Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 92 of 208
Found at i:27320472 original size:19 final size:19
Alignment explanation
Indices: 27320448--27320487 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27320438 GTGTTGCCCA
*
27320448 TGTGTGACACATGCCCATG
1 TGTGTGACACACGCCCATG
* *
27320467 TGTGTGGCACACGCCCGTG
1 TGTGTGACACACGCCCATG
27320486 TG
1 TG
27320488 GCTAGGCTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (19 bp):
TGTGTGACACACGCCCATG
Found at i:27321431 original size:43 final size:43
Alignment explanation
Indices: 27321346--27321431 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
27321336 TCATATCTCA
* *
27321346 TTTCTCATCTCATAATCATTTCTCATATTTGTCATTTTAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGTCATCTCAATAT
* *
27321389 TTTCTCATCTCATATTCATTTCTCATCTTTGTCATCTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGTCATCTCAATAT
27321432 CAATCACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGTCATCTCAATAT
Found at i:27322645 original size:13 final size:13
Alignment explanation
Indices: 27322627--27322653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27322617 ACAACCATTT
27322627 ATTAAATGGTTTA
1 ATTAAATGGTTTA
27322640 ATTAAATGGTTTA
1 ATTAAATGGTTTA
27322653 A
1 A
27322654 ATTGTTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
ATTAAATGGTTTA
Found at i:27323156 original size:3 final size:3
Alignment explanation
Indices: 27323150--27323176 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27323140 CATCATGAGA
27323150 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
27323177 AGTTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27323475 original size:16 final size:16
Alignment explanation
Indices: 27323456--27323492 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
27323446 TTATTTTTTC
27323456 ATAAAA-TTAAAATAAA
1 ATAAAATTTAAAA-AAA
27323472 ATAAAATTTAAAAAAA
1 ATAAAATTTAAAAAAA
27323488 A-AAAA
1 ATAAAA
27323493 AAGGCGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAATTTAAAAAAA
Found at i:27323834 original size:22 final size:22
Alignment explanation
Indices: 27323806--27323866 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
27323796 NNNNNNNNAA
* * *
27323806 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
27323828 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
27323850 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
27323867 CGGGCCGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:27324087 original size:3 final size:3
Alignment explanation
Indices: 27324079--27324126 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
27324069 GTTAAAATAT
27324079 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27324127 AATCTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27328251 original size:22 final size:22
Alignment explanation
Indices: 27328226--27328269 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27328216 GTAACATAGT
27328226 GTCCAATTATCTGTTTTGTCAG
1 GTCCAATTATCTGTTTTGTCAG
27328248 GTCCAATTATCTGTTTTGTCAG
1 GTCCAATTATCTGTTTTGTCAG
27328270 ATAAACCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (22 bp):
GTCCAATTATCTGTTTTGTCAG
Found at i:27329994 original size:22 final size:22
Alignment explanation
Indices: 27329969--27330016 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27329959 ACGAATTCGG
*
27329969 AATTCAAATT-ATATAAAATTAA
1 AATTCAAATTAAT-TAAAAATAA
* *
27329991 AATTGAATTTAATTAAAAATAA
1 AATTCAAATTAATTAAAAATAA
27330013 AATT
1 AATT
27330017 TTATTTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTCAAATTAATTAAAAATAA
Found at i:27330022 original size:22 final size:22
Alignment explanation
Indices: 27329982--27330025 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27329972 TCAAATTATA
*
27329982 TAAAATTAAAATTGAATTTAAT
1 TAAAAATAAAATTGAATTTAAT
**
27330004 TAAAAATAAAATTTTATTTAAT
1 TAAAAATAAAATTGAATTTAAT
27330026 CGAACAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAATAAAATTGAATTTAAT
Found at i:27333183 original size:32 final size:33
Alignment explanation
Indices: 27333147--27333230 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 33
27333137 CTAAAGTTAT
27333147 TGAAAAAATTATATTATTTATAAAA-AGTATTA
1 TGAAAAAATTATATTATTTATAAAACAGTATTA
** * ** * *
27333179 TGAAAATTTTAGACAATTTATAAAACATTTTTA
1 TGAAAAAATTATATTATTTATAAAACAGTATTA
27333212 T-AAAAAATTTATATTATTT
1 TGAAAAAA-TTATATTATTT
27333231 TATTTAATTT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
32 24 0.63
33 14 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (33 bp):
TGAAAAAATTATATTATTTATAAAACAGTATTA
Found at i:27334694 original size:90 final size:88
Alignment explanation
Indices: 27334554--27334740 Score: 218
Period size: 90 Copynumber: 2.1 Consensus size: 88
27334544 CTCAATTTAA
*
27334554 AAAAAAAACCAATTAAGTCCCTCTTTTTTTTGCACTCAATTGAGCACTTGAATTTTCAAAATGCA
1 AAAAAAAACCAATTAAGTCCCTCTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
*
27334619 TCAAAAAGGCCCTCAAAC-CTTT
66 TCAAAAAGACCCTCAAACTCTTT
* * * *
27334641 AAAAAAAAGCAATTAA-TCCCCTACTTTTTTTTTTGTACTCCATTG-GTTACTTGAACTTTCAAA
1 AAAAAAAACCAATTAAGT-CCCT-C--TTTTTTTTGCACTCAATTGAG-CACTTGAACTTTCAAA
* * *
27334704 ATGCATCAACAAGACCTTCAAACTTTTT
61 ATGCATCAAAAAGACCCTCAAACTCTTT
27334732 ACAAAAAAA
1 A-AAAAAAA
27334741 AAAAAGCAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
86 1 0.01
87 19 0.23
88 1 0.01
89 1 0.01
90 51 0.61
91 4 0.05
92 7 0.08
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (88 bp):
AAAAAAAACCAATTAAGTCCCTCTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
TCAAAAAGACCCTCAAACTCTTT
Found at i:27334786 original size:20 final size:20
Alignment explanation
Indices: 27334761--27334800 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27334751 TAAACCCTTG
*
27334761 TTTTTATTAAAAATTAGAAT
1 TTTTTATAAAAAATTAGAAT
27334781 TTTTTATAAAAAATTAGAAT
1 TTTTTATAAAAAATTAGAAT
27334801 CAATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTATAAAAAATTAGAAT
Found at i:27334856 original size:28 final size:28
Alignment explanation
Indices: 27334789--27334892 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 28
27334779 ATTTTTTATA
27334789 AAAAATTAGAATCAATAAAATTTATAAATATT
1 AAAAATTAGAA--AA-AAAATTTA-AAATATT
* ** *
27334821 ATTAAATTTTAATAAAAATTTAAAATATT
1 A-AAAATTAGAAAAAAAATTTAAAATATT
*
27334850 AAAAATTAGAAAAAAAATATAAAAT-TGT
1 AAAAATTAGAAAAAAAATTTAAAATAT-T
* *
27334878 AAAAAATATAAAAAA
1 AAAAATTAGAAAAAA
27334893 TTGTAAAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.02
28 33 0.56
29 8 0.14
30 8 0.14
31 1 0.02
32 1 0.02
33 7 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTAGAAAAAAAATTTAAAATATT
Found at i:27334892 original size:38 final size:39
Alignment explanation
Indices: 27334842--27334939 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
27334832 ATAAAAATTT
* *
27334842 AAAATATTAAAAATTAGAAAAAAAATAT-AAAATTGTAA
1 AAAATATAAAAAATTAGAAAAAAAATATAAAAATCGTAA
* ***
27334880 AAAATATAAAAAATT-GTAAAATTTTATAAAAATCGTAA
1 AAAATATAAAAAATTAGAAAAAAAATATAAAAATCGTAA
*
27334918 AAAATTATAAAATATATAGAAA
1 AAAA-TATAAAAAAT-TAGAAA
27334940 TATAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 8 0.17
38 27 0.56
39 9 0.19
40 1 0.02
41 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (39 bp):
AAAATATAAAAAATTAGAAAAAAAATATAAAAATCGTAA
Found at i:27334921 original size:56 final size:54
Alignment explanation
Indices: 27334834--27335000 Score: 158
Period size: 56 Copynumber: 3.0 Consensus size: 54
27334824 AAATTTTAAT
* * *
27334834 AAAAATTTAAAATATTA-AAAATTAGAAAAAAAATATAAAATTGTAAAAAATATA
1 AAAAATTTAAAATTTTATAAAATTCGTAAAAAAATATAAAA-TGTAAAAAATATA
* * * *
27334888 AAAAATTGTAAAATTTTATAAAAATCGTAAAAAATTATAAAATATATAGAAATATAA
1 AAAAATT-TAAAATTTTATAAAATTCGTAAAAAAATATAAAATGTA-AAAAATAT-A
* * *
27334945 AAAAATATAAAATTTTAT-AAATTCGTTAGAAAATGATACAAAATGTAAAGAAATAT
1 AAAAATTTAAAATTTTATAAAATTCG-TA-AAAA-AATATAAAATGTAAA-AAATAT
27335001 TTCGTAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
54 7 0.08
55 18 0.20
56 39 0.43
57 12 0.13
58 15 0.16
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (54 bp):
AAAAATTTAAAATTTTATAAAATTCGTAAAAAAATATAAAATGTAAAAAATATA
Found at i:27334925 original size:19 final size:19
Alignment explanation
Indices: 27334832--27334929 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
27334822 TTAAATTTTA
*
27334832 ATAAAAATT-TAAAATA-T
1 ATAAAAATTGTAAAAAATT
* *
27334849 -TAAAAATTAGAAAAAAAAT
1 ATAAAAATT-GTAAAAAATT
27334868 AT-AAAATTGTAAAAAA-T
1 ATAAAAATTGTAAAAAATT
**
27334885 ATAAAAAATTGTAAAATTTT
1 AT-AAAAATTGTAAAAAATT
*
27334905 ATAAAAATCGTAAAAAATT
1 ATAAAAATTGTAAAAAATT
27334924 ATAAAA
1 ATAAAA
27334930 TATATAGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
16 8 0.12
17 3 0.05
18 12 0.18
19 39 0.59
20 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
ATAAAAATTGTAAAAAATT
Found at i:27335264 original size:18 final size:18
Alignment explanation
Indices: 27335243--27335301 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
27335233 TAAATATTAT
27335243 ATTTTTTATATTTTAATA
1 ATTTTTTATATTTTAATA
**
27335261 ATTTTTCTA-AAATTAATA
1 ATTTTT-TATATTTTAATA
*
27335279 ATTTTTTAT-TTTTTATA
1 ATTTTTTATATTTTAATA
27335296 ATTTTT
1 ATTTTT
27335302 AATTAGAGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 13 0.38
18 19 0.56
19 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTATATTTTAATA
Found at i:27335708 original size:12 final size:11
Alignment explanation
Indices: 27335672--27335710 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
27335662 AAAATAACTC
27335672 AAAA-TATAAA
1 AAAATTATAAA
27335682 AAAATTAT-AA
1 AAAATTATAAA
27335692 AAAATTCATAAA
1 AAAATT-ATAAA
27335704 AAAATTA
1 AAAATTA
27335711 GCATGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 12 0.46
11 6 0.23
12 8 0.31
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:27341725 original size:11 final size:11
