Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 59 of 64
Found at i:11952166 original size:57 final size:58
Alignment explanation
Indices: 11952105--11952219 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 58
11952095 ATTTTTTATA
11952105 TTTACTTATTATTTTCATAATATTTATATGTTGAGC-AACTTTTAACATCTGTATCAG
1 TTTACTTATTATTTTCATAATATTTATATGTTGAGCAAACTTTTAACATCTGTATCAG
11952162 TTTACTTATTATTTTCATAATATTTATATGTTGAGCAAACTTTTAACATCTGTATCAG
1 TTTACTTATTATTTTCATAATATTTATATGTTGAGCAAACTTTTAACATCTGTATCAG
11952220 CAAATGTTGG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 36 0.63
58 21 0.37
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (58 bp):
TTTACTTATTATTTTCATAATATTTATATGTTGAGCAAACTTTTAACATCTGTATCAG
Found at i:11952600 original size:20 final size:21
Alignment explanation
Indices: 11952575--11952613 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11952565 GTATGGTTTC
11952575 AATACAC-ATCGCATGAATCA
1 AATACACAATCGCATGAATCA
11952595 AATACACAATCGCATGAAT
1 AATACACAATCGCATGAAT
11952614 AAGATGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (21 bp):
AATACACAATCGCATGAATCA
Found at i:11953432 original size:50 final size:53
Alignment explanation
Indices: 11953236--11953434 Score: 212
Period size: 53 Copynumber: 3.8 Consensus size: 53
11953226 AAGAATCTTG
* * * ** *
11953236 GCAGAAGCCACAGAAAAGGATG-ATGTGTTGTC-AACGCTTTATGAACGTCTGA
1 GCAGAAACCACAG-AAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
*
11953288 GCAAAAACCACAAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCAC--AGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* * *
11953343 GCAGAAGCCACAGAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC-TC-GA
1 GCAGAAACCACAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* *
11953393 -CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTA
1 GCAGAAACCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTA
11953435 TGAACAGTGA
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
49 10 0.08
50 29 0.23
51 2 0.02
52 11 0.09
53 39 0.31
54 12 0.09
55 24 0.19
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (53 bp):
GCAGAAACCACAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
Found at i:11953843 original size:20 final size:22
Alignment explanation
Indices: 11953793--11953845 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
11953783 ATCTACACTC
11953793 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
11953815 TTTAAAGATGA-CGATTCTC-T
1 TTCAAAGATGATAGATTCTCTT
11953835 TTCAAAGATGA
1 TTCAAAGATGA
11953846 AAACTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.39
21 7 0.25
22 10 0.36
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:11954418 original size:76 final size:75
Alignment explanation
Indices: 11954234--11954453 Score: 364
Period size: 69 Copynumber: 3.0 Consensus size: 75
11954224 CTCAAATCCA
11954234 TCATCTGATGGATCAGTTTTTCCAGAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 TCATCTGATGGATCAGTTTTTCCAGAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
11954299 AG-AA---AT
66 AGAAATTCAT
11954305 TCA-CTGAT-GATCAGTTTTTCCAGAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 TCATCTGATGGATCAGTTTTTCCAGAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
11954368 AGAAATTCAT
66 AGAAATTCAT
*
11954378 TCATCTGATGGATCAGTTTTTCCAGAAAAAGTTCATAATGAGAAGAA-TCATCTGAAGAAGGGAA
1 TCATCTGATGGATCAGTTTTTCCAG-AAAGGTTCATAATGAGAAGAACTCATCTGAAGAA-GGAA
11954442 GAAGAAATTCAT
64 GAAGAAATTCAT
11954454 AATGAGAAGA
Statistics
Matches: 140, Mismatches: 1, Indels: 11
0.92 0.01 0.07
Matches are distributed among these distances:
69 57 0.41
70 7 0.05
71 3 0.02
73 5 0.04
74 5 0.04
75 27 0.19
76 36 0.26
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (75 bp):
TCATCTGATGGATCAGTTTTTCCAGAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAATTCAT
Found at i:11954636 original size:224 final size:224
Alignment explanation
Indices: 11954378--11955047 Score: 916
Period size: 224 Copynumber: 3.0 Consensus size: 224
11954368 AGAAATTCAT
*
11954378 TCATCTGATGGATCAGTTTTTCCAGAAAAAGTTCATAATGAGAAGAA-TCATCTGAAGAAGGGAA
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGGAA
*
11954442 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAATCCATCATCTGAT-GATCAAC
66 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAATCCATCATCTGATAGATCAGC
11954506 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAG
131 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT-AAGAAGGAAGAAGAAATTCA-AATGAG
11954571 AAGAATTTGTTCAACCTTTTGCTCAAATCCA
194 AAGAATTTGTTCAACCTTTTGCTCAAATCCA
11954602 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GGAA
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGGAA
*
11954666 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAG
66 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-AATCCATCATCTGATAGATCAG
*
11954731 CTTTTCCAGAAAAAGTTC-TAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAATTTAAATGAG
130 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT-AAGAAGGAAGAAGAAATTCAAATGAG
*
11954794 AAGAATTTGTTCAAACCTTTTGCTCAAATTCA
194 AAGAATTTGTTC-AACCTTTTGCTCAAATCCA
*
11954826 TCAT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAACTCATCTGAAG--GAGA
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG-AACTCATCTGAAGAAGGGA
* ** * * * *
11954888 AGAA-AAGTTCATAATGAGAAGAGCTTATTCAACCTTTCGCAT-AATTCTATCACAGAAGCAGAT
65 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAA-TCCAT--C---ATC---T
*
11954951 AGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--GAA-GAAGAAGA
120 -GA-TAG-ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAGAAGGAAGAAGA
* **
11955013 AGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
182 AATTCA-AATGAGAAGAATTTGTTCAACCTTTTGC
11955048 ATAATTCTAT
Statistics
Matches: 405, Mismatches: 19, Indels: 37
0.88 0.04 0.08
Matches are distributed among these distances:
221 2 0.00
222 35 0.09
223 65 0.16
224 136 0.34
225 56 0.14
226 23 0.06
227 2 0.00
230 5 0.01
231 22 0.05
232 18 0.04
233 22 0.05
234 19 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (224 bp):
TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGGAA
GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAATCCATCATCTGATAGATCAGC
TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAGAAGGAAGAAGAAATTCAAATGAGAA
GAATTTGTTCAACCTTTTGCTCAAATCCA
Found at i:11954661 original size:113 final size:113
Alignment explanation
Indices: 11954378--11955047 Score: 936
Period size: 111 Copynumber: 5.9 Consensus size: 113
11954368 AGAAATTCAT
*
11954378 TCATCTGATGGATCAGTTTTTCCAGAAAAAGTTCATAATGAGAAGAA-TCATCTGAAGAAGGGAA
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GGAA
11954442 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-AATCCA
65 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
* *
11954490 TCATCTGAT-GATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAG
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
11954554 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
66 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
11954602 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
11954667 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
66 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
11954715 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTC-TAATGAGAAGAACTCATCTGAAGAAGGAAG
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
* *
11954779 -AGAAATTTA-AATGAGAAGAATTTGTTCAAACCTTTTGCTCAAATTCA
66 AAGAAATTCATAATGAGAAGAATTTGTTC-AACCTTTTGCTCAAATCCA
*
11954826 TCAT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAACTCATCTGAAGGA-GAA
1 TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG-AACTCATCTGAAGAAGGAA
* ** * *
11954889 GAA-AAGTTCATAATGAGAAGAGCTTATTCAACCTTTCGCAT-AATTCTATCACAGAA
65 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAA----ATC-C---A
* ** * *
11954945 GCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G
1 TCATCT-GA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* **
11955009 AAGAAG---TTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
63 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11955048 ATAATTCTAT
Statistics
Matches: 513, Mismatches: 23, Indels: 36
0.90 0.04 0.06
Matches are distributed among these distances:
110 47 0.09
111 141 0.27
112 96 0.19
113 135 0.26
115 2 0.00
116 1 0.00
119 3 0.01
120 31 0.06
121 2 0.00
122 21 0.04
123 34 0.07
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
TCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
Found at i:11954908 original size:19 final size:19
Alignment explanation
Indices: 11954851--11954909 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
11954841 CTTTTCCAGA
11954851 AAAAGTTCATAATGAGAAG
1 AAAAGTTCATAATGAGAAG
* *
11954870 -AAA-CTCATCTGAAGGAGAAG
1 AAAAGTTCA--T-AATGAGAAG
11954890 AAAAGTTCATAATGAGAAG
1 AAAAGTTCATAATGAGAAG
11954909 A
1 A
11954910 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 10 0.32
20 9 0.29
21 3 0.10
22 3 0.10
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (19 bp):
AAAAGTTCATAATGAGAAG
Found at i:11954980 original size:123 final size:120
Alignment explanation
Indices: 11954836--11955186 Score: 494
Period size: 120 Copynumber: 2.9 Consensus size: 120
11954826 TCATTGATGG
*
11954836 ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAACTCATCTGAAGGAGAAGAAAAGTTCATA
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG-AACTCATCTGAAGGAGAAGAAAAGTTCA-A
*
11954901 ATGAGAAGAGCTTATTCAACCTTTCGCATAATTCTATCACAGAAGCAGATAGATTAGC
64 ATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG-AGATAGATTAGC
*
11954959 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG--AAGTTCACAA
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAGAAAAGTTCA-AA
* *
11955022 TGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGC
65 TGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAG-AAGAGATAGATTAGC
* * *
11955079 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGGGAAAGAAAAAGTTC--
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAG-AAG-AAAAGTTCAA
* * * * *
11955142 ATGAAAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
64 ATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG
11955187 GAAATAGGTC
Statistics
Matches: 206, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
120 108 0.52
121 41 0.20
122 18 0.09
123 33 0.16
124 6 0.03
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (120 bp):
ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAGAAAAGTTCAAAT
GAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGAGATAGATTAGC
Found at i:11955219 original size:120 final size:118
Alignment explanation
Indices: 11954843--11955233 Score: 459
Period size: 120 Copynumber: 3.2 Consensus size: 118
11954833 TGGATCAGCT
*
11954843 TTTCCAGAAAAAGTTCATAATGAGAAGAAACTCATCTGAAGGAGAAG-AAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAG-AACTCATCTGAAGG-GAAGAAAAAGTTC--AATGAGA
* *
11954907 AGAGCTTATTCAACCTTTCGCATAATTCTATCACAGAAGCAGATAGATTAGCATCAGC
