Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 135 of 770
Found at i:39616764 original size:46 final size:46
Alignment explanation
Indices: 39616592--39616764 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
39616582 AACCCACCCC
* * *
39616592 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGC-GTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTT-GCATCCA
* *
39616638 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTGCATCCA
* *
39616686 TCAG-GAACTCGGACTCAACTCAACGAGTTCGGACAATTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTGCATCCA
39616731 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39616765 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 3 0.03
46 60 0.55
47 29 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTGCATCCA
Found at i:39618194 original size:20 final size:20
Alignment explanation
Indices: 39618169--39618208 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39618159 TAAAATGTGT
39618169 GCCATTCATGTGTGGTGTTA
1 GCCATTCATGTGTGGTGTTA
39618189 GCCATTCATGTGTGGTGTTA
1 GCCATTCATGTGTGGTGTTA
39618209 AACATGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (20 bp):
GCCATTCATGTGTGGTGTTA
Found at i:39618747 original size:39 final size:39
Alignment explanation
Indices: 39618693--39618883 Score: 310
Period size: 39 Copynumber: 4.9 Consensus size: 39
39618683 AATGTTCGAG
39618693 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
*
39618732 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
*
39618771 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* * *
39618810 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
39618849 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
39618884 GGTTACCATA
Statistics
Matches: 141, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
39 124 0.88
40 17 0.12
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
Found at i:39620584 original size:31 final size:30
Alignment explanation
Indices: 39620549--39620609 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39620539 ATTTAATACG
39620549 AACTTTAAAAAAATTAACACTTTTGCCCCTA
1 AACTTTAAAAAAATT-ACACTTTTGCCCCTA
*** *
39620580 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
39620610 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:39628240 original size:17 final size:18
Alignment explanation
Indices: 39628208--39628242 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39628198 CAAAGCTAGG
39628208 ATGGGCTAAGTGGGCCCA
1 ATGGGCTAAGTGGGCCCA
*
39628226 ATGGGCT-ATTGGGCCCA
1 ATGGGCTAAGTGGGCCCA
39628243 TAATAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.23, G:0.37, T:0.20
Consensus pattern (18 bp):
ATGGGCTAAGTGGGCCCA
Found at i:39628341 original size:29 final size:29
Alignment explanation
Indices: 39628299--39628481 Score: 260
Period size: 29 Copynumber: 6.3 Consensus size: 29
39628289 GAAATCATGT
* *
39628299 ATATAAATGTGATTTGGGCCTAATGGGTC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
39628328 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
39628357 ATACGAATATGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39628386 GTATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
** *
39628415 ATACAAATATGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
39628444 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39628472 ATATGCATGT
1 ATATGAATGT
39628482 TTGTAGAGTT
Statistics
Matches: 136, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
28 23 0.17
29 113 0.83
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:39644562 original size:29 final size:29
Alignment explanation
Indices: 39644519--39644626 Score: 155
Period size: 29 Copynumber: 3.8 Consensus size: 29
39644509 GAAAGCATGT
*
39644519 ATATGAATGTGATTTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39644548 GTATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
39644577 ATACGAATATAATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39644606 ATATGAATGAGA-TTGGGCCTA
1 ATATGAATGTGATTTGGGCCTA
39644627 GTATGCCATA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
28 9 0.13
29 60 0.87
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:39645916 original size:22 final size:22
Alignment explanation
Indices: 39645891--39645934 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39645881 TGTACAATAA
*
39645891 GGAGTTTTCAATCATGGTACTT
1 GGAGTTTTCAAACATGGTACTT
39645913 GGAGTTTTCAAACATGGTACTT
1 GGAGTTTTCAAACATGGTACTT
39645935 CTTGTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (22 bp):
GGAGTTTTCAAACATGGTACTT
Found at i:39646887 original size:26 final size:26
Alignment explanation
Indices: 39646841--39646892 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
39646831 TATTTAATAT
* *
39646841 TAAATATAATTTAATATTTATCTTAA
1 TAAATATAATTTAATACTTATATTAA
*
39646867 TAAATATTATATTAAT-CTTATATTAA
1 TAAATATAAT-TTAATACTTATATTAA
39646893 AGTGATTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TAAATATAATTTAATACTTATATTAA
Found at i:39649734 original size:18 final size:18
Alignment explanation
Indices: 39649711--39649746 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39649701 AGCCGAAAAG
39649711 GGCAAAGCTATGGACATC
1 GGCAAAGCTATGGACATC
39649729 GGCAAAGCTATGGACATC
1 GGCAAAGCTATGGACATC
39649747 TTTGTCGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (18 bp):
GGCAAAGCTATGGACATC
Found at i:39658129 original size:40 final size:40
Alignment explanation
Indices: 39658009--39658213 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
39657999 ATTAAATGAT
* * ** * *
39658009 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
* * * *
39658049 ATCCGGGTTAAGA-CCGAAGGCAATT-ATGCTAG-TGACTAA
1 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TTAA
39658088 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
* * * **
39658128 ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
* * *
39658168 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
39658208 ATCCGG
1 ATCCGG
39658214 TTGTATTCCG
Statistics
Matches: 141, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.01
39 32 0.23
40 106 0.75
41 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
Found at i:39658178 original size:80 final size:77
Alignment explanation
Indices: 39658008--39658213 Score: 232
Period size: 80 Copynumber: 2.6 Consensus size: 77
39657998 AATTAAATGA
* * ** * *
39658008 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAAATCCGGGTTAAGACCGAAGGCAAT
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCGAAGGCAAT
*
39658073 TATGCTAGTGAC
66 TATGCAAGTGAC
* *
39658085 TAAATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGA-CCGAAGGC
* * *
39658150 ATTTGTGCAAGTCGTTC
63 AATTATGCAAGT-G-AC
* * *
39658167 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGG
39658214 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
79 45 0.41
80 60 0.55
81 1 0.01
82 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (77 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCGAAGGCAAT
TATGCAAGTGAC
Found at i:39666072 original size:40 final size:39
Alignment explanation
Indices: 39666015--39666199 Score: 217
Period size: 40 Copynumber: 4.6 Consensus size: 39
39666005 ATTAAATGAT
* * *
39666015 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGT-GTTAA
* * * *
39666055 ATCCGGGTTAAGACCCGAAGGCAATTATGCTAGTGACTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTG-TTAA
**
39666095 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAG-TGTTAA
* * **
39666135 ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTCT
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGT-GTTAA
39666175 ATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATT
39666200 CGTGCATGTG
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.02
40 122 0.97
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (39 bp):
ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTGTTAA
Found at i:39666151 original size:80 final size:80
Alignment explanation
Indices: 39666014--39666220 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
39666004 AATTAAATGA
* * ** * *
39666014 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAAATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAA
*
39666079 TTATGCTAGT-G-AC
66 TTATGCAAGTCGTAC
* *
39666092 TAAATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGC
* * *
39666157 ATTTGTGCAAGTCGTTC
64 AATTATGCAAGTCGTAC
* * *
39666174 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGG
39666221 TTGTATTCCG
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
80 106 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAA
TTATGCAAGTCGTAC
Found at i:39666205 original size:40 final size:39
Alignment explanation
Indices: 39666013--39666220 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 39
