Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1908261 original size:19 final size:18
Alignment explanation
Indices: 1908204--1908265 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
1908194 AATTAATTTA
*
1908204 TGAATTTGAAAATAAGTTC
1 TGAATTTGAAAAT-TGTTC
*
1908223 TGAATCT-AAAATTGATTTC
1 TGAATTTGAAAATTG--TTC
1908242 TGAATTTGAAAATGTGTTC
1 TGAATTTGAAAAT-TGTTC
1908261 TGAAT
1 TGAAT
1908266 CTCAAAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 23 0.64
20 5 0.14
21 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (18 bp):
TGAATTTGAAAATTGTTC
Found at i:1908272 original size:19 final size:18
Alignment explanation
Indices: 1908219--1908293 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 18
1908209 TTGAAAATAA
1908219 GTTCTGAATCTAAAAT-T
1 GTTCTGAATCTAAAATGT
*
1908236 GATTTCTGAATTTGAAAATGT
1 G--TTCTGAATCT-AAAATGT
*
1908257 GTTCTGAATCTCAAAA-GA
1 GTTCTGAATCT-AAAATGT
*
1908275 GTTATGAATCTAAAATGT
1 GTTCTGAATCTAAAATGT
1908293 G
1 G
1908294 AAAGTATTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
17 5 0.11
18 13 0.28
19 22 0.47
20 5 0.11
21 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (18 bp):
GTTCTGAATCTAAAATGT
Found at i:1912440 original size:29 final size:29
Alignment explanation
Indices: 1912374--1912448 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
1912364 GTTAGTGACC
* **
1912374 AAAATGTAAATTTTG--AAAGTTTATGGTC
1 AAAATGT-AATTTTGAAAAAGTTTAAGGAA
* *
1912402 AAAGTATAATTTTGAAAAAGTTTAAGGAA
1 AAAATGTAATTTTGAAAAAGTTTAAGGAA
1912431 AAAATGTAATGTTT-AAAA
1 AAAATGTAAT-TTTGAAAA
1912449 GTTATGTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.19
28 5 0.14
29 22 0.59
30 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAAAGTTTAAGGAA
Found at i:1914140 original size:35 final size:35
Alignment explanation
Indices: 1914100--1914178 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1914090 GTTGAGTTGT
*
1914100 TATCGAATAGCGAAATGATTTTTATAACGAATAAG
1 TATCGAATAGCGAAATGATTTTTATAACAAATAAG
1914135 TATCGAATAGCGAAATGATTTTTATAACAAATAAG
1 TATCGAATAGCGAAATGATTTTTATAACAAATAAG
1914170 TATCGAATA
1 TATCGAATA
1914179 TATTATATGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (35 bp):
TATCGAATAGCGAAATGATTTTTATAACAAATAAG
Found at i:1914732 original size:15 final size:14
Alignment explanation
Indices: 1914708--1914737 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1914698 TGAAACTACC
1914708 ATTGATTATAAATG
1 ATTGATTATAAATG
1914722 ATTGCATTATAAATG
1 ATTG-ATTATAAATG
1914737 A
1 A
1914738 CAAATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (14 bp):
ATTGATTATAAATG
Found at i:1914866 original size:19 final size:19
Alignment explanation
Indices: 1914817--1914887 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1914807 TGAAAACTAG
* *
1914817 AAAAATGAGTTATTAATAT
1 AAAAATGAGTTATGAATCT
*
1914836 -AAAATTAGGTTATGAATCT
1 AAAAATGA-GTTATGAATCT
1914855 AAAAATGAGTTATGAA-CT
1 AAAAATGAGTTATGAATCT
*
1914873 GAAAA-GAGTTATGAA
1 AAAAATGAGTTATGAA
1914888 CCTGAAATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 10 0.22
18 12 0.27
19 17 0.38
20 6 0.13
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (19 bp):
AAAAATGAGTTATGAATCT
Found at i:1914883 original size:17 final size:19
Alignment explanation
Indices: 1914844--1914894 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
1914834 ATAAAATTAG
* *
1914844 GTTATGAATCTAAAAATGA
1 GTTATGAACCTGAAAATGA
1914863 GTTATGAA-CTGAAAA-GA
1 GTTATGAACCTGAAAATGA
1914880 GTTATGAACCTGAAA
1 GTTATGAACCTGAAA
1914895 TGTGAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (19 bp):
GTTATGAACCTGAAAATGA
Found at i:1921394 original size:24 final size:24
Alignment explanation
Indices: 1921340--1921394 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1921330 GCACCATGAT
*
1921340 ATGCACAATTCTAAAGACAAGTAC
1 ATGCACCATTCTAAAGACAAGTAC
1921364 ATGCACCATTCTAAAGACAAGTAC
1 ATGCACCATTCTAAAGACAAGTAC
*
1921388 ATTCACC
1 ATGCACC
1921395 TAGACACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (24 bp):
ATGCACCATTCTAAAGACAAGTAC
Found at i:1921511 original size:14 final size:15
Alignment explanation
Indices: 1921492--1921527 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1921482 ATGCACTCAG
*
1921492 TTCATGAATG-TTGA
1 TTCATGAATGATTCA
1921506 TTCATGAATGATTCA
1 TTCATGAATGATTCA
1921521 TTCATGA
1 TTCATGA
1921528 TTTAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (15 bp):
TTCATGAATGATTCA
Found at i:1922093 original size:21 final size:20
Alignment explanation
Indices: 1922063--1922102 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1922053 TGTACATATA
1922063 TAAATCATGGAAAAAACTAAG
1 TAAATCATGG-AAAAACTAAG
* *
1922084 TAAATTATGGATAAACTAA
1 TAAATCATGGAAAAACTAA
1922103 CTTAACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (20 bp):
TAAATCATGGAAAAACTAAG
Found at i:1923048 original size:21 final size:21
Alignment explanation
Indices: 1923023--1923071 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1923013 TCTATTTTAG
*
1923023 TTTCAATACTCCCAAATTCAT
1 TTTCAACACTCCCAAATTCAT
1923044 TTTCAACACTCCCAAATTCAT
1 TTTCAACACTCCCAAATTCAT
1923065 TTTCAAC
1 TTTCAAC
1923072 TACAACATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTCAACACTCCCAAATTCAT
Found at i:1924325 original size:42 final size:42
Alignment explanation
Indices: 1924260--1924379 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
1924250 GCCCACAACC
* *
1924260 TGCACTAAGTGTCA-TGGGCATACACTCTAGTGCTAAATCACA
1 TGCACTAAGTGT-ATTGGGTATACACTCTAATGCTAAATCACA
* *
1924302 TGCACAAAGTGTATTGGGTATACACTCTAATGCTAAATCACC
1 TGCACTAAGTGTATTGGGTATACACTCTAATGCTAAATCACA
* *
1924344 TGCACTAAGTGTCTTGGGTATGCACTCTAATGCTAA
1 TGCACTAAGTGTATTGGGTATACACTCTAATGCTAA
1924380 TCCGGATATC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
TGCACTAAGTGTATTGGGTATACACTCTAATGCTAAATCACA
Found at i:1944048 original size:26 final size:26
Alignment explanation
Indices: 1944000--1944049 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1943990 GCTTTTTTAA
*
1944000 ATGTACTGCATTTGAATTATTCATAT
1 ATGTACTGCATTTGAAATATTCATAT
* *
1944026 ATGTACTGTATTTGAAATGTTCAT
1 ATGTACTGCATTTGAAATATTCAT
1944050 TAATAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (26 bp):
ATGTACTGCATTTGAAATATTCATAT
Found at i:1945733 original size:24 final size:24
Alignment explanation
Indices: 1945706--1945751 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1945696 TGTAATACAC
*
1945706 TTTTCTCTGCTCTTGCGGCACATG
1 TTTTCTATGCTCTTGCGGCACATG
*
1945730 TTTTCTATGCTCTTGTGGCACA
1 TTTTCTATGCTCTTGCGGCACA
1945752 ATCATTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTTCTATGCTCTTGCGGCACATG
Found at i:1948900 original size:21 final size:21
Alignment explanation
Indices: 1948874--1948914 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1948864 AGGGAGTTTT
1948874 ATTAT-AGAAGTATCGATACTC
1 ATTATAAG-AGTATCGATACTC
1948895 ATTATAAGAGTATCGATACT
1 ATTATAAGAGTATCGATACT
1948915 GGAGTCTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (21 bp):
ATTATAAGAGTATCGATACTC
Found at i:1961660 original size:56 final size:57
Alignment explanation
Indices: 1961593--1961749 Score: 221
Period size: 56 Copynumber: 2.8 Consensus size: 57
1961583 TTATTCAACA
* *
1961593 GTAACATTCAACTCTCCTTCTTTATTAATCCATTTTAACTTATACCG-ACCTTCTTG
1 GTAACATTCAACTCTCCTTCTTCATTGATCCATTTTAACTTATACCGAACCTTCTTG
* * *
1961649 GTAACATTCAACTCTCCTCCTTCATTGATCTATTTTAACTTATA-CGAATCTTCTTG
1 GTAACATTCAACTCTCCTTCTTCATTGATCCATTTTAACTTATACCGAACCTTCTTG
* *
1961705 GTAACATTCAACTCTTC-TCATTCATTGAGCCATTTTAACTTATAC
1 GTAACATTCAACTCTCCTTC-TTCATTGATCCATTTTAACTTATAC
1961750 GGAGTTGGAG
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
55 3 0.03
56 86 0.97
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.42
Consensus pattern (57 bp):
GTAACATTCAACTCTCCTTCTTCATTGATCCATTTTAACTTATACCGAACCTTCTTG
Found at i:1965904 original size:8 final size:8
Alignment explanation
Indices: 1965894--1965960 Score: 71
Period size: 8 Copynumber: 8.4 Consensus size: 8
1965884 CTCAACGTAT
*
1965894 ATATATAT
1 ATATATAC
1965902 ATATATAC
1 ATATATAC
*
1965910 ATACATAC
1 ATATATAC
1965918 ATATATAC
1 ATATATAC
*
1965926 ATACATAC
1 ATATATAC
*
1965934 ATACATAC
1 ATATATAC
*
1965942 ATACATAC
1 ATATATAC
* *
1965950 TTACATAC
1 ATATATAC
1965958 ATA
1 ATA
1965961 CATATATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 53 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (8 bp):
ATATATAC
Found at i:1965923 original size:16 final size:16
Alignment explanation
Indices: 1965902--1965969 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
1965892 ATATATATAT
1965902 ATATATACATACATAC
1 ATATATACATACATAC
1965918 ATATATACATACATAC
1 ATATATACATACATAC
*
1965934 ATACATACATACATAC
1 ATATATACATACATAC
* * *
1965950 TTACATACATACATAT
1 ATATATACATACATAC
1965966 ATAT
1 ATAT
1965970 TCTCTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATATACATACATAC
Found at i:1965929 original size:4 final size:4
Alignment explanation
Indices: 1965906--1965964 Score: 100
Period size: 4 Copynumber: 14.8 Consensus size: 4
1965896 ATATATATAT
* *
1965906 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC TTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1965954 ATAC ATAC ATA
1 ATAC ATAC ATA
1965965 TATATTCTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:1972853 original size:20 final size:20
Alignment explanation
Indices: 1972828--1972927 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 20
1972818 ATTAAAAATA
1972828 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
1972848 CATGAAAGGATGCCATAACTAAAAATG