62 AGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCA-C
*
11954965 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA--GAAGAAGAAGTTCACAATGAGAA
1 -TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGGAAGAAAAAGTT--CAATGAGAA
* * *
11955028 GAGCTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
63 GAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATC-A-C
*
11955086 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGGGAAAGAAAAAGTTC-ATGAAAAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-GGG-AAGAAAAAGTTCAATGAGAAG
* * * * * * * *
11955150 AACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCA-
64 AGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAC
* *
11955204 TTCCCAGCGGAAAAGTTCATAATGAGAAGA
1 TTTCCAG-AG-AAAGTTCATAATGAGAAGA
11955234 GCTAATCCCA
Statistics
Matches: 235, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
118 6 0.03
119 5 0.02
120 122 0.52
121 51 0.22
122 14 0.06
123 27 0.11
124 10 0.04
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (118 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGGAAGAAAAAGTTCAATGAGAAGAG
CTTATTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAC
Found at i:11955402 original size:3 final size:3
Alignment explanation
Indices: 11955394--11955446 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
11955384 TTATTTAAAA
* *
11955394 ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT AAT ATAT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-TT ATT
11955441 A-T ATT A
1 ATT ATT A
11955447 CAAAACCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:11956653 original size:15 final size:15
Alignment explanation
Indices: 11956635--11956694 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
11956625 ATCCATTAGT
11956635 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
11956650 TTTTAAT-TTTTTAA
1 TTTTAATATTATTAC
*
11956664 TTTTAATTATTGTTA-
1 TTTTAA-TATTATTAC
*
11956679 TTTTATTTATTATTAC
1 TTTTA-ATATTATTAC
11956695 GTTTGATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.31
15 20 0.56
16 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:11956767 original size:14 final size:15
Alignment explanation
Indices: 11956750--11956782 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11956740 TATTATTAAG
11956750 TTATATAA-ATATAT
1 TTATATAATATATAT
*
11956764 TTATATAATATTTAT
1 TTATATAATATATAT
11956779 TTAT
1 TTAT
11956783 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:11959254 original size:14 final size:14
Alignment explanation
Indices: 11959216--11959254 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
11959206 ATTTTAAATA
*
11959216 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
11959230 TTTTACATTTGCAT
1 ATTTACATTTGCAT
11959244 ATTTACATTTG
1 ATTTACATTTG
11959255 TCATCTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:11962567 original size:17 final size:16
Alignment explanation
Indices: 11962543--11962574 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11962533 AAGAAAGAAG
11962543 AAAAAAAAAGGAAAAA
1 AAAAAAAAAGGAAAAA
11962559 AAAAGAAAAAGGAAAA
1 AAAA-AAAAAGGAAAA
11962575 TTGAATCAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAA
Found at i:11965023 original size:114 final size:114
Alignment explanation
Indices: 11964820--11965045 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
11964810 AAGTGCCATG
*
11964820 TGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
11964885 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGATTCGATAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
11964934 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
11964999 TGGTTCGATAGGAACCCTAGAACCAATCATTGGAATTAAAAGATGAA
66 TGATTCGATAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
11965046 CTGCATGATC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGATAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:11967071 original size:54 final size:52
Alignment explanation
Indices: 11966978--11967164 Score: 202
Period size: 54 Copynumber: 3.6 Consensus size: 52
11966968 AAGCCATAGA
* * *
11966978 AAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGAGCAAAAACCACAAG
1 AAAGGATGAATGTGTTGTCAAATGTTTTA-CAAC-TCTGAGCAAAAACCACAAG
* *
11967032 AAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGAGCAGAAGCCAC-AG
1 AAAGGATGAATGTGTTGTCAAATGTTTTAC-AAC-TCTGAGCAAAAACCACAAG
* * *
11967085 AAAAGGATGAATGTGTTGTCAAGTGTTTTACATCTC-GA--AAGAAACCACAGG
1 -AAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGAGCAA-AAACCACAAG
* *
11967136 AAAAGATGAATGTATTGTCAAATGTTTTA
1 AAAGGATGAATGTGTTGTCAAATGTTTTA
11967165 TGAACCAGTG
Statistics
Matches: 115, Mismatches: 14, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
49 1 0.01
50 32 0.28
51 3 0.03
52 2 0.02
53 4 0.03
54 73 0.63
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (52 bp):
AAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGAGCAAAAACCACAAG
Found at i:11967565 original size:22 final size:22
Alignment explanation
Indices: 11967536--11967590 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
11967526 ATCTACACTC
*
11967536 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGACATATTCTCTT
*
11967558 TTTAAAGATGACATATTCTCTT
1 TTCAAAGATGACATATTCTCTT
11967580 TTCAAAGATGA
1 TTCAAAGATGA
11967591 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGACATATTCTCTT
Found at i:11968188 original size:113 final size:113
Alignment explanation
Indices: 11967990--11969011 Score: 1682
Period size: 113 Copynumber: 9.0 Consensus size: 113
11967980 TAGCAAAGAT
*
11967990 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968055 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
11968103 TCAAATCCATCATCTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968168 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11968216 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968281 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
11968329 TC-AATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
11968393 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
11968441 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968506 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11968554 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968619 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
11968667 TCAAATACATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
11968732 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11968780 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** * *
11968845 AGGA-GAAGAA-AAAGTTCACAATGAGAAGAGCTTATTCAACCTTTCGC
66 AGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * *
11968892 AT-AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCATCT-GA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
* **
11968956 GAACTCATCTGAAGAA-GAAGAAG---TTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11969012 ATAATTCTAT
Statistics
Matches: 867, Mismatches: 27, Indels: 23
0.95 0.03 0.03
Matches are distributed among these distances:
111 3 0.00
112 146 0.17
113 622 0.72
116 3 0.00
117 1 0.00
120 35 0.04
121 2 0.00
122 1 0.00
123 54 0.06
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:11968870 original size:451 final size:451
Alignment explanation
Indices: 11967990--11969011 Score: 1680
Period size: 451 Copynumber: 2.2 Consensus size: 451
11967980 TAGCAAAGAT
*
11967990 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT-A
11968055 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGA
65 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGA
11968120 TGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATT
130 TGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATT
*
11968185 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAG
195 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGCTTTTCCAG
11968250 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
260 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
11968315 GTTCAACCTTTTGCTCAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
325 GTTCAACCTTTTGCTCAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
* * * *
11968380 AGAACTCATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-
390 AGAACTCATCTGAAGAATGAAGAAGAAATTCACAATGAGAAGAACTTATTCAACCTTTCGCA
11968441 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT-A
11968506 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGA
65 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGA
* *
11968571 TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
130 TGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATT
11968636 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGCTTTTCCAG
195 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGCTTTTCCAG
11968701 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
260 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
*
11968766 GTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
325 GTTCAACCTTTTGCTC-AATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAG
* *
11968831 AAGAACTCATCTGAAGGA-GAAGAA-AAAGTTCACAATGAGAAGAGCTTATTCAACCTTTCGCA
389 AAGAACTCATCTGAAGAATGAAGAAGAAA-TTCACAATGAGAAGAACTTATTCAACCTTTCGCA
* ** * *
11968893 T-AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 TCAA----ATC-C---ATCATCT-GA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
* * **
11968957 AACTCATCT--GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
55 AACTCATCTAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11969012 ATAATTCTAT
Statistics
Matches: 536, Mismatches: 21, Indels: 21
0.93 0.04 0.04
Matches are distributed among these distances:
450 3 0.01
451 372 0.69
452 65 0.12
455 3 0.01
456 1 0.00
458 39 0.07
459 7 0.01
460 2 0.00
461 1 0.00
462 43 0.08
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (451 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAA
GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGAT
GGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTC
ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGCTTTTCCAGA
AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTCAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAA
GAACTCATCTGAAGAATGAAGAAGAAATTCACAATGAGAAGAACTTATTCAACCTTTCGCA
Found at i:11969027 original size:120 final size:119
Alignment explanation
Indices: 11968800--11969153 Score: 510
Period size: 120 Copynumber: 2.9 Consensus size: 119
11968790 CATCTGATGG
*
11968800 ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAGAAAAAGTTCACA
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A--AGAAGAAAAAGTTCACA
*
11968865 ATGAGAAGAGCTTATTCAACCTTTCGCATAATTCTATCACAGAAGCAGATAGATTAGC
63 ATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG-AGATAGATTAGC
*
11968923 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATG
* *
11968988 AGAAGAGCTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGC
66 AGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAG-AAGAGATAGATTAGC
* * *