39666003 CAATTAAATG
* * ** *
39666013 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTT
* * * * *
39666053 AAATCCGGGTTAAGACCCGAAGGCAATT-ATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTG-TT
*
39666093 AAATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAG-TGTT
* * *
39666133 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTT
* *
39666173 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTT
39666213 ATATCCGG
1 ATATCCGG
39666221 TTGTATTCCG
Statistics
Matches: 145, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.03
40 135 0.93
41 5 0.03
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTT
Found at i:39668629 original size:61 final size:59
Alignment explanation
Indices: 39668557--39668672 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 59
39668547 AGTCATTATC
** * * * *
39668557 TTAATATTAAATTTAATTTAATATTTGTCTT-ATAGATAATATTCTATTATTTTAATAATAT
1 TTAATATTAAATCAAATCTAATATTTATCTTGAT--A-AATATTATATTAATTTAATAATAT
39668618 TTAATATTAAATCAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATCAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
39668673 TGAAAGTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 18 0.38
60 1 0.02
61 27 0.56
62 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATCAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAATAT
Found at i:39675212 original size:42 final size:40
Alignment explanation
Indices: 39675153--39675271 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 40
39675143 GAAGTTCGAA
*
39675153 CTCGTTGAGTGGTCTGAGTTTGTGAGATATGTG-GCATCCAAG
1 CTCGTTGAGTGGTCTGAGTTTATG-G--ATGTGAGCATCCAAG
*
39675195 CTCGTTGAGTGGTCTGAGTCCATTATGGATGTGAGCATCCGAG
1 CTCGTTGAGTGGTCTGAGT---TTATGGATGTGAGCATCCAAG
*
39675238 CTCGATGAGTGGTCTGAGTTCATAATGGATGTGA
1 CTCGTTGAGTGGTCTGAGTT--T-ATGGATGTGA
39675272 TACATGTGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
40 1 0.01
42 25 0.37
43 36 0.54
44 1 0.01
45 4 0.06
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.32
Consensus pattern (40 bp):
CTCGTTGAGTGGTCTGAGTTTATGGATGTGAGCATCCAAG
Found at i:39675247 original size:43 final size:43
Alignment explanation
Indices: 39675181--39675271 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
39675171 TTTGTGAGAT
* *
39675181 ATGTG-GCATCCAAGCTCGTTGAGTGGTCTGAGTCCATTATGG
1 ATGTGAGCATCCAAGCTCGATGAGTGGTCTGAGTCCATAATGG
* *
39675223 ATGTGAGCATCCGAGCTCGATGAGTGGTCTGAGTTCATAATGG
1 ATGTGAGCATCCAAGCTCGATGAGTGGTCTGAGTCCATAATGG
39675266 ATGTGA
1 ATGTGA
39675272 TACATGTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 5 0.11
43 39 0.89
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (43 bp):
ATGTGAGCATCCAAGCTCGATGAGTGGTCTGAGTCCATAATGG
Found at i:39678891 original size:15 final size:15
Alignment explanation
Indices: 39678866--39678923 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
39678856 GAGATGACAT
*
39678866 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* *
39678881 GAAGTCCAAGACAAA
1 GAAATCCAAGATAAA
**
39678896 GAAATCCTGGATAAA
1 GAAATCCAAGATAAA
39678911 GAAATCCAAGATA
1 GAAATCCAAGATA
39678924 CAATATCATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.55, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:39686329 original size:44 final size:44
Alignment explanation
Indices: 39686266--39686530 Score: 246
Period size: 44 Copynumber: 6.0 Consensus size: 44
39686256 CATCGTGGCG
* * * * * * *
39686266 AATCTTACCTCTCTGAAGTTGTAGTGGAGCAGATTGAAGCCATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
* * *
39686310 AATCTTATCTACCTGAAGTTGCAGTAGAGCAAATTAAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
* * *
39686354 AATCTTATCTCCCTGAAATTGCAGTAGAGCAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-CA
** * * * *
39686399 AATCTTATCTCTATGACGTTGTAGTAGACCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
* * * *
39686443 AATC-T-TCTCCCTAAAGTAGCAGTGGAGCAAATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
* ** * *
39686485 AATCTTATTTCCCTGAAAGTTGTTGTGGAACAGATTAAAGCTACA
1 AATCTTATCTCCCTG-AAGTTGCAGTAGAGCAGATTAAAGCTACA
39686530 A
1 A
39686531 GTTACAAATC
Statistics
Matches: 175, Mismatches: 42, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
42 31 0.18
43 2 0.01
44 82 0.47
45 60 0.34
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
Found at i:39686578 original size:51 final size:52
Alignment explanation
Indices: 39686477--39686594 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 52
39686467 GAGCAAATTA
** *** *
39686477 AAGCTACAAATCTTATTTCCCTGAAAGTTGTTGTGGAACAGATTAAAGCTAC
1 AAGCTACAAATCTTAAATCCCTGAAAGTTGCAATGGAACAGACTAAAGCTAC
* * *
39686529 AAGTTACAAATCTTAAATCCCTG-AAGTTGCAATGGAATAGACTAGAGCTAC
1 AAGCTACAAATCTTAAATCCCTGAAAGTTGCAATGGAACAGACTAAAGCTAC
39686580 AAGCTACAAATCTTA
1 AAGCTACAAATCTTA
39686595 TCTCCTTGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 36 0.64
52 20 0.36
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (52 bp):
AAGCTACAAATCTTAAATCCCTGAAAGTTGCAATGGAACAGACTAAAGCTAC
Found at i:39687143 original size:3 final size:3
Alignment explanation
Indices: 39687129--39687242 Score: 106
Period size: 3 Copynumber: 38.7 Consensus size: 3
39687119 ATTACACATC
*
39687129 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * * * * *
39687177 ATT ATT ATG GTA ACT AGT ATA ACT ATT GTT GTT ATT ATT A-A ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39687224 ATT -TT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
39687243 AGTGTATTAT
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
2 3 0.03
3 86 0.97
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:39688507 original size:20 final size:20
Alignment explanation
Indices: 39688482--39688536 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
39688472 AAGCTTATGC
39688482 TAAGTAAATGGAATGAAAAG
1 TAAGTAAATGGAATGAAAAG
*
39688502 TAAGTAAAT-GAAGTGGAAAG
1 TAAGTAAATGGAA-TGAAAAG
39688522 TAAGTAAATGGAATG
1 TAAGTAAATGGAATG
39688537 GTTCATCGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGGAATGAAAAG
Found at i:39690542 original size:65 final size:65
Alignment explanation
Indices: 39690457--39690586 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 65
39690447 TTTTCACTTA
39690457 AAAAGTATAGAAAGTTCAATAATGATATATTAAAA-TAACGATGATGAAAGACTAAGTTGGTCAC
1 AAAAGTATAGAAAGTTCAATAATGATATATTAAAATTAACGATGATGAAAGACTAAGTTGGTCAC
39690521 AAAAGTATTAGAAAGTTCAATAATGATATATTAAAATTAACGATGATGAAAGACTAAGTTGGTCA
1 AAAAGTA-TAGAAAGTTCAATAATGATATATTAAAATTAACGATGATGAAAGACTAAGTTGGTCA
39690586 C
65 C
39690587 TTCTTATGTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 7 0.11
65 28 0.44
66 29 0.45
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.28
Consensus pattern (65 bp):
AAAAGTATAGAAAGTTCAATAATGATATATTAAAATTAACGATGATGAAAGACTAAGTTGGTCAC
Found at i:39693214 original size:32 final size:29
Alignment explanation
Indices: 39693178--39693277 Score: 85
Period size: 32 Copynumber: 3.2 Consensus size: 29
39693168 AAAAATTTGC
39693178 AAAAATATAAAATTTAGTAAATAAATATTTA
1 AAAAATATAAAATTTA-TAAA-AAATATTTA
* *
39693209 GAAAAACT-TAAAATTTATTTAAAAATATATA
1 -AAAAA-TATAAAATTTA-TAAAAAATATTTA
* *
39693240 AAAAATATTAAAAAGTTATAAAAAAATCTTTA
1 AAAAATA-T-AAAATTTAT-AAAAAATATTTA
39693272 AAAAAT
1 AAAAAT
39693278 TTTCTTGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
29 1 0.02
30 5 0.09
31 10 0.18
32 39 0.70
33 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATATAAAATTTATAAAAAATATTTA
Found at i:39693248 original size:21 final size:22
Alignment explanation
Indices: 39693224--39693275 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
39693214 ACTTAAAATT
39693224 TATTTAAAAA--TATATAAAAAA
1 TATTTAAAAAGTTATA-AAAAAA
39693245 TA-TTAAAAAGTTATAAAAAAA
1 TATTTAAAAAGTTATAAAAAAA
*
39693266 TCTTTAAAAA
1 TATTTAAAAA
39693276 ATTTTCTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TATTTAAAAAGTTATAAAAAAA
Found at i:39693250 original size:20 final size:20
Alignment explanation
Indices: 39693227--39693264 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39693217 TAAAATTTAT
39693227 TTAAAAA-TATATAAAAAATA
1 TTAAAAAGT-TATAAAAAATA
39693247 TTAAAAAGTTATAAAAAA
1 TTAAAAAGTTATAAAAAA
39693265 ATCTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
TTAAAAAGTTATAAAAAATA
Found at i:39693251 original size:31 final size:33
Alignment explanation
Indices: 39693178--39693252 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
39693168 AAAAATTTGC
*
39693178 AAAAATA-TAAAATTTAGTAAATAAATATTTAG
1 AAAAATATTAAAATTTAGTAAATAAATATATAG
* * *
39693210 AAAAA-CTTAAAATTTATTTAA-AAATATATA-
1 AAAAATATTAAAATTTAGTAAATAAATATATAG
39693240 AAAAATATTAAAA
1 AAAAATATTAAAA
39693253 AGTTATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.14
31 14 0.39
32 17 0.47