Alignment explanation
Indices: 27341686--27341748 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
27341676 CAACCTTAAA
*
27341686 CACCACCTAAC
1 CACCACCAAAC
* *
27341697 AACCACCAAAT
1 CACCACCAAAC
27341708 CACCACCAAAC
1 CACCACCAAAC
* *
27341719 CATCACCATAC
1 CACCACCAAAC
* **
27341730 AACCACCACTC
1 CACCACCAAAC
27341741 CACCACCA
1 CACCACCA
27341749 TTCAACCACC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.41, C:0.51, G:0.00, T:0.08
Consensus pattern (11 bp):
CACCACCAAAC
Found at i:27341734 original size:22 final size:22
Alignment explanation
Indices: 27341687--27341758 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
27341677 AACCTTAAAC
* * *
27341687 ACCACCTAACAACCACCAAATC-
1 ACCACCAAACCACCACCATA-CA
*
27341709 ACCACCAAACCATCACCATACA
1 ACCACCAAACCACCACCATACA
** *
27341731 ACCACCACTCCACCACCATTCA
1 ACCACCAAACCACCACCATACA
27341753 ACCACC
1 ACCACC
27341759 GTAACATCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 1 0.02
22 40 0.98
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (22 bp):
ACCACCAAACCACCACCATACA
Found at i:27342669 original size:18 final size:19
Alignment explanation
Indices: 27342641--27342677 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27342631 GCAATCACAT
27342641 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
27342660 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
27342678 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:27346908 original size:35 final size:36
Alignment explanation
Indices: 27346819--27346912 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 36
27346809 CATTGATTTA
* * *
27346819 TTGATATTCTGTTTCGCATGTTGAGCATGCTATTATT
1 TTGA-ATTCTGATTCGCATGTTAAGAATGCTATTATT
* * *
27346856 TTGACTAC-GATTTGCATGTTAAGGAAT-CTATTATT
1 TTGAATTCTGATTCGCATGTTAA-GAATGCTATTATT
27346891 TT-AATTCTGATTCGCATGTTAA
1 TTGAATTCTGATTCGCATGTTAA
27346913 ACGTGCCCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
34 3 0.07
35 34 0.74
36 5 0.11
37 4 0.09
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (36 bp):
TTGAATTCTGATTCGCATGTTAAGAATGCTATTATT
Found at i:27360078 original size:28 final size:28
Alignment explanation
Indices: 27360009--27360328 Score: 283
Period size: 28 Copynumber: 11.4 Consensus size: 28
27359999 TAGTTTTTGC
* *
27360009 AAGGAAACCTTTGTGGCTATCTC--TAA
1 AAGGAAGCCTTTGTGGCTATCTCTGTTA
* *
27360035 AAGGATGCCTTCGTGGCTATCTCTGTTA
1 AAGGAAGCCTTTGTGGCTATCTCTGTTA
* * *
27360063 AAGGAAGCCTTTGTGGCAATCCCTATTA
1 AAGGAAGCCTTTGTGGCTATCTCTGTTA
*
27360091 AAGGAAGCCTTTATGG-TGATCTCTGTTA
1 AAGGAAGCCTTTGTGGCT-ATCTCTGTTA
* * * ** *
27360119 AATGAAGCTTTTGTTGAGATCTCTATTA
1 AAGGAAGCCTTTGTGGCTATCTCTGTTA
27360147 AAGGAAGCCTTTGTGG-TGATCTCTGTTA
1 AAGGAAGCCTTTGTGGCT-ATCTCTGTTA
* * *
27360175 AAAGAAGCCTTTG-GGGTGATCTCTATTA
1 AAGGAAGCCTTTGTGGCT-ATCTCTGTTA
*
27360203 AAGGAAGCCTTTGTGGCTATTTCTGTTAA
1 AAGGAAGCCTTTGTGGCTATCTCTGTT-A
*
27360232 AAGGAAGTCTTTGTGGCTATCTCTGTTAA
1 AAGGAAGCCTTTGTGGCTATCTCTGTT-A
** * *
27360261 AAGGATTCCTTTATGGCTACCTCAT-TTAA
1 AAGGAAGCCTTTGTGGCTATCTC-TGTT-A
* * *
27360290 AAGCATGTCTTTGTGGCTATCTCTGTTA
1 AAGGAAGCCTTTGTGGCTATCTCTGTTA
*
27360318 AATGAATGCCT
1 AAGGAA-GCCT
27360329 CGTGCCAAAC
Statistics
Matches: 237, Mismatches: 46, Indels: 19
0.78 0.15 0.06
Matches are distributed among these distances:
26 20 0.08
27 2 0.01
28 138 0.58
29 76 0.32
30 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (28 bp):
AAGGAAGCCTTTGTGGCTATCTCTGTTA
Found at i:27360113 original size:56 final size:56
Alignment explanation
Indices: 27360009--27360421 Score: 295
Period size: 56 Copynumber: 7.3 Consensus size: 56
27359999 TAGTTTTTGC
* * * *
27360009 AAGGAAACCTTTGTGGCTATCTCTA--AAAGGATGCCTTCGTGGCTATCTCTGTTA
1 AAGGAAGCCTTTGTGGCAATCTCTATTAAAGGAAGCCTTTGTGGCTATCTCTGTTA
* *
27360063 AAGGAAGCCTTTGTGGCAATCCCTATTAAAGGAAGCCTTTATGG-TGATCTCTGTTA
1 AAGGAAGCCTTTGTGGCAATCTCTATTAAAGGAAGCCTTTGTGGCT-ATCTCTGTTA
* * *
27360119 AATGAAGCTTTTGTTG-AGATCTCTATTAAAGGAAGCCTTTGTGG-TGATCTCTGTTA
1 AAGGAAGCCTTTGTGGCA-ATCTCTATTAAAGGAAGCCTTTGTGGCT-ATCTCTGTTA
* * ** *
27360175 AAAGAAGCCTTTGGGGTGATCTCTATTAAAGGAAGCCTTTGTGGCTATTTCTGTTAA
1 AAGGAAGCCTTTGTGGCAATCTCTATTAAAGGAAGCCTTTGTGGCTATCTCTGTT-A
* * * ** * *
27360232 AAGGAAGTCTTTGTGGCTATCTCTGTTAAAAGGATTCCTTTATGGCTACCTCAT-TTAA
1 AAGGAAGCCTTTGTGGCAATCTCTATT-AAAGGAAGCCTTTGTGGCTATCTC-TGTT-A
* * * * * * * * * * *
27360290 AAGCATGTCTTTGTGGCTATCTCTGTTAAATGAATGCC-TCGTGCCAAACTCTATTAA
1 AAGGAAGCCTTTGTGGCAATCTCTATTAAAGGAA-GCCTTTGTGGCTATCTCTGTT-A
* * * ** * * *
27360347 AAGTACGCCTTCGTGGCAA-GACTATAAAAGGAAAGCCTTTGTGGCTATCTTTG-GA
1 AAGGAAGCCTTTGTGGCAATCTCTATTAAAGG-AAGCCTTTGTGGCTATCTCTGTTA
*
27360402 AAGGAAAACCTTTGTGGCAA
1 AAGG-AAGCCTTTGTGGCAA
27360422 AATATGAAGA
Statistics
Matches: 286, Mismatches: 59, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
54 22 0.08
55 6 0.02
56 142 0.50
57 65 0.23
58 50 0.17
59 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (56 bp):
AAGGAAGCCTTTGTGGCAATCTCTATTAAAGGAAGCCTTTGTGGCTATCTCTGTTA
Found at i:27360618 original size:18 final size:18
Alignment explanation
Indices: 27360595--27360633 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27360585 TGAAGTAACA
27360595 AAGAAATGGGTGAATTCT
1 AAGAAATGGGTGAATTCT
*
27360613 AAGAAATGGGTGAATTTT
1 AAGAAATGGGTGAATTCT
27360631 AAG
1 AAG
27360634 TTAACTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (18 bp):
AAGAAATGGGTGAATTCT
Found at i:27361496 original size:11 final size:11
Alignment explanation
Indices: 27361480--27361507 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
27361470 CACTTTAGTC
27361480 AAAATTCATTT
1 AAAATTCATTT
27361491 AAAATTCATTT
1 AAAATTCATTT
27361502 AAAATT
1 AAAATT
27361508 TTATGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAATTCATTT
Found at i:27363130 original size:20 final size:21
Alignment explanation
Indices: 27363098--27363139 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
27363088 TGACAAGCTT
*
27363098 AAATATCAATTTAACCACTAA
1 AAATATCAATTTAAACACTAA
27363119 AAATAT-AATTTAAACACTAA
1 AAATATCAATTTAAACACTAA
27363139 A
1 A
27363140 GTTTACAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATCAATTTAAACACTAA
Found at i:27366264 original size:72 final size:72
Alignment explanation
Indices: 27366154--27366296 Score: 189
Period size: 72 Copynumber: 2.0 Consensus size: 72
27366144 GCCCATATGC
* * * *
27366154 AGATAAAACATATCAGAAAATACTAGTTGCACATATAGTTTAACAGATAAAAAATATG-TGATTG
1 AGATAAAACAGATCAGAAAATACTAATTGAACATATAGTTTAACAGATAAAAAACATGCT-ATTG
27366218 GCATATTT
65 GCATATTT
* * * * *
27366226 AGATAAAACAGATCGGAACATACTAATTGAACTTATAGTTTAACATATCAAAAACATGCTATTGG
1 AGATAAAACAGATCAGAAAATACTAATTGAACATATAGTTTAACAGATAAAAAACATGCTATTGG
27366291 CATATT
66 CATATT
27366297 CAGCCATCAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 60 0.98
73 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (72 bp):
AGATAAAACAGATCAGAAAATACTAATTGAACATATAGTTTAACAGATAAAAAACATGCTATTGG
CATATTT
Found at i:27369452 original size:67 final size:68
Alignment explanation
Indices: 27369381--27369712 Score: 372
Period size: 67 Copynumber: 5.0 Consensus size: 68
27369371 GCCATAACTG
* *
27369381 AGCTATGATCTTACACATCATACC-CAATGATTAATGT-CTGAGCAGACTCTCTATGTTGCCATA
1 AGCTATGATCTTACACATCATACCTC-ATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATA
27369444 GCCA
65 GCCA
* * **
27369448 AGCTATGGTCTTACACATCATACCTCATGTTTAATGTCCT-AGCGGACTCTCTATATTATCATAG
1 AGCTATGATCTTACACATCATACCTCATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATAG
27369512 TCC-
66 -CCA
* ** * * ** **** *
27369515 AGCTATAATCTTACACATCATACCTCATGTTTAATGTCCT-AGTAGATTCACTACATTATTGTCG
1 AGCTATGATCTTACACATCATACCTCATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATAG
* *
27369579 TCG
66 CCA
* * *
27369582 AGCTATGGTCTTGCACATCATACCTCATGTTTAATGTCATG-GCGGACTCTCTATGTTGCCATAG
1 AGCTATGATCTTACACATCATACCTCATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATAG
27369646 CCA
66 CCA
* *
27369649 AGTTATGATCTTACACATCATACCCCATGTTTAATGTCCTG-GCGGACTCTCTATGTTGCCATAG
1 AGCTATGATCTTACACATCATACCTCATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATAG
27369713 TCGAGCTCTA
Statistics
Matches: 221, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
66 1 0.00
67 215 0.97
68 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (68 bp):
AGCTATGATCTTACACATCATACCTCATGTTTAATGTCCTGAGCGGACTCTCTATGTTGCCATAG
CCA
Found at i:27369738 original size:201 final size:201
Alignment explanation
Indices: 27369380--27369744 Score: 536
Period size: 201 Copynumber: 1.8 Consensus size: 201
27369370 TGCCATAACT
27369380 GAGCTATGATCTTACACATCATACCCAATGATTAATGTCTGAGCAGACTCTCTATGTTGCCATAG
1 GAGCTATGATCTTACACATCATACCCAATGATTAATGTCTGAGCAGACTCTCTATGTTGCCATAG
* * *
27369445 CCAAGCTATGGTCTTACACATCATACCTCATGTTTAATGTCCTAGCGGACTCTCTATATTATCAT
66 CCAAGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTAGCGGACTCTCTATATTACCAT
* * *
27369510 AGTCCAGCTATAATCTTACACATCATACCTCATGTTTAATGTCCTAGTAGATTCACTACATTATT
131 AGTCCAGCTATAACCCTACACATCATACCCCATGTTTAATGTCCTAGTAGATTCACTACATTATT
27369575 GTCGTC
196 GTCGTC
* * * *
27369581 GAGCTATGGTCTTGCACATCATACCTC-ATGTTTAATGTCATG-GCGGACTCTCTATGTTGCCAT
1 GAGCTATGATCTTACACATCATACC-CAATGATTAATGTC-TGAGCAGACTCTCTATGTTGCCAT
* * * *
27369644 AGCCAAGTTATGATCTTACACATCATACCCCATGTTTAATGTCCTGGCGGACTCTCTATGTTGCC
64 AGCCAAGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTAGCGGACTCTCTATATTACC
* * * *
27369709 ATAGTCGAGCTCTAGCCCTACATATCATACCCCATG
129 ATAGTCCAGCTATAACCCTACACATCATACCCCATG
27369745 GTGAACTGTC
Statistics
Matches: 144, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
201 141 0.98
202 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (201 bp):
GAGCTATGATCTTACACATCATACCCAATGATTAATGTCTGAGCAGACTCTCTATGTTGCCATAG
CCAAGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTAGCGGACTCTCTATATTACCAT
AGTCCAGCTATAACCCTACACATCATACCCCATGTTTAATGTCCTAGTAGATTCACTACATTATT
GTCGTC
Found at i:27369739 original size:134 final size:134
Alignment explanation
Indices: 27369381--27369719 Score: 421
Period size: 134 Copynumber: 2.5 Consensus size: 134
27369371 GCCATAACTG
* *
27369381 AGCTATGATCTTACACATCATACCCAATGATTAATGT-CTGAGCAGACTCTCTATGTTGCCATAG
1 AGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTG-GCAGACTCTCTATGTTGCCATAG
* * * *
27369445 CCAAGCTATGGTCTTACACATCATACCTCATGTTTAATGTCCTAGCGGACTCTCTATATTATCAT
65 TCGAGCTATGGTCTTACACATCATACCTCATGTTTAATGTCATAGCGGACTCTCTATATTACCAT
27369510 AGTCC
130 AGTCC
* * * * * * ** **** *
27369515 AGCTATAATCTTACACATCATACCTCATGTTTAATGTCCTAGTAGATTCACTACATTATTGTCGT
1 AGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTGGCAGACTCTCTATGTTGCCATAGT
* * * *
27369580 CGAGCTATGGTCTTGCACATCATACCTCATGTTTAATGTCATGGCGGACTCTCTATGTTGCCATA
66 CGAGCTATGGTCTTACACATCATACCTCATGTTTAATGTCATAGCGGACTCTCTATATTACCATA
27369645 G-CC
131 GTCC
* *
27369648 AAGTTATGATCTTACACATCATACCCCATGTTTAATGTCCTGGCGGACTCTCTATGTTGCCATAG
1 -AGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTGGCAGACTCTCTATGTTGCCATAG
27369713 TCGAGCT
65 TCGAGCT
27369720 CTAGCCCTAC
Statistics
Matches: 165, Mismatches: 38, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
133 2 0.01
134 161 0.98
135 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (134 bp):
AGCTATGATCTTACACATCATACCCCATGTTTAATGTCCTGGCAGACTCTCTATGTTGCCATAGT
CGAGCTATGGTCTTACACATCATACCTCATGTTTAATGTCATAGCGGACTCTCTATATTACCATA
GTCC
Found at i:27381247 original size:19 final size:19
Alignment explanation
Indices: 27381210--27381248 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27381200 TGTCCTTCAG
*
27381210 AAAATAGAAAAGAAAAACA
1 AAAATAGAAAACAAAAACA
*
27381229 AAAATAGAAAACAATAACA
1 AAAATAGAAAACAAAAACA
27381248 A
1 A
27381249 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAATAGAAAACAAAAACA
Found at i:27389064 original size:10 final size:10
Alignment explanation
Indices: 27389051--27389075 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27389041 ACCTATTCAT
27389051 AATATGCCAA
1 AATATGCCAA
27389061 AATATGCCAA
1 AATATGCCAA
27389071 AATAT
1 AATAT
27389076 ATCAATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (10 bp):
AATATGCCAA
Found at i:27398709 original size:22 final size:22
Alignment explanation
Indices: 27398684--27398736 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
27398674 ATGGCCCTTG
27398684 TAATTAAAATTTCATTATTTTA
1 TAATTAAAATTTCATTATTTTA
*
27398706 TAATTAAAATTTCATTATTTTG
1 TAATTAAAATTTCATTATTTTA
27398728 TAATTAAAA
1 TAATTAAAA
27398737 ATAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTAAAATTTCATTATTTTA
Found at i:27398745 original size:23 final size:22
Alignment explanation
Indices: 27398697--27398745 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27398687 TTAAAATTTC
***
27398697 ATTATTTTATAATTAAAATTTC
1 ATTATTTTATAATTAAAATAAA
*
27398719 ATTATTTTGTAATTAAAAATAAA
1 ATTATTTTATAATT-AAAATAAA
27398742 ATTA
1 ATTA
27398746 ATAGAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTATTTTATAATTAAAATAAA
Found at i:27399327 original size:9 final size:9
Alignment explanation
Indices: 27399313--27399414 Score: 82
Period size: 9 Copynumber: 10.8 Consensus size: 9
27399303 AATTTTTTTC
27399313 ATAAAAATT
1 ATAAAAATT
*
27399322 ATAAAATTT
1 ATAAAAATT
27399331 ATTAAAAA-T
1 A-TAAAAATT
*
27399340 ATTAAAATTT
1 A-TAAAAATT
27399350 ATATAAAATT
1 ATA-AAAATT
27399360 ATAAAAA-T
1 ATAAAAATT
*
27399368 ATGGAAAACTT
1 AT--AAAAATT
*
27399379 ATAAATATT
1 ATAAAAATT
27399388 ATAAAAATT
1 ATAAAAATT
*
27399397 ATTATAAATT
1 A-TAAAAATT
27399407 ATTAAAAA
1 A-TAAAAA
27399415 CATATTAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
8 3 0.04
9 37 0.49
10 33 0.43
11 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:27399336 original size:19 final size:19
Alignment explanation
Indices: 27399314--27399414 Score: 79
Period size: 19 Copynumber: 5.3 Consensus size: 19
27399304 ATTTTTTTCA
27399314 TAAAAATTATAAAATTTAT
1 TAAAAATTATAAAATTTAT
27399333 TAAAAA-TATTAAAATTTA-
1 TAAAAATTA-TAAAATTTAT
*
27399351 TATAAAATTATAAAA-ATAT
1 TA-AAAATTATAAAATTTAT
* *
27399370 GGAAAACTTAT-AAATATTA-
1 -TAAAAATTATAAAAT-TTAT
27399389 TAAAAATTATTATAAA-TTAT
1 TAAAAATTA-TA-AAATTTAT
27399409 TAAAAA
1 TAAAAA
27399415 CATATTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
18 16 0.25
19 35 0.54
20 11 0.17
21 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAAATTATAAAATTTAT
Found at i:27399353 original size:12 final size:11
Alignment explanation
Indices: 27399321--27399367 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
27399311 TCATAAAAAT
27399321 TATAAAATTTA
1 TATAAAATTTA
*
27399332 T-TAAAA-ATA
1 TATAAAATTTA
27399341 T-TAAAATTTA
1 TATAAAATTTA
27399351 TATAAAA-TTA
1 TATAAAATTTA
27399361 TA-AAAAT
1 TATAAAAT
27399368 ATGGAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 12 0.39
10 13 0.42
11 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAAAATTTA
Found at i:27399364 original size:28 final size:27
Alignment explanation
Indices: 27399316--27399413 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 27
27399306 TTTTTTCATA
*
27399316 AAAATTATA-AAATTTATTAAAAATATT
1 AAAATTATATAAAATTA-TAAAAATATT
*
27399343 AAAATTTATATAAAATTATAAAAATATGG
1 AAAA-TTATATAAAATTATAAAAATAT-T
*
27399372 AAAACTTATA-AATATTATAAAAATTATT
1 AAAA-TTATATAAAATTATAAAAA-TATT
27399400 ATAAATTAT-TAAAA
1 A-AAATTATATAAAA
27399414 ACATATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.07
28 34 0.58
29 21 0.36
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAATTATATAAAATTATAAAAATATT
Found at i:27399425 original size:66 final size:60
Alignment explanation
Indices: 27399313--27399490 Score: 154
Period size: 66 Copynumber: 2.9 Consensus size: 60
27399303 AATTTTTTTC
* * * *
27399313 ATAAAAATTATAAAATTTATTA-AAAATATTAAAATTTATATAAAATTATAAAAATATGGAAAAC
1 ATAAATATTATAAAAATTATTATAAATTATTAAAA--AATAT-AAATTATAAAAA-A---AAAAC
27399377 TT
59 TT
27399379 ATAAATATTATAAAAATTATTATAAATTATTAAAAACATATTAAATT-TCAAAAAAAAAACTT
1 ATAAATATTATAAAAATTATTATAAATTATTAAAAA-ATA-TAAATTAT-AAAAAAAAAACTT
* *
27399441 ATAAATAATA-AAAAATTCA-AATAAATTA-T-AAAAATA-AAATTATAAAAAAA
1 ATAAATATTATAAAAATT-ATTATAAATTATTAAAAAATATAAATTATAAAAAAA
27399491 GTTACTTGAA
Statistics
Matches: 100, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
56 12 0.12
57 1 0.01
58 3 0.03
59 4 0.04
60 1 0.01
61 15 0.15
62 17 0.17
65 2 0.02
66 33 0.33
67 12 0.12
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (60 bp):
ATAAATATTATAAAAATTATTATAAATTATTAAAAAATATAAATTATAAAAAAAAAACTT
Found at i:27399475 original size:13 final size:14
Alignment explanation
Indices: 27399428--27399488 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
27399418 ATTAAATTTC
*
27399428 AAAAAAAAAACTTAT
1 AAAAATAAAA-TTAT
*
27399443 AAATAATAAAA-AAT
1 AAA-AATAAAATTAT
**
27399457 TCAAAT-AAATTAT
1 AAAAATAAAATTAT
27399470 AAAAATAAAATTAT
1 AAAAATAAAATTAT
27399484 AAAAA
1 AAAAA
27399489 AAGTTACTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
12 3 0.08
13 9 0.25
14 15 0.42
15 3 0.08
16 6 0.17
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATAAAATTAT
Found at i:27401011 original size:20 final size:20
Alignment explanation
Indices: 27400986--27401050 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
27400976 CCCTTCCATA
27400986 TACTTACTTTCCATTGCATT
1 TACTTACTTTCCATTGCATT
27401006 TACTTACTTTCCATTGCATT
1 TACTTACTTTCCATTGCATT
*
27401026 TACTTACTTTTCATTGCATT
1 TACTTACTTTCCATTGCATT
27401046 TACTT
1 TACTT
27401051 TAGCTTAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (20 bp):
TACTTACTTTCCATTGCATT
Found at i:27401292 original size:43 final size:43
Alignment explanation
Indices: 27401240--27401480 Score: 308
Period size: 43 Copynumber: 5.6 Consensus size: 43
27401230 TATGTGAAAA
* *
27401240 AAACGCCGCTAAAGATCATGGCCTTTAGCGGTGCTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* * *
27401283 AAACGCCGCTAAAGATAATGACCTTTAGCAGCGCTTCTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* *
27401326 AAACGCCGCTAAAGATCATGACCTTTAGCAGCGCTTCTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
27401369 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGC-TTTTATCAC
* * * ** *
27401413 AAACGCCACTATAA-AACA-AACCTTTAGCGGCGCTTTTCGCAA
1 AAACGCCGCTA-AAGATCATGACCTTTAGCGGCGCTTTTATCAC
* *
27401455 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGATCATGACCTTTA
27401481 AAAGAAGATA
Statistics
Matches: 180, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
41 6 0.03
42 24 0.13
43 127 0.71
44 21 0.12
45 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
Found at i:27404725 original size:13 final size:13
Alignment explanation
Indices: 27404707--27404772 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
27404697 AGTTCTTCAT
*
27404707 TGCTTTTGTAAAG
1 TGCTTTTGAAAAG
*
27404720 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
27404733 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
27404746 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
27404759 TACTGTTGAAAAG
1 TGCTTTTGAAAAG
27404772 T
1 T
27404773 TTAGTTTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:27404745 original size:26 final size:26
Alignment explanation
Indices: 27404716--27404772 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
27404706 TTGCTTTTGT
*
27404716 AAAGTGCTTTTGAAAAATGCTGTGGA
1 AAAGTGCTTTTGAAAAATACTGTGGA
* * *
27404742 AAAGTGCTTTTGAGAAGTACTGTTGA
1 AAAGTGCTTTTGAAAAATACTGTGGA
27404768 AAAGT
1 AAAGT
27404773 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (26 bp):
AAAGTGCTTTTGAAAAATACTGTGGA
Found at i:27405277 original size:13 final size:13
Alignment explanation
Indices: 27405261--27405286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27405251 TTTCAGAAGT
27405261 ACTTTTGAAAAGC
1 ACTTTTGAAAAGC