1 CATGAAAGGATG-CAT---T---AAGG
1972875 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
1972895 CAAGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
1972915 CAAGAAAGGATGC
1 CATGAAAGGATGC
1972928 CATAACTAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
20 47 0.67
21 3 0.04
23 1 0.01
24 1 0.01
26 3 0.04
27 15 0.21
ACGTcount: A:0.44, C:0.12, G:0.27, T:0.17
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:1972871 original size:47 final size:47
Alignment explanation
Indices: 1972814--1972907 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
1972804 AGTTTTAGAG
* *
1972814 CATAATTAAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATACATGAAAGGATGCATTAAGGCAAGAAAGGATGC
*
1972861 CATAACTAAAAATGCATGAAAGGATGCATTAAGGCAAGAAAGGATGC
1 CATAACTAAAAATACATGAAAGGATGCATTAAGGCAAGAAAGGATGC
1972908 ATTAAGGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (47 bp):
CATAACTAAAAATACATGAAAGGATGCATTAAGGCAAGAAAGGATGC
Found at i:1972905 original size:67 final size:66
Alignment explanation
Indices: 1972831--1972978 Score: 224
Period size: 67 Copynumber: 2.2 Consensus size: 66
1972821 AAAAATACAT
* *
1972831 GAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAGGC
1 GAAAGGATGCATTAAGGCAAGAAAGGATGCCATAACT-AAAATGCATGAAAGAATGCATTAAGGC
1972896 AA
65 AA
* *
1972898 GAAAGGATGCATTAAGGCAAGAAAGGATGCCATAACTAAAATGCATGGAAGAATGCATTAAGTCA
1 GAAAGGATGCATTAAGGCAAGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAGGCA
*
1972963 T
66 A
*
1972964 GATAGGATGCCATTA
1 GAAAGGATG-CATTA
1972979 TTTAAATGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
66 33 0.45
67 41 0.55
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (66 bp):
GAAAGGATGCATTAAGGCAAGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAGGCA
A
Found at i:1974978 original size:262 final size:263
Alignment explanation
Indices: 1974512--1975036 Score: 989
Period size: 262 Copynumber: 2.0 Consensus size: 263
1974502 CACTCCCCAT
1974512 CATATTAAAAGAGGCAAGGGATCGAGTTCCAGATTTTCAGATAGACACCGTTTTGCGAAAGCTTC
1 CATATTAAAAGAGGCAAGGGATCGAGTTCCAGATTTTCAGATAGACACCGTTTTGCGAAAGCTTC
1974577 AAAGAAAAATAGAAAATCTTAGTCTTATGTTGCGAGCTCAGGTAGAGCAACAGGAGAGAAAATTC
66 AAAGAAAAATAGAAAATCTTAGTCTTATGTTGCGAGCTCAGGTAGAGCAACAGGAGAGAAAATTC
*
1974642 CATATCAGACATGTGGCAAGTTGCATAGTGGAACATGCAGACTACTCAGTGGAGCTTGTTTCCAA
131 CATATCAGACATGTGGCAAGTTGCATAGTGGAACATGCAGACTACTCAGTAGAGCTTGTTTCCAA
*
1974707 TGTGGAGAGATGGGTCACTTCGCTCGAAACTGTCCTAAGAAATATTTGGACAACTCGATGCAATC
196 TGTGGAGAGACGGGTCACTTCGCTCGAAACTGTCCTAAGAAATATTTGGACAACTCGATGCAATC
1974772 TGA
261 TGA
*
1974775 CATATTAAAAGAGGCAAGGGATCGAGTTCCATATTTTCAGATAGACACCGTTTTGCGAAAGCTTC
1 CATATTAAAAGAGGCAAGGGATCGAGTTCCAGATTTTCAGATAGACACCGTTTTGCGAAAGCTTC
*
1974840 AAAGAAAAATAGACAATCTTAGTCTTATGTTG-GAGCTCAGGTAGAGCAACAGGAGAGAAAATTC
66 AAAGAAAAATAGAAAATCTTAGTCTTATGTTGCGAGCTCAGGTAGAGCAACAGGAGAGAAAATTC
*
1974904 CATGTCAGACATGTGGCAAGTTGCATAGTGGAACATGCAGACTACTCAGTAGAGCTTGTTTCCAA
131 CATATCAGACATGTGGCAAGTTGCATAGTGGAACATGCAGACTACTCAGTAGAGCTTGTTTCCAA
*
1974969 TGTGGAGAGACGGGTCACTTCGTTCGAAACTGTCCTAAGAAATATTTGGACAACTCGATGCAATC
196 TGTGGAGAGACGGGTCACTTCGCTCGAAACTGTCCTAAGAAATATTTGGACAACTCGATGCAATC
1975034 TGA
261 TGA
1975037 AAGATCAGTA
Statistics
Matches: 256, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
262 161 0.63
263 95 0.37
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (263 bp):
CATATTAAAAGAGGCAAGGGATCGAGTTCCAGATTTTCAGATAGACACCGTTTTGCGAAAGCTTC
AAAGAAAAATAGAAAATCTTAGTCTTATGTTGCGAGCTCAGGTAGAGCAACAGGAGAGAAAATTC
CATATCAGACATGTGGCAAGTTGCATAGTGGAACATGCAGACTACTCAGTAGAGCTTGTTTCCAA
TGTGGAGAGACGGGTCACTTCGCTCGAAACTGTCCTAAGAAATATTTGGACAACTCGATGCAATC
TGA
Found at i:1979101 original size:47 final size:47
Alignment explanation
Indices: 1979047--1979192 Score: 220
Period size: 47 Copynumber: 3.1 Consensus size: 47
1979037 AGTTTTAGAG
* *
1979047 CATAACTAAAAATGCATGAAAGGATGCATTAAGGTATAAAAGGATGC
1 CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
1979094 CATAACTAAAAATGCATAAAAGGATACATTAAGGCATGAAAGGATGT
1 CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
1979141 CAAAACTAAAAATGCATGAAAGAATGCATTAAGGCATGATAGGATGC
1 CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1979188 CATAA
1 CATAA
1979193 TTTAAATGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 87 1.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.21
Consensus pattern (47 bp):
CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:1980200 original size:2 final size:2
Alignment explanation
Indices: 1980181--1980226 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1980171 AGGAACCAAT
*
1980181 TA TA -A TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1980220 TA T- TA TA
1 TA TA TA TA
1980227 GTTAATGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1987592 original size:26 final size:26
Alignment explanation
Indices: 1987563--1987615 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1987553 TATCCAAATA
1987563 GAGGCTATCCTTGAACCTCCTATAGT
1 GAGGCTATCCTTGAACCTCCTATAGT
1987589 GAGGCTATCCTTGAACCTCCTATAGT
1 GAGGCTATCCTTGAACCTCCTATAGT
1987615 G
1 G
1987616 GTGAGCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (26 bp):
GAGGCTATCCTTGAACCTCCTATAGT
Found at i:1994789 original size:2 final size:2
Alignment explanation
Indices: 1994782--1994822 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1994772 ACAAATTAAC
1994782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1994823 ATCACTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1998788 original size:20 final size:20
Alignment explanation
Indices: 1998760--1998816 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1998750 ACAAAATTGG
*
1998760 CGGTTTTTTCTGATTTTTTA
1 CGGTTTTTTCCGATTTTTTA
*
1998780 CGTTTTTTTCCGATTTTTTA
1 CGGTTTTTTCCGATTTTTTA
*
1998800 CGGTTTTTTCCGGTTTT
1 CGGTTTTTTCCGATTTT
1998817 CAACCGATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.63
Consensus pattern (20 bp):
CGGTTTTTTCCGATTTTTTA
Found at i:1998813 original size:10 final size:10
Alignment explanation
Indices: 1998760--1998816 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
1998750 ACAAAATTGG
1998760 CGGTTTTTTC
1 CGGTTTTTTC
* * *
1998770 TGATTTTTTA
1 CGGTTTTTTC
*
1998780 CGTTTTTTTC
1 CGGTTTTTTC
* *
1998790 CGATTTTTTA
1 CGGTTTTTTC
1998800 CGGTTTTTTC
1 CGGTTTTTTC
1998810 CGGTTTT
1 CGGTTTT
1998817 CAACCGATCC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.63
Consensus pattern (10 bp):
CGGTTTTTTC
Found at i:2004247 original size:29 final size:31
Alignment explanation
Indices: 2004214--2004290 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
2004204 ACATTTTGGC
*
2004214 TAGTGACCAAAATATAAAATTT-GAAAA-TT
1 TAGTGACCAAAGTATAAAATTTGGAAAAGTT
*
2004243 TAGTGACCAAAGTATAAACTTTGGAAAAGTT
1 TAGTGACCAAAGTATAAAATTTGGAAAAGTT
* *
2004274 TAGGGAGCAAAGTATAA
1 TAGTGACCAAAGTATAA
2004291 TTTTCAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (31 bp):
TAGTGACCAAAGTATAAAATTTGGAAAAGTT
Found at i:2004285 original size:31 final size:29
Alignment explanation
Indices: 2004218--2004290 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
2004208 TTTGGCTAGT
* *
2004218 GACCAAAATATAAAATTTGAAAATTTAGT
1 GACCAAAGTATAAAATTTGAAAATTTAGG
*
2004247 GACCAAAGTATAAACTTTGGAAAAGTTTAGG
1 GACCAAAGTATAAAATTT-GAAAA-TTTAGG
*
2004278 GAGCAAAGTATAA
1 GACCAAAGTATAA
2004291 TTTTCAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 16 0.42
30 5 0.13
31 17 0.45
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (29 bp):
GACCAAAGTATAAAATTTGAAAATTTAGG
Found at i:2004769 original size:20 final size:20
Alignment explanation
Indices: 2004744--2004790 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
2004734 TTGTTTAGAA
2004744 ATTTCATGACAATTCTTCTC
1 ATTTCATGACAATTCTTCTC
2004764 ATTTCATGACAATTCTTCTC
1 ATTTCATGACAATTCTTCTC
2004784 ATCTTCA
1 AT-TTCA
2004791 AGCTATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.45
Consensus pattern (20 bp):
ATTTCATGACAATTCTTCTC
Found at i:2005740 original size:53 final size:52
Alignment explanation
Indices: 2005678--2005822 Score: 133
Period size: 53 Copynumber: 2.8 Consensus size: 52
2005668 ATATATATAT
* *
2005678 ACATGTATATTTGGAAAACATATA--TATATATATATATATATGGTTTTGAAAAG
1 ACATATATATTTAGAAAACATATACTTATATA-ATATATATATGGTTTTG--AAG
* * *
2005731 ATATATATATTTTA-AAAAC-TATACTTTTATAATATATATATTGTTTTGAAG
1 ACATATATA-TTTAGAAAACATATACTTATATAATATATATATGGTTTTGAAG
*
2005782 ACATATA-ATTTAGAAAA-ATATAGCGTATATAAT-TAATATAT
1 ACATATATATTTAGAAAACATATA-CTTATATAATAT-ATATAT
2005823 TATTATATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
49 4 0.05
50 10 0.13
51 23 0.30
52 4 0.05
53 28 0.36
54 8 0.10
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (52 bp):
ACATATATATTTAGAAAACATATACTTATATAATATATATATGGTTTTGAAG
Found at i:2005747 original size:18 final size:20
Alignment explanation
Indices: 2005711--2005747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2005701 ATATATATAT
*
2005711 ATATATATGGTTTTGAAAAG
1 ATATATATGATTTTGAAAAG
2005731 ATATATAT-ATTTT-AAAA
1 ATATATATGATTTTGAAAA
2005748 ACTATACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (20 bp):
ATATATATGATTTTGAAAAG
Found at i:2005813 original size:51 final size:52
Alignment explanation
Indices: 2005702--2005823 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 52
2005692 AAAACATATA
* * * *
2005702 TATATATATATATATATGGTTTTGAAAAGATATATATATTTTAAAAACTATACT
1 TATATA-ATATATATATTGTTTTG-AAAGACATATATATTTTAAAAAATATACG
*
2005756 TTTATAATATATATATTGTTTTG-AAGACATATA-A-TTTAGAAAAATATAGCG