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (33 bp):
AAAAATATTAAAATTTAGTAAATAAATATATAG
Found at i:39694054 original size:33 final size:33
Alignment explanation
Indices: 39694019--39694094 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
39694009 TAATTTAGTA
* *
39694019 AAAAAATTTTAGAAAATT-TTAATA-TTTATTTT
1 AAAAAATATTA-AAAATTGTTAAAATTTTATTTT
*
39694051 AAAATATATTAAAAATTGTTAAAATTTTATTTT
1 AAAAAATATTAAAAATTGTTAAAATTTTATTTT
* *
39694084 TAAAATTATTA
1 AAAAAATATTA
39694095 TAATTTAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 6 0.17
32 14 0.39
33 16 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
AAAAAATATTAAAAATTGTTAAAATTTTATTTT
Found at i:39694191 original size:20 final size:21
Alignment explanation
Indices: 39694159--39694217 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
39694149 TTAAACTTTT
39694159 TTTTTACAA--TTTTAAAGAA
1 TTTTTACAATTTTTTAAAGAA
*
39694178 TTTTTA-AATTTTTTAAATAA
1 TTTTTACAATTTTTTAAAGAA
39694198 TTTTTACTAATTTTTATAAA
1 TTTTTAC-AATTTTT-TAAA
39694218 AAAATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 15 0.44
22 7 0.21
23 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTACAATTTTTTAAAGAA
Found at i:39695239 original size:37 final size:37
Alignment explanation
Indices: 39695189--39695261 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
39695179 CTCATGTTCA
39695189 TTGAGTATGTTAATATATGAATCCTTAACAATGTAGC
1 TTGAGTATGTTAATATATGAATCCTTAACAATGTAGC
39695226 TTGAGTATGTTAATATATGAATCCTTAACAATGTAG
1 TTGAGTATGTTAATATATGAATCCTTAACAATGTAG
39695262 TAAGCACCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (37 bp):
TTGAGTATGTTAATATATGAATCCTTAACAATGTAGC
Found at i:39697525 original size:23 final size:23
Alignment explanation
Indices: 39697499--39697543 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39697489 CCTGTTACAT
* *
39697499 GGCTCTTTGTGAGCTTCTTGATA
1 GGCTCTTCGTGAGCTTCCTGATA
39697522 GGCTCTTCGTGAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
39697544 TAAAAGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCTGATA
Found at i:39697632 original size:23 final size:27
Alignment explanation
Indices: 39697606--39697661 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
39697596 ATAGCCCAGA
39697606 TAAGCTTTCT-GA-T-A-GGCTCTTTG
1 TAAGCTTTCTAGATTAATGGCTCTTTG
39697629 TAAGC-TTCTAGATTAATGGCTCTTTG
1 TAAGCTTTCTAGATTAATGGCTCTTTG
*
39697655 TGAGCTT
1 TAAGCTT
39697662 CCTGTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 1 0.04
25 1 0.04
26 13 0.48
27 1 0.04
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
TAAGCTTTCTAGATTAATGGCTCTTTG
Found at i:39699928 original size:21 final size:21
Alignment explanation
Indices: 39699904--39699944 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39699894 TTTTACAATT
*
39699904 TAATCTTTGTGTTTTAATTAA
1 TAATCTTTGTGATTTAATTAA
* *
39699925 TAATTTTTTTGATTTAATTA
1 TAATCTTTGTGATTTAATTA
39699945 TTCAACCTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
TAATCTTTGTGATTTAATTAA
Found at i:39706697 original size:48 final size:48
Alignment explanation
Indices: 39706526--39706795 Score: 250
Period size: 46 Copynumber: 5.7 Consensus size: 48
39706516 TGATATGTGT
* * * * *
39706526 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATAT-TGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAT-ACAA
* * * * *
39706572 GCCAATGTAAGACATGTCTGGGACATGCATCGGCCAC-ATAT-TA-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACA-A
* *
39706618 GCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAA
* * * * ** * *
39706666 GCTAGTGTAAGACATGTCTAGGACATACATCAGCATTGAGA-CGAGAG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAA
*
39706713 GCTAGTGTAAGACATGTCTGGGACATGCATC-GACCTCGACATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CCTCGAGATATACAA
*
39706761 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGC
39706796 TTGTTGTGTG
Statistics
Matches: 189, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
45 1 0.01
46 76 0.40
47 39 0.21
48 65 0.34
49 7 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAA
Found at i:39706737 original size:95 final size:96
Alignment explanation
Indices: 39706623--39706795 Score: 287
Period size: 95 Copynumber: 1.8 Consensus size: 96
39706613 TAAGAGCCAA
*
39706623 TGTAAGACATGTCTGGGACATGCATC-AGCCTCGAGATATACAAGCTAGTGTAAGACATGTCTAG
1 TGTAAGACATGTCTGGGACATGCATCGA-CCTCGACATATACAAGCTAGTGTAAGACATGTCTAG
39706687 GACAT-ACATCAGCATTGAGACGAGAGGCTAG
65 GACATGACATCAGCATTGAGACGAGAGGCTAG
* *
39706718 TGTAAGACATGTCTGGGACATGCATCGACCTCGACATATACAAGCTAGTGTAAGACCTGTCTGGG
1 TGTAAGACATGTCTGGGACATGCATCGACCTCGACATATACAAGCTAGTGTAAGACATGTCTAGG
*
39706783 ACATGGCATCAGC
66 ACATGACATCAGC
39706796 TTGTTGTGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
95 64 0.89
96 8 0.11
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (96 bp):
TGTAAGACATGTCTGGGACATGCATCGACCTCGACATATACAAGCTAGTGTAAGACATGTCTAGG
ACATGACATCAGCATTGAGACGAGAGGCTAG
Found at i:39706935 original size:49 final size:49
Alignment explanation
Indices: 39706716--39706937 Score: 210
Period size: 49 Copynumber: 4.7 Consensus size: 49
39706706 ACGAGAGGCT
* * **
39706716 AGTGTAAGACATGTCTGGGACAT-GCATCGACCTCGACATATACAAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGGAAGTC
* * * *
39706763 TAGTGTAAGACCTGTCTGGGACATGGCATC-AGCTTG-T-TGT-G-TGTC
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGGAAGTC
* * *
39706808 AGGGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGAT-GAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATATATGGA-AGTC
*** * *
39706857 AGTGTAAGACCTGTCTGGGACACAACATCGGCCTCAATATATGGAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGGAAGTC
39706906 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
39706938 TTTGATGTGC
Statistics
Matches: 138, Mismatches: 26, Indels: 19
0.75 0.14 0.10
Matches are distributed among these distances:
44 29 0.21
45 3 0.02
46 4 0.03
47 2 0.01
48 27 0.20
49 71 0.51
50 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGGAAGTC
Found at i:39714635 original size:45 final size:46
Alignment explanation
Indices: 39714546--39714665 Score: 145
Period size: 45 Copynumber: 2.6 Consensus size: 46
39714536 TATGTGTGCT
* * * *
39714546 AGTGTAAGACATGTCTAGGACATGCATCAGCCACATATTGAGAGCG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCAACAGACTGAGAGCG
* *
39714592 A-TGTAAGACATGTCTAGGACATGCATCGGCAATGAGACT-AGAGCT
1 AGTGTAAGACATGTCTAGGACATGCATCGGCAA-CAGACTGAGAGCG
* *
39714637 AGTGTAAGACATGTTTGGGACATGCATCG
1 AGTGTAAGACATGTCTAGGACATGCATCG
39714666 ACCTTGAGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 35 0.55
46 29 0.45
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCAACAGACTGAGAGCG
Found at i:39714804 original size:49 final size:49
Alignment explanation
Indices: 39714731--39714857 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
39714721 TATTGTTAGG
* *
39714731 GTAAGACCTGTTTGGGACATGGCATCGACACT-GATAGATGAGAGC-CAGT
1 GTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATG-GAACTCAGT
* * *
39714780 GTAAGACCTGTCTAGGACACGGCATC-AGCCTCGATATATGGAACTCAGT
1 GTAAGACCTGTCTGGGACATGGCATCGA-CCTCGATAGATGGAACTCAGT
*
39714829 GTAAGACCTGTCTGGGACATGACATCGAC
1 GTAAGACCTGTCTGGGACATGGCATCGAC
39714858 TTTGATGTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
48 6 0.09
49 59 0.89
50 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (49 bp):
GTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGGAACTCAGT
Found at i:39714804 original size:92 final size:91
Alignment explanation
Indices: 39714640--39714807 Score: 198
Period size: 92 Copynumber: 1.8 Consensus size: 91
39714630 TAGAGCTAGT
* * * *
39714640 GTAAGACATGTTTGGGACATGCATCGACCTTGAGATATACAAGCTAGTGTAAGACTTGTTTGTAA
1 GTAAGACATGTTTGGGACATGCATCGACCTTGAGAGATACAAGCCAGTGTAAGACCTGTTAGTAA
*
39714705 CATGGCATCAGGTTGTTATTGTTAGG
66 CACGGCATCAGGTTGTTATTGTTAGG
* * *
39714731 GTAAGACCTGTTTGGGACATGGCATCGACAC-TGATAGATGA-GAGCCAGTGTAAGACCTGTCTA
1 GTAAGACATGTTTGGGACAT-GCATCGAC-CTTGAGAGAT-ACAAGCCAGTGTAAGACCTGT-TA
*
39714794 G-GACACGGCATCAG
62 GTAACACGGCATCAG
39714808 CCTCGATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
91 19 0.30
92 41 0.64
93 4 0.06
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (91 bp):
GTAAGACATGTTTGGGACATGCATCGACCTTGAGAGATACAAGCCAGTGTAAGACCTGTTAGTAA
CACGGCATCAGGTTGTTATTGTTAGG
Found at i:39716267 original size:23 final size:21
Alignment explanation
Indices: 39716211--39716255 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
39716201 GTTAAAAGAG
* *
39716211 CCACACGGGTGTGTCGCCTTT
1 CCACACAGGTGTGTCACCTTT
39716232 CCACACAGGTGTGTCACCTTT
1 CCACACAGGTGTGTCACCTTT
39716253 CCA
1 CCA
39716256 TACGAGCGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.36, G:0.22, T:0.27
Consensus pattern (21 bp):
