Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 24
Found at i:866720 original size:16 final size:17
Alignment explanation
Indices: 866696--866727 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
866686 TTATTTTGTT
866696 TTAATATTATTATTATA
1 TTAATATTATTATTATA
866713 TTAA-ATTATTATTAT
1 TTAATATTATTATTAT
866728 TAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATATTATTATTATA
Found at i:866722 original size:19 final size:19
Alignment explanation
Indices: 866700--866749 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
866690 TTTGTTTTAA
*
866700 TATTATTATTATATTAAAT
1 TATTATTATTATAATAAAT
866719 TATTATTATTA-AATAAAT
1 TATTATTATTATAATAAAT
*
866737 AATTTATTATTAT
1 TA-TTATTATTAT
866750 TACAGGCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATTATTATAATAAAT
Found at i:868186 original size:16 final size:16
Alignment explanation
Indices: 868165--868197 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
868155 TTGCTTTTAA
868165 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
868181 ATTTATTTATAATATT
1 ATTTATTTATAATATT
868197 A
1 A
868198 ATTTGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:868399 original size:31 final size:33
Alignment explanation
Indices: 868364--868426 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
868354 ATAATTAAAC
868364 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
868395 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
868427 TTAATATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:868575 original size:129 final size:129
Alignment explanation
Indices: 868419--868740 Score: 590
Period size: 129 Copynumber: 2.5 Consensus size: 129
868409 AATATTTATT
*
868419 TTTATTTATTAATATCAAATAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
*
868484 TTAAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTCA
66 TTAAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATATTTTAGTCA
868548 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
*
868613 TTTAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATATTTTAGTCA
66 TTAAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATATTTTAGTCA
* * *
868677 TTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTT
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTT
868741 CTAAATAAAT
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 187 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (129 bp):
TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
TTAAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATATTTTAGTCA
Found at i:868791 original size:26 final size:25
Alignment explanation
Indices: 868745--868796 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
868735 ATATTTCTAA
868745 ATAAATATATTTTATTTATAATATAT
1 ATAAATATATTTTATTTATAAT-TAT
868771 ATAAAT-TATTTT-TTCTAATAATTAT
1 ATAAATATATTTTATT-T-ATAATTAT
868796 A
1 A
868797 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.08
25 11 0.46
26 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAAATATATTTTATTTATAATTAT
Found at i:869291 original size:18 final size:16
Alignment explanation
Indices: 869264--869307 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
869254 TTTCTTTCAA
*
869264 ATTTTTTATTACTTATT
1 ATTTTTTATTA-TTAAT
869281 ATTTTTATATTATTAAT
1 ATTTTT-TATTATTAAT
869298 ATTTTTTATT
1 ATTTTTTATT
869308 TATGAAGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 16 0.64
18 5 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTTATTATTAAT
Found at i:870820 original size:8 final size:7
Alignment explanation
Indices: 870796--870837 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
870786 TTTTCATACA
870796 TGCA-TT
1 TGCATTT
870802 TGCATTT
1 TGCATTT
870809 TGCATCTT
1 TGCAT-TT
870817 TGCATTT
1 TGCATTT
* *
870824 TTCATTG
1 TGCATTT
870831 TGCATTT
1 TGCATTT