1 TATATAATATATATATTGTTTTGAAAGACATATATATTTTA-AAAAATATA-CG
2005807 TATATAAT-TAATATATT
1 TATATAATAT-ATATATT
2005824 ATTATATTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
49 4 0.07
50 10 0.17
51 24 0.41
53 16 0.27
54 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (52 bp):
TATATAATATATATATTGTTTTGAAAGACATATATATTTTAAAAAATATACG
Found at i:2007065 original size:26 final size:25
Alignment explanation
Indices: 2007023--2007081 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
2007013 ATTTCATATC
2007023 ATTTTATTATTAATATTATTAT-TCGTT
1 ATTTT-TTATTAATATT-TTATATC-TT
*
2007050 ATTTTTTATTATTATTTTATATCTT
1 ATTTTTTATTAATATTTTATATCTT
2007075 -TTTTTTA
1 ATTTTTTA
2007082 AATACTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.23
25 6 0.20
26 12 0.40
27 5 0.17
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTTTTATTAATATTTTATATCTT
Found at i:2008173 original size:19 final size:19
Alignment explanation
Indices: 2008151--2008190 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2008141 TATGTTTAAA
2008151 TGTAATTAATATGTGTTAT
1 TGTAATTAATATGTGTTAT
*
2008170 TGTAATTAATATGTTTTAT
1 TGTAATTAATATGTGTTAT
2008189 TG
1 TG
2008191 AATATATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
TGTAATTAATATGTGTTAT
Found at i:2008343 original size:45 final size:45
Alignment explanation
Indices: 2008293--2008826 Score: 692
Period size: 45 Copynumber: 11.9 Consensus size: 45
2008283 AAAGGATGCC
* *
2008293 ATAGTTGAAATGTATATGGGTACATTATCAACGGAAAAGCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
2008338 TTAGTTGGAATATATATGGGTACATCATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** *
2008383 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
**
2008428 AT-GATTGAAATGTATATGGGTACATTATCAACAGAAAAACATACT
1 ATAG-TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2008473 TTAGTTGAAATGTATATGGGTAAATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
** * * * *
2008518 AGCGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
2008563 AGAGTTGAAATGTATATTGATACATTATCAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2008608 ATGGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTAGACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2008653 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2008698 AGAGTTGAAATGTATATGGGTACAATATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2008743 ATGGTTTAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
** * *
2008788 ATAGTTGAAATACATATGGGTGCATTATCAATAGAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
2008827 ATGTTATAGT
Statistics
Matches: 422, Mismatches: 65, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
44 1 0.00
45 420 1.00
46 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:2008503 original size:135 final size:135
Alignment explanation
Indices: 2008260--2008826 Score: 789
Period size: 135 Copynumber: 4.2 Consensus size: 135
2008250 AATACTAATG
*** * * *
2008260 CATATGGGTGCATTATTGGCATG-AAAGGATGCCATAGTTGAAATGTATATGGGTACATTATCAA
1 CATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTATCAA
* * * * *
2008324 CGGAAAAGCATACTTTAGTTGGAATATATATGGGTACATCATCAACAGAAAAGTATGCTAGAGTT
65 CAGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTT
2008389 GAAATA
130 GAAATA
*
2008395 CATATGGGTGCATTATCAACAGAAAAGTATACTATGA-TTGAAATGTATATGGGTACATTATCAA
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTA-GAGTTGAAATGTATATGGGTACATTATCAA
* * * *
2008459 CAGAAAAACATACTTTAGTTGAAATGTATATGGGTAAATTATCAACAGAAAAGTATGCTAGCGTT
65 CAGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTT
*
2008524 GAAATG
130 GAAATA
* * * *
2008530 CATATGGGTGCATTATCAATAGAAAAGTATGCTAGAGTTGAAATGTATATTGATACATTATCAAT
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTATCAAC
* * * *
2008595 AGAAAAGTATACTATGGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTA-GACTATAGTT
66 AGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATG-CTAGAGTT
*
2008659 GAAATG
130 GAAATA
*
2008665 CATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACAATATCAAC
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTATCAAC
* * * * *
2008730 AGAAAAGTATACTATGGTTTAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTG
66 AGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTG
2008795 AAATA
131 AAATA
*
2008800 CATATGGGTGCATTATCAATAGAAAAG
1 CATATGGGTGCATTATCAACAGAAAAG
2008827 ATGTTATAGT
Statistics
Matches: 389, Mismatches: 38, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
134 4 0.01
135 384 0.99
136 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (135 bp):
CATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTATCAAC
AGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTG
AAATA
Found at i:2015132 original size:45 final size:45
Alignment explanation
Indices: 2014576--2015110 Score: 703
Period size: 45 Copynumber: 11.9 Consensus size: 45
2014566 AAAGGATGTC
* ** *
2014576 ATAGTTGAAATGTATATGGGTACATTATCAACATAAAAAAATAGT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2014621 TTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
2014666 AGAGTTGAAATGTCTGTGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2014711 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAAGCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAG-AAAAGTATACT
* * *
2014757 TTAGTTGAAATGTATATGTGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
2014802 AGAATTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACC
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2014847 AGAGTTAAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2014892 ATGGTTGAAATGTATAAGGGTACATTATCTACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** * *
2014937 ATAGTTGAAATGCATATGGGTGTATTATCAACAGAAATGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
2014982 ACAGTTAAAATGTATATGTGTACATTATCAACAGAAAAGTATATT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
2015027 AT-GTTTGAAATGTATATTGGTACATTATCAACAGAAAAGTATACT
1 ATAG-TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2015072 ATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
2015111 ATGTTATATT
Statistics
Matches: 420, Mismatches: 67, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.00
45 377 0.90
46 42 0.10
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:2015171 original size:135 final size:134
Alignment explanation
Indices: 2014626--2015171 Score: 479
Period size: 135 Copynumber: 4.0 Consensus size: 134
2014616 ATAGTTTAGT
* * * *
2014626 TGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTC-TGTGGGTGCA
1 TGAAATGTATAAGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATG-CATATGGGTGCA
* ** * * * * * *
2014690 TTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAAGCATA
65 TTATCAACAGAAAAGTATGCTACAGTTAAAATGCATATGTGTA-ATTATAAACAG-AAAAGGAGA
* **
2014755 CTT-TAGT
128 -TTACAAA
* * * * *
2014762 TGAAATGTATATGTGTACATTATCAACAGAAAAGTATGCTAGAATTGAAATGCATATGGGTGCAT
1 TGAAATGTATAAGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCAT
* * * * * * * * *
2014827 TATCAACAGAAAAGTATACCAGAGTTAAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
66 TATCAACAGAAAAGTATGCTACAGTTAAAATGCATATGTGTA-ATTATAAACAGAAAAGGAGATT
****
2014892 ATGGT
130 ACAAA
* *
2014897 TGAAATGTATAAGGGTACATTATCTACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGTAT
1 TGAAATGTATAAGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCAT
* * * * *
2014962 TATCAACAGAAATGTATGCTACAGTTAAAATGTATATGTGTACATTATCAACAGAAAAGTATATT
66 TATCAACAGAAAAGTATGCTACAGTTAAAATGCATATGTGTA-ATTATAAACAGAAAAGGAGATT
****
2015027 ATGTT
130 ACAAA
**
2015032 TGAAATGTATATTGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCAT
1 TGAAATGTATAAGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCAT
* * * * * * * * *
2015097 TATCAACATAAAAG-ATGTTATATTTTAAAGTGCATACTGGTGT-ATTATAAATATAAAGGGAGG
66 TATCAACAGAAAAGTATGCTACA-GTTAAAATGCATA-T-GTGTAATTATAAACAGAAAAGGAGA
2015160 TTACAAA
128 TTACAAA
2015167 TGAAA
1 TGAAA
2015172 ATAAAGAATT
Statistics
Matches: 359, Mismatches: 46, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
134 7 0.02
135 237 0.66
136 111 0.31
137 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (134 bp):
TGAAATGTATAAGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCAT
TATCAACAGAAAAGTATGCTACAGTTAAAATGCATATGTGTAATTATAAACAGAAAAGGAGATTA
CAAA
Found at i:2021512 original size:45 final size:45
Alignment explanation
Indices: 2020946--2021478 Score: 721
Period size: 45 Copynumber: 11.9 Consensus size: 45
2020936 AAAGGATGTC
*
2020946 ATAGTTGAAATGTATATAGGTACATTATCAACAGAAAA-TCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT-ATACT
* * *
2020991 TTAGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
2021036 AGAGTTGAAATGCATGTGGGTGCATTATCAACAGAAAAATATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2021081 ATGGTTGAAATGTATATGGATACATTATCAGCAG-AAA-TCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT-ATACT
* * * *
2021125 TTAGTTGAAATATATATGGGTACATTATCAATAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
2021170 AGAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
2021215 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2021260 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATATT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
2021305 ATAATTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
2021350 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
2021395 ATGGTTGAAATGTATATGGTTACATTATCAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
2021440 ATAGTTGAAATGCATATGGGTTCATTATCAACAGAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