CCACACAGGTGTGTCACCTTT
Found at i:39718310 original size:15 final size:15
Alignment explanation
Indices: 39718278--39718306 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39718268 ATTTTCAATG
39718278 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
39718293 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
39718307 ATTTTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:39719125 original size:15 final size:15
Alignment explanation
Indices: 39719105--39719134 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39719095 GTGAAAATAT
39719105 ATTTGAATAAGTTTA
1 ATTTGAATAAGTTTA
*
39719120 ATTTGAATATGTTTA
1 ATTTGAATAAGTTTA
39719135 GATCAAGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
ATTTGAATAAGTTTA
Found at i:39721208 original size:30 final size:29
Alignment explanation
Indices: 39721174--39721234 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
39721164 GTGTAATATA
39721174 AACATATAAGAAAAATA-ATAGATATAAAGT
1 AACATATAA-AAAAATACATAGATAT-AAGT
* *
39721204 AACATATAAAACAATACATATATATAAGT
1 AACATATAAAAAAATACATAGATATAAGT
39721233 AA
1 AA
39721235 TAAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.25
Consensus pattern (29 bp):
AACATATAAAAAAATACATAGATATAAGT
Found at i:39721325 original size:20 final size:22
Alignment explanation
Indices: 39721278--39721328 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
39721268 TAATTTAAGG
39721278 AAAATAATATATATAATAAGTA
1 AAAATAATATATATAATAAGTA
* *
39721300 ATAATAATA-ATAT-ATAATTA
1 AAAATAATATATATAATAAGTA
39721320 AAAATAATA
1 AAAATAATA
39721329 CTCATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATAATATATATAATAAGTA
Found at i:39721325 original size:23 final size:22
Alignment explanation
Indices: 39721280--39721328 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
39721270 ATTTAAGGAA
*
39721280 AATAATATATATAATAAGTAAT
1 AATAATATATATAATAAGAAAT
39721302 AATAATAATATATAATTAA-AAAT
1 AATAAT-ATATATAA-TAAGAAAT
39721325 AATA
1 AATA
39721329 CTCATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 15 0.62
24 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATAATATATATAATAAGAAAT
Found at i:39726791 original size:25 final size:26
Alignment explanation
Indices: 39726762--39726819 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
39726752 TTTGATACTT
*
39726762 ATATTAATAGT-ATTTTATTAAT-TTA
1 ATATTAA-AGTGATTATATTAATATTA
*
39726787 ATATTAAAGTGATTATCTTAATATTA
1 ATATTAAAGTGATTATATTAATATTA
39726813 A-ATTAAA
1 ATATTAAA
39726820 TTTAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 22 0.76
26 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
ATATTAAAGTGATTATATTAATATTA
Found at i:39726812 original size:31 final size:29
Alignment explanation
Indices: 39726777--39726834 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
39726767 AATAGTATTT
*
39726777 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
39726808 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
39726835 GTAGATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:39726882 original size:12 final size:12
Alignment explanation
Indices: 39726865--39726889 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39726855 TTTTAATAAG
39726865 ATTTAATATTAA
1 ATTTAATATTAA
39726877 ATTTAATATTAA
1 ATTTAATATTAA
39726889 A
1 A
39726890 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:39729357 original size:20 final size:20
Alignment explanation
Indices: 39729332--39729380 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
39729322 CGTGACTTGG
* *
39729332 TATTGATACTAATTTAAAAT
1 TATTGATACTAATCTAAAAA
**
39729352 TATTGATACTCGTCTAAAAA
1 TATTGATACTAATCTAAAAA
39729372 TATTGATAC
1 TATTGATAC
39729381 GAGAGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (20 bp):
TATTGATACTAATCTAAAAA
Found at i:39729545 original size:22 final size:20
Alignment explanation
Indices: 39729520--39729565 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
39729510 TTTTCAACAC
*
39729520 CATTGCATCAAGATTTCTTCAA
1 CATTGCATCAA-AATT-TTCAA
*
39729542 CATTGCTTCAAAATTTTCAA
1 CATTGCATCAAAATTTTCAA
39729562 CATT
1 CATT
39729566 TCAACATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (20 bp):
CATTGCATCAAAATTTTCAA
Found at i:39730215 original size:15 final size:15
Alignment explanation
Indices: 39730170--39730216 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 15
39730160 ATGTTTCCGC
39730170 TATTTTAA--TTTAT
1 TATTTTAATTTTTAT
39730183 TATTTTAACCTTTATTAT
1 TATTTTAA--TTT-TTAT
39730201 TATTTTAATTTTTAT
1 TATTTTAATTTTTAT
39730216 T
1 T
39730217 TAATATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 8 0.28
15 5 0.17
16 3 0.10
17 1 0.03
18 12 0.41
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTAATTTTTAT
Found at i:39732395 original size:20 final size:19
Alignment explanation
Indices: 39732372--39732411 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
39732362 TAAAATGACC
39732372 TCAATCAAGTTAGAATT-TTT
1 TCAATCAA-TTA-AATTGTTT
39732392 TCAATCAATTAAATTGTTT
1 TCAATCAATTAAATTGTTT
39732411 T
1 T
39732412 TAAAACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (19 bp):
TCAATCAATTAAATTGTTT
Found at i:39736809 original size:62 final size:59
Alignment explanation
Indices: 39736723--39736856 Score: 162
Period size: 62 Copynumber: 2.2 Consensus size: 59
39736713 TCAAAAAATA
* * * *
39736723 ATATTATTTTAAT-AGATTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATAAATATT
1 ATATTAATTTAATAAGATTTAATATTAAATTAAATCTAATATCTATC-T-TA-ATAAATATT
* * *
39736784 CTATTAATTTAATAAGATTTAATATTAAATTTAATCTAATATCTATCTTAATAAGTATT
1 ATATTAATTTAATAAGATTTAATATTAAATTAAATCTAATATCTATCTTAATAAATATT
*
39736843 ATATTAATGTAATA
1 ATATTAATTTAATA
39736857 TTAAAGTGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.32
60 2 0.03
61 12 0.19
62 29 0.46
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.49
Consensus pattern (59 bp):
ATATTAATTTAATAAGATTTAATATTAAATTAAATCTAATATCTATCTTAATAAATATT
Found at i:39736995 original size:26 final size:24
Alignment explanation
Indices: 39736965--39737015 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
39736955 AAGTTGTAGG
39736965 AGAAAATTCTCTAAAGAAATTATTTC
1 AGAAAATT-TCTAAAGAAATT-TTTC
* *
39736991 AGAAAATTTCTAGAGATATTTTTC
1 AGAAAATTTCTAAAGAAATTTTTC
39737015 A
1 A
39737016 TATTTATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 8 0.35
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (24 bp):
AGAAAATTTCTAAAGAAATTTTTC
Found at i:39738934 original size:15 final size:16
Alignment explanation
Indices: 39738907--39738959 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
39738897 ATCAAAATTT
*
39738907 TATATAT-ATAATTGCA
1 TATATATCA-AATTACA
39738923 TA-ATATCAAATTACA
1 TATATATCAAATTACA
39738938 TATTATATCAAATTA-A
1 TA-TATATCAAATTACA
39738954 TATATA
1 TATATA
39738960 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 16 0.48
16 6 0.18
17 11 0.33
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (16 bp):
TATATATCAAATTACA
Found at i:39738945 original size:17 final size:16
Alignment explanation
Indices: 39738925--39738956 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
39738915 TAATTGCATA
39738925 ATATCAAATTACATATT
1 ATATCAAATTA-ATATT
39738942 ATATCAAATTAATAT
1 ATATCAAATTAATAT
39738957 ATAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATCAAATTAATATT
Found at i:39740805 original size:11 final size:11
Alignment explanation
Indices: 39740791--39740824 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39740781 GTACAAATTT
39740791 TAAAAAAAATA
1 TAAAAAAAATA
*
39740802 TAAAAAATATA
1 TAAAAAAAATA
39740813 TAAAAACAAATA
1 TAAAAA-AAATA
39740825 AATAAAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAAAAATA
Found at i:39740885 original size:19 final size:18
Alignment explanation
Indices: 39740845--39740942 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 18
39740835 ATAAAAATCC
* *
39740845 TAAAAATTCTAAAA-TATT
1 TAAAAATTATAAAACT-TA
39740863 TAAAAATTATATAAACTTA
1 TAAAAATTATA-AAACTTA
* * *
39740882 TAAAAAGTAGAAAAATTAGA
1 TAAAAATTATAAAACTT--A
* *
39740902 AAAAAATCATAAAAACTTA
1 TAAAAATTAT-AAAACTTA
*
39740921 TAAATATTATCAAAACTTA
1 TAAAAATTAT-AAAACTTA
39740940 TAA
1 TAA
39740943 TAAAAATAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
18 15 0.25
19 32 0.52
20 8 0.13
21 6 0.10
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAATTATAAAACTTA
Found at i:39740923 original size:10 final size:9
Alignment explanation
Indices: 39740833--39740955 Score: 70
Period size: 9 Copynumber: 13.1 Consensus size: 9
39740823 TAAATAAAGC
39740833 TTATAAAAA
1 TTATAAAAA
**
39740842 TCCTAAAAA
1 TTATAAAAA
*
39740851 TTCTAAAATA
1 TTATAAAA-A
39740861 TT-TAAAAA
1 TTATAAAAA
*
39740869 TTATATAAAC
1 TTATA-AAAA
39740879 TTATAAAAA
1 TTATAAAAA
* *
