34061658 TTAAAACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:34067463 original size:10 final size:11
Alignment explanation
Indices: 34067436--34067464 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34067426 GGTAATTAAA
34067436 AATATTTTTTT
1 AATATTTTTTT
34067447 AATATTTTTTT
1 AATATTTTTTT
34067458 AA-ATTTT
1 AATATTTT
34067465 CAATAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:34073529 original size:18 final size:18
Alignment explanation
Indices: 34073496--34073530 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34073486 GTCCTCTTAT
*
34073496 TCTTCGGGATCTTCCTCC
1 TCTTCGGGATCCTCCTCC
*
34073514 TCTTCGGGGTCCTCCTC
1 TCTTCGGGATCCTCCTC
34073531 ATCAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.40, G:0.20, T:0.37
Consensus pattern (18 bp):
TCTTCGGGATCCTCCTCC
Found at i:34076304 original size:26 final size:26
Alignment explanation
Indices: 34076246--34076304 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
34076236 TTCTTTTAAG
34076246 TTAGAA-AATTCTTTTTGAGTTTTAT
1 TTAGAAGAATTCTTTTTGAGTTTTAT
**
34076271 TTTCAAGAATT-TTTGTTGAGTTTCT-T
1 TTAGAAGAATTCTTT-TTGAGTTT-TAT
34076297 TTAGAAGA
1 TTAGAAGA
34076305 CTTATAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
25 7 0.26
26 19 0.70
27 1 0.04
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (26 bp):
TTAGAAGAATTCTTTTTGAGTTTTAT
Found at i:34077745 original size:16 final size:17
Alignment explanation
Indices: 34077712--34077745 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34077702 AGATTCATCC
34077712 TCGAATCTTGGCTTTGA
1 TCGAATCTTGGCTTTGA
34077729 TCGAATCTTGG-TTTGA
1 TCGAATCTTGGCTTTGA
34077745 T
1 T
34077746 TTGCTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (17 bp):
TCGAATCTTGGCTTTGA
Found at i:34078872 original size:14 final size:14
Alignment explanation
Indices: 34078853--34078879 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34078843 AAATTATAAA
34078853 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
34078867 TTTAGGGTTTAGA
1 TTTAGGGTTTAGA
34078880 ATTTGTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:34080097 original size:60 final size:60
Alignment explanation
Indices: 34079919--34080104 Score: 248
Period size: 60 Copynumber: 3.1 Consensus size: 60
34079909 GTGCCCCTGC
* * * ** * **
34079919 GTGCCCATGTATACACTCTGGTGTCTCTATTTGCACGCCTGTGCTCCTGTTCGCACTTCA
1 GTGCCCCTATATACACTCTGGTGTCCCTATTTGCACGTATGTGCCCCTGTTCGCACTTTG
* * *
34079979 ATGCCCCTATATACACTCTGGTGTCCCTGTTTGCACGTATGTGCCCTTGTTCGCACTTTG
1 GTGCCCCTATATACACTCTGGTGTCCCTATTTGCACGTATGTGCCCCTGTTCGCACTTTG
*
34080039 GTGCCCCTATATACACT-TCGGTGTCCCTATTTGCACGTATCTGCCCCTGTTCGCACTTTG
1 GTGCCCCTATATACACTCT-GGTGTCCCTATTTGCACGTATGTGCCCCTGTTCGCACTTTG
34080099 GTGCCC
1 GTGCCC
34080105 ATGACTGTAC
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
59 1 0.01
60 109 0.99
ACGTcount: A:0.13, C:0.32, G:0.20, T:0.35
Consensus pattern (60 bp):
GTGCCCCTATATACACTCTGGTGTCCCTATTTGCACGTATGTGCCCCTGTTCGCACTTTG
Found at i:34080103 original size:20 final size:20
Alignment explanation
Indices: 34079992--34080104 Score: 61
Period size: 20 Copynumber: 5.7 Consensus size: 20
34079982 CCCCTATATA
* * *
34079992 CACTCTGGTGTCCCTGTTTG
1 CACTTTGGTGCCCCTGTTCG
* *
34080012 CACGTAT-GTGCCCTTGTTCG
1 CAC-TTTGGTGCCCCTGTTCG
* *
34080032 CACTTTGGTGCCCCTATAT-A
1 CACTTTGGTGCCCCTGT-TCG
* * * *
34080052 CACTTCGGTGTCCCTATTTG
1 CACTTTGGTGCCCCTGTTCG
* *
34080072 CACGTAT-CTGCCCCTGTTCG
1 CAC-TTTGGTGCCCCTGTTCG
34080092 CACTTTGGTGCCC
1 CACTTTGGTGCCC
34080105 ATGACTGTAC
Statistics
Matches: 68, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 5 0.07
20 59 0.87
21 4 0.06
ACGTcount: A:0.11, C:0.33, G:0.21, T:0.35
Consensus pattern (20 bp):
CACTTTGGTGCCCCTGTTCG
Found at i:34083350 original size:4 final size:4
Alignment explanation
Indices: 34083341--34083379 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
34083331 ATGAGTTATT
* * *
34083341 TAAG TAAG TAAG TAAG TAAA CAAG TAAG CAAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
34083380 AGAAGTGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (4 bp):
TAAG
Found at i:34089580 original size:23 final size:24
Alignment explanation
Indices: 34089530--34089580 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
34089520 TTACTTATAA
* *
34089530 ATTTTTAATAAATTTAAAATTTTT
1 ATTTTTAATAAATTTAAAATTATG
* *
34089554 ATTTTT-ATATATTTTAAATTATG
1 ATTTTTAATAAATTTAAAATTATG
34089577 ATTT
1 ATTT
34089581 CATTATGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTTTAATAAATTTAAAATTATG
Found at i:34094223 original size:26 final size:26
Alignment explanation
Indices: 34094194--34094245 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
34094184 TTCAATGCAT
34094194 ATTACTTGATCATATCCAAAGGACAA
1 ATTACTTGATCATATCCAAAGGACAA
34094220 ATTACTTGATCATATCCAAAGGACAA
1 ATTACTTGATCATATCCAAAGGACAA
34094246 CTCAGCCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (26 bp):
ATTACTTGATCATATCCAAAGGACAA
Found at i:34100105 original size:138 final size:140
Alignment explanation
Indices: 34099729--34100261 Score: 698
Period size: 140 Copynumber: 3.8 Consensus size: 140
34099719 ATTCGCAATC
* * * * *
34099729 ATCTAACCATCTAACGAAAGGAGCTAACATGTT-AAAAATATTAATTAAAATAATAAAAAATGCT
1 ATCTAACCATCTAACGAAA-AAACTAATATGTTAAAAAACATTAATTAAAA-AATTAAAAA-GCT
** * *
34099793 TGAAGCAACATGAAATGCAAAATACAAATGTGATTAGTAGAGGAATCCAACTCGAGACTC-AAGA