27405274 ACTTTTGAAAAGC
1 ACTTTTGAAAAGC
27405287 TAAAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ACTTTTGAAAAGC
Found at i:27406123 original size:11 final size:11
Alignment explanation
Indices: 27406109--27406168 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 11
27406099 AAAATAAAAG
*
27406109 TTTAAAATCTT
1 TTTAAAATCAT
27406120 TTTAAAAT--T
1 TTTAAAATCAT
* *
27406129 TTTAAAA-AAA
1 TTTAAAATCAT
27406139 TTTAAAATC-T
1 TTTAAAATCAT
27406149 TTTAAAATTCAT
1 TTTAAAA-TCAT
27406161 TTTAAAAT
1 TTTAAAAT
27406169 TTTAAATCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 8 0.20
10 14 0.34
11 11 0.27
12 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAAATCAT
Found at i:27406167 original size:29 final size:29
Alignment explanation
Indices: 27406102--27406176 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
27406092 TATTATAAAA
27406102 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAA-TTTAAAATCTTTTTAAAATTTTT
*
27406132 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 -ATAAAATTTAAAATCTTTTTAAAATT--TTT
*
27406163 -TAAAATTTTAAATC
1 ATAAAATTTAAAATC
27406177 ACGAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 22 0.56
30 9 0.23
31 8 0.21
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
ATAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:27406173 original size:30 final size:30
Alignment explanation
Indices: 27406102--27406174 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
27406092 TATTATAAAA
*
27406102 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAAATTTAAAATCTTTTTAAAATTTTT
*
27406132 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 ATAAAAATTTAAAATCTTTTTAAAATT--TTT
*
27406163 -TAAAATTTTAAA
1 ATAAAAATTTAAA
27406175 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.27
30 24 0.65
31 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (30 bp):
ATAAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:27406174 original size:20 final size:20
Alignment explanation
Indices: 27406109--27406171 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
27406099 AAAATAAAAG
*
27406109 TTTAAAATCTTTTTAAAATT
1 TTTAAAATCATTTTAAAATT
* *
27406129 TTTAAAA-AAATTTAAAATCT
1 TTTAAAATCATTTTAAAAT-T
27406149 TTTAAAATTCATTTTAAAATT
1 TTTAAAA-TCATTTTAAAATT
27406170 TT
1 TT
27406172 AAATCACGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.23
20 15 0.43
21 3 0.09
22 9 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATCATTTTAAAATT
Found at i:27406832 original size:7 final size:7
Alignment explanation
Indices: 27406820--27407025 Score: 56
Period size: 7 Copynumber: 28.9 Consensus size: 7
27406810 ACTAGTTAAT
27406820 CTAAACC
1 CTAAACC
27406827 CTAAACC
1 CTAAACC
*
27406834 ATAAA-C
1 CTAAACC
27406840 CTAAACC
1 CTAAACC
*
27406847 CGAAAACC
1 C-TAAACC
*
27406855 CTAAAATC
1 CT-AAACC
* *
27406863 ATAAATC
1 CTAAACC
*
27406870 ATAAACC
1 CTAAACC
* *
27406877 ATAATCC
1 CTAAACC
27406884 CTAAACC
1 CTAAACC
*
27406891 CATAATCC
1 C-TAAACC
*
27406899 ATAAACC
1 CTAAACC
*
27406906 ATAAACC
1 CTAAACC
**** *
27406913 CCGGGCT
1 CTAAACC
*
27406920 TTAAACC
1 CTAAACC
*
27406927 ATAAACC
1 CTAAACC
* *
27406934 ATAATCC
1 CTAAACC
27406941 CTAAACC
1 CTAAACC
*
27406948 CATAATCC
1 C-TAAACC
*
27406956 ATAAACC
1 CTAAACC
* **
27406963 TTAAAATG
1 CT-AAACC
*
27406971 GT-AACAC
1 CTAAAC-C
27406978 CTAAACC
1 CTAAACC
* *
27406985 TTAAACT
1 CTAAACC
27406992 CTAAACC
1 CTAAACC
* *
27406999 ATATACC
1 CTAAACC
27407006 CTAAACC
1 CTAAACC
**
27407013 AAAAACC
1 CTAAACC
27407020 CTAAAC
1 CTAAAC
27407026 TATAGTGATA
Statistics
Matches: 140, Mismatches: 51, Indels: 16
0.68 0.25 0.08
Matches are distributed among these distances:
6 7 0.05
7 105 0.75
8 28 0.20
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:27406840 original size:14 final size:14
Alignment explanation
Indices: 27406821--27407025 Score: 103
Period size: 14 Copynumber: 13.9 Consensus size: 14
27406811 CTAGTTAATC
27406821 TAAACCCTAAACCA
1 TAAACCCTAAACCA
27406835 TAAA-CCTAAACCCGA
1 TAAACCCTAAA-CC-A
*
27406850 -AAACCCTAAAATCA
1 TAAACCCT-AAACCA
* *
27406864 TAAATCATAAACCA
1 TAAACCCTAAACCA
*
27406878 TAATCCCTAAACCCA
1 TAAACCCTAAA-CCA
* *
27406893 TAATCCATAAACCA
1 TAAACCCTAAACCA
27406907 TAAACCCCGGGCTTTAAACCA
1 TAAA--CC---C--TAAACCA
* * *
27406928 TAAACCATAATCCC
1 TAAACCCTAAACCA
*
27406942 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
*
27406957 TAAACCTTAAA--A
1 TAAACCCTAAACCA
* *
27406969 TGGTAACACCTAAACCT
1 T--AAAC-CCTAAACCA
*
27406986 TAAACTCTAAACCA
1 TAAACCCTAAACCA
*
27407000 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
27407014 AAAACCCTAAAC
1 TAAACCCTAAAC
27407026 TATAGTGATA
Statistics
Matches: 145, Mismatches: 27, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
12 2 0.01
13 6 0.04
14 75 0.52
15 43 0.30
16 5 0.03
17 1 0.01
19 2 0.01
21 11 0.08
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:27406873 original size:36 final size:36
Alignment explanation
Indices: 27406828--27406912 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
27406818 ATCTAAACCC
27406828 TAAACCATAAACC-TAAACCCGAAAACCCTAAAAT-CA
1 TAAACCATAAACCATAAACCC-AAAACCC-AAAATCCA
* * * *
27406864 TAAATCATAAACCATAATCCCTAAACCCATAATCCA
1 TAAACCATAAACCATAAACCCAAAACCCAAAATCCA
27406900 TAAACCATAAACC
1 TAAACCATAAACC
27406913 CCGGGCTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 4 0.10
36 32 0.76
37 6 0.14
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.18
Consensus pattern (36 bp):
TAAACCATAAACCATAAACCCAAAACCCAAAATCCA
Found at i:27406885 original size:29 final size:29
Alignment explanation
Indices: 27406853--27406962 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
27406843 AACCCGAAAA
*
27406853 CCCTAAAATCATAAAT-CATAAACCATAAT
1 CCCTAAAACCAT-AATCCATAAACCATAAT
* *
27406882 CCCTAAACCCATAATCCATAAACCATAAA
1 CCCTAAAACCATAATCCATAAACCATAAT
**** ** *
27406911 CCC-CGGGCTTTAAACCATAAACCATAAT
1 CCCTAAAACCATAATCCATAAACCATAAT
*
27406939 CCCTAAACCCATAATCCATAAACC
1 CCCTAAAACCATAATCCATAAACC
27406963 TTAAAATGGT
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
28 23 0.38
29 38 0.62
ACGTcount: A:0.45, C:0.33, G:0.03, T:0.20
Consensus pattern (29 bp):
CCCTAAAACCATAATCCATAAACCATAAT
Found at i:27406967 original size:22 final size:21
Alignment explanation
Indices: 27406920--27407025 Score: 72
Period size: 21 Copynumber: 5.0 Consensus size: 21
27406910 ACCCCGGGCT
*
27406920 TTAAACCATAAACCATAATCC
1 TTAAACCATAAACCATAAACC
* *
27406941 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
***
27406963 TTAAAATGGTAACACC-TAAACC
1 TT-AAACCATAA-ACCATAAACC
*
27406985 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
* * *
27407006 CTAAACCAAAAACCCTAAAC
1 TTAAACCATAAACCATAAAC
27407026 TATAGTGATA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
20 4 0.06
21 29 0.45
22 26 0.41
23 5 0.08
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:27407322 original size:41 final size:41
Alignment explanation
Indices: 27407270--27407657 Score: 454
Period size: 41 Copynumber: 9.5 Consensus size: 41
27407260 GTGCTACCTG
* * * * * *
27407270 AAAAACACCGCTAAAGCCCCGAGAATTAGCGACGTTTTCCC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
* * * *
27407311 AAAAATGCCGCTAAAGCCTTGAGCATTAGTGGCGCATTCTC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
* * *
27407352 AAAAACGCCGCTAAATCCCTGAGTATTAGCAGCGCTTT-TC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
** * * * * *
27407392 AAAAACGCCGCTAAAGTACTAAACATTAGTGGAGCTTTCTA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
* *
27407433 AAAAACGCCGCTAAATCCCTAAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
* * *
27407474 AAAAACACCACTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
* * * * *
27407515 AGAAATGCTGCTAAATCCCTGAGCATTAGCGGTGCTTTCTC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
*
27407556 AAAAACACCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTTTCTC
* * *
27407598 AAAAACGCCACTGAAGCCCTGAGCATTAGCGGCGCTTTCTT
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
27407639 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
27407658 AGAAAGCTCA
Statistics
Matches: 286, Mismatches: 59, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
40 31 0.11
41 218 0.76
42 37 0.13
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTC
Found at i:27407490 original size:163 final size:162
Alignment explanation
Indices: 27407200--27407657 Score: 504
Period size: 163 Copynumber: 2.8 Consensus size: 162
27407190 TAAATTATTT
* * * * *
27407200 TAAATCCCTGAGCATTAGCAGTGCTTTTTAGAAAACGCCGCTAAA-AATAGAGTATTCGCGGTGC
1 TAAATCCCTGAGCATTAGCAGTGCTTTTCA-AAAACGCCGCTAAAGACTA-AGCATTAGCGGAGC
** * * * * * * * *
27407264 TACCTGAAAAACACCGCTAAAGCCCCGAGAATTAGCGACGTTTTCCCAAAAATGCCGCTAAAGCC
64 TTTCTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCC
* *
27407329 TTGAGCATTAGTGGCGCATTCTCAAAAACGCCGC
129 CTGAGCATTAGCGGCGCATTCTCAAAAACGCCGC
* * * *
27407363 TAAATCCCTGAGTATTAGCAGCGCTTTTCAAAAACGCCGCTAAAGTACTAAACATTAGTGGAGCT
1 TAAATCCCTGAGCATTAGCAGTGCTTTTCAAAAACGCCGCTAAAG-ACTAAGCATTAGCGGAGCT
* * * *
27407428 TTCTAAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCGCTTTCTCAAAAACACCACTAAAGCCC
65 TTCTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * * *
27407493 TGAGCATTAGCGGCGCTTTCTTAGAAATGCTGC
130 TGAGCATTAGCGGCGCATTCTCAAAAACGCCGC
* * * * *
27407526 TAAATCCCTGAGCATTAGCGGTGCTTTCTCAAAAACACCGCTAAAAGCCCTGAGCATTAGCGGCG
1 TAAATCCCTGAGCATTAGCAGTGCTTT-TCAAAAACGCCGCT-AAAG-ACTAAGCATTAGCGGAG
* * * *
27407591 CTTTCTCAAAAACGCCACTGAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAGC
63 CTTTCTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGC
27407656 CC
128 CC
27407658 AGAAAGCTCA
Statistics
Matches: 243, Mismatches: 48, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
162 14 0.06
163 138 0.57
164 16 0.07
165 75 0.31
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (162 bp):