39740888 GTAGAAAAA
1 TTATAAAAA
*
39740897 TTAGAAAAAAA
1 TT--ATAAAAA
*
39740908 TCATAAAAA
1 TTATAAAAA
*
39740917 CTTATAAATA
1 -TTATAAAAA
*
39740927 TTATCAAAAC
1 TTAT-AAAAA
39740937 TTATAATAAA
1 TTATAA-AAA
*
39740947 -AATAAAAA
1 TTATAAAAA
39740955 T
1 T
39740956 ATTTAAATTA
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
8 6 0.07
9 48 0.55
10 27 0.31
11 7 0.08
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (9 bp):
TTATAAAAA
Found at i:39741547 original size:3 final size:3
Alignment explanation
Indices: 39741539--39741577 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
39741529 AAGAGCTTTA
*
39741539 ATT ATT ATT ATT ATT ATT ATT ATT ATG ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39741578 TGGATTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:39745181 original size:40 final size:40
Alignment explanation
Indices: 39745079--39745257 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 40
39745069 TATTCGAATG
* *
39745079 ATATCCGGGCTAAG-TCCGAAGGC-TTT-TGTTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCT-AGTGACT
* * * *
39745117 ATATCC-GACTAAGATCCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * *
39745156 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
*
39745196 ATATCCGGGCTAAGTCCC-AAGGCATTTATGCTAGTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
39745234 CAT-TCCGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
39745258 CTTGTGCGAG
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
37 6 0.05
38 30 0.26
39 39 0.33
40 42 0.36
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:39745218 original size:79 final size:78
Alignment explanation
Indices: 39745113--39745257 Score: 195
Period size: 79 Copynumber: 1.8 Consensus size: 78
39745103 TTTGTTAAGT
* *
39745113 GACTATATCCGACTAAGATCCGAAGGCATTTATGCGAGTTA-CTATATCCGGGCCAAAACCCGAA
1 GACTATATCCGACTAAGATCCCAAGGCATTTATGCGAGTGATC-AT-TCCGGGCCAAAACCCGAA
39745177 GGCATTTGTGCTAGC
64 GGCATTTGTGCTAGC
* * * *
39745192 GACTATATCCGGGCTAAG-TCCCAAGGCATTTATGCTAGTGATCATTCCGGGCTAAGACCCGAAG
1 GACTATATCC-GACTAAGATCCCAAGGCATTTATGCGAGTGATCATTCCGGGCCAAAACCCGAAG
39745256 GC
65 GC
39745258 CTTGTGCGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 19 0.33
79 32 0.55
80 7 0.12
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (78 bp):
GACTATATCCGACTAAGATCCCAAGGCATTTATGCGAGTGATCATTCCGGGCCAAAACCCGAAGG
CATTTGTGCTAGC
Found at i:39745280 original size:39 final size:40
Alignment explanation
Indices: 39745079--39745280 Score: 175
Period size: 39 Copynumber: 5.2 Consensus size: 40
39745069 TATTCGAATG
* * *
39745079 ATATCCGGGCTAAG-TCCGAAGGC-TTT-TGTTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCT-AGTGATT
* * * * * *
39745117 ATATCC-GACTAAGATCCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * *
39745156 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
39745196 ATATCCGGGCTAAGTCCC-AAGGCATTTATGCTAGTGATC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
39745235 AT-TCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
39745273 ATATCCGG
1 ATATCCGG
39745281 TTAAATCCCG
Statistics
Matches: 133, Mismatches: 25, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
37 6 0.05
38 41 0.31
39 44 0.33
40 42 0.32
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:39753309 original size:40 final size:40
Alignment explanation
Indices: 39753208--39753392 Score: 228
Period size: 40 Copynumber: 4.6 Consensus size: 40
39753198 TTATTCGATG
* * * *
39753208 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCT-AGTGACT
* * * *
39753249 ATATCCGGACTAAGATCCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * *
39753289 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
*
39753329 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
39753368 CATATCCGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
39753393 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 94 0.78
41 26 0.21
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:39762374 original size:170 final size:170
Alignment explanation
Indices: 39762080--39762417 Score: 622
Period size: 170 Copynumber: 2.0 Consensus size: 170
39762070 CATTACTATG
*
39762080 CAAAAATACATTTTTAACTGTCAGAAATCATCACACTATCGTATTAACACTATATGGCATGTATA
1 CAAAAACACATTTTTAACTGTCAGAAATCATCACACTATCGTATTAACACTATATGGCATGTATA
* *
39762145 GCTAGACTCATATACGCTACGTTAGTCCTAGAATCGACTAAACCGTAGCTCTAATACCAATAAAA
66 GCTAGACTCATATACGCTACGTTAGTCCTAAAATCGACTAAACCGTAACTCTAATACCAATAAAA
* *
39762210 TGTAACACCCCTAACCCGAATCTGATTGCCGGATTAAGTA
131 TGTAACACCCCTAACCCGAATCCGATTGCCAGATTAAGTA
39762250 CAAAAACACATTTTTAACTGTCAGAAATCATCACACTATCGTATTAACACTATATGGCATGTATA
1 CAAAAACACATTTTTAACTGTCAGAAATCATCACACTATCGTATTAACACTATATGGCATGTATA
*
39762315 GCTAGACTCATATACGCTACGTTAGTCCTAAAATCGACTAAACCGTAACTCTGATACCAATAAAA
66 GCTAGACTCATATACGCTACGTTAGTCCTAAAATCGACTAAACCGTAACTCTAATACCAATAAAA
39762380 TGTAACACCCCTAACCCGAATCCGATTGCCAGATTAAG
131 TGTAACACCCCTAACCCGAATCCGATTGCCAGATTAAG
39762418 GCTAAGGGGT
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 162 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (170 bp):
CAAAAACACATTTTTAACTGTCAGAAATCATCACACTATCGTATTAACACTATATGGCATGTATA
GCTAGACTCATATACGCTACGTTAGTCCTAAAATCGACTAAACCGTAACTCTAATACCAATAAAA
TGTAACACCCCTAACCCGAATCCGATTGCCAGATTAAGTA
Found at i:39763516 original size:38 final size:39
Alignment explanation
Indices: 39763400--39763547 Score: 201
Period size: 39 Copynumber: 3.8 Consensus size: 39
39763390 ACATATTTCT
* *
39763400 AGCACGTAGCCTGCGGACCTTAAGTTC-GATTATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTTCGGA-TATAATTCC
** * *
39763439 AGCACATAGCCTGTAGACCTTAAGTCCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTTCGGATATAATTCC
*
39763478 AGCACATAGCTTGCGGACCCT-AGTTCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTTCGGATATAATTCC
*
39763516 AGCACATAGCCTGCGGACCCTAAGTTCTGATA
1 AGCACATAGCCTGCGGACCCTAAGTTCGGATA
39763548 AACATCACTA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 36 0.38
39 58 0.60
40 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (39 bp):
AGCACATAGCCTGCGGACCCTAAGTTCGGATATAATTCC
Found at i:39763540 original size:77 final size:78
Alignment explanation
Indices: 39763386--39763540 Score: 206
Period size: 77 Copynumber: 2.0 Consensus size: 78
39763376 GGACTTTAGC
* * * *
39763386 CCGGACATATTTCTAGCACGTAGCCTGCGGACCTTAAGTTCGATTATAATTCCAGCACATAGCCT
1 CCGGACATAATTCCAGCACATAGCCTGCGGACCCTAAGTTCGATTATAATTCCAGCACATAGCCT
* *
39763451 GTAGACCTTAAGT
66 GCAGACCCTAAGT
* *
39763464 CCGGATATAATTCCAGCACATAGCTTGCGGACCCT-AGTTCGGA-TATAATTCCAGCACATAGCC
1 CCGGACATAATTCCAGCACATAGCCTGCGGACCCTAAGTTC-GATTATAATTCCAGCACATAGCC
*
39763527 TGCGGACCCTAAGT
65 TGCAGACCCTAAGT
39763541 TCTGATAAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 36 0.54
78 31 0.46
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (78 bp):
CCGGACATAATTCCAGCACATAGCCTGCGGACCCTAAGTTCGATTATAATTCCAGCACATAGCCT
GCAGACCCTAAGT
Found at i:39765377 original size:13 final size:13
Alignment explanation
Indices: 39765359--39765386 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39765349 TCAATTTATG
39765359 AAATAAAAAAATT
1 AAATAAAAAAATT
39765372 AAATAAAAAAATT
1 AAATAAAAAAATT
39765385 AA
1 AA
39765387 GAATGGTTCA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAAAAATT
Found at i:39765394 original size:45 final size:45
Alignment explanation
Indices: 39765343--39765432 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
39765333 ATTATATGGT
39765343 AATGGTTCAATTTATGAAAT-AAAAAAATTAAATAAAAAAATTAAG
1 AATGGTTCAATTTATGAAATAAAAAAAATTAAAT-AAAAAATTAAG
39765388 AATGGTTCAATTTATGAAATAAAAAAAATTAAATAAAAAATTAAG
1 AATGGTTCAATTTATGAAATAAAAAAAATTAAATAAAAAATTAAG
39765433 TTAAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 31 0.70
46 13 0.30
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (45 bp):
AATGGTTCAATTTATGAAATAAAAAAAATTAAATAAAAAATTAAG
Found at i:39774158 original size:20 final size:20
Alignment explanation
Indices: 39774130--39774168 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39774120 ATAGTATTTT
39774130 ATTAATTTAATATTAAATTG
1 ATTAATTTAATATTAAATTG
*
39774150 ATTATTTTAATATTAAATT
1 ATTAATTTAATATTAAATT
39774169 TAATTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTAATTTAATATTAAATTG
Found at i:39777219 original size:46 final size:46
Alignment explanation
Indices: 39777169--39777341 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
39777159 TGGTTGAGCA
*
39777169 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
39777215 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
39777262 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
39777308 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39777342 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:39777325 original size:93 final size:93