870838 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:870820 original size:15 final size:14
Alignment explanation
Indices: 870796--870837 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
870786 TTTTCATACA
870796 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
870809 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
870824 TTCATTGTGCATTT
1 TGCATTTTGCATTT
870838 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:870913 original size:12 final size:12
Alignment explanation
Indices: 870896--870935 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
870886 ACATTCACAT
870896 ATTTACATTTGC
1 ATTTACATTTGC
*
870908 ATTTACATTTGT
1 ATTTACATTTGC
*
870920 ATTTACCTTTGC
1 ATTTACATTTGC
870932 ATTT
1 ATTT
870936 TTTACGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:870947 original size:27 final size:27
Alignment explanation
Indices: 870895--870968 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
870885 TACATTCACA
870895 TATTTACATTTGCA---TTTACATTTG
1 TATTTACATTTGCATTTTTTACATTTG
* *
870919 TATTTACCTTTGCATTTTTTACGTTTG
1 TATTTACATTTGCATTTTTTACATTTG
*
870946 TATTTACATTTTCA-TTTTTACAT
1 TATTTACATTTGCATTTTTTACAT
870969 AATTACATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 13 0.31
26 8 0.19
27 21 0.50
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.58
Consensus pattern (27 bp):
TATTTACATTTGCATTTTTTACATTTG
Found at i:870951 original size:12 final size:12
Alignment explanation
Indices: 870895--870956 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 12
870885 TACATTCACA
870895 TATTTACATTTG
1 TATTTACATTTG
*
870907 CATTTACATTTG
1 TATTTACATTTG
*
870919 TATTTACCTTTG
1 TATTTACATTTG
* *
870931 CATTTTTTACGTTTG
1 ---TATTTACATTTG
870946 TATTTACATTT
1 TATTTACATTT
870957 TCATTTTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
12 30 0.75
15 10 0.25
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (12 bp):
TATTTACATTTG
Found at i:872947 original size:12 final size:11
Alignment explanation
Indices: 872909--872947 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
872899 TCCAGCAAAG
872909 AAAGAAGAAAA
1 AAAGAAGAAAA
*
872920 AAAAAAGAAAAA
1 AAAGAAG-AAAA
872932 AAAGAAGAAGAA
1 AAAGAAGAA-AA
872944 AAAG
1 AAAG
872948 GAAAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:877399 original size:54 final size:54
Alignment explanation
Indices: 877317--877525 Score: 321
Period size: 54 Copynumber: 3.9 Consensus size: 54
877307 GAAATCTTGG
* *
877317 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
*
877371 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAA
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* * * *
877425 CAGAAACCACAGGAAATGATGAATATGTTGTCAAATGTTTTAAGAACATCTGAG
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
877479 CA-AAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 CAGAAA-CCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
877526 CTGCTATTCT
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
53 3 0.02
54 138 0.98
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (54 bp):
CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:877923 original size:22 final size:22
Alignment explanation
Indices: 877897--877950 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
877887 CTCTTCAAAG
877897 ATGATAGATTCTCTTTTAAAAA
1 ATGATAGATTCTCTTTTAAAAA
* *
877919 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTAAAAA
*
877941 ATGAAAGATT
1 ATGATAGATT
877951 TATTGGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTAAAAA
Found at i:878764 original size:81 final size:81
Alignment explanation
Indices: 878651--878805 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 81
878641 TGAAGTTTCT
* * * *
878651 AAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGC
1 AAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAACCTTAGGGCCAGCTGTAAGCCCTACAGTGC