11969043 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGGGAAAGAAAAAGTTCAT
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA---G-AAGAAAAAGTTCAC
* * * * *
11969108 AATGAAAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
62 AATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG
11969154 GAAATAGGTC
Statistics
Matches: 210, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
120 111 0.53
121 3 0.01
122 1 0.00
123 47 0.22
124 48 0.23
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (119 bp):
ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATG
AGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGAGATAGATTAGC
Found at i:11969369 original size:3 final size:3
Alignment explanation
Indices: 11969361--11969422 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
11969351 ATTTTAAAAT
*
11969361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
11969407 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
11969423 CAAAACCCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:11970654 original size:15 final size:14
Alignment explanation
Indices: 11970634--11970693 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
11970624 ATCCATTAGT
11970634 TTTTAATATTATTA
1 TTTTAATATTATTA
* *
11970648 CTTTTAATTTTTTTAA
1 -TTTTAATATTATT-A
*
11970664 TTTTAATTATTGTTA
1 TTTTAA-TATTATTA
*
11970679 TTTT-ATTTTATTA
1 TTTTAATATTATTA
11970692 TT
1 TT
11970694 ACGTTTGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 22 0.59
16 6 0.16
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTAATATTATTA
Found at i:11972795 original size:42 final size:42
Alignment explanation
Indices: 11972748--11972866 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
11972738 GATTCACCTG
** * * *
11972748 TCATCGTTCAAGAGGTGCCTCCTATCATTCAAGAGGCTCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* *
11972790 TCATCGTTCAATAGGCCCCTCCCACCATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* * *
11972832 TCATCGTTCAATG-GGTCTCTCCCACCGTTCAAGAG
1 TCATCGTTCAA-GAGGCCCCTCCCACCATTCAAGAG
11972867 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
Found at i:11972841 original size:21 final size:21
Alignment explanation
Indices: 11972748--11972842 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
11972738 GATTCACCTG
**
11972748 TCATCGTTCAAGAGGTGCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
11972769 -CTATCATTCAAGAGGCTCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
*
11972790 TCATCGTTCAATAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
11972811 CCACCATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
11972832 TCATCGTTCAA
1 TCATCGTTCAA
11972843 TGGGTCTCTC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:11974289 original size:66 final size:64
Alignment explanation
Indices: 11974129--11974303 Score: 233
Period size: 66 Copynumber: 2.6 Consensus size: 64
11974119 TGAGGTACAC
* *
11974129 TTTTTTGCTTGTTTAATTGAATTTTATATTGAAAGTTGATTTGTTTAATTGATGGGGAAATAAAA
1 TTTTTTGCTTGTTTAATTG-A-TTTGTA---AAAGTTGATTTGTTTAATTGATGGAGAAATAAAA
11974194 ATTA
61 ATTA
* * * *
11974198 TTTTCTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTATAAATAAGAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGGAGAAATAAAAATTA
11974263 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
11974304 GTTTTAAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
64 17 0.18
65 17 0.18
66 39 0.40
67 5 0.05
68 1 0.01
69 18 0.19
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.53
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGGAGAAATAAAAATTA
Found at i:11974494 original size:14 final size:14
Alignment explanation
Indices: 11974473--11974511 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
11974463 GTCAAATTCA
11974473 CGTTGCGAATTTCG
1 CGTTGCGAATTTCG
11974487 -GTTTGCG-ATTTCG
1 CG-TTGCGAATTTCG
11974500 CGTTGCGAATTT
1 CGTTGCGAATTT
11974512 GACTTTCGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.13, C:0.18, G:0.28, T:0.41
Consensus pattern (14 bp):
CGTTGCGAATTTCG
Found at i:11974755 original size:18 final size:18
Alignment explanation
Indices: 11974732--11974767 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11974722 AAGCCGGTTG
*
11974732 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
11974750 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
11974768 ACTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:11977062 original size:24 final size:24
Alignment explanation
Indices: 11977035--11977088 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
11977025 TTGAAACATC
*
11977035 ATCAAAATCCTAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
11977059 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
11977083 ATCAAA
1 ATCAAA
11977089 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:11978059 original size:19 final size:20
Alignment explanation
Indices: 11978035--11978117 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 20
11978025 AACTAAAACC
11978035 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
11978054 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* *
11978074 AGTTGCGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
11978093 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
11978114 TGTT
1 TGTT
11978118 ACAAATTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.07
19 26 0.48
20 18 0.33
21 6 0.11
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:11978080 original size:20 final size:19
Alignment explanation
Indices: 11978055--11978114 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
11978045 TTAAATTCGT
*
11978055 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATC-A
*
11978075 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
*
11978094 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
11978113 GT
1 GT
11978115 GTTACAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:11978126 original size:21 final size:19
Alignment explanation
Indices: 11978081--11978127 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
11978071 TCGAGTTGCG
* *
11978081 AATTTGAAATTCAGTTGCG
1 AATTTGAAATTCAGTTACA
11978100 AATTTGAAATTCAGTGTTACA
1 AATTTGAAATTCA--GTTACA
11978121 AATTTGA
1 AATTTGA
11978128 CTATCGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.54
21 11 0.46
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (19 bp):
AATTTGAAATTCAGTTACA
Found at i:11978144 original size:20 final size:20
Alignment explanation
Indices: 11978121--11978305 Score: 111
Period size: 20 Copynumber: 9.2 Consensus size: 20
11978111 CAGTGTTACA
*
11978121 AATTTGACTATCGCGTTGCA
1 AATTTGACTATCGCGTTGCG
*
11978141 AATTTGACT-TCTGTGTTGCG
1 AATTTGACTATC-GCGTTGCG
* *
11978161 -ATTT-ACAGATTCGCGTTTCG
1 AATTTGAC-TA-TCGCGTTGCG
* *
11978181 AATTTGTCT-TCAGTGTTGCG
1 AATTTGACTATC-GCGTTGCG
11978201 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
* *
11978221 AATTTGACT-TCTGTGTTACG
1 AATTTGACTATC-GCGTTGCG
*
11978241 AATTTGACT-TCTGTGTTGCG
1 AATTTGACTATC-GCGTTGCG
*
11978261 -ATTT-ACAAATTCGCGTTGCG
1 AATTTGAC-TA-TCGCGTTGCG
*
11978281 -ATTT-ACATATTCGTGTTGCG
1 AATTTGAC-TA-TCGCGTTGCG
11978301 AATTT
1 AATTT
11978306 AGAAACTGGG
Statistics
Matches: 134, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.03
19 14 0.10
20 101 0.75
21 14 0.10
22 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
AATTTGACTATCGCGTTGCG
Found at i:11978219 original size:60 final size:60
Alignment explanation
Indices: 11978108--11978305 Score: 176
Period size: 60 Copynumber: 3.3 Consensus size: 60
11978098 CGAATTTGAA
* * * *
11978108 ATTCAGTGTTACAAATTTGACTATC-GCGTTGCAAATTTGACT-TCTGTGTTGCGATTTACAG
1 ATTC-GTGTTACGAATTTGACT-TCAGTGTTGCGAATTTGACTATC-GCGTTGCGATTTACAG
* * *
11978169 ATTCGCGTTTCGAATTTGTCTTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTT---G
1 ATTCGTGTTACGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCGTTGCG-ATTTACAG
* * *
11978227 ACTTCTGTGTTACGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGATTTACAT
1 A-TTC-GTGTTACGAATTTGACTTCAGTGTTGCGAATTTGAC-TA-TCGCGTTGCGATTTACAG
*
11978289 ATTCGTGTTGCGAATTT
1 ATTCGTGTTACGAATTT
11978306 AGAAACTGGG
Statistics
Matches: 113, Mismatches: 14, Indels: 21
0.76 0.09 0.14
Matches are distributed among these distances:
58 4 0.04
59 14 0.12
60 81 0.72
61 13 0.12
62 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (60 bp):
ATTCGTGTTACGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCGTTGCGATTTACAG
Found at i:11978261 original size:40 final size:40
Alignment explanation
Indices: 11978094--11978249 Score: 181
Period size: 40 Copynumber: 3.9 Consensus size: 40
11978084 TTGAAATTCA
* *
11978094 GTTGCGAATTTGAAATTCAGTGTTACAAATTTGACTATCGC
1 GTTGCGAATTTG-ACTTCAGTGTTACGAATTTGACTATCGC
* * * *
11978135 GTTGCAAATTTGACTTCTGTGTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGACTTCAGTGTTACGAATTTGAC-TA-TCGC
* * *
11978175 GTTTCGAATTTGTCTTCAGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTCAGTGTTACGAATTTGACTATCGC
*
11978215 GTTGCGAATTTGACTTCTGTGTTACGAATTTGACT
1 GTTGCGAATTTGACTTCAGTGTTACGAATTTGACT
11978250 TCTGTGTTGC
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 5 0.05
40 71 0.74
41 16 0.17
42 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCAGTGTTACGAATTTGACTATCGC
Found at i:11983953 original size:33 final size:32
Alignment explanation
Indices: 11983911--11984006 Score: 131
Period size: 33 Copynumber: 3.0 Consensus size: 32
11983901 TGGCAAGTTG
*
11983911 GAAATTTCATCTTGGTTGGTGGCCAACTTATT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATT
11983943 GAAAAATTCATCTTGGTTGGTGGCCAACTTATT
1 G-AAAATTCATCTTGGTTGGTGGCCAACTTATT
* * * *
11983976 GGAAATT-TTTTTGGTAGGTGGCCAACTTATT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATT
11984007 TTTCATGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
31 21 0.36
32 6 0.10
33 31 0.53
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.40
Consensus pattern (32 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATT
Found at i:11984045 original size:12 final size:12
Alignment explanation
Indices: 11984028--11984054 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11984018 ATCCCTAAAA
11984028 TATTAGGTTATT
1 TATTAGGTTATT
11984040 TATTAGGTTATT
1 TATTAGGTTATT
11984052 TAT
1 TAT
11984055 AAGTTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (12 bp):
TATTAGGTTATT
Found at i:11988766 original size:31 final size:33
Alignment explanation
Indices: 11988671--11988770 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
11988661 AGTTTGGCAA
* *
11988671 ATTGGAAATTTCATCTTGGTTGGTGGCCAACTT
1 ATTGGAAAATTCATCTTGGTTGGTGGTCAACTT
**
11988704 ATTAAAAAATTCATCTTGGTTGGT-GTCCAACTT
1 ATTGGAAAATTCATCTTGGTTGGTGGT-CAACTT
*
11988737 ATTGGAAAATTC-T-TTGGTAGGTGGTCAACTT
1 ATTGGAAAATTCATCTTGGTTGGTGGTCAACTT
11988768 ATT
1 ATT
11988771 TTTCATTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
31 17 0.29
32 4 0.07
33 37 0.64
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (33 bp):
ATTGGAAAATTCATCTTGGTTGGTGGTCAACTT