2021479 ATGTTATAGT
Statistics
Matches: 426, Mismatches: 58, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
43 1 0.00
44 36 0.08
45 387 0.91
46 2 0.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:2021539 original size:135 final size:135
Alignment explanation
Indices: 2020948--2021478 Score: 800
Period size: 135 Copynumber: 3.9 Consensus size: 135
2020938 AGGATGTCAT
* * *
2020948 AGTTGAAATGTATATAGGTACATTATCAACAGAAAA-TCATACTTTAGTTGAAATGTATATAGGT
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT-ATACTATAGTTGAAATGTATATGGGT
* * *
2021012 ACATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATGTGGGTGCATTATCAACAGAAAAATA
65 ACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTA
*
2021077 TACTATG
130 TGCTA-G
* * * *
2021084 -GTTGAAATGTATATGGATACATTATCAGCAG-AAA-TCATACTTTAGTTGAAATATATATGGGT
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT-ATACTATAGTTGAAATGTATATGGGT
* * *
2021146 ACATTATCAATAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTA
65 ACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTA
2021211 TGCTAG
130 TGCTAG
*
2021217 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTA
* * *
2021282 CATTATCAACAGAAAAGTATATTATAATTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT
66 CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT
2021347 GCTAG
131 GCTAG
* *
2021352 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGTTA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTA
* * *
2021417 CATTATCAATAGAAAAGTATACTATAGTTGAAATGCATATGGGTTCATTATCAACAGAAAAG
66 CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
2021479 ATGTTATAGT
Statistics
Matches: 366, Mismatches: 26, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
133 1 0.00
134 123 0.34
135 241 0.66
136 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (135 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTA
CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT
GCTAG
Found at i:2031641 original size:28 final size:28
Alignment explanation
Indices: 2031601--2031657 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2031591 TTCATGTCAC
2031601 AACTCTCGGAAAAGGGAACTTCCTTCAA
1 AACTCTCGGAAAAGGGAACTTCCTTCAA
2031629 AACTCTCGGAAAAGGGAACTTCCTTCAA
1 AACTCTCGGAAAAGGGAACTTCCTTCAA
2031657 A
1 A
2031658 GATCGCTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (28 bp):
AACTCTCGGAAAAGGGAACTTCCTTCAA
Found at i:2032974 original size:29 final size:27
Alignment explanation
Indices: 2032920--2033019 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
2032910 CTTTGAAGAC
* *
2032920 ATATATAGATGATATT-TGAAATTATAG
1 ATATATATAT-ATATTATGAAATTATAT
*
2032947 CTATATATATATATTATGAAATTATAT
1 ATATATATATATATTATGAAATTATAT
*
2032974 ATAGTAAATTATATATTATG-AA-TATAT
1 ATA-TATA-TATATATTATGAAATTATAT
* *
2033001 ATA-ACATATA-ATTTTGAAA
1 ATATATATATATATTATGAAA
2033020 ACAGATAGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
23 5 0.08
24 6 0.10
25 2 0.03
26 5 0.08
27 28 0.45
28 5 0.08
29 11 0.18
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
ATATATATATATATTATGAAATTATAT
Found at i:2033090 original size:25 final size:26
Alignment explanation
Indices: 2033024--2033095 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
2033014 TTGAAAACAG
* *
2033024 ATAGTTTTCAAAAATATATATAATATAA
1 ATAGTTTT-GAAAACATATATAATAT-A
* * *
2033052 ATAATTTCGGAAACATATATAATAT-
1 ATAGTTTTGAAAACATATATAATATA
2033077 ATAGTTTTGAAAACATATA
1 ATAGTTTTGAAAACATATA
2033096 GTTTTTAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 16 0.44
27 14 0.39
28 6 0.17
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.38
Consensus pattern (26 bp):
ATAGTTTTGAAAACATATATAATATA
Found at i:2033096 original size:16 final size:16
Alignment explanation
Indices: 2033075--2033111 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2033065 CATATATAAT
2033075 ATATAGTTTTGAAAAC
1 ATATAGTTTTGAAAAC
* *
2033091 ATATAGTTTTTAAAAT
1 ATATAGTTTTGAAAAC
2033107 ATATA
1 ATATA
2033112 ATATATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (16 bp):
ATATAGTTTTGAAAAC
Found at i:2033202 original size:17 final size:17
Alignment explanation
Indices: 2033180--2033212 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2033170 TATTATTATA
*
2033180 TTATTTTTGTTTTATTC
1 TTATTTTTATTTTATTC
2033197 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
2033213 TTTAGGTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTTTATTTTATTC
Found at i:2033759 original size:94 final size:93
Alignment explanation
Indices: 2033599--2033785 Score: 365
Period size: 94 Copynumber: 2.0 Consensus size: 93
2033589 ATTTTACGAT
2033599 TTAGAAGTTTTTTAAGAAATCGAGCACAATAAGAAAACCAAATTGAATAAAATCCAAAACTCAAG
1 TTAGAAGTTTTTTAAGAAATCGAGCACAATAAGAAAACCAAATTGAATAAAATCCAAAACTCAAG
2033664 GATATACAAGCATGCTAGTTAACAGAAC
66 GATATACAAGCATGCTAGTTAACAGAAC
2033692 TTAGAAGTTTTTTTAAGAAATCGAGCACAATAAGAAAACCAAATTGAATAAAATCCAAAACTCAA
1 TTAGAAG-TTTTTTAAGAAATCGAGCACAATAAGAAAACCAAATTGAATAAAATCCAAAACTCAA
2033757 GGATATACAAGCATGCTAGTTAACAGAAC
65 GGATATACAAGCATGCTAGTTAACAGAAC
2033786 CTAGCAAAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 7 0.08
94 86 0.92
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (93 bp):
TTAGAAGTTTTTTAAGAAATCGAGCACAATAAGAAAACCAAATTGAATAAAATCCAAAACTCAAG
GATATACAAGCATGCTAGTTAACAGAAC
Found at i:2039489 original size:29 final size:30
Alignment explanation
Indices: 2039454--2039527 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
2039444 TATGGTCAAA
*
2039454 AATCAATAAGACCACCGAACT-TTCAATTG
1 AATCAATAAGACCACCCAACTATTCAATTG
* *
2039483 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATAAGACCACCCAACTATTCAATTG
*
2039513 ATTCAATCAA-ACCAC
1 AATCAAT-AAGACCAC
2039528 TAGCCGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 19 0.50
30 18 0.47
31 1 0.03
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (30 bp):
AATCAATAAGACCACCCAACTATTCAATTG
Found at i:2039519 original size:30 final size:29
Alignment explanation
Indices: 2039454--2039527 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
2039444 TATGGTCAAA
* *
2039454 AATCAATAAGACCACCGAACTTTCAATTG
1 AATCAATCAGACCACCCAACTTTCAATTG
*
2039483 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATCAGACCACCCAACT-TTCAATTG
* *
2039513 ATTCAATCAAACCAC
1 AATCAATCAGACCAC
2039528 TAGCCGTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (29 bp):
AATCAATCAGACCACCCAACTTTCAATTG
Found at i:2040776 original size:6 final size:6
Alignment explanation
Indices: 2040757--2040788 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2040747 GTGCCCTCTC
2040757 CCCCTT CTCCCTT CCCCTT CCCCTT CCCCTT C
1 CCCCTT C-CCCTT CCCCTT CCCCTT CCCCTT C
2040789 TATATCGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCCTT
Found at i:2041282 original size:21 final size:21
Alignment explanation
Indices: 2041245--2041309 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
2041235 AAAAAGTGGG
*
2041245 TTTTTTTGTTAATAAATTAAAA
1 TTTTTTTATTAA-AAATTAAAA
*
2041267 TTTTTTTATTAAAAA-TAATA
1 TTTTTTTATTAAAAATTAAAA
2041287 TTTTTATTATTAAAAATTTAAAA
1 TTTTT-TTATTAAAAA-TTAAAA
2041310 ATTAAACCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.24
21 13 0.35
22 11 0.30
23 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTTTTATTAAAAATTAAAA
Found at i:2041983 original size:42 final size:42
Alignment explanation
Indices: 2041927--2042043 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
2041917 TTTTTTCGAA
*
2041927 TTTTCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATT
1 TTTTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
* * *
2041969 TTTTCGCGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTTTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
** *
2042011 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCG
1 TTTTCGTGTTTGTTTCACGTAATTCGTTTTCCG
2042044 GATGTAATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (42 bp):
TTTTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
Found at i:2042222 original size:58 final size:57
Alignment explanation
Indices: 2042157--2042271 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 57
2042147 GAATAAATAC
*
2042157 TCAAAATAAT-TTTATTTTATGAATTTAATATTAATAA-AATATTTTAATATCATTTTTA
1 TCAAAATAATATTTA-TTTATGAA-TTAATATTAATAATAATATTATAATAT-ATTTTTA
* ** * *
2042215 TCAAAATATTATTTATTTATTTATTAATATTTATAATAATATTATATTATATTTTTA
1 TCAAAATAATATTTATTTATGAATTAATATTAATAATAATATTATAATATATTTTTA
2042272 ATATTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
57 19 0.39
58 26 0.53
59 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (57 bp):
TCAAAATAATATTTATTTATGAATTAATATTAATAATAATATTATAATATATTTTTA
Found at i:2042256 original size:33 final size:32
Alignment explanation
Indices: 2042218--2042300 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 32
2042208 ATTTTTATCA
*
2042218 AAATATTATT-TATT-TATTTATTAATATTTAT
1 AAATAATATTATATTATATTT-TTAATATTTAT
2042249 -AATAATATTATATTATATTTTTAATATTATAT
1 AAATAATATTATATTATATTTTTAATATT-TAT
2042281 AAATAATCAATTATATTATA
1 AAATAAT--ATTATATTATA
2042301 ATAATATAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 8 0.18
31 12 0.27
32 8 0.18
33 6 0.13
35 11 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
AAATAATATTATATTATATTTTTAATATTTAT
Found at i:2042257 original size:22 final size:22
Alignment explanation
Indices: 2042232--2042280 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
2042222 ATTATTTATT
2042232 TATT-TATTAATATTTATAATAA
1 TATTATATT-ATATTTATAATAA
2042254 TATTATATTATATTT-T--TAA
1 TATTATATTATATTTATAATAA