63 TGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATCAAACTCGAGACTCAAAG-
34099857 ATGTAATTACAACT
127 ATGTAATTACAACT
* *
34099871 ATGTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAATTTAAAAAGCTTGA
1 ATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAATTAAAAAGCTTGA
* * * *
34099936 AGCAACATGAAATAAAAAATACAAGTTTGAGTAGAAGAGAAATCAAACTCGAGACTCAAAGATGT
66 AGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATCAAACTCGAGACTCAAAGATGT
** *
34100001 AACAATAACT
131 AATTACAACT
* * * *
34100011 ATCTAACCATCTAAC-AAAAGAATTAATATGTT-AACAA-ATTAATTAAAAATTTAAAAAGATTG
1 ATCTAACCATCTAACGAAAA-AACTAATATGTTAAAAAACATTAATTAAAAAATTAAAAAGCTTG
* * * * * *
34100073 AAGCAACATGAGACAAAAAATACAAATGTGAGTAGTAGATGAATCCAACTCGAGACTTAAGGATG
65 AAGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATCAAACTCGAGACTCAAAGATG
34100138 TAATTACAACT
130 TAATTACAACT
* *
34100149 ATCTAACCATCTAACGAAAAACCTAATATGTTAAAAAACATTAATTAAAAAATTAAAAAGCTTAA
1 ATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAATTAAAAAGCTTGA
* *
34100214 AGCAACATGAAATAAAAAATACAAATGTGAGCAGGAGAGGAATCAAAC
66 AGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATCAAAC
34100262 CTAGAACTCA
Statistics
Matches: 338, Mismatches: 47, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
138 112 0.33
139 16 0.05
140 156 0.46
141 20 0.06
142 34 0.10
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (140 bp):
ATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAATTAAAAAGCTTGA
AGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATCAAACTCGAGACTCAAAGATGT
AATTACAACT
Found at i:34100144 original size:278 final size:282
Alignment explanation
Indices: 34099729--34100261 Score: 813
Period size: 278 Copynumber: 1.9 Consensus size: 282
34099719 ATTCGCAATC
* * *
34099729 ATCTAACCATCTAACGAAAGGAGCTAACATGTTAAAAATATTAATTAAAATAATAAAAAATGCTT
1 ATCTAACCATCTAACGAAAAGAACTAACATGTTAAAAATATTAATTAAAATAATAAAAAATGATT
*** *
34099794 GAAGCAACATGAAATGCAAAATACAAATGTGATTAGTAGAGGAATCCAACTCGAGACTCAAGAAT
66 GAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGAGGAATCCAACTCGAGACTCAAGAAT
* *
34099859 GTAATTACAACTATGTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAATT
131 GTAATTACAACTATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAAT
* * * *
34099924 TAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAGTTTGAGTAGAAGAGAAATCAAACTCGAG
196 TAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGCAGAAGAGAAATCAAACTCGAG
34099989 ACTCAAAGATGTAACAATAACT
261 ACTCAAAGATGTAACAATAACT
* * * * *
34100011 ATCTAACCATCTAAC-AAAAGAATTAATATGTTAACAA-ATTAATTAAAA-ATTTAAAAA-GATT
1 ATCTAACCATCTAACGAAAAGAACTAACATGTTAAAAATATTAATTAAAATAATAAAAAATGATT
* * * *
34100072 GAAGCAACATGAGACAAAAAATACAAATGTGAGTAGTAGATGAATCCAACTCGAGACTTAAGGAT
66 GAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGAGGAATCCAACTCGAGACTCAAGAAT
*
34100137 GTAATTACAACTATCTAACCATCTAACGAAAAACCTAATATGTTAAAAAACATTAATTAAAAAAT
131 GTAATTACAACTATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAAT
* *
34100202 TAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGCAGGAGAGGAATCAAAC
196 TAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGCAGAAGAGAAATCAAAC
34100262 CTAGAACTCA
Statistics
Matches: 226, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
278 176 0.78
279 7 0.03
280 11 0.05
281 17 0.08
282 15 0.07
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (282 bp):
ATCTAACCATCTAACGAAAAGAACTAACATGTTAAAAATATTAATTAAAATAATAAAAAATGATT
GAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGAGGAATCCAACTCGAGACTCAAGAAT
GTAATTACAACTATCTAACCATCTAACGAAAAAACTAATATGTTAAAAAACATTAATTAAAAAAT
TAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGCAGAAGAGAAATCAAACTCGAG
ACTCAAAGATGTAACAATAACT
Found at i:34105719 original size:18 final size:18
Alignment explanation
Indices: 34105690--34105736 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
34105680 TCAACATCAT
34105690 AATTAGAATAAAATATTTA
1 AATTA-AATAAAATATTTA
34105709 AATTAAATAAAATATTTA
1 AATTAAATAAAATATTTA
34105727 AATTAAATAA
1 AATTAAATAA
34105737 CGATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATTAAATAAAATATTTA
Found at i:34111211 original size:3 final size:3
Alignment explanation
Indices: 34111203--34111237 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
34111193 TGAATTCTAA
34111203 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34111238 AGAAATGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34112020 original size:29 final size:29
Alignment explanation
Indices: 34111935--34112020 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
34111925 GGGTTTAAAA
* *
34111935 GTTCTGAAAAAAATAA-TTTGTACAATATGG
1 GTTCTG-AAAAAATAATTTTG-ACGAGATGG
* * *
34111965 GTT-TGAAAAAATATTTTTGAGGGGATGG
1 GTTCTGAAAAAATAATTTTGACGAGATGG
34111993 GTTCT-AAAGAAATAATTTTGACGAGATG
1 GTTCTGAAA-AAATAATTTTGACGAGATG
34112021 AGTTGAGTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
28 19 0.42
29 23 0.51
30 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
GTTCTGAAAAAATAATTTTGACGAGATGG
Found at i:34114312 original size:42 final size:43
Alignment explanation
Indices: 34114245--34114349 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
34114235 GATTTGAGAT
* * *
34114245 TTACGTGTAAGACCATGTTTGGGACA-TTAGC-GC-TGTATATGA
1 TTACATGTAAGACCATGTCTAGGACAGTT-GCAGCAT-TATATGA
* * *
34114287 TTACATGTAAGACCCTGTCTAGGACAGTTGCATCATTATTTGA
1 TTACATGTAAGACCATGTCTAGGACAGTTGCAGCATTATATGA
*
34114330 TTACATGTAAGACCACGTCT