878716 ATG-ATGTTTCCAAAAA
66 A-GAATGTTTCCAAAAA
* *
878732 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGCCAGCTGTAAGCCCTACAGTGC
1 AAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAACCTTAGGGCCAGCTGTAAGCCCTACAGTGC
878797 AGAATGTTT
66 AGAATGTTT
878806 TTTCTTAAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 66 0.99
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (81 bp):
AAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAACCTTAGGGCCAGCTGTAAGCCCTACAGTGC
AGAATGTTTCCAAAAA
Found at i:879028 original size:113 final size:113
Alignment explanation
Indices: 878816--879543 Score: 1007
Period size: 113 Copynumber: 6.5 Consensus size: 113
878806 TTTCTTAAAG
*
878816 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * *
878881 GAAGAATTTTTTCAA-CTTGTTGTTTGAATTCATCACTCGATGGATCAA
66 GAAGAACTTGTTCAACCTT-TTGCTCGAATTCATCACTCGATGGATCAA
*
878929 CTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
878994 GAAGAGCTTGTTCAGCCTTTTGCTCAAATCCATCACTTGATGGATCAGA
66 GAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCA-A
*
879043 -TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * * *
879107 GAAGAGCTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAA
*
879155 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * ** *
879220 GAAGAATTTGTTCAACTTTTTGTTTGAATTCAT-TTTCGATGGATTAA
66 GAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAA
* * * *
879267 CTCTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTTATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * *
879332 GAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATTATTCGATGGATCAG
66 GAAGAACTTGTTCAACCTTTT-GCTCGAATTCATCACTCGATGGATCAA
* * * * * *
879380 CATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGAAAGAAGAAGTTTATAATG
1 CTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
879444 AGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAA
65 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAA
*
879493 CTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
879544 CTTGTTCAAT
Statistics
Matches: 550, Mismatches: 57, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
111 4 0.01
112 96 0.17
113 440 0.80
114 10 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAA
Found at i:879432 original size:338 final size:339
Alignment explanation
Indices: 878814--879543 Score: 1128
Period size: 338 Copynumber: 2.2 Consensus size: 339
878804 TTTTTCTTAA
878814 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
1 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* * *
878879 GAGAAGAATTTTTTCAACTTGTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAG
66 GAGAAGAATTTGTTCAACTTGTTGTTTGAATTCATCACTCGATGGATCAACTCTTCCAAAGAAAG
* *
878944 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAG
131 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAG
* *
879009 CCTTTTGCTCAAATCCATCACTTGATGGATCAGATTTTCCAGAGAAAGTTCATAATGAGAAGAAC
196 ACTTTTGCTCAAATCCATCACTTGATGGATCAGATTTGCCAGAGAAAGTTCATAATGAGAAGAAC
* * *
879074 TCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGCTCAAATCCA
261 TCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTCAAATCCA
*
879139 TCACTTGATGGATC
326 TCACTCGATGGATC
879153 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
1 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* ** *
879218 GAGAAGAATTTGTTCAACTTTTTGTTTGAATTCAT-TTTCGATGGATTAACTCTTCCAAAGAAAG
66 GAGAAGAATTTGTTCAACTTGTTGTTTGAATTCATCACTCGATGGATCAACTCTTCCAAAGAAAG
* *
879282 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTTATAATGAGAAGAACTTGTTCA-
131 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAG
** * * *
879346 ACTTTTCGCTTGAATTCATTA-TTCGATGGATCAGCA-TTGCCA-AGTAGAGTTCATAATGAGAA
196 ACTTTT-GCTCAAATCCATCACTT-GATGGATCAG-ATTTGCCAGAG-AAAGTTCATAATGAGAA