Found at i:11990981 original size:20 final size:20
Alignment explanation
Indices: 11990952--11990990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11990942 ATTTCACCAC
*
11990952 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
11990972 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
11990991 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:11997745 original size:22 final size:22
Alignment explanation
Indices: 11997702--11997746 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
11997692 AGAGATAAGG
*
11997702 AAAATAAAAATAAAACTATAAA
1 AAAATAAAAATAAAACAATAAA
11997724 AAAATAAAAAT-AAACAAGTAAA
1 AAAATAAAAATAAAACAA-TAAA
11997746 A
1 A
11997747 TAAAAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAAAATAAAACAATAAA
Found at i:11999389 original size:20 final size:20
Alignment explanation
Indices: 11999360--11999398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11999350 ATTTCACCAC
*
11999360 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
11999380 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
11999399 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:12009220 original size:70 final size:70
Alignment explanation
Indices: 12009107--12009245 Score: 278
Period size: 70 Copynumber: 2.0 Consensus size: 70
12009097 ATTAACTTTT
12009107 TCGTTTAGCTTAAGAAATTAAGGGTTAAATCATGATAATTAGAATGTTGATATGTATATGTATGA
1 TCGTTTAGCTTAAGAAATTAAGGGTTAAATCATGATAATTAGAATGTTGATATGTATATGTATGA
12009172 TTGTC
66 TTGTC
12009177 TCGTTTAGCTTAAGAAATTAAGGGTTAAATCATGATAATTAGAATGTTGATATGTATATGTATGA
1 TCGTTTAGCTTAAGAAATTAAGGGTTAAATCATGATAATTAGAATGTTGATATGTATATGTATGA
12009242 TTGT
66 TTGT
12009246 GTTGATATCG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (70 bp):
TCGTTTAGCTTAAGAAATTAAGGGTTAAATCATGATAATTAGAATGTTGATATGTATATGTATGA
TTGTC
Found at i:12009699 original size:22 final size:22
Alignment explanation
Indices: 12009667--12009725 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
12009657 AATCGAGGGT
*
12009667 TTCATAGGTCCTTCGGGACATA
1 TTCACAGGTCCTTCGGGACATA
*
12009689 TTCACATGTCCTTCGGGACATA
1 TTCACAGGTCCTTCGGGACATA
12009711 TTCACAGGTCCTTCG
1 TTCACAGGTCCTTCG
12009726 TAACAAGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (22 bp):
TTCACAGGTCCTTCGGGACATA
Found at i:12018284 original size:21 final size:21
Alignment explanation
Indices: 12018258--12018301 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12018248 GCATCAAGGT
12018258 TTTTGTAGACGCCATGAAATC
1 TTTTGTAGACGCCATGAAATC
* * *
12018279 TTTTGTCGAGGCCATGAATTC
1 TTTTGTAGACGCCATGAAATC
12018300 TT
1 TT
12018302 GCAATGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
TTTTGTAGACGCCATGAAATC
Found at i:12018638 original size:31 final size:31
Alignment explanation
Indices: 12018598--12018672 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
12018588 AATCTCATGA
* *
12018598 TGGTTGCCTTTACATAATAGGCACGCATTAT
1 TGGTCGCCTTGACATAATAGGCACGCATTAT
12018629 TGGTCGCCTTGACATAATAGGCACGCATTAT
1 TGGTCGCCTTGACATAATAGGCACGCATTAT
12018660 TGGTCGCCTTGAC
1 TGGTCGCCTTGAC
12018673 TTCTCTTACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (31 bp):
TGGTCGCCTTGACATAATAGGCACGCATTAT
Found at i:12019892 original size:21 final size:19
Alignment explanation
Indices: 12019854--12019899 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
12019844 ATTTAATCCT
12019854 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
12019874 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
12019895 A-TAAT
1 ACTAAT
12019900 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:12024977 original size:14 final size:14
Alignment explanation
Indices: 12024942--12024977 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12024932 AAAATATTTG
12024942 TTGGGATGAATTCT
1 TTGGGATGAATTCT
* *
12024956 TAGAGATGAATTCT
1 TTGGGATGAATTCT
12024970 TTGGGATG
1 TTGGGATG
12024978 CAATATAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.39
Consensus pattern (14 bp):
TTGGGATGAATTCT
Found at i:12025504 original size:2 final size:2
Alignment explanation
Indices: 12025497--12025536 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12025487 TATCACTCCG
12025497 AT AT AT AT 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 AT AT AT AT
12025537 CTTTAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12030114 original size:32 final size:31
Alignment explanation
Indices: 12030047--12030120 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 31
12030037 TAAAAATTTG
*
12030047 AATTGTTATAAAATAAATATTAAATTTTATCA
1 AATT-TTATAAAATAAATATTAAATTTTATAA
*
12030079 AATTATTATAAAAT-GATCATTAAA-TTTATTAA
1 AATT-TTATAAAATAAAT-ATTAAATTTTA-TAA
12030111 AATTTTATAA
1 AATTTTATAA
12030121 TTATTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (31 bp):
AATTTTATAAAATAAATATTAAATTTTATAA
Found at i:12033122 original size:22 final size:23
Alignment explanation
Indices: 12033096--12033182 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 23
12033086 CCAAACAACC
12033096 GAAAACGTGCCA-AAAGACATAA
1 GAAAACGTGCCATAAAGACATAA
* * *
12033118 GAAAACGTGTCATAAAGGCATAG
1 GAAAACGTGCCATAAAGACATAA
* * * * *
12033141 GAAAACATGCCATACAGGCAGAG
1 GAAAACGTGCCATAAAGACATAA
*
12033164 GAAAACGTGCTATACAAGA
1 GAAAACGTGCCATA-AAGA
12033183 AGACTTGTTG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 11 0.21
23 39 0.75
24 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (23 bp):
GAAAACGTGCCATAAAGACATAA
Found at i:12033139 original size:23 final size:23
Alignment explanation
Indices: 12033096--12033173 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
12033086 CCAAACAACC
* *
12033096 GAAAACGTGCCA-AAAGACATAA
1 GAAAACGTGCCATAAAGGCATAG
*
12033118 GAAAACGTGTCATAAAGGCATAG
1 GAAAACGTGCCATAAAGGCATAG
* * *
12033141 GAAAACATGCCATACAGGCAGAG
1 GAAAACGTGCCATAAAGGCATAG
12033164 GAAAACGTGC
1 GAAAACGTGC
12033174 TATACAAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 11 0.23
23 36 0.77
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (23 bp):
GAAAACGTGCCATAAAGGCATAG
Found at i:12046807 original size:20 final size:20
Alignment explanation
Indices: 12046782--12046842 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
12046772 TTTTGGTGCA
12046782 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCTT
* * *
12046802 GAGGGAACCGATTCCCACCAT
1 GAGGGAATCGA-TCCCCCCTT
12046823 -AGGGGAATCGATACCCCCCT
1 GA-GGGAATCGAT-CCCCCCT
12046843 GGGGTTCTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCTT
Found at i:12066214 original size:2 final size:2
Alignment explanation
Indices: 12066207--12066250 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12066197 AATAAAAATG
12066207 AT AT AT AT AT 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 AT AT AT AT AT
12066249 AT
1 AT
12066251 GCATATTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12068338 original size:20 final size:20
Alignment explanation
Indices: 12068313--12068363 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
12068303 TATTCCCTGT
*
12068313 TAATCTTACATTCATATTAG
1 TAATCTTACATTCATACTAG
* *
12068333 TAATCTTACATTCCTACTGG
1 TAATCTTACATTCATACTAG
12068353 TAATCTTACAT
1 TAATCTTACAT
12068364 CCCGTGAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (20 bp):
TAATCTTACATTCATACTAG
Found at i:12070014 original size:24 final size:21
Alignment explanation
Indices: 12069987--12070032 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 21
12069977 TATACACGTT
12069987 TAAATTTTAAAATAATATTAATTA
1 TAAATTTT--AATAATA-TAATTA
12070011 TAAATTTTAATAATATAATTA
1 TAAATTTTAATAATATAATTA
12070032 T
1 T
12070033 GGATGTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
24 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTTAATAATATAATTA
Found at i:12074007 original size:30 final size:29
Alignment explanation
Indices: 12073951--12074013 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
12073941 TATTGATGGA
* *
12073951 TTTAAATATTTAAATTAAATTCATATTCCT
1 TTTAAATATTCAAATTAAATGCATATT-CT
*
12073981 TTTAAATATTACAAATTAAA-GGATATTCT
1 TTTAAATATT-CAAATTAAATGCATATTCT
12074010 TTTA
1 TTTA
12074014 TTTGAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 15 0.52
31 8 0.28
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAAATATTCAAATTAAATGCATATTCT
Found at i:12074177 original size:63 final size:65
Alignment explanation
Indices: 12074071--12074228 Score: 171
Period size: 63 Copynumber: 2.4 Consensus size: 65
12074061 AGGTATTTAT
* * *
12074071 TATCTATTTAACTTTGAATATTAAAAGATAATTATATACTTTGAAAATTT-A-AAACGAAAATAA
1 TATCTATTTAAATTTGAATATTAAAAGATAATTAAATACTTTGAAAATTTAATAAAAGAAAATAA
* * * *
12074134 TATCTATTTAAATTTGAATAGTAAAAGA-AGTTTAAAT-CGTTTGAATATTTCAAATTAAAAGAT
1 TATCTATTTAAATTTGAATATTAAAAGATA-ATTAAATAC-TTTGAAAATTT--AA-TAAAAGAA
*
12074197 AATAT
61 AATAA
12074202 TATCTATTTAAATTTGAATATTAAAAG
1 TATCTATTTAAATTTGAATATTAAAAG
12074229 TATTTAGTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
63 41 0.52
66 1 0.01
68 35 0.44
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (65 bp):
TATCTATTTAAATTTGAATATTAAAAGATAATTAAATACTTTGAAAATTTAATAAAAGAAAATAA
Found at i:12074225 original size:34 final size:33
Alignment explanation
Indices: 12074068--12074228 Score: 106
Period size: 34 Copynumber: 4.9 Consensus size: 33
12074058 AATAGGTATT
*
12074068 TATTATCTATTTAACTTTGAATATTAAAAG--A
1 TATTATCTATTTAAATTTGAATATTAAAAGAAA
* * *
12074099 TA--AT-TATAT-ACTTTGAAAATTTAAAACGAAAA
1 TATTATCTATTTAAATTTGAATA-TTAAAA-G-AAA
* * *
12074131 TAATATCTATTTAAATTTGAATAGTAAAAGAAG
1 TATTATCTATTTAAATTTGAATATTAAAAGAAA
* *
12074164 T-TTAAATCGT-TTGAATATTTCAA-ATTAAAAGATAA
1 TATT--ATC-TATTTAA-ATTTGAATATTAAAAGA-AA
12074199 TATTATCTATTTAAATTTGAATATTAAAAG
1 TATTATCTATTTAAATTTGAATATTAAAAG
12074229 TATTTAGTTG
Statistics
Matches: 99, Mismatches: 14, Indels: 31
0.69 0.10 0.22
Matches are distributed among these distances:
27 9 0.09
28 10 0.10
29 3 0.03
31 2 0.02
32 4 0.04
33 10 0.10
34 33 0.33
35 18 0.18
36 10 0.10
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (33 bp):
TATTATCTATTTAAATTTGAATATTAAAAGAAA
Found at i:12079762 original size:63 final size:65
Alignment explanation
Indices: 12079640--12079803 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 65
12079630 AGGTATTTAT
* * *
12079640 TATCTATTTAACTTTGAATATTAAAAAGATAATTATATACTTTGAATATTTCAAATT-AAA-ATA
1 TATCTATTTAAATTTGAATATTAAAAGGAT-ATTAAATACTTTGAATATTTCAAATTAAAAGATA
12079703 A
65 A
*
12079704 TATCTATTTAAATTTGAATACTAAAAGGAGT-TTAAAT-CTTTCGAATATTTCAAATTAAAAGAT
1 TATCTATTTAAATTTGAATATTAAAAGGA-TATTAAATACTTT-GAATATTTCAAATTAAAAGAT
12079767 AA
64 AA
*
12079769 TATTGCCTGTTTAAATTTGAATATTAAAA-GATATT
1 TA-T--CTATTTAAATTTGAATATTAAAAGGATATT
12079804 TAGTTGGAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
62 4 0.05
63 19 0.22
64 29 0.34
65 7 0.08
66 2 0.02
67 4 0.05
68 21 0.24
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (65 bp):
TATCTATTTAAATTTGAATATTAAAAGGATATTAAATACTTTGAATATTTCAAATTAAAAGATAA
Found at i:12082884 original size:32 final size:32
Alignment explanation