TAAATCCCTGAGCATTAGCAGTGCTTTTCAAAAACGCCGCTAAAGACTAAGCATTAGCGGAGCTT
TCTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCT
GAGCATTAGCGGCGCATTCTCAAAAACGCCGC
Found at i:27407528 original size:82 final size:82
Alignment explanation
Indices: 27407200--27407657 Score: 465
Period size: 82 Copynumber: 5.6 Consensus size: 82
27407190 TAAATTATTT
* * * ** * * *
27407200 TAAATCCCTGAGCATTAGCAGTGCTTT-TTAGAAAACGCCGCTAAA--AATAGAGTATTCGCGGT
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCA-AAAACGCCGCTAAAGCCCT-GAGCATTAGCGGC
** * *
27407262 GCTACCTGAAAAACACCGC
64 GCTTTCTCAAAAACGCCGC
* * * * * * * * *
27407281 TAAAGCCCCGAGAATTAGCGACGTTTTCCCAAAAATGCCGCTAAAGCCTTGAGCATTAGTGGCGC
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
*
27407346 ATTCTCAAAAACGCCGC
66 TTTCTCAAAAACGCCGC
* * ** * * * *
27407363 TAAATCCCTGAGTATTAGCAGCGCTTT-TCAAAAACGCCGCTAAAGTACTAAACATTAGTGGAGC
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
*
27407427 TTTCTAAAAAACGCCGC
66 TTTCTCAAAAACGCCGC
* * *
27407444 TAAATCCCTAAGCATTAGCGGCGCTTTCTCAAAAACACCACTAAAGCCCTGAGCATTAGCGGCGC
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
* * * *
27407509 TTTCTTAGAAATGCTGC
66 TTTCTCAAAAACGCCGC
* *
27407526 TAAATCCCTGAGCATTAGCGGTGCTTTCTCAAAAACACCGCTAAAAGCCCTGAGCATTAGCGGCG
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCG
*
27407591 CTTTCTCAAAAACGCCAC
65 CTTTCTCAAAAACGCCGC
* * *
27407609 TGAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCC
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
27407658 AGAAAGCTCA
Statistics
Matches: 307, Mismatches: 65, Indels: 9
0.81 0.17 0.02
Matches are distributed among these distances:
81 101 0.33
82 133 0.43
83 73 0.24
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (82 bp):
TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
TTTCTCAAAAACGCCGC
Found at i:27407609 original size:124 final size:123
Alignment explanation
Indices: 27407318--27407654 Score: 444
Period size: 124 Copynumber: 2.7 Consensus size: 123
27407308 CCCAAAAATG
* * * * * * *
27407318 CCGCTAAAGCCTTGAGCATTAGTGGCGCATTCTCAAAAACGCCGCTAAATCCCTGAGTATTAGCA
1 CCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCCTGAGCATTAGCG
* * *
27407383 GCGCTTT-TCAAAAACGCCGCTAAAGTACTAAACATTAGTGGAGCTTTCTAAAAAACG
66 GCGCTTTCTTAAAAACGCCGCTAAAGTACTAAACATTAGCGGAGCTTTCTAAAAAACA
* * *
27407440 CCGCTAAATCCCTAAGCATTAGCGGCGCTTTCTCAAAAACACCACTAAAGCCCTGAGCATTAGCG
1 CCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCCTGAGCATTAGCG
* * * * * * * *
27407505 GCGCTTTCTTAGAAATGCTGCTAAA-TCCCTGAGCATTAGCGGTGCTTTCTCAAAAACA
66 GCGCTTTCTTAAAAACGCCGCTAAAGT-ACTAAACATTAGCGGAGCTTTCTAAAAAACA
*
27407563 CCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTGAAGCCCTGAGCATTAGC
1 CCGCT-AAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCCTGAGCATTAGC
27407628 GGCGCTTTCTTAAAAACGCCGCTAAAG
65 GGCGCTTTCTTAAAAACGCCGCTAAAG
27407655 CCCAGAAAGC
Statistics
Matches: 183, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
122 63 0.34
123 42 0.23
124 78 0.43
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (123 bp):
CCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCCTGAGCATTAGCG
GCGCTTTCTTAAAAACGCCGCTAAAGTACTAAACATTAGCGGAGCTTTCTAAAAAACA
Found at i:27408786 original size:44 final size:45
Alignment explanation
Indices: 27408700--27408824 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 45
27408690 GTTTGATTCG
* ** * *
27408700 TGATGCCATAACATCTTTCAACTAAGGTCTTACTCAATAGAATCA
1 TGATGCCATAACGTCTTTCAGTTATGGTCTTACTCGATAGAATCA
*
27408745 TGATGCCATAACGTCTTT-AGTTATGGTCTTACTCGATAGAATCG
1 TGATGCCATAACGTCTTTCAGTTATGGTCTTACTCGATAGAATCA
* * * * *
27408789 TGATACCGTAACGTCTTTCAGTCATGGCCATACTCG
1 TGATGCCATAACGTCTTTCAGTTATGGTCTTACTCG
27408825 TTTCTGGTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 37 0.54
45 31 0.46
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGTTATGGTCTTACTCGATAGAATCA
Found at i:27408880 original size:46 final size:46
Alignment explanation
Indices: 27408827--27408957 Score: 217
Period size: 46 Copynumber: 2.8 Consensus size: 46
27408817 CATACTCGTT
*
27408827 TCTGGTATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTTATTC
1 TCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTATTTATTC
* *
27408873 TCTGGTATAGTGCCATAGTGCCTTTCAACTATGGTATTATTTATTC
1 TCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTATTTATTC
* *
27408919 TCTGGTATAGTGCCATAATGTCTATCAACTATGGTCTTA
1 TCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTA
27408958 ATCATTTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (46 bp):
TCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTATTTATTC
Found at i:27418129 original size:18 final size:18
Alignment explanation
Indices: 27418103--27418140 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27418093 TTTAGGTAAC
27418103 TTGGAAAGTAAATTACAA
1 TTGGAAAGTAAATTACAA
* *
27418121 TTGGGAAGTAAATTGCAA
1 TTGGAAAGTAAATTACAA
27418139 TT
1 TT
27418141 CAGTTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (18 bp):
TTGGAAAGTAAATTACAA
Found at i:27432173 original size:50 final size:49
Alignment explanation
Indices: 27432049--27432234 Score: 212
Period size: 50 Copynumber: 3.8 Consensus size: 49
27432039 GATAATAACA
* * * **
27432049 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATTTGG
* *
27432098 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-TTGG
* ** **
27432148 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATTTGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATTT-GG
**
27432198 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
27432235 CCTGTCATAA
Statistics
Matches: 115, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
48 3 0.03
49 39 0.34
50 73 0.63
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATTTGG
Found at i:27433656 original size:12 final size:12
Alignment explanation
Indices: 27433631--27433669 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27433621 ACTCACTTCT
* *
27433631 TTACTTACTCAC
1 TTACTTGCTTAC
*
27433643 TTACTTGTTTAC
1 TTACTTGCTTAC
27433655 TTACTTGCTTAC
1 TTACTTGCTTAC
27433667 TTA
1 TTA
27433670 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:27434059 original size:50 final size:49
Alignment explanation
Indices: 27433918--27434093 Score: 167
Period size: 50 Copynumber: 3.5 Consensus size: 49
27433908 TTTTCTGTAC
* * * *
27433918 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGT-TCTCATATCGG
1 TGCCAACGCTATATCCCAGA-ATGGTCTTACATGGGA-TCTCTCATCTCGG
* * * * *
27433968 TGCCCATGATATGTCCCAGAATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAACGCTATATCCCAGAATGGTCTTAC-ATGGGATCTCTCATCTCGG
* *
27434017 TGCCAACGCTATATCCTATACATGGTCTTACATGGGATCTCTCATCTCGG
1 TGCCAACGCTATATCCCAGA-ATGGTCTTACATGGGATCTCTCATCTCGG
* * *
27434067 TGCCAACGCCATGTCCCTGACATGGTC
1 TGCCAACGCTATATCCCAGA-ATGGTC
27434094 ATTCCCTTAA
Statistics
Matches: 103, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 39 0.38
50 64 0.62
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCCAACGCTATATCCCAGAATGGTCTTACATGGGATCTCTCATCTCGG
Found at i:27435989 original size:20 final size:20
Alignment explanation
Indices: 27435964--27436004 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27435954 CTCATGGTAG
*
27435964 TGTGTTTGAAAACCGTAACT
1 TGTGTTAGAAAACCGTAACT
*
27435984 TGTGTTAGGAAACCGTAACT
1 TGTGTTAGAAAACCGTAACT
27436004 T
1 T
27436005 TGCTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (20 bp):
TGTGTTAGAAAACCGTAACT
Found at i:27442890 original size:11 final size:11
Alignment explanation
Indices: 27442829--27442939 Score: 73
Period size: 11 Copynumber: 9.8 Consensus size: 11
27442819 TATTTTTTAA
27442829 TTTTAAAATAT
1 TTTTAAAATAT
* *
27442840 TTTTTACATACT
1 TTTTAAAATA-T
*
27442852 TTTTAAATTA-
1 TTTTAAAATAT
*
27442862 ATTT-AAATAT
1 TTTTAAAATAT
**
27442872 TTAAAAAATAT
1 TTTTAAAATAT
27442883 TTTTAAAATACT
1 TTTTAAAATA-T
** *
27442895 TTTTAATTTTTAA
1 TTTTAA--AATAT
27442908 TTTTAAAATAT
1 TTTTAAAATAT
*
27442919 TTTTAAAATTAA
1 TTTTAAAA-TAT
27442931 TTTTAAAAT
1 TTTTAAAAT
27442940 TAAGTTTTTT
Statistics
Matches: 74, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 33 0.45
12 25 0.34
13 6 0.08
14 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:27442940 original size:12 final size:12
Alignment explanation
Indices: 27442904--27442947 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
27442894 TTTTTAATTT
27442904 TTAATTTTAAAA
1 TTAATTTTAAAA
*
27442916 -TATTTTTAAAA
1 TTAATTTTAAAA
27442927 TTAATTTTAAAA
1 TTAATTTTAAAA
27442939 TTAAGTTTT
1 TTAA-TTTT
27442948 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 14 0.50
13 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:27445458 original size:21 final size:21
Alignment explanation
Indices: 27445432--27445495 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
27445422 AGGTTGGTTT
*
27445432 TTCTACAATATTACTCTTTGA
1 TTCTACAATATTAATCTTTGA
27445453 TTCTACAATATTAATCTTTGA
1 TTCTACAATATTAATCTTTGA
*
27445474 ---TACAATACTAATCTTTGA
1 TTCTACAATATTAATCTTTGA
27445492 TTCT
1 TTCT
27445496 TTCTTCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 17 0.45
21 21 0.55
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (21 bp):
TTCTACAATATTAATCTTTGA
Found at i:27445479 original size:18 final size:18
Alignment explanation
Indices: 27445435--27445492 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
27445425 TTGGTTTTTC
*
27445435 TACAATATTACTCTTTGA
1 TACAATATTAATCTTTGA
27445453 TTCTACAATATTAATCTTTGA
1 ---TACAATATTAATCTTTGA
*
27445474 TACAATACTAATCTTTGA
1 TACAATATTAATCTTTGA
27445492 T
1 T
27445493 TCTTTCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 18 0.51
21 17 0.49
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (18 bp):
TACAATATTAATCTTTGA
Found at i:27447330 original size:23 final size:23
Alignment explanation