* * * *
879408 GAACTCATTTGAAGAAGAAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAA
257 GAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTCAAA
*
879473 TTCATCACTCGATGGATC
322 TCCATCACTCGATGGATC
* *
879491 AACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
879544 CTTGTTCAAT
Statistics
Matches: 358, Mismatches: 29, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
337 9 0.03
338 250 0.70
339 99 0.28
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (339 bp):
AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
GAGAAGAATTTGTTCAACTTGTTGTTTGAATTCATCACTCGATGGATCAACTCTTCCAAAGAAAG
TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAG
ACTTTTGCTCAAATCCATCACTTGATGGATCAGATTTGCCAGAGAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTCAAATCCA
TCACTCGATGGATC
Found at i:879928 original size:20 final size:20
Alignment explanation
Indices: 879903--879962 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
879893 TTTTATTTCA
879903 TTTGTTTTATTTATTATTAT
1 TTTGTTTTATTTATTATTAT
879923 TTTGTTTTA-TTATTATTAT
1 TTTGTTTTATTTATTATTAT
* *
879942 TAT-TATTATATTATTATTAT
1 TTTGTTTTAT-TTATTATTAT
879962 T
1 T
879963 AAATAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.11
19 12 0.33
20 20 0.56
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTGTTTTATTTATTATTAT
Found at i:879983 original size:3 final size:3
Alignment explanation
Indices: 879913--879963 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
879903 TTTGTTTTAT
*
879913 TTA TTA TTA TT- TTG TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
879958 TTA TTA
1 TTA TTA
879964 AATAAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:881438 original size:16 final size:16
Alignment explanation
Indices: 881417--881449 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
881407 TTGCTTTTAA
881417 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
881433 ATTTATTTATAATATT
1 ATTTATTTATAATATT
881449 A
1 A
881450 ATTTGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:881643 original size:33 final size:33
Alignment explanation
Indices: 881606--881674 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
881596 TTTTAAATAA
881606 TTAAA-CATTATAAAATTT-ATAATTTAGTTTTAT
1 TTAAATCATT-TAAAATTTAAT-ATTTAGTTTTAT
* * *
881639 TTAAATTATTTAAATTTTAATATTTATTTTTAT
1 TTAAATCATTTAAAATTTAATATTTAGTTTTAT
881672 TTA
1 TTA
881675 TTAATATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (33 bp):
TTAAATCATTTAAAATTTAATATTTAGTTTTAT
Found at i:881823 original size:130 final size:129
Alignment explanation
Indices: 881667--881989 Score: 549
Period size: 129 Copynumber: 2.5 Consensus size: 129
881657 AATATTTATT
*
881667 TTTATTTATTAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATATA
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATAT-T-
***
881732 TTTTTTTTA-AAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTC
64 TTTTTAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTC
881796 A
129 A
881797 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
881862 TTTAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTCA
66 TTTAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTCA
* * * *
881926 TTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTATGATATTT
1 TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTT
881990 CTAAATAAAT
Statistics
Matches: 184, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
128 6 0.03
129 117 0.64
130 61 0.33
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (129 bp):
TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTT
TTTAAAATAAATATCTTACTATATTAAAATAAATTTTTATTATCTTAAGAAAATGTTTTAGTCA
Found at i:882017 original size:23 final size:26
Alignment explanation
Indices: 881985--882034 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
881975 CCTTTTATGA