Indices: 12082843--12082927 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
12082833 CCCTCCTTAA
12082843 GGACACTATGAGATCCACCCCGTGGTAGATAG
1 GGACACTATGAGATCCACCCCGTGGTAGATAG
12082875 GGACACTATGAGATCCACCCCGTGGTAGATAG
1 GGACACTATGAGATCCACCCCGTGGTAGATAG
*
12082907 GGACACTATGAGATCCCCCCC
1 GGACACTATGAGATCCACCCC
12082928 TCCATTGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (32 bp):
GGACACTATGAGATCCACCCCGTGGTAGATAG
Found at i:12086577 original size:21 final size:21
Alignment explanation
Indices: 12086552--12086608 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
12086542 ATATTAAAAC
12086552 ATTTATTAAAAATAGATATA-
1 ATTTATTAAAAATAGATATAT
* *
12086572 ATTT-TATAAAAGTAAGATATTT
1 ATTTAT-TAAAAAT-AGATATAT
12086594 ATTTATTTAAAAATA
1 ATTTA-TTAAAAATA
12086609 TAAGAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
19 1 0.03
20 10 0.34
21 6 0.21
22 5 0.17
23 6 0.21
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTATTAAAAATAGATATAT
Found at i:12086608 original size:128 final size:123
Alignment explanation
Indices: 12086458--12086687 Score: 302
Period size: 128 Copynumber: 1.8 Consensus size: 123
12086448 TATATATAAG
* * * *
12086458 AGATATTTATTTATTTAGAAATATCAA-AAAAGGGAT-TCTAGGTGCTTTAAGACAACTCTTTTT
1 AGATATTTATTTATTTAAAAATAT-AAGAAAAGGGATATCCAGGTGCTTTAAGACAA-TCCTTTC
*
12086521 TTAATATTAAAAAATAAATAAATATTAAAACATTTATTAAAAATAGATATAATTTTATAAAAGTA
64 TTAATA-T---AAATAAATAAATATTAAAACA-TGATTAAAAATAGATATAATTTTATAAAAGTA
* * *
12086586 AGATATTTATTTATTTAAAAATATAAGAAAATGGATATCCAGTTGCTTTAAGACTATCCTTTCTT
1 AGATATTTATTTATTTAAAAATATAAGAAAAGGGATATCCAGGTGCTTTAAGACAATCCTTTCTT
*
12086651 AATATAAATAAATAAATATTAAAATATGATTAAAAAT
66 AATATAAATAAATAAATATTAAAACATGATTAAAAAT
12086688 TAATTTATGT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
123 10 0.11
124 20 0.22
127 3 0.03
128 42 0.46
129 16 0.18
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.38
Consensus pattern (123 bp):
AGATATTTATTTATTTAAAAATATAAGAAAAGGGATATCCAGGTGCTTTAAGACAATCCTTTCTT
AATATAAATAAATAAATATTAAAACATGATTAAAAATAGATATAATTTTATAAAAGTA
Found at i:12086890 original size:29 final size:27
Alignment explanation
Indices: 12086841--12086903 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
12086831 TAAACAATTA
* *
12086841 TTAAAATAAATAAAATTATAACTATATAT
1 TTAAAATAAATAAAATAATAA--AAATAT
*
12086870 TTAAAATATAA-AAAGTAATAAAAATAT
1 TTAAAATA-AATAAAATAATAAAAATAT
12086897 TTAAAAT
1 TTAAAAT
12086904 TAGTGACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 12 0.40
29 16 0.53
30 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
TTAAAATAAATAAAATAATAAAAATAT
Found at i:12087418 original size:11 final size:11
Alignment explanation
Indices: 12087402--12087426 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12087392 AGAGAAAAAA
12087402 TTCTCTCTAGC
1 TTCTCTCTAGC
12087413 TTCTCTCTAGC
1 TTCTCTCTAGC
12087424 TTC
1 TTC
12087427 CCTCACCGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.36, G:0.08, T:0.48
Consensus pattern (11 bp):
TTCTCTCTAGC
Found at i:12088293 original size:3 final size:3
Alignment explanation
Indices: 12088287--12088357 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
12088277 TAATTTTTTT
*
12088287 TAA TAA TAA TAA TAC TAA TAAA TAA TAA TAA T-A TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
12088331 TAG TAA TAAA TAA -AA TAG TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA
12088358 CAAATGGATG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 45 0.79
4 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12088310 original size:13 final size:13
Alignment explanation
Indices: 12088287--12088357 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
12088277 TAATTTTTTT
12088287 TAATAAT-AATAA
1 TAATAATAAATAA
*
12088299 TACTAATAAATAA
1 TAATAATAAATAA
12088312 TAATAAT--ATAA
1 TAATAATAAATAA
*
12088323 -AATAAT-AATAG
1 TAATAATAAATAA
*
12088334 TAATAAATAAAATAG
1 TAAT-AAT-AAATAA
12088349 TAATAATAA
1 TAATAATAA
12088358 CAAATGGATG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 6 0.12
11 7 0.14
12 9 0.18
13 16 0.32
14 3 0.06
15 9 0.18
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:12088310 original size:16 final size:16
Alignment explanation
Indices: 12088287--12088354 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
12088277 TAATTTTTTT
*
12088287 TAAT-AATAATAATAC
1 TAATAAATAATAATAG
*
12088302 TAATAAATAATAATAA
1 TAATAAATAATAATAG
12088318 T-ATAAAATAATAATAG
1 TAAT-AAATAATAATAG
12088334 TAATAAATAA-AATAG
1 TAATAAATAATAATAG
12088349 TAATAA
1 TAATAA
12088355 TAACAAATGG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
15 17 0.35
16 29 0.60
17 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATAAATAATAATAG
Found at i:12094588 original size:200 final size:198
Alignment explanation
Indices: 12094169--12094669 Score: 616
Period size: 200 Copynumber: 2.5 Consensus size: 198
12094159 AGTATATCGG
* * * *
12094169 TATATTTATA-CCGGTAATATTGAAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTT
1 TATATTTATATCAGGT-ACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGAT-GTTT
* * * *
12094233 TTGGATCGATACAATTT--TAAGTGTATCGACACTTTATACATGCACCTCGTTGGACATTCATTA
64 TGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATACATGCACCCCGTTGGACATTCATTA
* * *
12094296 TGGAAAAAAGTATCGACACAAACTTAAAAAGTGTTGATACATTATTTAGACCTATTTTCTCATAA
128 TGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATCTAGACCTAATTTCTCATAA
12094361 AACCGA
193 AACCGA
* * * * *
12094367 TATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATTATCGGTTTCGATGTTTGT
1 TATATTTATATCAGGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTT-T
***
12094432 GGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCCCGTTTGG-CATTCATTAT
65 GGGATCGATACTTTTAATAAATGTATCGACACTTTATACATGCACCCCG-TTGGACATTCATTAT
* ** * *
12094496 GGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACTTTATGCT-GACCTAATTTCTTATA
129 GGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT-CTAGACCTAATTTCTCATA
*
12094560 AAACCGG
192 AAACCGA
* * *
12094567 TATATTTATGTCAGTTACATTGTAAATTTACCTATTACATTACAATTATCAGTTTCGATGTTATT
1 TATATTTATATCAGGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTT-TT
* * *
12094632 GAGATCGATACTTTTAATAAATGTATTGATACTTTATA
65 GGGATCGATACTTTTAATAAATGTATCGACACTTTATA
12094670 TTCTGGACAA
Statistics
Matches: 259, Mismatches: 36, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
197 6 0.02
198 58 0.22
199 44 0.17
200 149 0.58
201 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
TATATTTATATCAGGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTG
GGATCGATACTTTTAATAAATGTATCGACACTTTATACATGCACCCCGTTGGACATTCATTATGG
AAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATCTAGACCTAATTTCTCATAAAAC
CGA
Found at i:12094801 original size:177 final size:178
Alignment explanation
Indices: 12094495--12094834 Score: 463
Period size: 177 Copynumber: 1.9 Consensus size: 178
12094485 GCATTCATTA
* ** * *
12094495 TGGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACTTTATGCTGACCTAATTTCTTATA
1 TGGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACCTAATTTCTAATA
*
12094560 AAACCGGTATATTTATGTCAGTTACATTGTAAATTTACCTATTACATTACAATTATCAGTTTCGA
66 AAACCGGTATATTTATGACAGTTACATTGTAAATTTACCTATTACATTACAATTATCAGTTTCGA
12094625 TGTTATTGA-GATCGATACTTTTA-ATAAATGTATTGATACTTTATATTC
131 TGTT-TTGAGGATCGATACTTTTAGA-AAATGTATTGATACTTTATATTC
* * * **
12094673 TGGACAATAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGTTGACTTGTTTTCTAAT-
1 TGGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACCTAATTTCTAATA
* * * **
12094737 TAACCGGTATATTTAT-ACAGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCG
66 AAACCGGTATATTTATGACA-GTTACATTGTAAATTTACCTATTACATTACAATTATCAGTTTCG
* *
12094801 ATGTTTTTAGGGTCGATACTTTTAGAAAATGTAT
130 ATGTTTTGAGGATCGATACTTTTAGAAAATGTAT
12094835 CGACACCTAT
Statistics
Matches: 141, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
176 5 0.04
177 81 0.57
178 55 0.39
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (178 bp):
TGGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACCTAATTTCTAATA
AAACCGGTATATTTATGACAGTTACATTGTAAATTTACCTATTACATTACAATTATCAGTTTCGA
TGTTTTGAGGATCGATACTTTTAGAAAATGTATTGATACTTTATATTC
Found at i:12097353 original size:19 final size:19
Alignment explanation
Indices: 12097308--12097356 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12097298 TTACATTCAC
12097308 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
** *
12097327 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
12097346 ATACAAAATTA
1 ATACAAAATTA
12097357 ACCCTACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:12099515 original size:18 final size:18
Alignment explanation
Indices: 12099469--12099516 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
12099459 GATACATTTG
* *
12099469 CTGAAATTTATATTGAAA
1 CTGAAATTCAAATTGAAA
* *
12099487 CTCAAACTCAAATTGAAA
1 CTGAAATTCAAATTGAAA
*
12099505 TTGAAATTCAAA
1 CTGAAATTCAAA
12099517 CTCCAATTAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.31
Consensus pattern (18 bp):
CTGAAATTCAAATTGAAA
Found at i:12100825 original size:3 final size:3
Alignment explanation
Indices: 12100810--12100853 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
12100800 ACTTGTTTGG
* * * *
12100810 ATC ATC ATA ATC ATC ATC ATC ATC ATC ATA ATC TTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
12100854 TGACCTCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:12101998 original size:18 final size:17
Alignment explanation
Indices: 12101977--12102019 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
12101967 TGATTTTCTC
12101977 AGAAGAAGCGATTGT-TTG
1 AGAAGAAG-G-TTGTGTTG
12101995 AGAAGAAGGTTGTGGTTG
1 AGAAGAAGGTTGT-GTTG
12102013 AGAAGAA
1 AGAAGAA
12102020 CTGGGTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 1 0.04
18 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.23
Consensus pattern (17 bp):
AGAAGAAGGTTGTGTTG
Found at i:12102803 original size:203 final size:199
Alignment explanation
Indices: 12102325--12102829 Score: 575
Period size: 199 Copynumber: 2.5 Consensus size: 199
12102315 CACGATTTTT
* * * * * *
12102325 AAAATGATATCGACACAAATTTAACAATTGTCGATAC-TTTATACTA-ACTTATTTTCTCATAAA
1 AAAATG-TATCGACACAAATTAAAAAAGTGTCGATACATTT-T-CTAGACATATTCTCACATAAA
* * * * * * *
12102388 ACCGGTATATTTATATCGGTTACATTGAAAATTTACCAATTACATTATAATTATCAGTTTCGATG
63 ACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATAACATTACAATCATCAGTTTCAATG
* * *
12102453 TTTTTGGGATCGACACTTTTTAAAAATGTATCGACACTTAATGGGTACACCCTTTTGGCATTCAT
128 TTTCTGGGATCGACACTTTTTAAAAATGTATCGACAATTAATGCGTACACCCTTTTGGCATTCAT
*
12102518 TCTGGAC
193 TCCGGAC
* * * ** * * * * *
12102525 AAAAAGTATCCAAACAAATTCCATAAGTATCGATACATTTTCTAGACCTATTCTCGCATAAAACT
1 AAAATGTATCGACACAAATTAAAAAAGTGTCGATACATTTTCTAGACATATTCTCACATAAAACC
* * **
12102590 GGTATATTTATACCAGTTATATTGAAAAATTACCTATAACATTACAATCATGGGTTTCAATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATAACATTACAATCATCAGTTTCAATGTTT
* * * * * *