Indices: 27447299--27447342 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27447289 ACTTGTATAA
* *
27447299 TATGTGAACCGTACATGTTTAGT
1 TATGGGAACCATACATGTTTAGT
*
27447322 TATGGGAACCATACTTGTTTA
1 TATGGGAACCATACATGTTTA
27447343 TATGCGAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (23 bp):
TATGGGAACCATACATGTTTAGT
Found at i:27447351 original size:21 final size:21
Alignment explanation
Indices: 27447289--27447352 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
27447279 GATAAGCAAA
* * *
27447289 ACTTGTATAATATGTGAACCGT
1 ACTTGT-TTATATGCGAACCAT
* *
27447311 ACATGTTTAGTTATGGGAACCAT
1 ACTTGTTTA--TATGCGAACCAT
27447334 ACTTGTTTATATGCGAACC
1 ACTTGTTTATATGCGAACC
27447353 CTAAATTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 11 0.32
22 5 0.15
23 18 0.53
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (21 bp):
ACTTGTTTATATGCGAACCAT
Found at i:27460622 original size:23 final size:23
Alignment explanation
Indices: 27460592--27460638 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
27460582 TATTTGATTG
* *
27460592 TGATTTTTAACATATAAATGTTA
1 TGATTTTTAACATAGAAAAGTTA
27460615 TGATTTTTAACATAGAAAAGTTA
1 TGATTTTTAACATAGAAAAGTTA
27460638 T
1 T
27460639 TATGTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (23 bp):
TGATTTTTAACATAGAAAAGTTA
Found at i:27462088 original size:43 final size:43
Alignment explanation
Indices: 27462039--27462150 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
27462029 TGTTATTGTG
* *
27462039 TAAGACCACATCTGGGACGTTGGCATCGACT-TGTGTTTACATC
1 TAAGACCACGTCTGGGACGTTGGCATCG-CTATGTGATTACATC
** * *
27462082 TAAGACCTTGTCTGGGACAG-TGGCATCGTTATGTGATTACATG
1 TAAGACCACGTCTGGGAC-GTTGGCATCGCTATGTGATTACATC
27462125 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
27462151 TGTACGATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.03
43 55 0.95
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGTTGGCATCGCTATGTGATTACATC
Found at i:27463144 original size:23 final size:23
Alignment explanation
Indices: 27463114--27463187 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
27463104 ATTGGGTATA
*
27463114 TATATATGTTGGCCAATTTAGTG
1 TATATATGCTGGCCAATTTAGTG
* *
27463137 TATATATGCTGTCCAATTTGGTG
1 TATATATGCTGGCCAATTTAGTG
* ** *
27463160 TATAAACTGCTATCCAATTTGGTG
1 TATATA-TGCTGGCCAATTTAGTG
27463184 TATA
1 TATA
27463188 AATGGTGTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 25 0.56
24 20 0.44
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (23 bp):
TATATATGCTGGCCAATTTAGTG
Found at i:27463175 original size:24 final size:23
Alignment explanation
Indices: 27463126--27463191 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 23
27463116 TATATGTTGG
* * *
27463126 CCAATTTAGTGTATATATGCTGT
1 CCAATTTGGTGTATAAATGCTAT
27463149 CCAATTTGGTGTATAAACTGCTAT
1 CCAATTTGGTGTATAAA-TGCTAT
27463173 CCAATTTGGTGTATAAATG
1 CCAATTTGGTGTATAAATG
27463192 GTGTCTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (23 bp):
CCAATTTGGTGTATAAATGCTAT
Found at i:27463219 original size:23 final size:23
Alignment explanation
Indices: 27463135--27463219 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
27463125 GCCAATTTAG
* ** *
27463135 TGTATATATGCTGTCCAATTTGG
1 TGTATAAATGCTGTCTGATTTGA
* ** *
27463158 TGTATAAACTGCTATCCAATTTGG
1 TGTATAAA-TGCTGTCTGATTTGA
*
27463182 TGTATAAATGGTGTCTGATTTGA
1 TGTATAAATGCTGTCTGATTTGA
27463205 TGTATAAGA-GCTGTC
1 TGTATAA-ATGCTGTC
27463220 CAAGCAGGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
23 29 0.56
24 23 0.44
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (23 bp):
TGTATAAATGCTGTCTGATTTGA
Found at i:27464745 original size:12 final size:13
Alignment explanation
Indices: 27464726--27464756 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
27464716 ATTCTTTCTC
27464726 TCTTTTCTCAATT
1 TCTTTTCTCAATT
27464739 T-TTTTCTCAATT
1 TCTTTTCTCAATT
27464751 TCTTTT
1 TCTTTT
27464757 GCTCCACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTTTCTCAATT
Found at i:27467199 original size:32 final size:32
Alignment explanation
Indices: 27467107--27467218 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
27467097 TGAGATGCTT
* *
27467107 TAATGCATGACCTAATTAAATGCTAC--ACATA
1 TAATGCAAGACATAATTAAA-GCTACAAACATA
* * *
27467138 TAATGCAAGACATAATTTAAAGATGCAAACACA
1 TAATGCAAGACATAA-TTAAAGCTACAAACATA
**
27467171 TAATGCAATTCATAATTAAAGCTACAAACATA
1 TAATGCAAGACATAATTAAAGCTACAAACATA
27467203 TAATGCAAGACATAAT
1 TAATGCAAGACATAAT
27467219 ATGCAAGCTT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 16 0.24
32 33 0.50
33 17 0.26
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (32 bp):
TAATGCAAGACATAATTAAAGCTACAAACATA
Found at i:27469896 original size:12 final size:12
Alignment explanation
Indices: 27469879--27469910 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
27469869 AATATTAACA
27469879 TGTTGTGATGAC
1 TGTTGTGATGAC
27469891 TGTTGTGATGAC
1 TGTTGTGATGAC
27469903 TGTTGTGA
1 TGTTGTGA
27469911 CGATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (12 bp):
TGTTGTGATGAC
Found at i:27471789 original size:17 final size:17
Alignment explanation
Indices: 27471768--27471810 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
27471758 ACGGAATTAG
27471768 AATTTAGTTGAGAAAATT
1 AATTTAGTTGAG-AAATT
*
27471786 -ATTTAATTGAGAAATT
1 AATTTAGTTGAGAAATT
27471802 AATTTAGTT
1 AATTTAGTT
27471811 AATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (17 bp):
AATTTAGTTGAGAAATT
Found at i:27472731 original size:25 final size:25
Alignment explanation
Indices: 27472674--27472731 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
27472664 AAAAGCATTC
*
27472674 ATTCATTAGGTCATATATACTTAGG
1 ATTCATTTGGTCATATATACTTAGG
27472699 ATTCATTTGGTCATATATACTTAGG
1 ATTCATTTGGTCATATATACTTAGG
27472724 ATTCATTT
1 ATTCATTT
27472732 TATTTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (25 bp):
ATTCATTTGGTCATATATACTTAGG
Found at i:27492346 original size:4 final size:4
Alignment explanation
Indices: 27492339--27492368 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
27492329 ATGATTTTTC
27492339 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
27492369 AGTTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:27496172 original size:137 final size:137
Alignment explanation
Indices: 27495824--27496337 Score: 773
Period size: 137 Copynumber: 3.8 Consensus size: 137
27495814 ACTGGTCCTA
* * *
27495824 AATGTCCTAT-CGGTGGCTGAGTT-CTGACATTTGTTGCGGATACTCGACAACTTGTGTGAGCAG
1 AATGTCCT-TCCGGTGGCTGAGTTCCAG-CATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAG
* *
27495887 CACTGTGTAGCTACGTTCCAACCGACAGCTTGTGTGAGCAGACCTAGGTTATCATGTTTCAGGTG
64 CACTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTG
*
27495952 TTGGTGTTG
129 TTGGTGATG
* *
27495961 -ATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGGAGATACTCGATAGCTTGTGTGAGCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
* * *
27496025 CTGTGTAGCTACATTCCAACCGATAGCTTGTGTGAGCAAACCCAGGTTATCATGTTTTAGGTGTT
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
27496090 GGTGATG
131 GGTGATG
* **
27496097 AATGTCCTTCCGGTGGCTGAGTTCTAGCATTTGTTGCAGATACTCGACAGCTTACGTGAGCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
* * * *
27496162 CTGTGTAGCTACATTCCAATCAACAGCTTGTGTGAGCAGACCCAGGTTATCATCTTTCAAGTGTT
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
*
27496227 GGTGCTG
131 GGTGATG
* *
27496234 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGTAGATACTCGACAGCTTGTGTGACCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
** *
27496299 CTGTGTAGCTACATTCCAATTGACAGCTTGTGTAAGCAG
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAG
27496338 GCTCATTTAT
Statistics
Matches: 342, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
135 1 0.00
136 120 0.35
137 221 0.65
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (137 bp):
AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
GGTGATG
Found at i:27500874 original size:22 final size:22
Alignment explanation
Indices: 27500849--27500920 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
27500839 ATAATATCTC
27500849 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
27500871 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
27500893 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
27500915 CTCATG
1 CTCATG
27500921 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:27502891 original size:25 final size:25
Alignment explanation
Indices: 27502859--27502956 Score: 60
Period size: 25 Copynumber: 4.0 Consensus size: 25
27502849 AGCTCTCCCT
27502859 TGAGCCATATAATC-GGAAGCTCATA
1 TGAGCCATATAA-CAGGAAGCTCATA
* * * * *
27502884 TGAGCCATGTAACGGGAAACTTATC
1 TGAGCCATATAACAGGAAGCTCATA
* **
27502909 TGGGCTGTATAAC-GGAAAGCTCATA
1 TGAGCCATATAACAGG-AAGCTCATA
*
27502934 AGAG-C-TATAATCAGGAAGCTCAT
1 TGAGCCATATAA-CAGGAAGCTCAT
27502957 GCAAGCCTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
23 5 0.09
24 12 0.22
25 38 0.69
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATA
Found at i:27503084 original size:26 final size:26
Alignment explanation
Indices: 27503054--27503113 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
27503044 GTAGCTCTGG
27503054 AGAGCCATTAATTAG-GAAGCTCATAA
1 AGAGCCATTAA-TAGAGAAGCTCATAA
* * *
27503080 AGAGCCTTTAATCGAGAAGCTCATGA
1 AGAGCCATTAATAGAGAAGCTCATAA
27503106 AGAGCCAT
1 AGAGCCAT
27503114 ACATCGGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
AGAGCCATTAATAGAGAAGCTCATAA
Found at i:27503119 original size:26 final size:25
Alignment explanation
Indices: 27503069--27503135 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
27503059 CATTAATTAG
*
27503069 GAAGCTCATAAAGAGCCTTTAATCGA
1 GAAGCTCAT-AAGAGCCTATAATCGA
*
27503095 GAAGCTCATGAAGAGCC-ATACATCGG
1 GAAGCTCAT-AAGAGCCTATA-ATCGA
*
27503121 GACGCTCATAAGAGC
1 GAAGCTCATAAGAGC