*
881985 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
882008 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
882034 T
1 T
882035 TTTCTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:886657 original size:20 final size:21
Alignment explanation
Indices: 886624--886666 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
886614 TGTTCATTTA
* *
886624 AATGATAAACGAACATAAACG
1 AATGATAAAAGAACACAAACG
886645 AATG-TAAAAGAACACAAACG
1 AATGATAAAAGAACACAAACG
886665 AA
1 AA
886667 CGAACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (21 bp):
AATGATAAAAGAACACAAACG
Found at i:886973 original size:10 final size:10
Alignment explanation
Indices: 886958--886982 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
886948 GCCCTCTATT
886958 TGAACATAAA
1 TGAACATAAA
886968 TGAACATAAA
1 TGAACATAAA
886978 TGAAC
1 TGAAC
886983 GAACATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (10 bp):
TGAACATAAA
Found at i:887948 original size:16 final size:14
Alignment explanation
Indices: 887918--887951 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
887908 AGTTTTAAGG
887918 ATTAAATTTAATAA
1 ATTAAATTTAATAA
887932 ATTAATATTTAAATAA
1 ATTAA-ATTT-AATAA
887948 ATTA
1 ATTA
887952 CACAACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATTTAATAA
Found at i:887949 original size:71 final size:70
Alignment explanation
Indices: 887796--887935 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 70
887786 TAGATGAAAT
* *
887796 CAAAAAATAAATATGTATGAGCAAATTTCATATACAAATATAATTTTAAGGACAAAATTGAAATA
1 CAAAAAATAAATAAGTATGAGCAAATTTCATATAAAAATATAATTTTAAGGACAAAATTGAAATA
887861 AATTA
66 AATTA
* * ** *
887866 CAAAAATATAAATAAGTATG-GACCAATTTCATATAAAAATATAGTTTTAAGGATTAAATT-TAA
1 CAAAAA-ATAAATAAGTATGAG-CAAATTTCATATAAAAATATAATTTTAAGGACAAAATTGAAA
887929 TAAATTA
64 TAAATTA
887936 ATATTTAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
70 16 0.26
71 45 0.74
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (70 bp):
CAAAAAATAAATAAGTATGAGCAAATTTCATATAAAAATATAATTTTAAGGACAAAATTGAAATA
AATTA
Found at i:888461 original size:21 final size:21
Alignment explanation
Indices: 888423--888484 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
888413 AAAGTTCCCT
**
888423 TTCAAAATTTCCCCAAAAAAA
1 TTCAAAATTTCCTTAAAAAAA
888444 TTCAAAATTTCCTTAAAAACAA
1 TTCAAAATTTCCTTAAAAA-AA
*
888466 --CAAAATTTTCCTTCAAAAA
1 TTCAAAA-TTTCCTTAAAAAA
888485 CCAATCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.17
21 28 0.78
22 2 0.06
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (21 bp):
TTCAAAATTTCCTTAAAAAAA
Found at i:888469 original size:20 final size:22
Alignment explanation
Indices: 888446--888485 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
888436 CAAAAAAATT
888446 CAAAA-TTTCCTT-AAAAACAA
1 CAAAATTTTCCTTCAAAAACAA
888466 CAAAATTTTCCTTCAAAAAC
1 CAAAATTTTCCTTCAAAAAC
888486 CAATCTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (22 bp):
CAAAATTTTCCTTCAAAAACAA
Found at i:888756 original size:14 final size:13
Alignment explanation
Indices: 888731--888768 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
888721 TAATAAAATT
888731 ATTATAATTAAGA
1 ATTATAATTAAGA
*
888744 TTTATAATATAAGA
1 ATTATAAT-TAAGA
888758 ATTATAATTAA
1 ATTATAATTAA
888769 TATAGAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (13 bp):
ATTATAATTAAGA
Found at i:895484 original size:18 final size:18
Alignment explanation
Indices: 895461--895495 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
895451 AGCCCACTGC
895461 CCATTTAAATTTTAAAAT
1 CCATTTAAATTTTAAAAT
895479 CCATTTAAATTTTAAAA
1 CCATTTAAATTTTAAAA
895496 CTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
CCATTTAAATTTTAAAAT
Found at i:900315 original size:23 final size:23
Alignment explanation
Indices: 900285--900329 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