12102655 CTGGGATCGATACTTTTTATAAATGTATCGACAATTTATGCGTGCACCATTTTTTGGGCATTTAT
131 CTGGGATCGACACTTTTTAAAAATGTATCGACAATTAATGCGTACACC--CTTTT-GGCATTCAT
12102720 TCCGGAC
193 TCCGGAC
*
12102727 AAAATGTATCGACACATAATTAAAAAAGTGTCGATACATTTTGTAGACATATTCTCACATAAAAC
1 AAAATGTATCGACACA-AATTAAAAAAGTGTCGATACATTTTCTAGACATATTCTCACATAAAAC
12102792 CGGTATATTTATACCGGTTACATT-ACAAAATTACCTAT
65 CGGTATATTTATACCGGTTACATTGA-AAAATTACCTAT
12102830 TATATTATAA
Statistics
Matches: 252, Mismatches: 46, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
198 3 0.01
199 135 0.54
200 8 0.03
201 4 0.02
202 28 0.11
203 74 0.29
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (199 bp):
AAAATGTATCGACACAAATTAAAAAAGTGTCGATACATTTTCTAGACATATTCTCACATAAAACC
GGTATATTTATACCGGTTACATTGAAAAATTACCTATAACATTACAATCATCAGTTTCAATGTTT
CTGGGATCGACACTTTTTAAAAATGTATCGACAATTAATGCGTACACCCTTTTGGCATTCATTCC
GGAC
Found at i:12103223 original size:199 final size:200
Alignment explanation
Indices: 12102861--12103249 Score: 572
Period size: 199 Copynumber: 1.9 Consensus size: 200
12102851 TTTATTTGTG
* * ** *
12102861 CACCCTTTTGGGCATTCCTTCTGGACAAACAATATTAACACAAATTCCATAAGTGTCGATACATT
1 CACCATTTTGGGCATTCATTCTGGACAAACAATAACAACACAAATTCCAAAAGTGTCGATACATT
* *
12102926 ATGTAGACATATTCTCTCATAAAAACGGTATAGTTTTACCGGTTACGTTGAAAAATTACCTATTA
66 ATGTAGACATATTCTCACATAAAAACGGTATAGTTTTACCGGTTACATTGAAAAATTACCTATTA
*
12102991 CATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT
131 CATTATAATTATGGGTTTCAATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT
12103056 GCGTT
196 GCGTT
* * *
12103061 CACCATTTTGGG-ATTCATTCTGGACAAA-AAGTAACGACACCAATTTCAAAAGTGTCGATACAT
1 CACCATTTTGGGCATTCATTCTGGACAAACAA-TAACAACACAAATTCCAAAAGTGTCGATACAT
* *
12103124 TATGTAGACCTATTCTCACAT-AAAACTGGTATA-TTTATACCGGTTATATT-ACAAAATTACCT
65 TATGTAGACATATTCTCACATAAAAAC-GGTATAGTTT-TACCGGTTACATTGA-AAAATTACCT
* *
12103186 ATTACATTATAATTATGGGTTTCAATGTTTTTGGGATCGATATTTTTTATAAATGTATCGACAC
127 ATTACATTATAATTATGGGTTTCAATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACAC
12103250 ATCTGCTTAC
Statistics
Matches: 170, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
198 11 0.06
199 148 0.87
200 11 0.06
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
CACCATTTTGGGCATTCATTCTGGACAAACAATAACAACACAAATTCCAAAAGTGTCGATACATT
ATGTAGACATATTCTCACATAAAAACGGTATAGTTTTACCGGTTACATTGAAAAATTACCTATTA
CATTATAATTATGGGTTTCAATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT
GCGTT
Found at i:12103290 original size:15 final size:15
Alignment explanation
Indices: 12103266--12103304 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12103256 TTACATATTT
*
12103266 TTTGGAAACTTTACG
1 TTTGGGAACTTTACG
*
12103281 TTTGTGAACTTTACG
1 TTTGGGAACTTTACG
12103296 TTTGGGAAC
1 TTTGGGAAC
12103305 CATACTGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (15 bp):
TTTGGGAACTTTACG
Found at i:12103643 original size:19 final size:19
Alignment explanation
Indices: 12103621--12103663 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
12103611 TCATATATAG
12103621 AATTATAAATCGTATACAA
1 AATTATAAATCGTATACAA
*
12103640 AATTATAAATCTTATACAA
1 AATTATAAATCGTATACAA
12103659 AATTA
1 AATTA
12103664 ACCCTACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTATAAATCGTATACAA
Found at i:12105269 original size:15 final size:16
Alignment explanation
Indices: 12105217--12105302 Score: 59
Period size: 18 Copynumber: 5.0 Consensus size: 16
12105207 TTCCTCCTCA
*
12105217 TTTCCTCCATCTTTTC
1 TTTCTTCCATCTTTTC
12105233 -TTCTTTCTCTATCTTTTC
1 TTTC-TTC-C-ATCTTTTC
*
12105251 TTCTTTCTCCATCTTTTC
1 TT-TCT-TCCATCTTTTC
12105269 TTCTTCTTCCATCTTTTC
1 -T-TTCTTCCATCTTTTC
*
12105287 -TTCTTCACATTTTTTC
1 TTTCTTC-CATCTTTTC
12105303 AGTTCATTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
15 9 0.16
16 10 0.18
17 1 0.02
18 27 0.47
19 6 0.11
20 4 0.07
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCTTCCATCTTTTC
Found at i:12105292 original size:18 final size:18
Alignment explanation
Indices: 12105221--12105291 Score: 117
Period size: 18 Copynumber: 3.9 Consensus size: 18
12105211 TCCTCATTTC
12105221 CTCCATCTTTTCTTCTTT
1 CTCCATCTTTTCTTCTTT
*
12105239 CTCTATCTTTTCTTCTTT
1 CTCCATCTTTTCTTCTTT
12105257 CTCCATCTTTTCTTC-TT
1 CTCCATCTTTTCTTCTTT
12105274 CTTCCATCTTTTCTTCTT
1 C-TCCATCTTTTCTTCTT
12105292 CACATTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 3 0.06
18 45 0.92
19 1 0.02
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (18 bp):
CTCCATCTTTTCTTCTTT
Found at i:12105514 original size:33 final size:33
Alignment explanation
Indices: 12105477--12105576 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
12105467 CCATCTTAAG
12105477 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
* * *
12105510 TTCACCCCTCAACACCTCAATTTTTTTCACCAA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
12105543 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
12105576 T
1 T
12105577 CTATCTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:12105635 original size:21 final size:21
Alignment explanation
Indices: 12105610--12105653 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12105600 TCCCTTATGC
* *
12105610 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTCTCTCTCCGACT
12105631 CTCTCAAGTCTCTCTCCGACT
1 CTCTCAAGTCTCTCTCCGACT
12105652 CT
1 CT
12105654 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.39, G:0.11, T:0.36
Consensus pattern (21 bp):
CTCTCAAGTCTCTCTCCGACT
Found at i:12108352 original size:182 final size:182
Alignment explanation
Indices: 12108104--12108637 Score: 822
Period size: 182 Copynumber: 2.9 Consensus size: 182
12108094 TTCGAGATAG
*
12108104 GTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACT
1 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
12108169 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAAAGTGTCGATACTTATATTAAATTATCG
66 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
*
12108234 ACAATTTAAATATATTCGGTCGCTCTATACTGATTTTGTCCTTTAGAGACCA
131 ACAATTTCAATATATTCGGTCGCTCTATACTGATTTTGTCCTTTAGAGACCA
* * *
12108286 GTTTTGTCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTGTTATAAAGTATCAACACT
1 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* * *
12108351 TTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCA
66 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
* * * * * *
12108416 ACAGTTTCAATATA-TCTGGTCAC-CTTATACCGGTTTTTTCCTTTAGAGACCG
131 ACAATTTCAATATATTC-GGTCGCTC-TATACTGATTTTGTCCTTTAGAGACCA
* *
12108468 GTTTTGTCATATTTTTATCTGTTATATCGTTGTGGATCAATACATTGTTATAAAGTATCGACACT
1 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
*
12108533 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
66 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
* * *
12108598 ACACTTTCAATATATAT-GGTCGTTCTATACTGTTTTTGTC
131 ACAATTTCAATATAT-TCGGTCGCTCTATACTGATTTTGTC
12108638 ATATTTTTAC
Statistics
Matches: 316, Mismatches: 31, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
181 3 0.01
182 311 0.98
183 1 0.00
184 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
ACAATTTCAATATATTCGGTCGCTCTATACTGATTTTGTCCTTTAGAGACCA
Found at i:12108736 original size:162 final size:162
Alignment explanation
Indices: 12108469--12108774 Score: 551
Period size: 162 Copynumber: 1.9 Consensus size: 162
12108459 TAGAGACCGG
12108469 TTTTGTCATATTTTTATCTGTTATATCGTTGTGGATCAATACATTGTTATAAAGTATCGACACTT
1 TTTTGTCATATTTTTATCTGTTATATCGTTGTGGATCAATACATTGTTATAAAGTATCGACACTT
*
12108534 TATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCGA
66 TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCGA
12108599 CACTTTCAATATATATGGTCGTTCTATACTGT
131 CACTTTCAATATATATGGTCGTTCTATACTGT
*
12108631 TTTTGTCATATTTTTA-CTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
1 TTTTGTCATATTTTTATC-TGTTATATCGTTGTGGATCAATACATTGTTATAAAGTATCGACACT
* * *
12108695 TTATAGGCTCTGAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCT
65 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCG
12108760 ACACTTTCAATATAT
130 ACACTTTCAATATAT
12108775 TCGGTACCGC
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
161 1 0.01
162 137 0.99
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (162 bp):
TTTTGTCATATTTTTATCTGTTATATCGTTGTGGATCAATACATTGTTATAAAGTATCGACACTT
TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTATCGA
CACTTTCAATATATATGGTCGTTCTATACTGT
Found at i:12131016 original size:202 final size:202
Alignment explanation
Indices: 12130670--12131073 Score: 808
Period size: 202 Copynumber: 2.0 Consensus size: 202
12130660 GAACAAATAA
12130670 ATAACACTCAAGAATGTATACAATTGAGCACAAATAGTGTTCTTGAAAGCAACAAGAATATTGAA
1 ATAACACTCAAGAATGTATACAATTGAGCACAAATAGTGTTCTTGAAAGCAACAAGAATATTGAA
12130735 TGGAAATAGGCTTGAAAATGCTCAAACAATAAGTTTAGGGCTTTCTCTTTGATTCTCTAGCTTCT
66 TGGAAATAGGCTTGAAAATGCTCAAACAATAAGTTTAGGGCTTTCTCTTTGATTCTCTAGCTTCT
12130800 CTTCTTAATTGTTGTTGATCAATGGCTTCAGAACTTGTTTAAATACACATTTGATCACTTCTGAA
131 CTTCTTAATTGTTGTTGATCAATGGCTTCAGAACTTGTTTAAATACACATTTGATCACTTCTGAA
12130865 CGTTGGG
196 CGTTGGG
12130872 ATAACACTCAAGAATGTATACAATTGAGCACAAATAGTGTTCTTGAAAGCAACAAGAATATTGAA
1 ATAACACTCAAGAATGTATACAATTGAGCACAAATAGTGTTCTTGAAAGCAACAAGAATATTGAA
12130937 TGGAAATAGGCTTGAAAATGCTCAAACAATAAGTTTAGGGCTTTCTCTTTGATTCTCTAGCTTCT
66 TGGAAATAGGCTTGAAAATGCTCAAACAATAAGTTTAGGGCTTTCTCTTTGATTCTCTAGCTTCT
12131002 CTTCTTAATTGTTGTTGATCAATGGCTTCAGAACTTGTTTAAATACACATTTGATCACTTCTGAA
131 CTTCTTAATTGTTGTTGATCAATGGCTTCAGAACTTGTTTAAATACACATTTGATCACTTCTGAA
12131067 CGTTGGG
196 CGTTGGG
12131074 GGTCATTAGT
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 202 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (202 bp):
ATAACACTCAAGAATGTATACAATTGAGCACAAATAGTGTTCTTGAAAGCAACAAGAATATTGAA
TGGAAATAGGCTTGAAAATGCTCAAACAATAAGTTTAGGGCTTTCTCTTTGATTCTCTAGCTTCT
CTTCTTAATTGTTGTTGATCAATGGCTTCAGAACTTGTTTAAATACACATTTGATCACTTCTGAA
CGTTGGG
Found at i:12131359 original size:20 final size:20
Alignment explanation
Indices: 12131334--12131387 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
12131324 CGAAATATGG
12131334 GTGTATCGGTACATACAGGA
1 GTGTATCGGTACATACAGGA
12131354 GTGTATCGGTACATACAGGA
1 GTGTATCGGTACATACAGGA
12131374 GTGTATCGGTACAT
1 GTGTATCGGTACAT
12131388 CCCTTTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
GTGTATCGGTACATACAGGA
Found at i:12131682 original size:13 final size:13
Alignment explanation
Indices: 12131664--12131696 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
12131654 TAAGATTTTC
12131664 TTTGAAAATCATT
1 TTTGAAAATCATT
12131677 TTTG-AAATCATT
1 TTTGAAAATCATT
12131689 TTTGAAAA
1 TTTGAAAA
12131697 ATTACTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:12131951 original size:17 final size:18
Alignment explanation
Indices: 12131929--12131965 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12131919 GCAAAAATTA
12131929 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
12131946 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
12131964 AT
1 AT
12131966 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:12132783 original size:19 final size:17