2042273 TATTATAT
1 TATTATAT
2042281 AAATAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.42
21 1 0.04
22 10 0.38
23 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATATTATATTTATAATAA
Found at i:2042361 original size:27 final size:28
Alignment explanation
Indices: 2042331--2042393 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
2042321 TTTATTTTAA
2042331 TAATATAT-AATAAAATT-TTTATATATT
1 TAATA-ATGAATAAAATTATTTATATATT
* *
2042358 TAATAATGAATAATATTATTTATATGTT
1 TAATAATGAATAAAATTATTTATATATT
2042386 TAAATAAT
1 T-AATAAT
2042394 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 13 0.42
28 10 0.32
29 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATAATGAATAAAATTATTTATATATT
Found at i:2042388 original size:58 final size:56
Alignment explanation
Indices: 2042247--2042404 Score: 133
Period size: 58 Copynumber: 2.7 Consensus size: 56
2042237 ATTAATATTT
* *
2042247 ATAATAATATTATATTATATTTTTAATATTATATAA-ATAATCAATTATATTATAATA
1 ATAATAATATTAT-TTATA-TTTTAATAATATATAATAAAATCAATTATATTATAATA
* ** *
2042304 AT-ATAAGTTATTATATTTTTATTTTAATAATATATAATAAAAT-TTTTATATATTTAATA
1 ATAATAA--TA-T-TATTTATATTTTAATAATATATAATAAAATCAATTATAT-TATAATA
*
2042363 ATGAATAATATTATTTATATGTTTAAATAATATTTTAATAAA
1 AT-AATAATATTATTTATAT-TTT-AATAATA-TATAATAAA
2042405 GATATTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
56 4 0.05
57 10 0.12
58 27 0.33
59 26 0.32
60 11 0.13
61 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (56 bp):
ATAATAATATTATTTATATTTTAATAATATATAATAAAATCAATTATATTATAATA
Found at i:2042573 original size:20 final size:20
Alignment explanation
Indices: 2042537--2042576 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2042527 TAATAAAATT
2042537 ATAAAAAATAATATTTAATA
1 ATAAAAAATAATATTTAATA
*
2042557 ATAAATAAATTAT-TTTAATA
1 ATAAA-AAATAATATTTAATA
2042577 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATAATATTTAATA
Found at i:2042853 original size:21 final size:21
Alignment explanation
Indices: 2042811--2042853 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2042801 ATAATTCAAA
** *
2042811 TTCCAGTAATTCATTTTTCAG
1 TTCCAGTAATTCAAATTCCAG
2042832 TTCCAGTAATTCAAATTCCAG
1 TTCCAGTAATTCAAATTCCAG
2042853 T
1 T
2042854 AATTCATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:2042865 original size:15 final size:15
Alignment explanation
Indices: 2042787--2042867 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
2042777 TTCCAGAAAT
2042787 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
2042802 -TAATTCAAATTCCA
1 GTAATTCATTTTCCA
2042816 GTAATTCATTTTTCAGTTCCA
1 GTAATTCA---TT---TTCCA
**
2042837 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
2042852 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
2042867 G
1 G
2042868 AAAACCAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
14 12 0.24
15 26 0.51
21 13 0.25
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:2043387 original size:90 final size:89
Alignment explanation
Indices: 2043228--2043390 Score: 299
Period size: 90 Copynumber: 1.8 Consensus size: 89
2043218 CCTAACACAC
*
2043228 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
2043293 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAGAATTTAATAAT
*
2043317 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
2043382 ATTTAATTA
65 ATTTAATTA
2043391 GTTGAAATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 34 0.48
90 37 0.52
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTAGAATTTAATAAT
Found at i:2045862 original size:59 final size:59
Alignment explanation
Indices: 2045794--2045920 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
2045784 TTGTGAATGG
* * * * *
2045794 TCATTTATATTTTCACAAACATGTTCATGAATATAT-TCGTTTATCGTTCGA-GAACATGT
1 TCATTTATATGTTCACAAACATGTTCACGAACATATGT-GCTTAACGTTC-ATGAACATGT
* *
2045853 TCATTTATATGTTCACAAATATGTTCACGAACATGTGTGCTTAACGTTCATGAACATGT
1 TCATTTATATGTTCACAAACATGTTCACGAACATATGTGCTTAACGTTCATGAACATGT
2045912 TCATTTATA
1 TCATTTATA
2045921 CGCTCACGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.02
59 57 0.97
60 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (59 bp):
TCATTTATATGTTCACAAACATGTTCACGAACATATGTGCTTAACGTTCATGAACATGT
Found at i:2045912 original size:47 final size:47
Alignment explanation
Indices: 2045861--2045961 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
2045851 GTTCATTTAT
* * *
2045861 ATGTTCACAAATATGTTCACGAACATGTGTGCTTAACGTTCATGAAC
1 ATGTTCACAAATACGCTCACGAACATATGTGCTTAACGTTCATGAAC
*** * * *
2045908 ATGTTCATTTATACGCTCACGAACATATTTGTTTAACGTTTATGAAC
1 ATGTTCACAAATACGCTCACGAACATATGTGCTTAACGTTCATGAAC
2045955 ATGTTCA
1 ATGTTCA
2045962 TTTATATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (47 bp):
ATGTTCACAAATACGCTCACGAACATATGTGCTTAACGTTCATGAAC
Found at i:2045962 original size:47 final size:47
Alignment explanation
Indices: 2045877--2046012 Score: 155
Period size: 47 Copynumber: 2.9 Consensus size: 47
2045867 ACAAATATGT
* * *
2045877 TCACGAACATGTGTGCTTAACGTTCATGAACATGTTCATTTATACGC
1 TCACGAACATGTTTGTTTAACGTTTATGAACATGTTCATTTATACGC
* * *
2045924 TCACGAACATATTTGTTTAACGTTTATGAACATGTTCATTTATATGT
1 TCACGAACATGTTTGTTTAACGTTTATGAACATGTTCATTTATACGC
* * * *** *
2045971 TCATGACCATGTTTCTTTAGTATTTGTGAACATGTTCATTTA
1 TCACGAACATGTTTGTTTAACGTTTATGAACATGTTCATTTA
2046013 GTGTTCGTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (47 bp):
TCACGAACATGTTTGTTTAACGTTTATGAACATGTTCATTTATACGC
Found at i:2045981 original size:24 final size:24
Alignment explanation
Indices: 2045896--2046012 Score: 98
Period size: 24 Copynumber: 5.0 Consensus size: 24
2045886 TGTGTGCTTA
2045896 ACGTTCATGAACATGTTCATTTAT
1 ACGTTCATGAACATGTTCATTTAT
* * * **
2045920 ACGCTCACGAACATATTTGTTTA-
1 ACGTTCATGAACATGTTCATTTAT
*
2045943 ACGTTTATGAACATGTTCATTTAT
1 ACGTTCATGAACATGTTCATTTAT
* *
2045967 ATGTTCATGACCATGTTTC-TTTAGT
1 ACGTTCATGAACATG-TTCATTTA-T
**
2045992 A--TTTGTGAACATGTTCATTTA
1 ACGTTCATGAACATGTTCATTTA
2046013 GTGTTCGTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
22 3 0.04
23 30 0.42
24 34 0.47
25 5 0.07
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (24 bp):
ACGTTCATGAACATGTTCATTTAT
Found at i:2047693 original size:18 final size:18
Alignment explanation
Indices: 2047670--2047738 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
2047660 TTAATATACG
2047670 TCTGATAATTGTAAAACA
1 TCTGATAATTGTAAAACA
* * **
2047688 TCTGATAACTGAAAAATG
1 TCTGATAATTGTAAAACA
*
2047706 TTTGATAATTGT-AAACTA
1 TCTGATAATTGTAAAAC-A
*
2047724 TCTTATAATTGTAAA
1 TCTGATAATTGTAAA
2047739 CATTTAGAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
17 3 0.08
18 33 0.87
19 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (18 bp):
TCTGATAATTGTAAAACA
Found at i:2055603 original size:2 final size:2
Alignment explanation
Indices: 2055596--2055626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2055586 ATATGAAGAA
2055596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2055627 AAAGCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2057925 original size:20 final size:20
Alignment explanation
Indices: 2057895--2058043 Score: 113
Period size: 20 Copynumber: 7.3 Consensus size: 20
2057885 GTTTCCAGAT
*
2057895 TCGCAACGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
* ** *
2057915 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTATGAC-TA
** *
2057935 TTCGCGTTGCGATTTTTTGACTA
1 -TCGCAATGCGA-TTAT-GACTA
* *
2057958 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
2057978 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
*
2057998 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
2058018 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTATGACTA
2058038 TCGCAA
1 TCGCAA
2058044 CACTGAATTT
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.03
20 73 0.71
21 13 0.13
22 11 0.11
23 2 0.02
24 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:2058005 original size:40 final size:39
Alignment explanation
Indices: 2057895--2058043 Score: 127
Period size: 40 Copynumber: 3.7 Consensus size: 39
2057885 GTTTCCAGAT
* * *
2057895 TCGCAACGCGATTATGACTATCGCATTGCGATTTTCCAAA
1 TCGCAACGCGATTATGACTATCGCAATGCGATTAT-GAAA
*** * *
2057935 TTCGCGTTGCGATTTTTTGACTATCGCAATGCGAATATGTAAA
1 -TCGCAACGCGA--TTATGACTATCGCAATGCGATTATG-AAA
* * *
2057978 TCGCAATGCGATTATGACTATCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTATGACTATCGCAATGCGATTATGA-AA
* *
2058018 TCGCAACGCGATTCTGACTGTCGCAA
1 TCGCAACGCGATTATGACTATCGCAA
2058044 CACTGAATTT
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.01
40 46 0.53
41 8 0.09
42 9 0.10
43 23 0.26
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (39 bp):
TCGCAACGCGATTATGACTATCGCAATGCGATTATGAAA
Found at i:2058824 original size:24 final size:24
Alignment explanation
Indices: 2058792--2058845 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2058782 GTATTCGAAA
2058792 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2058816 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2058840 TTTGAT
1 TTTGAT
2058846 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2059064 original size:14 final size:14
Alignment explanation
Indices: 2059035--2059071 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2059025 AGAAAAAGAA
2059035 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
2059050 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
2059064 GAAGAAAA
1 GAAGAAAA
2059072 TGCCACAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:2061323 original size:20 final size:20
Alignment explanation
Indices: 2061293--2061497 Score: 184