27503136 TGTGGTGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 8 0.22
26 28 0.78
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCTATAATCGA
Found at i:27503782 original size:19 final size:18
Alignment explanation
Indices: 27503736--27503783 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
27503726 GATAGAATTT
*
27503736 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
27503755 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
27503773 TTGTATTAAAA
1 TTGTA-TAAAA
27503784 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:27504780 original size:111 final size:111
Alignment explanation
Indices: 27504586--27504808 Score: 419
Period size: 111 Copynumber: 2.0 Consensus size: 111
27504576 CATGAAGTAT
* *
27504586 TTCCCGCCGAGCAAGAATGCCAAGTTGTGGAATGAGATCACTGCCTTCCAAAAAATGGATGATGA
1 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
27504651 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
66 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
*
27504697 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAACAAATAGATGATGA
1 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
27504762 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
66 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
27504808 T
1 T
27504809 GCCCTCATCA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (111 bp):
TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
Found at i:27513519 original size:19 final size:18
Alignment explanation
Indices: 27513478--27513515 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27513468 AATTTTTGTC
*
27513478 ATAAAATAATTAATTTTT
1 ATAAAATAATTAAATTTT
27513496 ATAAAATAATTAAATTTT
1 ATAAAATAATTAAATTTT
27513514 AT
1 AT
27513516 TAAAGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAAATAATTAAATTTT
Found at i:27514155 original size:14 final size:14
Alignment explanation
Indices: 27514132--27514161 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27514122 CGTCCCTCAT
*
27514132 TCACATCTCTTCTC
1 TCACAACTCTTCTC
27514146 TCACAACTCTTCTC
1 TCACAACTCTTCTC
27514160 TC
1 TC
27514162 CTCTCTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:27516189 original size:14 final size:14
Alignment explanation
Indices: 27516172--27516202 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
27516162 ATTAATTTTC
27516172 CATGGATGGATCAT
1 CATGGATGGATCAT
27516186 CATGGATGGATCAT
1 CATGGATGGATCAT
27516200 CAT
1 CAT
27516203 ACTTATCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (14 bp):
CATGGATGGATCAT
Found at i:27524255 original size:17 final size:18
Alignment explanation
Indices: 27524233--27524273 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
27524223 CATTTCTTTT
27524233 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
27524250 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
27524268 T-TTTTG
1 TCTTTTG
27524274 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:27529808 original size:18 final size:18
Alignment explanation
Indices: 27529785--27529823 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27529775 AGGAAGATAG
27529785 TGACCCACTCACATATGA
1 TGACCCACTCACATATGA
*
27529803 TGACCCACTTACATATGA
1 TGACCCACTCACATATGA
27529821 TGA
1 TGA
27529824 AGAGATGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (18 bp):
TGACCCACTCACATATGA
Found at i:27540941 original size:44 final size:45
Alignment explanation
Indices: 27540862--27541084 Score: 148
Period size: 44 Copynumber: 4.8 Consensus size: 45
27540852 CATGGCAGAT
* *
27540862 CTTATCTTCCTGAAGTTGGAGTGGAGCAGATTGAAGCCACT-AGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* * * * * **
27540906 CTTATCTCCCTGAAGTTGCAGCGGAACAGACTGAAGACAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* * *
27540951 CTTATCTCCCT-ATCA-TTGCAGTGGAACAGATTAAAGCTACAAATCATGGCAGAT
1 CTTATCTCCCTGA--AGTTGCAGTGGAGCAGATTGAAGC--C--A-C-T-G-AG-C
* * *
27541005 CTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCAC-CAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* ** *
27541049 CTTATCTCCATGAAGTTGCAGCAGAGCAGACTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
27541085 ACAGCAGATC
Statistics
Matches: 139, Mismatches: 26, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
44 66 0.47
45 32 0.23
46 1 0.01
47 1 0.01
49 2 0.01
50 1 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 30 0.22
55 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
Found at i:27541799 original size:143 final size:143
Alignment explanation
Indices: 27540707--27541791 Score: 1405
Period size: 143 Copynumber: 7.6 Consensus size: 143
27540697 GATTGAAGTC
* * * * * * * *
27540707 ATTACGGCAAATCTCATCTTCTTAAAGTTGCAGTGCAGCATATTGAAGTCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * * * * * *
27540772 CTAAAGTTACAGCAGAGCAGACTAAAGATAGTGGATCTGATCTCCCTGGAGTTACAGTGGAATAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
**
27540837 ATTAACTCTACAA
131 ATTAAAGCTACAA
* * *
27540850 ATCATGGCAGATCTTATCTTCCTGAAGTTGGAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
27540915 CTGAAGTTGCAGCGGAACAGACTGAAGACAGTGAATCTTATCTCCCTATCATTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
27540980 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* *
27540993 ATCATGGCAGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * ** *
27541058 ATGAAGTTGCAGCAGAGCAGACTGAAGACAGCAGATCTTATTTATCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
27541123 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
27541136 ATTATGGCAAATTTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * *
27541201 CTGAAGTTGTAGCAGAGCAGACTAAAGATAGCGAATCTTATTTCCCTAGTGTTGTAGTGGAACAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
27541266 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
27541279 ATTTTGGCGGATATTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGACACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* *
27541344 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGTGGATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
27541409 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
27541422 ATTATGGCAGATCTTATCTTTCTAAAGTTGCAGTAGAGCAGATTGAAACCACCAGCCTTGTCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
27541487 CTGAAGTTGCAGCGTAGCAGACTGAAGATAGCGGATCTTATTTCCCTGGCGTTGCAGTGGAATAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
*
27541552 ATTAAAGCTAAAA
131 ATTAAAGCTACAA
** * *
27541565 ATTATGGTGGATATTATTTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
27541630 CTAAATTTACAGCGGAGTAGACTGAAGACAGCGGATTTTATTTCCCTAGCGCTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
27541695 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
27541708 ACTATGACAGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTTAAGCTACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* *
27541773 TTGAAGTTGCAGTGGAGCA
66 CTGAAGTTGCAGCGGAGCA
27541792 AATTGAAGTT
Statistics
Matches: 814, Mismatches: 128, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
143 814 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (143 bp):
ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
ATTAAAGCTACAA
Found at i:27547212 original size:9 final size:10
Alignment explanation
Indices: 27547186--27547213 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27547176 TCGGTAGAAA
27547186 AAGAAAAAAT
1 AAGAAAAAAT
27547196 AAGAAAAAAT
1 AAGAAAAAAT
27547206 AAGAAAAA
1 AAGAAAAA
27547214 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAGAAAAAAT
Found at i:27562151 original size:11 final size:10
Alignment explanation
Indices: 27562137--27562188 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
27562127 ATTCTCTTTC
*
27562137 TTTTCTTTTGA
1 TTTTATTTT-A
27562148 TTTTATTTTA
1 TTTTATTTTA
27562158 TTTTATTTTTA
1 TTTTA-TTTTA
27562169 TTATTATTATTA
1 TT-TTATT-TTA
27562181 TTATTATT
1 TT-TTATT
27562189 GTTGTTGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 6 0.16
11 17 0.46
12 14 0.38
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:27562174 original size:3 final size:3
Alignment explanation
Indices: 27562150--27562188 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
27562140 TCTTTTGATT
*
27562150 TTA TT- TTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27562189 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:27562193 original size:3 final size:3
Alignment explanation
Indices: 27562187--27562221 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27562177 ATTATTATTA
27562187 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
27562222 ATTATTATAA
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:27563718 original size:36 final size:36
Alignment explanation
Indices: 27563664--27563781 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 36
27563654 CTCTCTATTT
* * *
27563664 TGGTGTGTTTCTGTTGGATTAAATCTTCGGAGC-TAC
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCAT-C
** ** *
27563700 TGGTGTGTTTCAGATGGATTAGCTCTAATGAGCATT
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
* *
27563736 TGGTGTGTTTCAGATGGACTAATTCTTCTGAGCATC
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
27563772 TGGTGTGTTT
1 TGGTGTGTTT
27563782 TGTTGGTATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
36 66 0.99
37 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.42
Consensus pattern (36 bp):
TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
Found at i:27572344 original size:19 final size:20
Alignment explanation
Indices: 27572307--27572346 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
27572297 AAACAAATTT
*
27572307 AGAAAATAACAAAAGAAATA
1 AGAAAATAACAAAAAAAATA
*
27572327 AGAAAA-AATAAAAAAAATA
1 AGAAAATAACAAAAAAAATA
27572346 A
1 A
27572347 AGGATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (20 bp):
AGAAAATAACAAAAAAAATA
Found at i:27576136 original size:20 final size:20
Alignment explanation