Alignment explanation
Indices: 12132759--12132805 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
12132749 GGACCCTTAG
*
12132759 TGCATCGGTGCACTAAGAA
1 TGCATCGATGCA-TAA-AA
12132778 TGCATCGATGCATAAAA
1 TGCATCGATGCATAAAA
12132795 TGCATTCGATG
1 TGCA-TCGATG
12132806 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATAAAA
Found at i:12132975 original size:65 final size:64
Alignment explanation
Indices: 12132778--12132984 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 64
12132768 GCACTAAGAA
* * *
12132778 TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAACCA-GAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTC-AATTAACTATGAGTGCATCGATGCATGGATGG
* * * * *
12132842 GGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTCTGAGTGCATCGATGCATAGTAT
1 TGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAACTATGAGTGCATCGATGCAT-GGAT
12132906 -G
63 GG
* *
12132907 TGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCTATG-GTGCATCGATGCATGGATC
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-ACTATGAGTGCATCGATGCATGGAT-
12132970 GG
63 GG
*
12132972 TGCATCGGTGCAT
1 TGCATCGATGCAT
12132985 CACTTTGAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
63 7 0.06
64 45 0.38
65 65 0.55
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAATTAACTATGAGTGCATCGATGCATGGATGG
Found at i:12133449 original size:2 final size:2
Alignment explanation
Indices: 12133442--12133491 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
12133432 AACATAGCCA
12133442 AT AT AT AT AT AT AT AT AT AT AT AT -T 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 AT AT AT AT AT
12133483 AT AT AT AT A
1 AT AT AT AT A
12133492 GCTTAAGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12135698 original size:21 final size:22
Alignment explanation
Indices: 12135640--12135723 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 22
12135630 AAAACCCGAT
12135640 GGATGCATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
* * *
12135662 GGCATGCATCGGTGCACCTTCAT
1 GG-ATGCATCGATGCACATTCAA
*
12135685 GG-TGTATCGATGCACATTCAAA
1 GGATGCATCGATGCACATTC-AA
12135707 GGGATGCATCGATGCAC
1 -GGATGCATCGATGCAC
12135724 TGTTAAGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 14 0.28
22 3 0.06
23 21 0.42
24 12 0.24
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (22 bp):
GGATGCATCGATGCACATTCAA
Found at i:12135734 original size:44 final size:44
Alignment explanation
Indices: 12135646--12135742 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
12135636 CGATGGATGC
* *
12135646 ATCGATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
* *
12135690 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCATGCATCGATGCACCT-TCATAGTGT
12135734 ATCGATGCA
1 ATCGATGCA
12135743 TGAAGCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 29 0.62
45 18 0.38
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
Found at i:12138978 original size:100 final size:100
Alignment explanation
Indices: 12138800--12138997 Score: 387
Period size: 100 Copynumber: 2.0 Consensus size: 100
12138790 ATTGTATTCA
*
12138800 ATGTCAATGACTTTACAACCATTAGTTTCAAACATGACATTGAATCCCTTATCACATAATTGACT
1 ATGTAAATGACTTTACAACCATTAGTTTCAAACATGACATTGAATCCCTTATCACATAATTGACT
12138865 AATACTCAAAAGATTATACTTTAACCCATTCACAT
66 AATACTCAAAAGATTATACTTTAACCCATTCACAT
12138900 ATGTAAATGACTTTACAACCATTAGTTTCAAACATGACATTGAATCCCTTATCACATAATTGACT
1 ATGTAAATGACTTTACAACCATTAGTTTCAAACATGACATTGAATCCCTTATCACATAATTGACT
12138965 AATACTCAAAAGATTATACTTTAACCCATTCAC
66 AATACTCAAAAGATTATACTTTAACCCATTCAC
12138998 GTATAAAATA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (100 bp):
ATGTAAATGACTTTACAACCATTAGTTTCAAACATGACATTGAATCCCTTATCACATAATTGACT
AATACTCAAAAGATTATACTTTAACCCATTCACAT
Found at i:12141564 original size:19 final size:17
Alignment explanation
Indices: 12141540--12141586 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
12141530 GGACCCTTAG
*
12141540 TGCATCGGTGCACTAAGAA
1 TGCATCGATGCA-TAA-AA
12141559 TGCATCGATGCATAAAA
1 TGCATCGATGCATAAAA
12141576 TGCATTCGATG
1 TGCA-TCGATG
12141587 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATAAAA
Found at i:12141630 original size:64 final size:63
Alignment explanation
Indices: 12141559--12141765 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
12141549 GCACTAAGAA
*
12141559 TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCGGAGTGCATCGATGCATGGTTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGGTTGG
* * * * *
12141623 TACATCGATGCATCAAATGAATTCGATGTTTTCATAAA-ACTCTGAATGCATCGATGCATAGTAT
1 TGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGT-T
12141687 -G
62 GG
* * * *
12141688 TGCATCGATGCATGAAATGCATTCTATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATT
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCATGG-TT
12141751 GG
62 GG
*
12141753 TGCATCGGTGCAT
1 TGCATCGATGCAT
12141766 CACTTTGAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 43 0.36
65 66 0.56
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGTTGG
Found at i:12144090 original size:13 final size:13
Alignment explanation
Indices: 12144067--12144092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12144057 TTTTATTTGA
12144067 ACATATTATTAAT
1 ACATATTATTAAT
12144080 ACATATTATTAAT
1 ACATATTATTAAT
12144093 TTTCACTAAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ACATATTATTAAT
Found at i:12153619 original size:16 final size:15
Alignment explanation
Indices: 12153600--12153629 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
12153590 ATCAAAATTA
12153600 AAATATATTATAAATG
1 AAATATA-TATAAATG
12153616 AAATATATATAAAT
1 AAATATATATAAAT
12153630 ATACACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AAATATATATAAATG
Found at i:12154809 original size:15 final size:16
Alignment explanation
Indices: 12154789--12154818 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12154779 CGACGGCTGG
12154789 AAACCCTAG-GGTTTC
1 AAACCCTAGTGGTTTC
12154804 AAACCCTAGTGGTTT
1 AAACCCTAGTGGTTT
12154819 ATTTTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (16 bp):
AAACCCTAGTGGTTTC
Found at i:12155189 original size:108 final size:109
Alignment explanation
Indices: 12154995--12155228 Score: 344
Period size: 108 Copynumber: 2.2 Consensus size: 109
12154985 GTCTACAATT
* * **
12154995 AACATATTAGGTTGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGGGGCTTTAGAAATCTGACG
1 AACATATTAGGTTGCGCATAAAATGTTACCAAAGTTTAAGCTGATGGGGCCTTAGAAATCCCACG
* * *
12155060 ATAACAAAATATGTTAAATACTTATTTTGTTATAAAT-ATTATC
66 ACAACAAAATAAGTTAAATACTTATTTTGTTATAAATAAATATC
* *
12155103 AACATATTAGGTTGTGCATAAAGTGTTACCAAAGTTTAAGCTGATGGGGCCTTAGAAATCCCACG
1 AACATATTAGGTTGCGCATAAAATGTTACCAAAGTTTAAGCTGATGGGGCCTTAGAAATCCCACG
* * *
12155168 ACAACAATATAAGTTATATACTTATTTTGTTATAAATAAATATT
66 ACAACAAAATAAGTTAAATACTTATTTTGTTATAAATAAATATC
*
12155212 AACATATTAAGTTGCGC
1 AACATATTAGGTTGCGC
12155229 CCAATAATGT
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 92 0.83
109 19 0.17
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (109 bp):
AACATATTAGGTTGCGCATAAAATGTTACCAAAGTTTAAGCTGATGGGGCCTTAGAAATCCCACG
ACAACAAAATAAGTTAAATACTTATTTTGTTATAAATAAATATC
Found at i:12156013 original size:12 final size:12
Alignment explanation
Indices: 12155996--12156020 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12155986 ATAGTGTACC
12155996 AAAAAGAAAAAA
1 AAAAAGAAAAAA
12156008 AAAAAGAAAAAA
1 AAAAAGAAAAAA
12156020 A
1 A
12156021 CACAAAATAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:12159887 original size:18 final size:18
Alignment explanation
Indices: 12159861--12159895 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12159851 TTTTAATTTA
12159861 AATTCAAATTCATTATTC
1 AATTCAAATTCATTATTC
* *
12159879 AATTTAAATTTATTATT
1 AATTCAAATTCATTATT
12159896 TCGATAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTCAAATTCATTATTC
Found at i:12167221 original size:21 final size:21
Alignment explanation
Indices: 12167172--12167223 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
12167162 TCGTGATTGT
* *
12167172 GGCCGTCACGGGCGCTATTAC
1 GGCCGTCGCGGACGCTATTAC
**
12167193 GGTTGTCGCGGACGCTATTAC
1 GGCCGTCGCGGACGCTATTAC
12167214 GGCCGTCGCG
1 GGCCGTCGCG
12167224 AGTAACTCGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.37, T:0.21
Consensus pattern (21 bp):
GGCCGTCGCGGACGCTATTAC
Found at i:12172212 original size:124 final size:124
Alignment explanation
Indices: 12172059--12172454 Score: 517
Period size: 124 Copynumber: 3.2 Consensus size: 124
12172049 ACAATACAAG
* * * * *
12172059 CTTGGATTTCAACTTCACGACAAAGGATATTCAAGTTAAGGCTCAACTTCACAATGAATAGTTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTTAACTTCACAACGAATGGGTCA
* *
12172124 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTAACCAGTAACATTCATCTTCAA
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAA
* *
12172183 CTTGGATTTCAACTTCACGACGAATGATATTCAAGTTAAAGCTTAACTTCACAACGAATGGGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTTAACTTCACAACGAATGGGTCA
* * * * * *
12172248 TCTACGGTTTCAACTTCACAACAAATGGAATCGTGCTCACTAGCAACATTCATCTTTAGA
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCA-A
* * * * *
12172308 -TTGGATTTCAACTTCACGACGAAGGATATCCAATTTGAGGCTTAACTTCACAACGAAGGGGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTTAACTTCACAACGAATGGGTCA
* * * *
12172372 TCCATGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAATATTCATCTTC-A
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAA
* * *
12172430 GTGTGGATTTTAACTTCACAACGAA
1 CT-TGGATTTCAACTTCACGACGAA
12172455 TGACGTCCAA
Statistics
Matches: 235, Mismatches: 34, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
122 1 0.00
123 1 0.00
124 232 0.99
125 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (124 bp):
CTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTTAACTTCACAACGAATGGGTCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAA
Found at i:12172496 original size:124 final size:122
Alignment explanation
Indices: 12172060--12172516 Score: 482
Period size: 124 Copynumber: 3.7 Consensus size: 122
12172050 CAATACAAGC
* * * * * * * **
12172060 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTTAAGGCTCAACTTCACAATGAATAGTTCAT
1 TTGGATTTCAACTTCACGACGAATGATATCCAA-TTAAAGCTTAACTTCACAACGAATGGGCCAT
* * *
12172125 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTAACCAGTAACATTCATCTTCAAC
65 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTC-AG
* *
12172184 TTGGATTTCAACTTCACGACGAATGATATTCAAGTTAAAGCTTAACTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTCACGACGAATGATATCCAA-TTAAAGCTTAACTTCACAACGAATGGGCCAT
* * * * * *
12172249 CTACGGTTTCAACTTCACAACAAATGGAATCGTGCTCACTAGCAACATTCATCTTTAG
65 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAG
* * * *
12172307 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTTGAGGCTTAACTTCACAACGAAGGGGCCA
1 -TTGGATTTCAACTTCACGACGAATGATATCCAA-TTAAAGCTTAACTTCACAACGAATGGGCCA
* * * *