Period size: 20 Copynumber: 10.8 Consensus size: 20
2061283 TTACACATTC
*
2061293 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2061313 ATTTAACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
2061332 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
** * *
2061347 ATTTCTCTATCGCAACTCAA
1 ATTTGACTATCGCAACGCGA
*
2061367 ATTTGACTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
2061387 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
2061407 A----A--ATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
2061421 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2061441 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
2061461 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
2061481 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2061498 AGAAAATCGC
Statistics
Matches: 151, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
14 22 0.15
15 3 0.02
16 1 0.01
18 1 0.01
19 2 0.01
20 121 0.80
21 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2061344 original size:34 final size:34
Alignment explanation
Indices: 2061301--2061477 Score: 142
Period size: 34 Copynumber: 4.9 Consensus size: 34
2061291 TCATTTGAAT
*
2061301 ATCGCAACGCGAATTTAACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
** *
2061335 ATCGCAACGCGAATTTCTCTATCGCAACTCAAATTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAA----A
*
2061373 CTATCGCAACG-GCTATTTGACTATCGCAACG-AGAAA
1 --ATCGCAACGCG-AATTTGACTATCGCAACGCA-AAA
* *
2061409 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
*
2061449 ATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
2061478 GGTATTTGAC
Statistics
Matches: 116, Mismatches: 11, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
34 56 0.48
35 2 0.02
36 2 0.02
38 1 0.01
39 3 0.03
40 52 0.45
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:2061413 original size:54 final size:54
Alignment explanation
Indices: 2061355--2061457 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
2061345 GAATTTCTCT
*
2061355 ATCGCAAC-TCAAATTTGACTATCGCAACG-GCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGT-AAATTTGACTATCGCAACGCG-AATTTGACTATCGCAACGAGAAA
* *
2061409 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGAGTATCGCAACG
1 ATCGCAACGTAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
2061458 CGAATTTGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (54 bp):
ATCGCAACGTAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
Found at i:2061414 original size:74 final size:74
Alignment explanation
Indices: 2061293--2061477 Score: 248
Period size: 74 Copynumber: 2.5 Consensus size: 74
2061283 TTACACATTC
* *
2061293 ATTTGAATATCGCAACGCGAATTTAACTATCGCAACGCAAAAATCGCAACGCGAATTTCTCTATC
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTCACTATC
*
2061358 GCAACTCAA
66 GCAACGCAA
* * * *
2061367 ATTTGACTATCGCAACG-GCTATTTGACTATCGCAACG-AGAAAATCGCAACGTGAATTTGACTA
1 ATTTGAATATCGCAACGCG-AATTTGACTATCGCAACGCA-AAAATCGCAACGCGAATTTCACTA
*
2061430 TCGCAACGCGA
64 TCGCAACGCAA
* *
2061441 ATTTGAGTATCGCAACGCGAATTTGATTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACG
2061478 GGTATTTGAC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
73 2 0.02
74 94 0.97
75 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (74 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTCACTATC
GCAACGCAA
Found at i:2061454 original size:94 final size:94
Alignment explanation
Indices: 2061335--2061537 Score: 298
Period size: 94 Copynumber: 2.2 Consensus size: 94
2061325 CAACGCAAAA
* *
2061335 ATCGCAACGCGAATTTCTCTATCGCAACTCAAATTTGACTATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTCACTATCGCAACGCAAATTTGACTATCGCAACGGCTATTTGACTATCGC
* * *
2061400 AACGAGAAAATCGCAACGTGAATTTGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
* * * * *
2061429 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTCACTATCGCAACGCAAATTTGACTATCGCAACGGCTATTTGACTATCGC
*
2061494 AACGAGAAAATCGCAAAGCGTATTAGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
*
2061523 ATCGCAACGCAAATT
1 ATCGCAACGCGAATT
2061538 GACTTTCGCG
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTCACTATCGCAACGCAAATTTGACTATCGCAACGGCTATTTGACTATCGC
AACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:2061565 original size:20 final size:20
Alignment explanation
Indices: 2061536--2061593 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2061526 GCAACGCAAA
2061536 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2061556 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2061576 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
2061594 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:2063845 original size:20 final size:20
Alignment explanation
Indices: 2063820--2063867 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2063810 GCGATTCTCT
2063820 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2063840 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2063860 CGTTGCGA
1 CGTTGCGA
2063868 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2065778 original size:20 final size:20
Alignment explanation
Indices: 2065755--2065810 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2065745 TCTGAAACTT
2065755 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
2065775 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
2065795 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
2065811 TTTGACTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2065816 original size:20 final size:20
Alignment explanation
Indices: 2065758--2065829 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
2065748 GAAACTTAAA
* **
2065758 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
2065778 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
2065798 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* *
2065818 ATTGTAACGCGA
1 ATCGCAACGCGA
2065830 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2066250 original size:22 final size:22
Alignment explanation
Indices: 2066225--2066266 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2066215 AGATAGACAA
2066225 ATTTCACTGAAGATGGGGACTG
1 ATTTCACTGAAGATGGGGACTG
** *
2066247 ATTTCGTTGGAGATGGGGAC
1 ATTTCACTGAAGATGGGGAC
2066267 AGATGTTGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.29
Consensus pattern (22 bp):
ATTTCACTGAAGATGGGGACTG
Found at i:2066608 original size:20 final size:20
Alignment explanation
Indices: 2066585--2066622 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2066575 ATGTAAATCG
2066585 CAATGCGAGTATGACTATAT
1 CAATGCGAGTATGACTATAT
* *
2066605 CAATGCGATTCTGACTAT
1 CAATGCGAGTATGACTAT
2066623 CGCAACGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
CAATGCGAGTATGACTATAT
Found at i:2066682 original size:40 final size:40
Alignment explanation
Indices: 2066612--2066687 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
2066602 TATCAATGCG
*
2066612 ATTCTGACTATCGCAACGAGATTCTAACTATCGCAACACC
1 ATTCTGACTATCGCAACGAGATGCTAACTATCGCAACACC
* * *
2066652 ATTCTGACTGTCGCAACGCGATGCTGACTATCGCAA
1 ATTCTGACTATCGCAACGAGATGCTAACTATCGCAA
2066688 TACGATTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (40 bp):
ATTCTGACTATCGCAACGAGATGCTAACTATCGCAACACC
Found at i:2066693 original size:20 final size:20
Alignment explanation
Indices: 2066610--2066694 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
2066600 TATATCAATG
2066610 CGATTCTGACTATCGCAACGA
1 CGATTCTGACTATCGCAAC-A
*
2066631 -GATTCTAACTATCGCAACA
1 CGATTCTGACTATCGCAACA
* * *
2066650 CCATTCTGACTGTCGCAACG
1 CGATTCTGACTATCGCAACA
* *
2066670 CGATGCTGACTATCGCAATA
1 CGATTCTGACTATCGCAACA
2066690 CGATT
1 CGATT
2066695 TTCAAAGTGC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (20 bp):
CGATTCTGACTATCGCAACA
Found at i:2066909 original size:22 final size:22
Alignment explanation
Indices: 2066870--2066911 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2066860 GCAACATCCC
* *
2066870 TCCCCATCTCCGATGAAATCAG
1 TCCCCAGCTCCGACGAAATCAG
*
2066892 TCCCCAGCTCCGGCGAAATC
1 TCCCCAGCTCCGACGAAATC
2066912 CGTCTATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (22 bp):
TCCCCAGCTCCGACGAAATCAG
Found at i:2067402 original size:20 final size:20
Alignment explanation
Indices: 2067312--2067403 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
2067302 TTTTAGTTAT
2067312 GCGTTGCGATTTTCA-TTTC
1 GCGTTGCGATTTTCATTTTC
*** **
2067331 GCGTTGCGATAGGCAAATTC
1 GCGTTGCGATTTTCATTTTC
**
2067351 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATTTTCATTTTC
* *
2067371 GTGTTGCAATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
*
2067391 GTGTTGCGATTTT
1 GCGTTGCGATTTT
2067404 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTC
Found at i:2067410 original size:20 final size:20
Alignment explanation
Indices: 2067367--2067410 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2067357 CGATAGTCAT
* *
2067367 TTTCGTGTTGCAATTTTCAT
1 TTTCGTGTTGCAATTTTAAG
*
2067387 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
2067407 TTTC
1 TTTC
2067411 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:2069004 original size:21 final size:21
Alignment explanation
Indices: 2068975--2069020 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2068965 TGGTGCATGG
*
2068975 CGTGTTGAGGT-GTCTACTTTA
1 CGTGGTGAGGTAGTC-ACTTTA
*
2068996 CGTGGTGAGGTAGTCGCTTTA
1 CGTGGTGAGGTAGTCACTTTA
2069017 CGTG
1 CGTG
2069021 AGATGGTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.13, C:0.15, G:0.35, T:0.37
Consensus pattern (21 bp):
CGTGGTGAGGTAGTCACTTTA