900275 AGTGTAAACT
900285 GTTTGTATACTGAATTATGCTTG
1 GTTTGTATACTGAATTATGCTTG
900308 GTTTGTATACTGAATTATGCTT
1 GTTTGTATACTGAATTATGCTT
900330 CCAGTTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (23 bp):
GTTTGTATACTGAATTATGCTTG
Found at i:900606 original size:30 final size:30
Alignment explanation
Indices: 900548--900606 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
900538 ACCGAAATTT
** ** *
900548 GTTCGGTTCGGTTAATTTTTTCATAAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
900578 GTTCGGTTCGGTTAATGGTTAAAGAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAA
900607 CAAATTCGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.37
Consensus pattern (30 bp):
GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
Found at i:904186 original size:15 final size:14
Alignment explanation
Indices: 904146--904188 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
904136 TGATCATTGC
*
904146 TTTTCTTTCCTTCG
1 TTTTCTTTTCTTCG
*
904160 TGTTTCTGTTCTTCG
1 T-TTTCTTTTCTTCG
904175 TTTTCTTTTTCTTC
1 TTTTC-TTTTCTTC
904189 TAGATGCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.67
Consensus pattern (14 bp):
TTTTCTTTTCTTCG
Found at i:904588 original size:31 final size:31
Alignment explanation
Indices: 904553--904613 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
904543 AAGAATCATT
*
904553 AATTTAATGTTTAAATTTTAAATAAAATATC
1 AATTTAATGTTTAAATTTAAAATAAAATATC
* *
904584 AATTTAATTTTTAAATTTAAAATATAATAT
1 AATTTAATGTTTAAATTTAAAATAAAATAT
904614 TGCTTTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
AATTTAATGTTTAAATTTAAAATAAAATATC
Found at i:905621 original size:30 final size:30
Alignment explanation
Indices: 905546--905631 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
905536 TTTGATCAGA
* *
905546 TTTAAAAGTTAAATTATTATTTTATTAAAAC
1 TTTAAAGGTTAAATTAATATTTTA-TAAAAC
* *
905577 TTTAAAGATTAAATTAATATTTTATATAA-
1 TTTAAAGGTTAAATTAATATTTTATAAAAC
* **
905606 TTGTAGAGGTTAAATTCGTATTTTAT
1 TT-TAAAGGTTAAATTAATATTTTAT
905632 CTTAAGTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.04
30 23 0.50
31 21 0.46
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTAAAGGTTAAATTAATATTTTATAAAAC
Found at i:907479 original size:4 final size:4
Alignment explanation
Indices: 907470--907494 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
907460 GTCATTGTTC
907470 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
907495 TATCAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:907912 original size:15 final size:15
Alignment explanation
Indices: 907892--907922 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
907882 TTAACACAAG
907892 AAACTAACCAAATAA
1 AAACTAACCAAATAA
907907 AAACTAACCAAATAA
1 AAACTAACCAAATAA
907922 A
1 A
907923 CTCGAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACTAACCAAATAA
Found at i:910637 original size:2 final size:2
Alignment explanation
Indices: 910632--910669 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
910622 AAAAATCTGA
910632 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
910670 GAATACTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:919369 original size:14 final size:14
Alignment explanation
Indices: 919352--919378 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
919342 AAATAGTTTC
919352 TGGAAAATGAATTT
1 TGGAAAATGAATTT
919366 TGGAAAATGAATT
1 TGGAAAATGAATT
919379 AAATTTCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (14 bp):
TGGAAAATGAATTT
Found at i:923916 original size:283 final size:283
Alignment explanation
Indices: 923409--923975 Score: 1089
Period size: 283 Copynumber: 2.0 Consensus size: 283
923399 GAGAGTGCCC
*
923409 TATACAGATCAATGGAGAGATTTTTCTGGCCGACCTGATGGAGTTACCCTTTGAAGAGTTCGATT
1 TATACAGATCAATGGAAAGATTTTTCTGGCCGACCTGATGGAGTTACCCTTTGAAGAGTTCGATT