Indices: 27576085--27576139 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
27576075 TATAATAACG
* *
27576085 AAACGATAGTAAAACAATAA
1 AAACAATAGCAAAACAATAA
* * *
27576105 AACACAACAGCAAAACGATGA
1 AA-ACAATAGCAAAACAATAA
27576126 AAACAATAGCAAAA
1 AAACAATAGCAAAA
27576140 TACATCAGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.64, C:0.16, G:0.11, T:0.09
Consensus pattern (20 bp):
AAACAATAGCAAAACAATAA
Found at i:27576439 original size:16 final size:16
Alignment explanation
Indices: 27576418--27576456 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
27576408 ATTTAATAAA
27576418 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
27576434 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
27576450 ATTCTTA
1 ATTCTTA
27576457 TAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTCTTAATAATCAAT
Found at i:27581970 original size:13 final size:13
Alignment explanation
Indices: 27581944--27581980 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
27581934 AAACATCAAC
27581944 TAATTTTT-TATA
1 TAATTTTTATATA
27581956 T-ATTTTTCATATA
1 TAATTTTT-ATATA
27581969 TAATTTTTATAT
1 TAATTTTTATAT
27581981 GTTAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 1 0.05
13 9 0.41
14 6 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TAATTTTTATATA
Found at i:27582329 original size:46 final size:46
Alignment explanation
Indices: 27582280--27582405 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 46
27582270 ATGCAGGTGA
*
27582280 AAAAAT-ATTGATATTTGAATTAATTATTTGAAATATTTCACATAT
1 AAAAATAATTGATATTTGAAATAATTATTTGAAATATTTCACATAT
*** * *
27582325 AAAAATAAAAAATATTTGAAATAATTTTTTTGAAATATTTCACATGT
1 AAAAATAATTGATATTTGAAATAA-TTATTTGAAATATTTCACATAT
27582372 AAAAATAATTGTGATATTTGAAATAATTATTTGA
1 AAAAATAA-T-TGATATTTGAAATAATTATTTGA
27582406 TTTTATAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 6 0.09
46 13 0.19
47 28 0.42
48 7 0.10
49 13 0.19
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (46 bp):
AAAAATAATTGATATTTGAAATAATTATTTGAAATATTTCACATAT
Found at i:27583383 original size:19 final size:19
Alignment explanation
Indices: 27583359--27583399 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
27583349 TGATTTATTC
27583359 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
27583378 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
27583397 TAA
1 TAA
27583400 CTTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:27588872 original size:41 final size:41
Alignment explanation
Indices: 27588788--27588875 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
27588778 ACCGGCTTTT
* * *
27588788 AGCCTGCTAGACTTATTGTCTGAAATGTATCACCGACATTA
1 AGCCTGCTAGACGTATAGTCTGAAATGTATCACCGACAATA
*
27588829 AGCCTGCTAGACGTATAGTCTGAATAAT-T-TCACTGACAATA
1 AGCCTGCTAGACGTATAGTCTG-A-AATGTATCACCGACAATA
27588870 AGCCTG
1 AGCCTG
27588876 ATAGGCACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 36 0.88
42 2 0.05
43 3 0.07
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACGTATAGTCTGAAATGTATCACCGACAATA
Found at i:27592435 original size:49 final size:49
Alignment explanation
Indices: 27592321--27592498 Score: 180
Period size: 49 Copynumber: 3.6 Consensus size: 49
27592311 TCATGAGAGG
* * * **
27592321 TCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGATATGAGAAC
** *
27592371 TCCCCCGTAAGACCATGTCGGGGACATGGCATGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAGAAC
* * * * * **
27592420 TCCCATGTAAAACCATATCTGGGATATGGCATTG-ACAG-TACAAGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAG-AAC
27592468 ATCCCATGTAAGACCATGTCTGGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
27592499 TTTGGCATGT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
47 4 0.04
48 6 0.06
49 69 0.66
50 26 0.25
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAGAAC
Found at i:27592505 original size:99 final size:102
Alignment explanation
Indices: 27592264--27592506 Score: 244
Period size: 99 Copynumber: 2.4 Consensus size: 102
27592254 GGGTAAAGAG
* **
27592264 ATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATCATGAGAGGTCCCATGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGC-TTGGCATC--T-AGATCATGAGAACTCCCATGT
* * * * * * * *
27592329 AAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAG
62 AAAACCATATCTGGGATATGGCATTGGCACAGACAAGAAAC
* ** * * *
27592370 GTCCCCCGTAAGACCATGTCGGGGACATGGCATGGCA-C-CGAT-ATGAGAACTCCCATGTAAAA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCTTGGCATCTAGATCATGAGAACTCCCATGTAAAA
27592432 CCATATCTGGGATATGGCATT-G-ACAGTACAAGAAAC
66 CCATATCTGGGATATGGCATTGGCACAG-ACAAGAAAC
27592468 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGC-TTGGCAT
27592507 GTTATTATCA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
97 3 0.03
98 33 0.29
99 41 0.37
100 3 0.03
104 1 0.01
105 5 0.04
106 26 0.23
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (102 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCTTGGCATCTAGATCATGAGAACTCCCATGTAAAA
CCATATCTGGGATATGGCATTGGCACAGACAAGAAAC
Found at i:27598028 original size:50 final size:50
Alignment explanation
Indices: 27597923--27598089 Score: 178
Period size: 50 Copynumber: 3.4 Consensus size: 50
27597913 GGGGTGTTAC
* *
27597923 ACATGGTCTTACATGGGATGTT-TCTTGTAC--TGCCAATGCCATATCCCAG
1 ACATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCCAATGCCATATCCCAG
* * * *
27597972 ATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAA
1 ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
** ** * **
27598022 ACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACACCATATCCCAG
1 ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
27598072 ACATGGTCTTACATGGGA
1 ACATGGTCTTACATGGGA
27598090 CCTCTCATGA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 4 0.04
49 21 0.22
50 71 0.74
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
Found at i:27599936 original size:21 final size:21
Alignment explanation
Indices: 27599912--27600012 Score: 78
Period size: 21 Copynumber: 4.8 Consensus size: 21
27599902 CAGAAGCTCT
* *
27599912 TAAGAGCTGAACGGAAACCCA
1 TAAGAGCTAAACGGAAACTCA
* * *
27599933 TAAGGGTTAAACAGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
*
27599954 AAAGAGCTAAACGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * *
27599975 TATGAGTTAAAC-AAAAGCTCG
1 TAAGAGCTAAACGGAAA-CTCA
* *
27599996 TGAGAGCTAAATGGAAA
1 TAAGAGCTAAACGGAAA
27600013 GTAAACACGA
Statistics
Matches: 59, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (21 bp):
TAAGAGCTAAACGGAAACTCA
Found at i:27599940 original size:42 final size:42
Alignment explanation
Indices: 27599858--27600012 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 42
27599848 CCGAAGGCTG
* ** ** * *
27599858 AACAGAAGCTCATAAGAGCCAAACAAAAACGTATACGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* *
27599900 AACAGAAGCTCTTAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * * *
27599942 AACAGAAACTCAAAAGAGCTAAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * *
27599984 AACAAAAGCTCGTGAGAGCTAAATGGAAA
1 AACAGAAGCTCATAAGAGCTAAACGGAAA
27600013 GTAAACACGA
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
Found at i:27600358 original size:20 final size:20
Alignment explanation
Indices: 27600333--27600373 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27600323 AGTATCTACG
27600333 AGCTCTTAATCTAAAATATA
1 AGCTCTTAATCTAAAATATA
27600353 AGCTCTTAATCTAAAATATA
1 AGCTCTTAATCTAAAATATA
27600373 A
1 A
27600374 AATTACTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
AGCTCTTAATCTAAAATATA
Found at i:27600459 original size:26 final size:26
Alignment explanation
Indices: 27600430--27600482 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
27600420 ATTAATACCC
27600430 CTTAATTTTTCAAATTTACACAATTA
1 CTTAATTTTTCAAATTTACACAATTA
27600456 CTTAATTTTTCAAATTTACACAATTA
1 CTTAATTTTTCAAATTTACACAATTA
27600482 C
1 C
27600483 CCCAACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (26 bp):
CTTAATTTTTCAAATTTACACAATTA
Found at i:27604292 original size:12 final size:12
Alignment explanation
Indices: 27604275--27604300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27604265 TATAAAATTT
27604275 ATATATAAAAAA
1 ATATATAAAAAA
27604287 ATATATAAAAAA
1 ATATATAAAAAA
27604299 AT
1 AT
27604301 TAGTTGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATATAAAAAA
Found at i:27604468 original size:129 final size:135
Alignment explanation
Indices: 27604248--27604494 Score: 382
Period size: 129 Copynumber: 1.9 Consensus size: 135
27604238 TATATATGAA
* *
27604248 AAAATAAATATTTTACATATAAAATTTATATATAAAAAAATATATAAAAAAATTAGTTGATGTTT
1 AAAATAAATATTTTACATATAAAAATTATATATAAAAAAATATATAAAAAAATAAGTTGATGTTT
* * *
27604313 TTAAAAATAAAATATATTTAACATAATGATATATA-AAAATATATTTTCATTACATCCACAATGT
66 TTAAAAATAAAATATATTTAACATAATAATATATATAAAAAATATTTCCATTACATCCACAATGT
27604377 ATGTG
131 ATGTG
27604382 AAAA-AAATATTTTACATA-AAAAATTATATAT-AAAAAA-ATAT-AAAAAATAAG-TGATGTTT
1 AAAATAAATATTTTACATATAAAAATTATATATAAAAAAATATATAAAAAAATAAGTTGATGTTT
*
27604441 TTAAAAGATAAAATATATTTAATATAATAATATATATAAAAAATATTTCCATTA
66 TTAAAA-ATAAAATATATTTAACATAATAATATATATAAAAAATATTTCCATTA
27604495 TATAATTACA
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
128 14 0.13
129 36 0.34
130 19 0.18
131 6 0.06
132 12 0.11
133 14 0.13
134 4 0.04
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (135 bp):
AAAATAAATATTTTACATATAAAAATTATATATAAAAAAATATATAAAAAAATAAGTTGATGTTT
TTAAAAATAAAATATATTTAACATAATAATATATATAAAAAATATTTCCATTACATCCACAATGT
ATGTG
Found at i:27604543 original size:15 final size:16
Alignment explanation
Indices: 27604518--27604547 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27604508 TTATTATTTT
27604518 TTATATAAAAAATAAG
1 TTATATAAAAAATAAG
27604534 TTAT-TAAAAAATAA
1 TTATATAAAAAATAA
27604548 AAAAAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TTATATAAAAAATAAG
Done.