Found at i:2069139 original size:18 final size:18
Alignment explanation
Indices: 2069116--2069165 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2069106 TTTACTCGTA
2069116 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2069134 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2069152 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2069166 GCTTTCGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:2069197 original size:20 final size:20
Alignment explanation
Indices: 2069170--2069257 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
2069160 TAGATTGCTT
*
2069170 TCGCAACGCGAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* *
2069190 TTGCAACGCAAAAATGACTG
1 TCGCAACGCAAAAATGACTA
2069210 TCGCAACGCAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* * **
2069230 TCGCAATGCGAATTTGACTA
1 TCGCAACGCAAAAATGACTA
2069250 TCGCAACG
1 TCGCAACG
2069258 AGAGAATCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:2069325 original size:20 final size:20
Alignment explanation
Indices: 2069300--2069388 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
2069290 GTGATTCTCT
2069300 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
**
2069320 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCA
** **
2069340 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCA
* **
2069360 CGTTACGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCA
2069380 CGTTGCGAT
1 CGTTGCGAT
2069389 TTTAAGTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:2069969 original size:21 final size:21
Alignment explanation
Indices: 2069874--2069981 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
2069864 GCCCGACTCA
2069874 CCTATCATCGTTCAAGAGGCTTC
1 CCTATCATCGTTCAAGAGGC--C
*
2069897 CC-CT-ATCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
** *
2069916 CCTATCATCCCTCAAGAGTCC
1 CCTATCATCGTTCAAGAGGCC
** *
2069937 CCTCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* * * *
2069958 ACTGTCATCGTTGAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
2069979 CCT
1 CCT
2069982 CCCAACATTC
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 58 0.89
22 1 0.02
23 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:2069975 original size:42 final size:42
Alignment explanation
Indices: 2069903--2069985 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2069893 CTTCCCCTAT
*
2069903 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
2069945 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2069986 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:2071410 original size:14 final size:14
Alignment explanation
Indices: 2071376--2071437 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2071366 TTGCTTGTTT
*
2071376 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
2071390 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
2071404 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
2071419 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2071433 TAATT
1 -AATT
2071438 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2071589 original size:20 final size:20
Alignment explanation
Indices: 2071536--2071589 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2071526 AGGTACACTT
* **
2071536 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
2071556 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
*
2071576 TCGGAACGCGAAAG
1 TCGCAACGCGAAAG
2071590 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:2071657 original size:20 final size:20
Alignment explanation
Indices: 2071632--2071910 Score: 209
Period size: 20 Copynumber: 14.8 Consensus size: 20
2071622 GCGATTTTCT
* * *
2071632 CGTTGCGATAGTTAAATACC
1 CGTTGCGATAGTCAAATTCG
*
2071652 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2071672 TGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
2071692 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2071712 TGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
2071726 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
2071745 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
** *
2071766 CGTTGCGATAGAGAAATTTG
1 CGTTGCGATAGTCAAATTCG
**
2071786 CGTTGCGAT--T----TTTA
1 CGTTGCGATAGTCAAATTCG
*
2071800 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
2071820 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2071840 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
2071854 AGTTGCGATAATCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
2071874 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
2071894 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2071911 GAATGTGTAA
Statistics
Matches: 208, Mismatches: 31, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
14 33 0.16
16 3 0.01
18 2 0.01
19 1 0.00
20 167 0.80
21 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2071730 original size:74 final size:74
Alignment explanation
Indices: 2071652--2071848 Score: 272
Period size: 74 Copynumber: 2.7 Consensus size: 74
2071642 GTTAAATACC
* * * *
2071652 CGTTGCGATAATCAAATTCGTGTTGCGATACTCAAATTCGCGTTGCGATAGTCAAATTCGTGTTG
1 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTG
2071717 CGATTTTCT-
66 CGATTTT-TA
* * * *
2071726 CGTTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGCGTTGCGATAGAGAAATTTGCGTT
1 CGTTGCGATAGTCAAATTCG-TGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
2071790 GCGATTTTTA
65 GCGATTTTTA
* *
2071800 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCATTGCGAT
1 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
2071849 TTTTGAGTTG
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
73 3 0.03
74 103 0.95
75 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTG
CGATTTTTA
Found at i:2071753 original size:94 final size:94
Alignment explanation
Indices: 2071592--2071794 Score: 300
Period size: 94 Copynumber: 2.2 Consensus size: 94
2071582 CGCGAAAGTC
* *
2071592 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTTAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
* *
2071657 CGATAATCAAATTCGTGTTGCGATACTCA
66 CGATAATCAAATTCGCGTTGCGATACACA
* *
2071686 AATTCGCGTTGCGATAGTCAAATTCG-TGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTT
1 AATTCGCGTTGCGATAGTCAAATACGCT-TTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTT
* * *
2071750 GCGATAGTCAAATTCGCGTTGCGATAGAGA
65 GCGATAATCAAATTCGCGTTGCGATACACA
*
2071780 AATTTGCGTTGCGAT
1 AATTCGCGTTGCGAT
2071795 TTTTACGTTG
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 1 0.01
94 97 0.99
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAATCAAATTCGCGTTGCGATACACA
Found at i:2071804 original size:54 final size:55
Alignment explanation
Indices: 2071746--2071902 Score: 228
Period size: 54 Copynumber: 2.9 Consensus size: 55
2071736 GTCAAATAGC
**
2071746 CGTTGCGATAGTCAAATTCGCGTTGCGATAGAGAAATTTGCGTTGCGATTTTT-A
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTGA
* * * *
2071800 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCATTGCGATTTTTGA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTGA
* *
2071855 -GTTGCGATAATCAAATTTGCGTTGCGATAGTCAAATTTGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGAT
2071903 ATTCAAATGA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 89 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (55 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTGA
Found at i:2072133 original size:140 final size:140
Alignment explanation
Indices: 2071881--2072150 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
2071871 TTGCGTTGCG
* * *
2071881 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAATTGAACATATCA
1 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2071946 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2072011 AATACACATA
131 AATACACATA
*
2072021 ATAGTCAAATTTGCATTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
2072086 TAGCAATGTTCAAACTCAAGTTACTAATGCATGCCTAACTGAAAATGTTAAAGGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2072151 TACAACGTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2072233 original size:18 final size:18
Alignment explanation
Indices: 2072210--2072245 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2072200 AAGCCGGTTG
*
2072210 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2072228 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2072246 CCTTTTTCTT
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:2075425 original size:20 final size:20
Alignment explanation
Indices: 2075363--2075473 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
2075353 AAATTCAGTG
* * *
2075363 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
*
2075383 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCATAATCGCA
*
2075403 TTGCGATAGTCATAATCGTA
1 TTGCGATAGTCATAATCGCA
* *
2075423 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
2075443 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
2075463 TTGCGATAGTC
1 TTGCGATAGTC
2075474 GAAAAATCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:2075490 original size:22 final size:22
Alignment explanation
Indices: 2075465--2075516 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
2075455 TATTCGCATT
2075465 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * * *
2075487 GCGA-ATTTGGAAAATTGCAAT
1 GCGATAGTCGAAAAATCGCAAC
2075508 GCGATAGTC
1 GCGATAGTC
2075517 AGAATCGCGT
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:2078616 original size:16 final size:16
Alignment explanation
Indices: 2078595--2078634 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2078585 GAGCCGAGTC