12172372 TCCATGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAATATTCATCTTCAG
64 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAG
* * ** * * * * *
12172431 TGTGGATTTTAACTTCACAACGAATGACGTCCAATTAAAAGCTCAATTTCATAGCGAATGAGCCA
1 T-TGGATTTCAACTTCACGACGAATGATATCCAATT-AAAGCTTAACTTCACAACGAATGGGCCA
* ***
12172496 TCTATAATTTCAACTTCACGA
64 TCCACGGTTTCAACTTCACGA
12172517 AGAAAGATAT
Statistics
Matches: 281, Mismatches: 49, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
123 4 0.01
124 277 0.99
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (122 bp):
TTGGATTTCAACTTCACGACGAATGATATCCAATTAAAGCTTAACTTCACAACGAATGGGCCATC
CACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTCAG
Found at i:12172509 original size:248 final size:248
Alignment explanation
Indices: 12172060--12172514 Score: 599
Period size: 248 Copynumber: 1.8 Consensus size: 248
12172050 CAATACAAGC
* * * **
12172060 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTTAAGGCTCAACTTCACAATGAATAGTTCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGAGGCCAT
* * *
12172125 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTAACCAGTAACATTCATCTTCAACTTGGAT
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCAACCAGCAACATTCATCTTCAACTTGGAT
* * * * * * **
12172190 TTCAACTTCACGACGAATGATATTCAAGTTAAAGCTTAACTTCACAACGAATGGGTCATCTACGG
131 TTCAACTTCACAACGAATGACATCCAAGTTAAAGCTCAACTTCACAACGAATGAGCCATCTACAA
12172255 TTTCAACTTCACAACAAATGGAATCGTGCTCACTAGCAACATTCATCTTTAGA
196 TTTCAACTTCACAACAAATGGAATCGTGCTCACTAGCAACATTCATCTTTAGA
* * * * *
12172308 TTGGATTTCAACTTCACGACGAAGGATATCCAATTTGAGGCTTAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGAGGCCAT
* * * *
12172373 CCATGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAATATTCATCTTC-AGTGTGGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCAACCAGCAACATTCATCTTCAACT-TGGA
* * * * * *
12172437 TTTTAACTTCACAACGAATGACGTCCAA-TTAAAAGCTCAATTTCATAGCGAATGAGCCATCTAT
130 TTTCAACTTCACAACGAATGACATCCAAGTT-AAAGCTCAACTTCACAACGAATGAGCCATCTAC
12172501 AATTTCAACTTCAC
194 AATTTCAACTTCAC
12172515 GAAGAAAGAT
Statistics
Matches: 174, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
247 4 0.02
248 170 0.98
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (248 bp):
TTGGATTTCAACTTCACGACAAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGAGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCAACCAGCAACATTCATCTTCAACTTGGAT
TTCAACTTCACAACGAATGACATCCAAGTTAAAGCTCAACTTCACAACGAATGAGCCATCTACAA
TTTCAACTTCACAACAAATGGAATCGTGCTCACTAGCAACATTCATCTTTAGA
Found at i:12172740 original size:21 final size:21
Alignment explanation
Indices: 12172716--12172850 Score: 74
Period size: 21 Copynumber: 7.3 Consensus size: 21
12172706 ACTTAAAACA
12172716 AAGTTTTGTCTCTCTTGAGAC
1 AAGTTTTGTCTCTCTTGAGAC
*
12172737 AAG---T-T-TCTCTTGAAAC
1 AAGTTTTGTCTCTCTTGAGAC
12172753 ATA-TTTTGTCTCTCTTGAGAC
1 A-AGTTTTGTCTCTCTTGAGAC
*
12172774 -AG--TT-TC-C-CTTGAAAC
1 AAGTTTTGTCTCTCTTGAGAC
*
12172789 AAATTTTGTCTCTCTTGAGAC
1 AAGTTTTGTCTCTCTTGAGAC
*
12172810 -AG--TT-TC-C-CTTGAAAC
1 AAGTTTTGTCTCTCTTGAGAC
* *
12172825 AAATTTTGTCTCCCTTGAGAC
1 AAGTTTTGTCTCTCTTGAGAC
12172846 -AGTTT
1 AAGTTT
12172851 CTCTTGAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 39
0.63 0.07 0.29
Matches are distributed among these distances:
15 14 0.16
16 15 0.18
17 6 0.07
18 9 0.11
19 6 0.07
20 8 0.09
21 27 0.32
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (21 bp):
AAGTTTTGTCTCTCTTGAGAC
Found at i:12172785 original size:36 final size:36
Alignment explanation
Indices: 12172684--12172863 Score: 263
Period size: 36 Copynumber: 4.9 Consensus size: 36
12172674 AAATAAGGGG
** *
12172684 TTGTCTCTCTTGAGACTA-TTTTACTTAAAACAAAGTT
1 TTGTCTCTCTTGAGAC-AGTTTCCCTTGAAACAAA-TT
* *
12172721 TTGTCTCTCTTGAGACAAGTTTCTCTTGAAACATATT
1 TTGTCTCTCTTGAGAC-AGTTTCCCTTGAAACAAATT
12172758 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
12172794 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
* *
12172830 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
12172864 ATCTTTGAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
36 86 0.65
37 35 0.26
38 12 0.09
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
Found at i:12172989 original size:58 final size:58
Alignment explanation
Indices: 12172881--12173000 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 58
12172871 AATATGTATT
* ** * * *
12172881 TCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTC
1 TCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTC
* *
12172939 TCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTC
1 TCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTC
12172997 TCTT
1 TCTT
12173001 GAGACAGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (58 bp):
TCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTC
Found at i:12172999 original size:37 final size:36
Alignment explanation
Indices: 12172944--12173021 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 36
12172934 GTCTCTCTTA
* *
12172944 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTAG
*
12172980 AAACAAAGTTTTATCTCTCTTGAGACAGTTTCTCTAG
1 AAACAAA-TTTTATCTCTCTTGAGACAGTTTCCCTAG
12173017 AAACA
1 AAACA
12173022 CCAACCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 7 0.18
37 31 0.82
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (36 bp):
AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTAG
Found at i:12173926 original size:23 final size:23
Alignment explanation
Indices: 12173900--12173977 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
12173890 CACCACAGCT
12173900 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
12173923 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
12173946 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
12173969 TATAATAAT
1 CAT-ATAAT
12173978 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:12174147 original size:103 final size:103
Alignment explanation
Indices: 12173984--12174201 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
12173974 TAATGTCCAT
* *
12173984 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
12174049 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
12174087 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
12174152 GACTTCACACATGTTTCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
12174190 AAGGACCACATA
1 AAGGACCACATA
12174202 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12179566 original size:23 final size:23
Alignment explanation
Indices: 12179540--12179606 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
12179530 CACCACAACT
12179540 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
12179563 CATATAATTGCACCGGAGTGTCG
1 CATATAATTGCACCGAAGTGCCA
* * *
12179586 CGTAGAATTGCACCGTAGTGC
1 CATATAATTGCACCGAAGTGC
12179607 TATATAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:12179795 original size:103 final size:103
Alignment explanation
Indices: 12179624--12179824 Score: 375
Period size: 103 Copynumber: 2.0 Consensus size: 103
12179614 TAATGTCCAT
* *
12179624 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
12179689 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
12179727 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
12179792 GACTTCACACATGTTCCAAAGAATACATATATG
66 GACTTCACACATGTTCCAAAGAATACATATATG
12179825 CCAACTATAC
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12180737 original size:64 final size:63
Alignment explanation
Indices: 12180585--12180746 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 63
12180575 TTCCCTATCG
* * ** * ** *
12180585 GTGCATCGATGCACTACATGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
* * * *
12180648 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTT-TTAGATTAAAA
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACCAAATACATTCGATGTTTGTT-GATT-AAA
12180711 GA
62 GA
*
12180713 GTGCATCGATGCACTACCTGTGCATCGATACACC
1 GTGCATCGATGCACTACCTGTGCATCGATGCACC
12180747 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
63 5 0.06
64 68 0.86
65 6 0.08
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
Found at i:12181617 original size:35 final size:34
Alignment explanation
Indices: 12181556--12181675 Score: 167
Period size: 35 Copynumber: 3.6 Consensus size: 34
12181546 CCTAGAGACA
12181556 GTTTCTCTTGAAACAAAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAAAAAAAAACCTTTGAAATC
12181590 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACA-AAAAAAAACCTTTGAAATC
* *
12181625 GTTTCTCTTTG--A-AAAATAAACCCTTTGAAAAT-
1 GTTTCTC-TTGAAACAAAAAAAAACCTTTG-AAATC
12181657 GTTTCTCTTGAAACAAAAA
1 GTTTCTCTTGAAACAAAAA
12181676 GACCCTCGAG
Statistics
Matches: 77, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
31 3 0.04
32 19 0.25
33 6 0.08
34 20 0.26
35 26 0.34
36 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACAAAAAAAAACCTTTGAAATC
Found at i:12183678 original size:2 final size:2
Alignment explanation
Indices: 12183667--12183725 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
12183657 TGTAAAGTTT
12183667 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12183708 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
12183726 ACTATCTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12185082 original size:23 final size:22
Alignment explanation
Indices: 12185059--12185101 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12185049 CTAAATAAGC
12185059 CCAAAAATCGTATCTACTAAAG
1 CCAAAAATCGTATCTACTAAAG
* * *
12185081 CCTAGAATCGTATCTTCTAAA
1 CCAAAAATCGTATCTACTAAA
12185102 CTCGCGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
CCAAAAATCGTATCTACTAAAG
Found at i:12186811 original size:24 final size:23
Alignment explanation
Indices: 12186764--12186822 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
12186754 AAAATTTTAG
12186764 AAATATAAATTAAATTATCAATAA
1 AAATATAAATTAAATTAT-AATAA
12186788 AAATATAATATCTAAATTAT-ATAA
1 AAATATAA-AT-TAAATTATAATAA
* *
12186812 AGATTTAAATT
1 AAATATAAATT
12186823 TTCGAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 18 0.58
25 2 0.06
26 8 0.26
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATATAAATTAAATTATAATAA
Found at i:12190496 original size:3 final size:3
Alignment explanation
Indices: 12190490--12190564 Score: 109
Period size: 3 Copynumber: 24.7 Consensus size: 3
12190480 CTCCATTTTC
12190490 TAT TAT TAT TATT TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
12190536 TAT TAT T-T TATT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
12190565 CAAACAGGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.06
3 54 0.81
4 9 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12196006 original size:15 final size:15
Alignment explanation
Indices: 12195986--12196017 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12195976 GATCAATACC
12195986 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
12196001 TTTTGCATACATTCA
1 TTTTGCATACATGCA
12196016 TT
1 TT
12196018 ATTCATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Done.