1 TTACATGTAAGACCATGTCT
34114350 GGCACGTTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 24 0.46
43 27 0.52
44 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTAGGACAGTTGCAGCATTATATGA
Found at i:34116850 original size:31 final size:31
Alignment explanation
Indices: 34116812--34116870 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
34116802 ATTAAAAAGA
*
34116812 TTAAAATTTATTCTTACCATTTGCAATTGGT
1 TTAAAATTTATTATTACCATTTGCAATTGGT
34116843 TTAAAATTTATTATTACCATTTGCAATT
1 TTAAAATTTATTATTACCATTTGCAATT
34116871 AGTTGACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
TTAAAATTTATTATTACCATTTGCAATTGGT
Found at i:34117015 original size:18 final size:19
Alignment explanation
Indices: 34116992--34117037 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
34116982 ATAAAAAATA
*
34116992 ATAAAATTTATAATTTA-G
1 ATAAAATTTAGAATTTAGG
*
34117010 ATAAAA-ATAGAATTTAGG
1 ATAAAATTTAGAATTTAGG
*
34117028 AAAAAATTTA
1 ATAAAATTTA
34117038 AGAGATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (19 bp):
ATAAAATTTAGAATTTAGG
Found at i:34119029 original size:29 final size:30
Alignment explanation
Indices: 34118973--34119029 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
34118963 ATTTTGTAGC
* * **
34118973 AAAATTCAATAAATTTCAAAGTTTAATAAA
1 AAAATTCAATAAATATAAAAGTCGAATAAA
34119003 AAAATTCAAT-AATATAAAAGTCGAATA
1 AAAATTCAATAAATATAAAAGTCGAATA
34119030 TTAAATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAATTCAATAAATATAAAAGTCGAATAAA
Found at i:34120311 original size:13 final size:15
Alignment explanation
Indices: 34120288--34120319 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34120278 AATCCCACCC
34120288 AATACACAGAT-ACA
1 AATACACAGATAACA
34120302 AATA-ACAGATAACA
1 AATACACAGATAACA
34120316 AATA
1 AATA
34120320 TATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (15 bp):
AATACACAGATAACA
Found at i:34121561 original size:69 final size:68
Alignment explanation
Indices: 34121450--34121586 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 68
34121440 GGGACTTGAA
*
34121450 CCCAAGACTTTAAACACACAATCAGAACACTTAACCATCGAAGTAGATTACTTATTTATGACAAA
1 CCCAAGACTTTAAACACACAATCAGAACACTTAACCACCGAAGTAGA-TACTTATTTATGACAAA
34121515 TTTC
65 TTTC
34121519 CCCAAGACTTTAAACACACAATCAGAACACTTAACCACCGAAGTAGATACTTATTTATGACAAAT
1 CCCAAGACTTTAAACACACAATCAGAACACTTAACCACCGAAGTAGATACTTATTTATGACAAAT
34121584 TTC
66 TTC
34121587 ACAAAAACAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 21 0.31
69 46 0.69
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (68 bp):
CCCAAGACTTTAAACACACAATCAGAACACTTAACCACCGAAGTAGATACTTATTTATGACAAAT
TTC
Found at i:34123690 original size:45 final size:45
Alignment explanation
Indices: 34123592--34123779 Score: 247
Period size: 45 Copynumber: 4.2 Consensus size: 45
34123582 AATAATAACA
* * * *
34123592 GATACACGGTGG-ATCAGCACATAGC-ACCACCTTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
* * * *
34123635 GATACTCGGTGGAATCAGCACATAGCAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
34123680 -AGTACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
* *
34123725 GATACCCGGTGGAATCAGTACACAACAACCGCCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
*
34123770 GGTACCCGGT
1 GATACCCGGT
34123780 ACACGTAGTA
Statistics
Matches: 131, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
43 11 0.08
44 14 0.11
45 105 0.80
46 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
Found at i:34125244 original size:31 final size:29
Alignment explanation
Indices: 34125209--34125302 Score: 107
Period size: 29 Copynumber: 3.1 Consensus size: 29
34125199 GTATTAGGAG
34125209 GTCCCTATATTATTGAAACTAGATCAAATTA
1 GTCCCTATATTATT-AAA-TAGATCAAATTA
* * *
34125240 GTCCCTCTATTATTAAATGGATCAATTTA
1 GTCCCTATATTATTAAATAGATCAAATTA
* * *
34125269 GTCCCTATACTATTAAAAAGAATCAAATAA
1 GTCCCTATATTATTAAATAG-ATCAAATTA
34125299 GTCC
1 GTCC
34125303 ATATTGTAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
29 26 0.49
30 14 0.26
31 13 0.25
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (29 bp):
GTCCCTATATTATTAAATAGATCAAATTA
Found at i:34125533 original size:29 final size:31
Alignment explanation
Indices: 34125469--34125535 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
34125459 ATTTGGTCTT
*
34125469 ATTTGATTCATTTTAATAGTACAAGGATCAA
1 ATTTGATCCATTTTAATAGTACAAGGATCAA
*
34125500 A-TTGATCCA-TTTAATAGTA-GAGCGA-CAA
1 ATTTGATCCATTTTAATAGTACAAG-GATCAA
34125528 ATTTGATC
1 ATTTGATC
34125536 AAATCCCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.19
29 18 0.56
30 7 0.22
31 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (31 bp):
ATTTGATCCATTTTAATAGTACAAGGATCAA
Found at i:34133011 original size:10 final size:9
Alignment explanation
Indices: 34132994--34133019 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
34132984 TTTTCTTTTT
34132994 ATAAAAAAA
1 ATAAAAAAA
34133003 ATAAAAAAA
1 ATAAAAAAA
34133012 ATAAAAAA
1 ATAAAAAA
34133020 TTTATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:34138206 original size:27 final size:28
Alignment explanation
Indices: 34138163--34138226 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 28
34138153 GAACATATCT
34138163 TAACATAT-AAAAGCATATTATAAATCA
1 TAACATATCAAAAGCATATTATAAATCA
*
34138190 TACCATATCAAAA-CATATTATAAATCA
1 TAACATATCAAAAGCATATTATAAATCA
34138217 TAACATATCA
1 TAACATATCA
34138227 TATCATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.30
Consensus pattern (28 bp):