Alignment explanation
Indices: 39777166--39777336 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
39777156 GGATGGTTGA
* *
39777166 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
39777231 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
39777259 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
39777324 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39777337 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39777603 original size:19 final size:20
Alignment explanation
Indices: 39777566--39777603 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39777556 ATAAGGTGGT
39777566 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
39777586 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
39777604 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:39784790 original size:46 final size:46
Alignment explanation
Indices: 39784740--39784911 Score: 190
Period size: 45 Copynumber: 3.7 Consensus size: 46
39784730 TGGTTGAGCA
*
39784740 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
39784786 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
39784833 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
39784879 -CCCAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39784912 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 14, Indels: 15
0.78 0.10 0.11
Matches are distributed among these distances:
43 6 0.06
45 32 0.30
46 30 0.29
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:39784855 original size:47 final size:47
Alignment explanation
Indices: 39784737--39784909 Score: 171
Period size: 46 Copynumber: 3.7 Consensus size: 47
39784727 GGATGGTTGA
* *
39784737 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* *
39784785 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--AG
* * * *
39784830 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* *
39784878 GC--CC-AGCTCATTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
39784910 TAGGGGCGGG
Statistics
Matches: 106, Mismatches: 12, Indels: 17
0.79 0.09 0.13
Matches are distributed among these distances:
43 6 0.06
45 29 0.27
46 31 0.29
47 29 0.27
48 6 0.06
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG
Found at i:39785173 original size:19 final size:20
Alignment explanation
Indices: 39785136--39785173 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39785126 ATAAGGTGGT
39785136 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
39785156 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
39785174 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:39793325 original size:68 final size:71
Alignment explanation
Indices: 39793229--39793363 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 71
39793219 TTTAATAGAT
* * *
39793229 TTAATATTACATTTAATTTAATAATTATC-CTA-CT-AGTATTATATTAATTTAATATTAAAGTG
1 TTAATATTAAATTTAATTTAATAATTATCTCTAGATAAATATTATATTAATTTAATATTAAAGTG
39793291 AGTATC
66 AGTATC
* ** *
39793297 TTAATATTAAATTTAATTTCATGTTTATCTTGTAGATAAATATTATATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATAATTATC-TCTAGATAAATATTATATTAATTTAATATTAAAGT
39793362 GA
65 GA
39793364 TTAAGTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 25 0.45
70 2 0.04
71 1 0.02
72 28 0.50
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (71 bp):
TTAATATTAAATTTAATTTAATAATTATCTCTAGATAAATATTATATTAATTTAATATTAAAGTG
AGTATC
Found at i:39794612 original size:2 final size:2
Alignment explanation
Indices: 39794605--39794629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39794595 TTAGGGATTT
39794605 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39794630 TTAAGTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39814495 original size:61 final size:61
Alignment explanation
Indices: 39814430--39814566 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 61
39814420 CAGAGTTAAC
* * *
39814430 TGGGCCTTAGCCAATATCCA-TATTAATCTGGGCCATAGCCC-CTTAC-AGTATCAGAGTATAT
1 TGGGCCTTAGCCCATAT-CAGTATCAATCTGGGCCATAGCCCTATTACAAGT-TCAGA-TATAT
** *
39814491 TGGGCC-TAGCCCATATCAGTATCAATCTGGGCTGTAGCCCTATTACAAGTTGAGATATAT
1 TGGGCCTTAGCCCATATCAGTATCAATCTGGGCCATAGCCCTATTACAAGTTCAGATATAT
39814551 TGGGCCTT-GCCCATAT
1 TGGGCCTTAGCCCATAT
39814567 TAACACAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
59 2 0.03
60 46 0.70
61 15 0.23
62 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (61 bp):
TGGGCCTTAGCCCATATCAGTATCAATCTGGGCCATAGCCCTATTACAAGTTCAGATATAT
Found at i:39814584 original size:20 final size:20
Alignment explanation
Indices: 39814559--39814604 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39814549 ATTGGGCCTT
39814559 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
39814579 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
39814598 GCCCATA
1 GCCCATA
39814605 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:39814613 original size:19 final size:20
Alignment explanation
Indices: 39814571--39814614 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
39814561 CCATATTAAC
** *
39814571 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
39814591 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
39814610 ACAGT
1 ACAGT
39814615 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:39827788 original size:2 final size:2
Alignment explanation
Indices: 39827783--39827817 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39827773 CAAAAAAATA
39827783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39827818 AACTACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39828924 original size:105 final size:105
Alignment explanation
Indices: 39828742--39828930 Score: 326
Period size: 105 Copynumber: 1.8 Consensus size: 105
39828732 ATGTTAATAT
*
39828742 ATGTAATTAGATCTCTCATTCCAAGTTTCATTTTTCGGAGTATTATTGAAGTTTGTATTTCTTCC
1 ATGTAATTACATCTCTCATTCCAAGTTTCATTTTTCGGAGTATTATTGAAGTTTGTATTTCTTCC
39828807 ACTCTAGCGTTTCTAGAAGTTCTGGATTGAAAATTTGAGA
66 ACTCTAGCGTTTCTAGAAGTTCTGGATTGAAAATTTGAGA
*
39828847 ATGTAATTACATCTCTCATTCCAAGTTTCATTTGTT-GGAGTATTATTTAAGTTTGTATTTCTTC
1 ATGTAATTACATCTCTCATTCCAAGTTTCATTT-TTCGGAGTATTATTGAAGTTTGTATTTCTTC
* *
39828911 CACTCTAGTGTTTCTGGAAG
65 CACTCTAGCGTTTCTAGAAG
39828931 ATATAAAACT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 77 0.97
106 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.44
Consensus pattern (105 bp):
ATGTAATTACATCTCTCATTCCAAGTTTCATTTTTCGGAGTATTATTGAAGTTTGTATTTCTTCC
ACTCTAGCGTTTCTAGAAGTTCTGGATTGAAAATTTGAGA
Found at i:39829610 original size:2 final size:2
Alignment explanation
Indices: 39829603--39829634 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39829593 TAATGCCTAA
39829603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39829635 CTAACTTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39836170 original size:30 final size:30
Alignment explanation
Indices: 39836136--39836216 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
39836126 TTCCACATGG
39836136 GTGATCCACATGCCCGTGTGTGACACACGA
1 GTGATCCACATGCCCGTGTGTGACACACGA
* * * * * *
39836166 GTGATCCACACGTCTGCGTGTGACACATGG
1 GTGATCCACATGCCCGTGTGTGACACACGA
*
39836196 GTAGA-CCACATGCCCATGTGT
1 GT-GATCCACATGCCCGTGTGT
39836217 CATGGCCGTG
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.22
Consensus pattern (30 bp):
GTGATCCACATGCCCGTGTGTGACACACGA
Found at i:39839966 original size:40 final size:39
Alignment explanation
Indices: 39839921--39840050 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
39839911 CGGAATACAA
39839921 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
39839961 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
39840001 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
39840041 CCGGATATAA
1 CCGGATATAA
39840051 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:39848938 original size:29 final size:29
Alignment explanation
Indices: 39848905--39848982 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
39848895 GTGACGAGAT
* *
39848905 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGAGCTGGAAAAATA
*
39848934 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGAGCTGGAAAAATA
* **
39848963 CGGCACTGGGTGTGCGAGCT
1 TGGCACTAAGTGTGCGAGCT
39848983 CGAGGGTATG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTGGAAAAATA
Found at i:39856787 original size:29 final size:29
Alignment explanation
Indices: 39856753--39856817 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
39856743 GTGACGAGAT
** *
39856753 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
*
39856782 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
39856811 CGGCACT
1 CGGCACT
39856818 GGGTGCGAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCAAGCTGGAAAAATA
Found at i:39858923 original size:40 final size:39
Alignment explanation
Indices: 39858878--39859005 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 39
39858868 CGGAATACAA
39858878 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
39858918 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
39858958 CCGGATGTAGCCGCTAGAAC-AATTGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
39858998 CCGGATAT
1 CCGGATAT
39859006 CATTCAATTG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:39866136 original size:29 final size:29
Alignment explanation
Indices: 39866103--39866205 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
39866093 CCTCCGAACT
** * * *
39866103 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
39866132 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39866161 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39866190 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39866206 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:39869543 original size:29 final size:29
Alignment explanation
Indices: 39869510--39869665 Score: 172
Period size: 29 Copynumber: 5.4 Consensus size: 29
39869500 CGAGATTGGT
39869510 ACTAAGTGTGCATGCTGGAAATATATGGC
1 ACTAAGTGTGCATGCTGGAAATATATGGC
39869539 ACTAAGTGTGCATGCTGGAAATATATGGC
1 ACTAAGTGTGCATGCTGGAAATATATGGC
*
39869568 ACTAAGTGTGCATGCTGGAAATATACGGC
1 ACTAAGTGTGCATGCTGGAAATATATGGC
** * ***
39869597 ACTGGGTGTGCGA-GCTCGAAGGGTATGGC
1 ACTAAGTGTGC-ATGCTGGAAATATATGGC
* ** * *
39869626 ACTATGTGTGCGGGCTTG-AATCACATGGC
1 ACTAAGTGTGCATGCTGGAAAT-ATATGGC
39869655 ACTAAGTGTGC
1 ACTAAGTGTGC
39869666 GAAATCGAGT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 105 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
ACTAAGTGTGCATGCTGGAAATATATGGC
Found at i:39875133 original size:29 final size:29
Alignment explanation
Indices: 39875100--39875259 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
39875090 GTGACGAGAT
39875100 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
39875129 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
39875158 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
39875187 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
39875216 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
39875245 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
39875260 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:39882986 original size:29 final size:29
Alignment explanation
Indices: 39882953--39883112 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
39882943 GTGACGAGAT
39882953 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
39882982 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
39883011 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
39883040 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
39883069 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
39883098 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
39883113 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:39886387 original size:18 final size:18
Alignment explanation
Indices: 39886344--39886379 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39886334 TCACCTAGAT
39886344 AATATCATCTACCATAAA
1 AATATCATCTACCATAAA
39886362 AATATCATCTACCATAAA
1 AATATCATCTACCATAAA
39886380 GGTATCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (18 bp):
AATATCATCTACCATAAA
Found at i:39901805 original size:24 final size:24
Alignment explanation
Indices: 39901773--39901821 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
39901763 TCCCTTATGA
*
39901773 TGGTCTACGAGACTTAAAACATAC
1 TGGTCTACGAGACCTAAAACATAC
39901797 TGGTCTACGAGACCTAAAACATAC
1 TGGTCTACGAGACCTAAAACATAC
39901821 T
1 T
39901822 TTTAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
TGGTCTACGAGACCTAAAACATAC
Found at i:39905756 original size:33 final size:33
Alignment explanation
Indices: 39905710--39905776 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
39905700 TAAAAAGCTC
*
39905710 AATTTGGATTGTTTGAAACTTTGATGTTCTTAT
1 AATTTGGACTGTTTGAAACTTTGATGTTCTTAT
*
39905743 AATTTGGACTGTTTGAAACTTTGATGTTTTTAT
1 AATTTGGACTGTTTGAAACTTTGATGTTCTTAT
39905776 A
1 A
39905777 GTTAAGCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.06, G:0.18, T:0.51
Consensus pattern (33 bp):
AATTTGGACTGTTTGAAACTTTGATGTTCTTAT
Found at i:39906185 original size:30 final size:30
Alignment explanation
Indices: 39906123--39906200 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
39906113 AGGAACTTCT
* ** * *
39906123 ACACGGGTGATCCACACTTTTGTGTGTGAC
1 ACACGGGTGATCCACACGTCCGTGTATAAC
39906153 ACACGGGTGATCCACACGTCCGTGTATAAC
1 ACACGGGTGATCCACACGTCCGTGTATAAC
39906183 ACACGGGTAGA-CCACACG
1 ACACGGGT-GATCCACACG
39906201 CCTGTGTGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 40 0.95
31 2 0.05
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.21
Consensus pattern (30 bp):
ACACGGGTGATCCACACGTCCGTGTATAAC
Found at i:39917559 original size:20 final size:19
Alignment explanation
Indices: 39917514--39917559 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
39917504 TAAAATAATC
*
39917514 TAATTTTAGTGTTAAAATT
1 TAATTTTTGTGTTAAAATT
39917533 T-ATTTTTGTAGTTAAAATT
1 TAATTTTTGT-GTTAAAATT
39917552 TAATTTTT
1 TAATTTTT
39917560 ATACATCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (19 bp):
TAATTTTTGTGTTAAAATT
Found at i:39918164 original size:31 final size:29
Alignment explanation
Indices: 39918117--39918197 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 29
39918107 ATTTATAAAA
* *
39918117 TTTTAAATTAATAATAAAATTATATTTTTATC
1 TTTTAAA--AATAATAAAATT-TAATTTAATC
*
39918149 TTTTTATAAATAATAAAAATTTAATTTAATC
1 -TTTTAAAAATAAT-AAAATTTAATTTAATC
*
39918180 TTTTAAAAATTATAAAAT
1 TTTTAAAAATAATAAAAT
39918198 ATAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 5 0.12
30 11 0.26
31 14 0.33
32 6 0.14
33 6 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTAAAAATAATAAAATTTAATTTAATC
Found at i:39918195 original size:30 final size:32
Alignment explanation
Indices: 39918117--39918196 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 32
39918107 ATTTATAAAA
* *
39918117 TTTTAAATTAATAAT-AAAATTATATTTTTATCT
1 TTTTAAA--AATAATAAAAATTATAATTTAATCT
*
39918150 TTTTATAAATAATAAAAATT-TAATTTAATC-
1 TTTTAAAAATAATAAAAATTATAATTTAATCT
*
39918180 TTTTAAAAATTATAAAA
1 TTTTAAAAATAATAAAA
39918197 TATAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 15 0.37
31 14 0.34
32 6 0.15
33 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTTAAAAATAATAAAAATTATAATTTAATCT
Found at i:39918220 original size:17 final size:16
Alignment explanation
Indices: 39918185--39918224 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
39918175 TAATCTTTTA
39918185 AAAATTA-TAAAATAT
1 AAAATTATTAAAATAT
39918200 -AAATTATTAAAATATT
1 AAAATTATTAAAATA-T
39918216 AAAATTATT
1 AAAATTATT
39918225 TATTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 1 0.05
17 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTATTAAAATAT
Found at i:39918254 original size:27 final size:27
Alignment explanation
Indices: 39918202--39918254 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
39918192 TAAAATATAA
* *
39918202 ATTATTAAAATATTAAAATTATTTATT
1 ATTATAAAAATATTAAAATTAATTATT
*
39918229 ATTATAAAAATA-TATAATTTAATTAT
1 ATTATAAAAATATTA-AAATTAATTAT
39918255 GCAAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTATAAAAATATTAAAATTAATTATT
Found at i:39920653 original size:23 final size:22
Alignment explanation
Indices: 39920611--39920653 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
39920601 TTTCTGACAC
39920611 TTAACAAGCTTATTTATAACTG
1 TTAACAAGCTTATTTATAACTG
39920633 TTAACAAGCTTATTTTATAAC
1 TTAACAAGCTTA-TTTATAAC
39920654 GGTTTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (22 bp):
TTAACAAGCTTATTTATAACTG
Found at i:39926386 original size:93 final size:93
Alignment explanation
Indices: 39926279--39926450 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
39926269 GCCCATAAGT
* *
39926279 GAACTCGGACTCAACTCAACAAGTTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39926344 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
39926372 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
39926437 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
39926451 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:39926446 original size:46 final size:46
Alignment explanation
Indices: 39926271--39926446 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
39926261 TGTAACCTGC
* * *
39926271 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
39926317 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* ***