2078595 GAGCTCGAGTATTACT
1 GAGCTCGAGTATTACT
*
2078611 GAGCTCGAGTATTGCT
1 GAGCTCGAGTATTACT
2078627 GAGCTCGA
1 GAGCTCGA
2078635 CTCAAACTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (16 bp):
GAGCTCGAGTATTACT
Found at i:2078786 original size:11 final size:11
Alignment explanation
Indices: 2078770--2078820 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2078760 CTTGAAACTC
2078770 AAGCTCGATTG
1 AAGCTCGATTG
2078781 AAGCTCGATTTTG
1 AAGCTCGA--TTG
*
2078794 -AGCTCGATTC
1 AAGCTCGATTG
* *
2078804 AAGCTCGTTTA
1 AAGCTCGATTG
2078815 AAGCTC
1 AAGCTC
2078821 AAAGATGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.06
11 22 0.65
12 7 0.21
13 3 0.09
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (11 bp):
AAGCTCGATTG
Found at i:2080156 original size:11 final size:11
Alignment explanation
Indices: 2080140--2080202 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2080130 GTATTATAGA
2080140 ATTTTTAATAT
1 ATTTTTAATAT
2080151 ATTTTTAA-AT
1 ATTTTTAATAT
2080161 -TTTTATAAT-T
1 ATTTT-TAATAT
*** * *
2080171 ATCAATAGTGT
1 ATTTTTAATAT
2080182 ATTTTTAATAT
1 ATTTTTAATAT
2080193 ATTTTTAATA
1 ATTTTTAATA
2080203 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.10
10 9 0.23
11 26 0.67
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:2084072 original size:141 final size:141
Alignment explanation
Indices: 2083855--2084117 Score: 422
Period size: 141 Copynumber: 1.9 Consensus size: 141
2083845 TAAACCGAAT
* *
2083855 TCATAACTAAAAATGCATGAACGGATGCATTAAGGCTTGAAAGGATGCCATAACTAAAAATGCAT
1 TCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAATGCAT
* *
2083920 GAACATATGCATTAAGGCATGAAAGGATACCATAACTA-AGAATGCATGAACGGATGCATTTAGG
66 GAACATATGCATTAAGGCATGAAAGGATACAATAACTAGA-AATGCATGAAAGGATGCATTTAGG
2083984 CATGAAAGGACG
130 CATGAAAGGACG
* *
2083996 TCATAACTAAAAATGCATGAACTGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAATGCGT
1 TCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAATGCAT
**
2084061 GAAC-TGATGCATTAAGGCATGAAAGGATGTAATAACTAGAAATGCATGAAAGGATGC
66 GAACAT-ATGCATTAAGGCATGAAAGGATACAATAACTAGAAATGCATGAAAGGATGC
2084118 TATGAAAATG
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
140 1 0.01
141 110 0.98
142 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (141 bp):
TCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAATGCAT
GAACATATGCATTAAGGCATGAAAGGATACAATAACTAGAAATGCATGAAAGGATGCATTTAGGC
ATGAAAGGACG
Found at i:2084117 original size:47 final size:47
Alignment explanation
Indices: 2083856--2084117 Score: 380
Period size: 47 Copynumber: 5.6 Consensus size: 47
2083846 AAACCGAATT
*
2083856 CATAACTAAAAATGCATGAACGGATGCATTAAGGCTTGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
** *
2083903 CATAACTAAAAATGCATGAACATATGCATTAAGGCATGAAAGGATAC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * *
2083950 CATAACTAAGAATGCATGAACGGATGCATTTAGGCATGAAAGGACGT
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
2083997 CATAACTAAAAATGCATGAACTGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * *
2084044 CATAAATAAAAATGCGTGAACTGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * *
2084091 AATAACTAGAAATGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGC
2084118 TATGAAAATG
Statistics
Matches: 190, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 190 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (47 bp):
CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:2087258 original size:24 final size:24
Alignment explanation
Indices: 2087224--2087332 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
2087214 AAACAGAGAT
*
2087224 ATCAGAAATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * * *
2087248 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAA
* *
2087272 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* * *
2087296 GTCATG-TATCAGAACATAATTCAA
1 ATCA-GAAATCAGAACAGAATTCAA
2087320 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2087333 TAAAATATTC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:2087293 original size:48 final size:48
Alignment explanation
Indices: 2087224--2087332 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
2087214 AAACAGAGAT
* * *
2087224 ATCAGAAATCAAAACAGAATTCAAATCA-GATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAAATCATG-TATCAGAACAGAATCCAA
* ** * *
2087272 ATCAGAAATCAGAACATAATTCAGGTCATGTATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAAATCATGTATCAGAACAGAATCCAA
2087320 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2087333 TAAAATATTC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAAATCATGTATCAGAACAGAATCCAA
Found at i:2090910 original size:30 final size:29
Alignment explanation
Indices: 2090862--2090935 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 29
2090852 TGGTATATAA
2090862 TTTTTAAAGTTAAGATAAAGTCAAAAAATAT
1 TTTTTAAAGTT-A-ATAAAGTCAAAAAATAT
*
2090893 TTTTCTAAAGTTAATAAAGTTAAAAAATAT
1 TTTT-TAAAGTTAATAAAGTCAAAAAATAT
*
2090923 TTTTTAGAGTTAA
1 TTTTTAAAGTTAA
2090936 GATAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 8 0.20
30 20 0.50
31 5 0.12
32 7 0.17
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (29 bp):
TTTTTAAAGTTAATAAAGTCAAAAAATAT
Found at i:2090918 original size:167 final size:160
Alignment explanation
Indices: 2090596--2090928 Score: 443
Period size: 167 Copynumber: 2.0 Consensus size: 160
2090586 TTTTTTTTAA
*
2090596 TTTTATCGTAAGAGTGGTTTAAAATGGACTAAGAGTGATATATATTTTATCTTAAATTTAAAATA
1 TTTTATCGTAAGAGTGGTTTAAAATGGACTAAAAGTGATATATATTTTATCTTAAATTTAAAATA
2090661 TATTTTTAAATTTTATCTTAAGAGTAGTATATAATTTTTAAAGTTAAGATAAAATAAAAAATAAG
66 TATTTTTAAATTTTATCTTAAGAGTAGTATATAATTTTTAAAGTTAAGATAAAATAAAAAATAAG
** * * **
2090726 TTTTAATTTTATCTTTACTTTAAAAACATTATT
131 TTTTAAAGTTA-CATAAAGTTAAAAA-A-TATT
* * *
2090759 TTTTATCTTAAGCGTGGTTTAAAAAAATGGACTAAAAGTGGTATATATTTTATCTTAAATTTAAA
1 TTTTATCGTAAGAGTGGTTT---AAAATGGACTAAAAGTGATATATATTTTATCTTAAATTTAAA
* * *
2090824 ATATATATTTTTAATTTTATCTTAAGAGTGGTATATAATTTTTAAAGTTAAGATAAAGTCAAAAA
63 ATATAT-TTTTAAATTTTATCTTAAGAGTAGTATATAATTTTTAAAGTTAAGATAAAAT-AAAAA
**
2090889 ATATTTTTCTAAAGTTA-ATAAAGTTAAAAAATATT
126 ATAAGTTT-TAAAGTTACATAAAGTTAAAAAATATT
2090924 TTTTA
1 TTTTA
2090929 GAGTTAAGAT
Statistics
Matches: 149, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
163 18 0.12
165 9 0.06
166 47 0.32
167 58 0.39
168 11 0.07
169 6 0.04
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (160 bp):
TTTTATCGTAAGAGTGGTTTAAAATGGACTAAAAGTGATATATATTTTATCTTAAATTTAAAATA
TATTTTTAAATTTTATCTTAAGAGTAGTATATAATTTTTAAAGTTAAGATAAAATAAAAAATAAG
TTTTAAAGTTACATAAAGTTAAAAAATATT
Found at i:2090961 original size:47 final size:46
Alignment explanation
Indices: 2090907--2090997 Score: 137
Period size: 47 Copynumber: 2.0 Consensus size: 46
2090897 CTAAAGTTAA
* * * *
2090907 TAAAGTTAAAAAATATTTTTTAGAGTTAAGATAAAATTTAAAAAAAT
1 TAAAGTTAAAAAATATTTTGTAAAGTTAAG-GAAAAGTTAAAAAAAT
2090954 TAAAGTTAAAAAATATTTTGTAAAGTTAAGGAAAAGTTAAAAAA
1 TAAAGTTAAAAAATATTTTGTAAAGTTAAGGAAAAGTTAAAAAA
2090998 TTGTTTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 12 0.30
47 28 0.70
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (46 bp):
TAAAGTTAAAAAATATTTTGTAAAGTTAAGGAAAAGTTAAAAAAAT
Found at i:2092338 original size:7 final size:7
Alignment explanation
Indices: 2092319--2092348 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2092309 CATGTAATTT
2092319 ATATATAA
1 ATATAT-A
2092327 ATATATA
1 ATATATA
2092334 ATATATA
1 ATATATA
2092341 ATATATA
1 ATATATA
2092348 A
1 A
2092349 GATTTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.73
8 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:2092360 original size:15 final size:14
Alignment explanation
Indices: 2092342--2092389 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2092332 TAATATATAA
2092342 TATATAAGATTTATG
1 TATAT-AGATTTATG
*
2092357 TATATAG-TTTATA
1 TATATAGATTTATG
*
2092370 TATATAGATATTAAG
1 TATATAGAT-TTATG
2092385 TATAT
1 TATAT
2092390 TATTACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 12 0.43
14 3 0.11
15 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TATATAGATTTATG
Found at i:2092543 original size:18 final size:18
Alignment explanation
Indices: 2092514--2092565 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
2092504 ATAATATAAG
2092514 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
2092531 TTTATATTATAAA-T-TA
1 TTTATATTATAAACTATA
** *
2092547 TAAATATTATAAGCTATA
1 TTTATATTATAAACTATA
2092565 T
1 T
2092566 ATAAATGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.41
17 8 0.28
18 9 0.31
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:2092636 original size:22 final size:22
Alignment explanation
Indices: 2092607--2092669 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
2092597 ATTATGTATT
2092607 AAAATATAT-GTATAAACTATA
1 AAAATATATAGTATAAACTATA
*
2092628 AAAAGTATATAGGTATAAATTATA
1 AAAA-TATATA-GTATAAACTATA
2092652 ATATAATATATAGATATA
1 A-A-AATATATAG-TATA
2092670 TTATATATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
24 13 0.37
25 11 0.31
26 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
AAAATATATAGTATAAACTATA
Found at i:2092670 original size:2 final size:2
Alignment explanation
Indices: 2092648--2092696 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
2092638 AGGTATAAAT
*
2092648 TA TA -A TA TA -A TA TA TA GA TA TA T- TA TA TA TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
2092688 TA TA TA TA T
1 TA TA TA TA T
2092697 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Done.