TAACATATCAAAAGCATATTATAAATCA
Found at i:34138939 original size:48 final size:49
Alignment explanation
Indices: 34138887--34139024 Score: 179
Period size: 49 Copynumber: 2.8 Consensus size: 49
34138877 ATCTGCATGG
* * * * *
34138887 TTTCACACAACCGTGTGCCCCAC-ACGCCTACCCACATGGCTTGCTTTA
1 TTTCAAACGACCGTGTGCCCTACAAGGCCTACCCACATGGCTTGCATTA
* *
34138935 TTTCAAACGGCCATGTGCCCTACAAGGCCTACCCACATGGCTTGCATTA
1 TTTCAAACGACCGTGTGCCCTACAAGGCCTACCCACATGGCTTGCATTA
* * *
34138984 TTTCAAAGGACCGTGTGTCCTACAAGGCTTACCCACATGGC
1 TTTCAAACGACCGTGTGCCCTACAAGGCCTACCCACATGGC
34139025 CTACAAAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
48 18 0.23
49 59 0.77
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (49 bp):
TTTCAAACGACCGTGTGCCCTACAAGGCCTACCCACATGGCTTGCATTA
Found at i:34141986 original size:114 final size:114
Alignment explanation
Indices: 34141853--34142083 Score: 390
Period size: 114 Copynumber: 2.0 Consensus size: 114
34141843 TTAAACTAAA
* *
34141853 TTTATATTAAATTTATATATTTTATAATTAAATTGAAATAAAAATTAAAATATCATTAAATGGTA
1 TTTATATTAAATTTATATATTTTATAATTAAATTGAAATAAAAATAAAAATATCATTAAATAGTA
* *
34141918 ATTCGGATTGGATTAAATTTAATTTATATAATCTTTATCCAAGGTCTTT
66 ATTCGGATTGGATTAAATTGAACTTATATAATCTTTATCCAAGGTCTTT
* *
34141967 TTTATATTAAATTTTTATATTTTATAATTAAATTTAAATAAAAATAAAAATATCATTAAATAGTA
1 TTTATATTAAATTTATATATTTTATAATTAAATTGAAATAAAAATAAAAATATCATTAAATAGTA
* *
34142032 ATTCGGATTGGATTAGATTGAACTTATATAATCTTTATCCAAGGTTTTT
66 ATTCGGATTGGATTAAATTGAACTTATATAATCTTTATCCAAGGTCTTT
34142081 TTT
1 TTT
34142084 TTATGTTTGA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (114 bp):
TTTATATTAAATTTATATATTTTATAATTAAATTGAAATAAAAATAAAAATATCATTAAATAGTA
ATTCGGATTGGATTAAATTGAACTTATATAATCTTTATCCAAGGTCTTT
Found at i:34143570 original size:17 final size:16
Alignment explanation
Indices: 34143532--34143570 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
34143522 TGATAACAAT
34143532 ATTTTTAATTATTTAA
1 ATTTTTAATTATTTAA
* *
34143548 AATTTTAATATATTTTA
1 ATTTTTAAT-TATTTAA
34143565 ATTTTT
1 ATTTTT
34143571 TTAAAAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTAATTATTTAA
Found at i:34143848 original size:22 final size:22
Alignment explanation
Indices: 34143807--34143848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
34143797 TGTTGGTAAC
*
34143807 TTTAAATTTGTTTAGTTTTTTT
1 TTTAAATTTGTATAGTTTTTTT
*
34143829 TTTAAATTT-TATAGTATTTT
1 TTTAAATTTGTATAGTTTTTT
34143849 GGTTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTAAATTTGTATAGTTTTTTT
Found at i:34150924 original size:15 final size:14
Alignment explanation
Indices: 34150896--34150932 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
34150886 TACCGATTTG
34150896 AAGTA-TTTTGGGT
1 AAGTATTTTTGGGT
34150909 AAGTATTTTATGGGT
1 AAGTATTTT-TGGGT
34150924 AAGTATTTT
1 AAGTATTTT
34150933 GATTTCGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 3 0.14
15 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
AAGTATTTTTGGGT
Found at i:34152674 original size:18 final size:19
Alignment explanation
Indices: 34152633--34152677 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
34152623 TAAAAAAAAC
34152633 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
34152652 A-TTTGTAAA-TGAATAAT-
1 ATTTTG-AAATTGAATAATG
34152669 ATTTTGAAA
1 ATTTTGAAA
34152678 ACGAACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:34156821 original size:9 final size:9
Alignment explanation
Indices: 34156807--34156868 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
34156797 TTCACATCCT
34156807 TCTCTCAAC
1 TCTCTCAAC
*
34156816 TCTCTCAAT
1 TCTCTCAAC
* *
34156825 TCTTTCAAAT
1 TCTCTC-AAC
34156835 TCTCTCAAAC
1 TCTCTC-AAC
* *
34156845 ACTCTCAAG
1 TCTCTCAAC
34156854 TCTCTCAAC
1 TCTCTCAAC
34156863 TCTCTC
1 TCTCTC
34156869 GCTTTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
9 28 0.64
10 16 0.36
ACGTcount: A:0.24, C:0.37, G:0.02, T:0.37
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:34164915 original size:27 final size:28
Alignment explanation
Indices: 34164878--34164934 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
34164868 TCAAATATTG
*
34164878 TAATATCATCA-TAT-ACATATCATTCAA
1 TAATATAATCATTATCACAT-TCATTCAA
*
34164905 TAATATAATCATTTTCACATTCATTCAA
1 TAATATAATCATTATCACATTCATTCAA
34164933 TA
1 TA
34164935 CATTGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 12 0.46
29 4 0.15
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATATAATCATTATCACATTCATTCAA
Found at i:34169123 original size:287 final size:287
Alignment explanation
Indices: 34168607--34169125 Score: 984
Period size: 287 Copynumber: 1.8 Consensus size: 287
34168597 CGAAAACCCG
*
34168607 AAAAATAAAGAACCATCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGGGTTCTAATCTAA
1 AAAAATAAAGAACCATCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
*
34168672 TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTTATATGTCAAATAATAA
66 TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
34168737 TAAAATAATCTAAACTAATCAATGTTTGACTGAAATAAATAAACAGAGTTTAACTAAAAGATTAT
131 TAAAATAATCTAAACTAATCAATGTTTGACTGAAATAAATAAACAGAGTTTAACTAAAAGATTAT
34168802 TTTTCAAATTTGACTAAAAATAGGAGTCATACTTAACAAATCTCCACCTTGACTCATATTTCCAC
196 TTTTCAAATTTGACTAAAAATAGGAGTCATACTTAACAAATCTCCACCTTGACTCATATTTCCAC
34168867 AACGCCATATTTGCCAACAAAAACTCA
261 AACGCCATATTTGCCAACAAAAACTCA
*
34168894 AAAAATAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
1 AAAAATAAAGAACCATCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
34168959 TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
66 TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
* *
34169024 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
131 TAAAATAATCTAAACTAATCAATGTTTGACTGAAATAAATAAACAGAGTTTAACTAAAAGATTAT
*
34169089 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAAC
196 TTTTCAAATTTGACTAAAAATAGGAGTCATACTTAAC
34169126 GTGGAAAAAC
Statistics
Matches: 226, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
287 226 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (287 bp):
AAAAATAAAGAACCATCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
TAAAATAATCTAAACTAATCAATGTTTGACTGAAATAAATAAACAGAGTTTAACTAAAAGATTAT
TTTTCAAATTTGACTAAAAATAGGAGTCATACTTAACAAATCTCCACCTTGACTCATATTTCCAC
AACGCCATATTTGCCAACAAAAACTCA
Found at i:34169533 original size:346 final size:346
Alignment explanation
Indices: 34168894--34169817 Score: 1776
Period size: 346 Copynumber: 2.7 Consensus size: 346
34168884 CAAAAACTCA
*
34168894 AAAAATAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
1 AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
* *
34168959 TGGGTGTTTTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
66 TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
34169024 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
131 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
34169089 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAACGTGGAAAAACCCCTCCAAAGAGGATAAA
196 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAACGTGGAAAAACCCCTCCAAAGAGGATAAA
34169154 AAACCACGGGCAAAGATAATTTTACTATAATGGAAAAAGAATGAAGAGTACAAAAGATGGAGATA
261 AAACCACGGGCAAAGATAATTTTACTATAATGGAAAAAGAATGAAGAGTACAAAAGATGGAGATA
34169219 AAACTAAACCCCGAAAACCCG
326 AAACTAAACCCCGAAAACCCG
34169240 AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
1 AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
34169305 TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
66 TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
34169370 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
131 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
34169435 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAACGTGGAAAAACCCCTCCAAAGAGGATAAA
196 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAACGTGGAAAAACCCCTCCAAAGAGGATAAA
34169500 AAACCACGGGCAAAGATAATTTTACTATAATGGAAAAAGAATGAAGAGTACAAAAGATGGAGATA
261 AAACCACGGGCAAAGATAATTTTACTATAATGGAAAAAGAATGAAGAGTACAAAAGATGGAGATA
34169565 AAACTAAACCCCGAAAACCCG
326 AAACTAAACCCCGAAAACCCG
34169586 AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
1 AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
34169651 TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
66 TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
* * * *
34169716 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAACAAATAAACAAAGTTTAATTAAAAGATTAT
131 TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
*
34169781 TTCTCAAATTTGACTGAAAATAGGAGTCATACTTAAC
196 TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAAC
34169818 AAATCTCCAC
Statistics
Matches: 570, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
346 570 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (346 bp):
AAAAACAAAGAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAA
TGGATGTTTTTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAA
TAAAATAATCTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTAT
TTTTCAAATTTGACTGAAAATAGGAGTCATACTTAACGTGGAAAAACCCCTCCAAAGAGGATAAA
AAACCACGGGCAAAGATAATTTTACTATAATGGAAAAAGAATGAAGAGTACAAAAGATGGAGATA
AAACTAAACCCCGAAAACCCG
Found at i:34175741 original size:30 final size:30
Alignment explanation
Indices: 34175705--34175764 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34175695 GGTCTCTTTC
34175705 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
1 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
34175735 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
1 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
34175765 TTAAGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (30 bp):
ATGTTTTCTAATTAAGTGATTAGAGTTTAT
Found at i:34178385 original size:28 final size:28
Alignment explanation
Indices: 34178354--34178893 Score: 184
Period size: 28 Copynumber: 19.4 Consensus size: 28
34178344 AGTCGTTTCA
* *
34178354 TGGATAGGTATCATTAGGAGTCGTACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* *
34178382 TGGATGGGTACCATTATGAGTCATACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** ***
34178410 T--AAAGAATACCAGTAGGAGTTGTATAA
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * * * * *
34178437 TAGATAGATACCTTTAAGAGTCGTATCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* ** *
34178465 TGGAT-GAGTACCAATAGGAGTTGTATCG
1 TGGATAG-GTACCATTAGGAGTCATACCG
** * *
34178493 TGGAGGGGTACTATTAGGAGTCATACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** ***
34178521 TGGAT-GATACCTTTAAGAGTTGTGTAG
1 TGGATAGGTACCATTAGGAGTCATACCG
**
34178548 TGGATAGGTACCATTAGGAGTTTTACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* *
34178576 TAGAT-GCGTACCTTTAGGAGTCATACCG
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * *
34178604 TGGGTAGGTACC-TATAGGAGTCATGCCA
1 TGGATAGGTACCAT-TAGGAGTCATACCG
* * * *
34178632 TGGAT-GAATACTATTATGAGTCATACCA
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * **
34178660 TGGATAGGTACCTTTAAGAGTCATGTCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** *
34178688 TAGAT-GGATACCACTAGAAGTTGTACCA
1 TGGATAGG-TACCATTAGGAGTCATACCG
** * * ** **
34178716 TGGAGGGGAACCATTAGGAATTTTATTG
1 TGGATAGGTACCATTAGGAGTCATACCG
* **
34178744 TGGAT-GGCTACTATTAGGAGTCATGTCG
1 TGGATAGG-TACCATTAGGAGTCATACCG
* * *
34178772 TGGAT-GGTACCGTTAGAAGTCATACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* ** *
34178799 TGGATAGGTACCTTTCA-GAGTTGTATCG
1 TGGATAGGTACCATT-AGGAGTCATACCG
* ** *
34178827 TGGATGGGTACCATTAGGAGTTGTACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* * ** *
34178855 TGGATGGGTACCTTTAGGAGTTGTATCG
1 TGGATAGGTACCATTAGGAGTCATACCG
*
34178883 TGGATGGGTAC
1 TGGATAGGTAC
34178894 TGTAACACCC
Statistics
Matches: 375, Mismatches: 119, Indels: 36
0.71 0.22 0.07
Matches are distributed among these distances:
26 2 0.01
27 59 0.16
28 304 0.81
29 10 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
TGGATAGGTACCATTAGGAGTCATACCG
Found at i:34178530 original size:83 final size:83
Alignment explanation
Indices: 34178443--34178602 Score: 207
Period size: 83 Copynumber: 1.9 Consensus size: 83
34178433 ATAATAGATA
* * * *
34178443 GATACCTTTAAGAGTCGTATCGTGGAT-GAGTACCAATAGGAGTTGTATCGTGGAGGGGTA-CTA
1 GATACCTTTAAGAGTCGTATAGTGGATAG-GTACCAATAGGAGTTGTACCGTAGAGGCGTACCT-
34178506 TTAGGAGTCATACCATGGAT
64 TTAGGAGTCATACCATGGAT
* * * * *
34178526 GATACCTTTAAGAGTTGTGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGATGCGTACCTTT
1 GATACCTTTAAGAGTCGTATAGTGGATAGGTACCAATAGGAGTTGTACCGTAGAGGCGTACCTTT
34178591 AGGAGTCATACC
66 AGGAGTCATACC
34178603 GTGGGTAGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 63 0.95
84 3 0.05
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (83 bp):
GATACCTTTAAGAGTCGTATAGTGGATAGGTACCAATAGGAGTTGTACCGTAGAGGCGTACCTTT
AGGAGTCATACCATGGAT
Found at i:34178541 original size:111 final size:111
Alignment explanation
Indices: 34178368--34178734 Score: 303
Period size: 111 Copynumber: 3.3 Consensus size: 111
34178358 TAGGTATCAT
* * * * * ** *
34178368 TAGGAGTCGTACCGTGGATGGGTACCATTATGAGTCATACCGT-AAAGAATACCAGTAGGAGTTG
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
* * * *
34178432 TATAATAGATAGATACCTTTAAGAGTCGTATCGTGGATGAGTACCAA
66 TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATG-GTACCAA
* * *
34178479 TAGGAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGATG-ATACCTTTAAGAGTTG
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
* * * * ** * **
34178543 TGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGATGCGTACCTT
66 TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATG-GTACCAA
* * * *
34178590 TAGGAGTCATACCGTGG-GTAGGTACC-TATAGGAGTCATGCCATGGATGAATA-CTATTATGAG
1 TAGGAGTCGTACCGTGGAG-GGGTACCAT-TAGGAGTCATACCATGGATGAATACCT-TTAAGAG
** ** * *
34178652 TCATACCATGGATAGGTACCTTTAAGAGTCATGTCGTAGATGGATACCAC
63 TTGTATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATGG-TACCAA
* * * *
34178702 TAGAAGTTGTACCATGGAGGGGAACCATTAGGA
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGA
34178735 ATTTTATTGT
Statistics
Matches: 197, Mismatches: 51, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
110 2 0.01
111 125 0.63
112 68 0.35
113 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (111 bp):
TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATGGTACCAA
Found at i:34178597 original size:139 final size:138
Alignment explanation
Indices: 34178417--34178893 Score: 447
Period size: 139 Copynumber: 3.4 Consensus size: 138
34178407 CCGTAAAGAA
* ** * * * *
34178417 TACCAGTAGGAGTTGTATAATAGATAGATACCTTTAAGAGTCGTATCGTGGATGAGTACCAATAG
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTACCAATAG
** * *
34178482 GAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGAT-GATACCTTTAAGAGTTGTGT
66 GAGTCATGTCGTGGA-GGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTGT
*
34178546 AGTGGATAGG
130 CGTGGAT-GG
* * * * * * * *
34178556 TACCATTAGGAGTTTTACCGTAGATGCGTACCTTTAGGAGTCATACCGTGGGT-AGGTACCTATA
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGA-GTACCAATA
* * ** * **
34178620 GGAGTCATGCCATGGATGAATACTATTATGAGTCATACCATGGATAGGTACCTTTAAGAGTCATG
65 GGAGTCATGTCGTGGA-GGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTG
*
34178685 TCGTAGATGG
129 TCGTGGATGG
* * * * * * ** * * *
34178695 ATACCACTAGAAGTTGTACCATGGAGGGGAACCATTAGGAATTTTATTGTGGATG-GCTACTATT
1 -TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAG-TACCAAT
* ** * * *
34178759 AGGAGTCATGTCGTGGATGGTACCGTTAGAAGTCATACCATGGATAGGTACCTTTCAGAGTTGTA
64 AGGAGTCATGTCGTGGAGGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTG
34178824 TCGTGGATGGG
129 TCGTGGAT-GG
* *
34178835 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTAC
34178894 TGTAACACCC
Statistics
Matches: 264, Mismatches: 67, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
138 1 0.00
139 181 0.69
140 82 0.31
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (138 bp):
TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTACCAATAG
GAGTCATGTCGTGGAGGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTGTC
GTGGATGG
Found at i:34178858 original size:56 final size:56
Alignment explanation
Indices: 34178307--34178893 Score: 206
Period size: 56 Copynumber: 10.6 Consensus size: 56
34178297 TTAGTAGAAG
* * * * **
34178307 GGTACCTTTAGGAG-T-TATTGT-GATAGGTACCACTAGAAGTCGTTTCATGGATA
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* * * * * *