39926363 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39926410 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39926447 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:39932468 original size:27 final size:28
Alignment explanation
Indices: 39932438--39932537 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 28
39932428 ATAGTGAGTC
39932438 CGCACACTTAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* *
39932465 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
39932493 CGCACACTTAGTGCTGTACAAATTAAAAACC
1 CGCACACTTAGTGCTATA-AAA-T-CAAACT
39932524 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39932538 CATTCTCATG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 2 0.03
30 1 0.02
31 18 0.29
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:39935290 original size:24 final size:24
Alignment explanation
Indices: 39935258--39935368 Score: 134
Period size: 24 Copynumber: 4.6 Consensus size: 24
39935248 TATCTCAAAT
*
39935258 GCACTATGTGTGCAATTTATTATA
1 GCACTATGTGTGCAATTTACTATA
* *
39935282 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCAATTTACTATA
* *
39935306 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCAATTTACTATA
** *
39935330 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGC-AATTTACTATA
39935354 GCACTATGTGTGCAA
1 GCACTATGTGTGCAA
39935369 CGTTTGGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
23 2 0.03
24 71 0.91
25 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCAATTTACTATA
Found at i:39940975 original size:40 final size:40
Alignment explanation
Indices: 39940867--39941076 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
39940857 CGGGATTTAA
* * * * *
39940867 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
39940907 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39940947 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39940987 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39941027 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39941067 CCGGATATAT
1 CCGGATATAT
39941077 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:39949109 original size:40 final size:40
Alignment explanation
Indices: 39949001--39949210 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
39948991 CGGGATTTAA
* * * * *
39949001 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
39949041 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39949081 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39949121 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39949161 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39949201 CCGGATATAT
1 CCGGATATAT
39949211 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:39953550 original size:30 final size:30
Alignment explanation
Indices: 39953514--39953614 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
39953504 GACAAGATTG
* * *
39953514 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
39953544 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
39953572 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
39953601 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39953615 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:39953626 original size:29 final size:28
Alignment explanation
Indices: 39953543--39953618 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
39953533 AAAATTGTAC
* *
39953543 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
39953571 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
39953600 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
39953619 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:39961441 original size:30 final size:30
Alignment explanation
Indices: 39961405--39961505 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
39961395 GACAAGATTG
* * *
39961405 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
39961435 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
39961463 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
39961492 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39961506 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:39961517 original size:29 final size:28
Alignment explanation
Indices: 39961434--39961509 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
39961424 AAAATTGTAC
* *
39961434 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
39961462 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
39961491 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
39961510 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:39968202 original size:41 final size:41
Alignment explanation
Indices: 39968157--39968235 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
39968147 TACATGGTAT
39968157 TGGCATTGAGATGAGTGCTAGTGTAAGACATGTTTGGGACA
1 TGGCATTGAGATGAGTGCTAGTGTAAGACATGTTTGGGACA
39968198 TGGCATTGAGATGAGTGCTAGTGTAAGACATGTTTGGG
1 TGGCATTGAGATGAGTGCTAGTGTAAGACATGTTTGGG
39968236 GCATACAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.25, C:0.09, G:0.35, T:0.30
Consensus pattern (41 bp):
TGGCATTGAGATGAGTGCTAGTGTAAGACATGTTTGGGACA
Found at i:39970171 original size:27 final size:28
Alignment explanation
Indices: 39970141--39970210 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
39970131 ATAGTGAATC
*
39970141 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
39970168 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
39970196 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39970211 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:39970282 original size:42 final size:42
Alignment explanation
Indices: 39970218--39970324 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
39970208 GCTGTACAAT
* *
39970218 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
39970260 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
39970302 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
39970325 GAGACCAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:39974828 original size:28 final size:27
Alignment explanation
Indices: 39974765--39974834 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
39974755 ATAGTGAGTC
39974765 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
39974792 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
39974820 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39974835 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:39983646 original size:27 final size:27
Alignment explanation
Indices: 39983608--39983899 Score: 207
Period size: 27 Copynumber: 10.9 Consensus size: 27
39983598 AATACTTTAG
* *
39983608 TTTACCAAATTACCAAAGTACCCCTGA
1 TTTACAAAATTACCAAAATACCCCTGA
* ***
39983635 TTTACAGAATTACCATTTTA-CCCTCGA
1 TTTACAAAATTACCAAAATACCCCT-GA
*
39983662 -TTAGCAAAATTACCAAAATA-CCCTGG
1 TTTA-CAAAATTACCAAAATACCCCTGA
***
39983688 TTTGTGAAATTACCAAAATACCCCTGA
1 TTTACAAAATTACCAAAATACCCCTGA
*** ***
39983715 TTTGTGAAATTATTGAAATA-CCCTCGA
1 TTTACAAAATTACCAAAATACCCCT-GA
* ** * *
39983742 CTTGTAAAATTACCAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCCTGA
*
39983769 TTTACAAAATTACCAAAATACCCCTAA
1 TTTACAAAATTACCAAAATACCCCTGA
*** * * *
39983796 TTTGTGAAATTACTAAAATACCCTTAA
1 TTTACAAAATTACCAAAATACCCCTGA
* **
39983823 CTTGTAAAATTACCAAAATACCCCT-A
1 TTTACAAAATTACCAAAATACCCCTGA
*
39983849 GTTTACAAAATTACCAAAATACCCCTGG
1 -TTTACAAAATTACCAAAATACCCCTGA
**
39983877 TTTGTAAAATTACCAAAATACCC
1 TTTACAAAATTACCAAAATACCC
39983900 TTATAGGGTA
Statistics
Matches: 212, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
26 27 0.13
27 182 0.86
28 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCCTGA
Found at i:39983802 original size:81 final size:80
Alignment explanation
Indices: 39983607--39983900 Score: 349
Period size: 81 Copynumber: 3.6 Consensus size: 80
39983597 GAATACTTTA
* * ** * *** *
39983607 GTTTACCAAATTACCAAAGTACCCCTGATTT-ACAGAATTACCATTTTACCCTCGA-TTAGCAAA
1 GTTTACAAAATTACCAAAATACCCCTGATTTGTGA-AATTACTAAAATACCCTCGACTT-GTAAA
39983670 ATTACCAAAATACCCTG
64 ATTACCAAAATACCCTG
*** * *
39983687 GTTTGTGAAATTACCAAAATACCCCTGATTTGTGAAATTATTGAAATACCCTCGACTTGTAAAAT
1 GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCTCGACTTGTAAAAT
39983752 TACCAAAATACCCTTG
66 TACCAAAATACCC-TG
* **
39983768 GTTTACAAAATTACCAAAATACCCCTAATTTGTGAAATTACTAAAATACCCTTAACTTGTAAAAT
1 GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCTCGACTTGTAAAAT
*
39983833 TACCAAAATACCCCTA
66 TACCAAAATA-CCCTG
* * *
39983849 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCT
1 GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCT
39983901 TATAGGGTAG
Statistics
Matches: 184, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
80 60 0.33
81 121 0.66
82 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (80 bp):
GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCTCGACTTGTAAAAT
TACCAAAATACCCTG
Done.