923474 TGATTCTCGACGTATATTGGTTGGACAAACATCGAGTAAATATTGATTTTGAGACTAAGAGAGCT
66 TGATTCTCGACGTATATTGGTTGGACAAACATCGAGTAAATATTGATTTTGAGACTAAGAGAGCT
*
923539 GTTCTGAAGACCCCAGATAATCGAAAGATTGTAATGATCGGGGAACGACGTGGATTTCTGACGAA
131 GTTCTGAAGACCCCAGATAATCAAAAGATTGTAATGATCGGGGAACGACGTGGATTTCTGACGAA
923604 TGTTGTGTCTACCTTGGTAGCGGAGAAGATGATCAGGAAGGGTTCCGAGGCGTTTCTTGCTTATA
196 TGTTGTGTCTACCTTGGTAGCGGAGAAGATGATCAGGAAGGGTTCCGAGGCGTTTCTTGCTTATA
923669 TTTTAGACACTGGGAGATCTCAA
261 TTTTAGACACTGGGAGATCTCAA
*
923692 TATACAGATCAATGGAAAGATTTTTCTGGCCGACCTGATGGAGTTACCCTTTGAAGAGTTTGATT
1 TATACAGATCAATGGAAAGATTTTTCTGGCCGACCTGATGGAGTTACCCTTTGAAGAGTTCGATT
* *
923757 TGATTCTTGGCGTATATTGGTTGGACAAACATCGAGTAAATATTGATTTTGAGACTAAGAGAGCT
66 TGATTCTCGACGTATATTGGTTGGACAAACATCGAGTAAATATTGATTTTGAGACTAAGAGAGCT
923822 GTTCTGAAGACCCCAGATAATCAAAAGATTGTAATGATCGGGGAACGACGTGGATTTCTGACGAA
131 GTTCTGAAGACCCCAGATAATCAAAAGATTGTAATGATCGGGGAACGACGTGGATTTCTGACGAA
923887 TGTTGTGTCTACCTTGGTAGCGGAGAAGATGATCAGGAAGGGTTCCGAGGCGTTTCTTGCTTATA
196 TGTTGTGTCTACCTTGGTAGCGGAGAAGATGATCAGGAAGGGTTCCGAGGCGTTTCTTGCTTATA
923952 TTTTAGACACTGGGAGATCTCAA
261 TTTTAGACACTGGGAGATCTCAA
923975 T
1 T
923976 CTGATATTGA
Statistics
Matches: 279, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
283 279 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (283 bp):
TATACAGATCAATGGAAAGATTTTTCTGGCCGACCTGATGGAGTTACCCTTTGAAGAGTTCGATT
TGATTCTCGACGTATATTGGTTGGACAAACATCGAGTAAATATTGATTTTGAGACTAAGAGAGCT
GTTCTGAAGACCCCAGATAATCAAAAGATTGTAATGATCGGGGAACGACGTGGATTTCTGACGAA
TGTTGTGTCTACCTTGGTAGCGGAGAAGATGATCAGGAAGGGTTCCGAGGCGTTTCTTGCTTATA
TTTTAGACACTGGGAGATCTCAA
Found at i:935142 original size:8 final size:8
Alignment explanation
Indices: 935129--935154 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
935119 CCAAAAAGGC
935129 TTAGTATT
1 TTAGTATT
935137 TTAGTATT
1 TTAGTATT
935145 TTAGTATT
1 TTAGTATT
935153 TT
1 TT
935155 GATTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (8 bp):
TTAGTATT
Found at i:936796 original size:45 final size:45
Alignment explanation
Indices: 936683--936812 Score: 131
Period size: 45 Copynumber: 2.9 Consensus size: 45
936673 TAATATAAAT
* * *
936683 ATATTGTCTAATTCATAATTAGTGCTACAACACA-TCAAACCAAC
1 ATATTGTCTAAGTCATAATTAGTACTACAACACATTAAAACCAAC
* *
936727 ACATTGT-TAAAGTCTATAATTAGTACTACAACACATTAAAACTTAA-
1 ATATTGTCT-AAGTC-ATAATTAGTACTACAACACATTAAAAC-CAAC
* * * *
936773 ATATTGTCTAAGTCATAAATAGTAGTACACCACTTTAAAA
1 ATATTGTCTAAGTCATAATTAGTACTACAACACATTAAAA
936813 GTTCACATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 10 0.14
45 41 0.58
46 16 0.23
47 3 0.04
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (45 bp):
ATATTGTCTAAGTCATAATTAGTACTACAACACATTAAAACCAAC
Found at i:939203 original size:21 final size:21
Alignment explanation
Indices: 939177--939216 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
939167 CAGATTCGCA
939177 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
939198 TTGCGATAGCACTGTTCAC
1 TTGCGATAGCACTGTTCAC
939217 ATTGGGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:939927 original size:21 final size:21
Alignment explanation
Indices: 939895--940008 Score: 192
Period size: 21 Copynumber: 5.4 Consensus size: 21
939885 ATTTTGATCA
939895 CTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
* **
939916 ATATAACAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
*
939937 CTATCGCAACGATGAACAGTG
1 CTATCGCAACGGTGAACAGTG
939958 CTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
939979 CTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
940000 CTATCGCAA
1 CTATCGCAA
940009 TGCGATTTTG
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.19
Consensus pattern (21 bp):
CTATCGCAACGGTGAACAGTG
Found at i:940024 original size:21 final size:21
Alignment explanation