34178360 GGTATCATTAGGAGTCGTACCGTGGATGGGTACCATTATG-AGTCATACC--GTAAA
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTA-GAAGTCATACCATGGATA
* ** ** * * * * * * *
34178414 GAATACCAGTAGGAGTTGTATAATAGATAGATACCTTTA-AGAGTCGTATCGTGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGA-AGTCATACCATGGATA
** * * *
34178470 GAGTACCAATAGGAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* * * * * * ** * *
34178526 GATACCTTTAAGAGTTGTGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGAT-
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
** * * * * *
34178581 GCGTACCTTTAGGAGTCATACCGTGGGTAGGTACC-TATAGGAGTCATGCCATGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCAT-TAGAAGTCATACCATGGATA
* * ** * * * * ** * *
34178637 GAATA-CTATTATGAGTCATACCATGGATAGGTACCTTTA-AGAGTCATGTCGTAGAT-
1 G-GTACCT-TTAGGAGTTGTATCGTGGATGGGTACCATTAGA-AGTCATACCATGGATA
** * * * * * ** ***
34178693 GGATACCACTAGAAGTTGTACCATGGAGGGGAACCATTAGGAA-TTTTATTGTGGAT-
1 GG-TACCTTTAGGAGTTGTATCGTGGATGGGTACCATTA-GAAGTCATACCATGGATA
** * *
34178749 GGCTA-CTATTAGGAGTCATGTCGTGGAT-GGTACCGTTAGAAGTCATACCATGGATA
1 GG-TACCT-TTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* ** *
34178805 GGTACCTTTCA-GAGTTGTATCGTGGATGGGTACCATTAGGAGTTGTACCATGGATG
1 GGTACCTTT-AGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
34178861 GGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
34178894 TGTAACACCC
Statistics
Matches: 391, Mismatches: 117, Indels: 49
0.70 0.21 0.09
Matches are distributed among these distances:
53 12 0.03
54 7 0.02
55 117 0.30
56 248 0.63
57 6 0.02
58 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (56 bp):
GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
Found at i:34181919 original size:18 final size:18
Alignment explanation
Indices: 34181896--34181940 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
34181886 CATGTGTAAA
34181896 GTTTTATTTCAG-GTTAGG
1 GTTTTATTT-AGAGTTAGG
*
34181914 GTTTTATTTTGAGTTAGG
1 GTTTTATTTAGAGTTAGG
34181932 GTTTTATTT
1 GTTTTATTT
34181941 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.58
Consensus pattern (18 bp):
GTTTTATTTAGAGTTAGG
Found at i:34182057 original size:23 final size:23
Alignment explanation
Indices: 34182012--34182057 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
34182002 TGCTATATAT
* * *
34182012 ATTTTTAATTTTTTATATATAAA
1 ATTTATAATTTTTGAGATATAAA
*
34182035 ATTTATAATTTTTGAGATGTAAA
1 ATTTATAATTTTTGAGATATAAA
34182058 GTTAACAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTTATAATTTTTGAGATATAAA
Found at i:34185554 original size:18 final size:18
Alignment explanation
Indices: 34185511--34185555 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
34185501 GTGGTGGGAC
*
34185511 CATCGGTATCGATTCTTG
1 CATCGGTGTCGATTCTTG
34185529 CATCGGTGTCGATTCTTG
1 CATCGGTGTCGATTCTTG
34185547 CATCGGTGT
1 CATCGGTGT
34185556 AGATGATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (18 bp):
CATCGGTGTCGATTCTTG
Found at i:34188074 original size:20 final size:20
Alignment explanation
Indices: 34188027--34188079 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
34188017 AAAATTGACT
* *
34188027 ATTTTTAGAATTCTTTTTGA
1 ATTTTTATAATTCTTGTTGA
* * *
34188047 AATCTTATAATTCTTGTTGG
1 ATTTTTATAATTCTTGTTGA
*
34188067 ATTTTTATGATTC
1 ATTTTTATAATTC
34188080 CAAAAGTTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.57
Consensus pattern (20 bp):
ATTTTTATAATTCTTGTTGA
Found at i:34191060 original size:50 final size:50
Alignment explanation
Indices: 34190949--34191144 Score: 194
Period size: 50 Copynumber: 3.8 Consensus size: 50
34190939 ATTTGGGTAA
* * *
34190949 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
*
34191005 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** * *
34191055 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** ** * * *
34191105 AGAACTATCGTGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
34191145 TAGTACAAGA
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 77 0.64
52 1 0.01
53 2 0.02
55 1 0.01
56 39 0.32
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:34193532 original size:31 final size:31
Alignment explanation
Indices: 34193497--34193562 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
34193487 TAATAGTTTG
*
34193497 GTGACATGAATAAAAATTTTCAAATAATTCA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
* * *
34193528 GTGACTTAAATGAAAATTTTCAAATAATTTA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
34193559 GTGA
1 GTGA
34193563 TGATTTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (31 bp):
GTGACATAAATAAAAATTTTCAAATAATTCA
Found at i:34194224 original size:20 final size:20
Alignment explanation
Indices: 34194197--34194241 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
34194187 TTTATACAAT
34194197 AATA-ATATTTTAATTTTTA
1 AATATATATTTTAATTTTTA
34194216 AATATATATTTTAATTTTTA
1 AATATATATTTTAATTTTTA
34194236 AATATA
1 AATATA
34194242 ATTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATATATATTTTAATTTTTA
Found at i:34195598 original size:15 final size:15
Alignment explanation
Indices: 34195578--34195606 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34195568 CCAGTCACAC
34195578 AGGCGTGTCTTACAT
1 AGGCGTGTCTTACAT
34195593 AGGCGTGTCTTACA
1 AGGCGTGTCTTACA
34195607 AACACGCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (15 bp):
AGGCGTGTCTTACAT
Found at i:34197791 original size:35 final size:35
Alignment explanation
Indices: 34197745--34197814 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
34197735 ATGGCATGAC
*
34197745 TTTACTAGCAACAGTGGAATTCATAGCTCAATTAA
1 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
34197780 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
1 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
34197815 AGAGTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
Found at i:34201431 original size:19 final size:18
Alignment explanation
Indices: 34201385--34201432 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
34201375 GATAGAATTT
*
34201385 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
34201404 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
34201422 TTGTATTAAAA
1 TTGTA-TAAAA
34201433 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:34204151 original size:27 final size:28
Alignment explanation
Indices: 34204088--34204155 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
34204078 TTCTTCGAAG
* *
34204088 TTTTCTTTTTCTTTTTCCTCTTTCTGGG
1 TTTTCTTTTTCTTTTTCCTCTTGCTGGA
** *
34204116 TTTTC-TTTTCTTTTTGTTCTTGCT-TA
1 TTTTCTTTTTCTTTTTCCTCTTGCTGGA
34204142 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
34204156 GAAAACTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 5 0.15
27 24 0.71
28 5 0.15
ACGTcount: A:0.01, C:0.18, G:0.07, T:0.74
Consensus pattern (28 bp):
TTTTCTTTTTCTTTTTCCTCTTGCTGGA
Found at i:34204826 original size:21 final size:22
Alignment explanation
Indices: 34204801--34204858 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
34204791 ATGTCCTTGG
*
34204801 CCCACACGGGCGTGTGCCTCAT
1 CCCACACAGGCGTGTGCCTCAT
* * *
34204823 -CCACATAGTCGTGTGCCTCCT
1 CCCACACAGGCGTGTGCCTCAT
*
34204844 CCCACACAAGCGTGT
1 CCCACACAGGCGTGT
34204859 TGACCCCTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.21
Consensus pattern (22 bp):
CCCACACAGGCGTGTGCCTCAT
Found at i:34210508 original size:50 final size:51
Alignment explanation
Indices: 34210451--34210550 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 51
34210441 GTTTTCTTTT
* *
34210451 CCTAATAAGATGTTGGACGGATTTGATGGGAAAGAATATGATTAC-TTCTC
1 CCTAATAAGATGTTGGACAGATTTGATGGGAAAAAATATGATTACATTCTC
34210501 CCTAATAAGATGTTGGACAGATTTGATGGGAAAAAATATGATTACATTCT
1 CCTAATAAGATGTTGGACAGATTTGATGGGAAAAAATATGATTACATTCT
34210551 AGATGGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 43 0.91
51 4 0.09
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (51 bp):
CCTAATAAGATGTTGGACAGATTTGATGGGAAAAAATATGATTACATTCTC
Found at i:34213283 original size:22 final size:22
Alignment explanation
Indices: 34213257--34213300 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34213247 ATTATGTGTA
34213257 TAATTCATAATATAA-TTAATTT
1 TAATT-ATAATATAATTTAATTT
* *
34213279 TAATTTTAATCTAATTTAATTT
1 TAATTATAATATAATTTAATTT
34213301 GGGTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTATAATATAATTTAATTT
Found at i:34218870 original size:12 final size:13
Alignment explanation
Indices: 34218853--34218881 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34218843 CTCATACATG
34218853 AATAAATAAA-GC
1 AATAAATAAATGC
34218865 AATAAATAAATGC
1 AATAAATAAATGC
34218878 AATA
1 AATA
34218882 GTTATAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:34220814 original size:25 final size:26
Alignment explanation
Indices: 34220780--34220828 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
34220770 TTGTAAAGAG
*
34220780 AAATTCTCTAAAGAGATTATTCTAGA
1 AAATTCTCTAAAGACATTATTCTAGA
* *
34220806 AAATT-TCTAGAGACATTTTTCTA
1 AAATTCTCTAAAGACATTATTCTA
34220829 ATTTACAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (26 bp):
AAATTCTCTAAAGACATTATTCTAGA
Found at i:34224317 original size:66 final size:66
Alignment explanation
Indices: 34224193--34224322 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
34224183 ATTTAAGATC
* * ** * *
34224193 ACCAAAATCCTTTTCAAAATCACAATATGAATTAACAAAATTCACATGCATAAGAACAAAAAAAT
1 ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAAT
34224258 T
66 T
* * * * *
34224259 ACCAAAAACCTATTCAAATTCATAATACAAATTAACGAAATTCACATATATAAAAACAACAAAA
1 ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAA
34224323 CATCTATTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (66 bp):
ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAAT
T
Found at i:34232243 original size:19 final size:19
Alignment explanation
Indices: 34232227--34232273 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
34232217 GTGTGCCCTG
34232227 GCCGTGTAGAAGTGCCCAA
1 GCCGTGTAGAAGTGCCCAA
* *
34232246 GTCGTGTGGAAGTGCCCAA
1 GCCGTGTAGAAGTGCCCAA
*
34232265 GCCATGTAG
1 GCCGTGTAG
34232274 GGGTCTACAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.19
Consensus pattern (19 bp):
GCCGTGTAGAAGTGCCCAA
Found at i:34235890 original size:47 final size:47
Alignment explanation
Indices: 34235832--34236066 Score: 452
Period size: 47 Copynumber: 5.0 Consensus size: 47
34235822 TATTTGAATA
*
34235832 AATGTGTAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34235879 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34235926 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34235973 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34236020 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34236067 TGTAACACCC
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 186 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Done.