Indices: 940000--940056 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
939990 GTGAACAGTG
940000 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGATTTTGGA
* *
940021 CTATCGCATTGCGAATTTGGA
1 CTATCGCAATGCGATTTTGGA
**
940042 AAATCGCAATGCGAT
1 CTATCGCAATGCGAT
940057 AGTCAGAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGATTTTGGA
Found at i:951443 original size:18 final size:19
Alignment explanation
Indices: 951420--951461 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
951410 GTAAGAAAAT
*
951420 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
951438 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
951456 ATTAAA
1 ATTAAA
951462 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:955036 original size:32 final size:32
Alignment explanation
Indices: 955000--955112 Score: 190
Period size: 32 Copynumber: 3.5 Consensus size: 32
954990 TGTTTTTGGT
955000 TTTTGCTAACGTGCGCCCAAGCCTCCCTTGAG
1 TTTTGCTAACGTGCGCCCAAGCCTCCCTTGAG
* *
955032 TTTTGCTAACATGCGCCCAAACCTCCCTTGAG
1 TTTTGCTAACGTGCGCCCAAGCCTCCCTTGAG
*
955064 TTTTGCTAACGTGCGCCCAAGCCTTCCTTGAG
1 TTTTGCTAACGTGCGCCCAAGCCTCCCTTGAG
*
955096 TTTTGCTAATGTGCGCC
1 TTTTGCTAACGTGCGCC
955113 GTTAATGAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.31
Consensus pattern (32 bp):
TTTTGCTAACGTGCGCCCAAGCCTCCCTTGAG
Found at i:964612 original size:4 final size:4
Alignment explanation
Indices: 964603--964638 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
964593 AAACAGATAG
964603 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
964639 GAAAAGGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:965408 original size:17 final size:17
Alignment explanation
Indices: 965377--965409 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
965367 AAATATTATT
965377 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
965394 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
965410 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:966109 original size:85 final size:86
Alignment explanation
Indices: 966000--966174 Score: 343
Period size: 85 Copynumber: 2.0 Consensus size: 86
965990 TAGGTAAAAA
966000 AAAATTAGATTGATTTTTTATCCAACTTTATGCATGTCTAGTAATAACACGACCACTTTGGTCTT
1 AAAATTAGATTGATTTTTTATCCAACTTTATGCATGTCTAGTAATAACACGACCACTTTGGTCTT
966065 ATCTCCGTACTCGAAACACAC
66 ATCTCCGTACTCGAAACACAC
966086 AAAA-TAGATTGATTTTTTATCCAACTTTATGCATGTCTAGTAATAACACGACCACTTTGGTCTT
1 AAAATTAGATTGATTTTTTATCCAACTTTATGCATGTCTAGTAATAACACGACCACTTTGGTCTT
966150 ATCTCCGTACTCGAAACACAC
66 ATCTCCGTACTCGAAACACAC
966171 AAAA
1 AAAA
966175 CATAGGTTAT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 85 0.96
86 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (86 bp):
AAAATTAGATTGATTTTTTATCCAACTTTATGCATGTCTAGTAATAACACGACCACTTTGGTCTT
ATCTCCGTACTCGAAACACAC
Found at i:970137 original size:157 final size:160
Alignment explanation
Indices: 969851--970167 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 160
969841 TTTACCCATT
969851 GAACTTTATAGATTGAATTTTTTTGGTCACTCGATCGTTTTCTCTCTAACTAAATGAATGGTATG
1 GAACTTTATAGATTGAATTTTTTTGGTCACTCGATCGTTTTCTCTCTAACTAAATGAATGGTATG
969916 GAAAAATTTAATATTAAATAGGCAACGTCAGATTGATATTAAATAACAATTACTAATATTTAATT
66 GAAAAATTTAATATTAAATAGGCAACGTCAGATTGATATTAAATAACAATTACTAATATTTAATT
969981 TT-AA-ATGA-TTTAACATAAAAAATAAAA
131 TTAAACATGATTTTAACATAAAAAATAAAA
970008 GAACTTTATAGATTGAATTTTTTTGGTCACTCGATCGTTTTCTCTCTAACTAAATGAATGGTATG
1 GAACTTTATAGATTGAATTTTTTTGGTCACTCGATCGTTTTCTCTCTAACTAAATGAATGGTATG
970073 GAAAAATTTAATATTAAATAGGCAACGTCAGATTGATATTAAATAACAATTACTAATATTTAATT
66 GAAAAATTTAATATTAAATAGGCAACGTCAGATTGATATTAAATAACAATTACTAATATTTAATT
970138 TTAAACATGATTTTAACATAAAAAATAAAA
131 TTAAACATGATTTTAACATAAAAAATAAAA
970168 ACAAACTAAA
Statistics
Matches: 157, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
157 132 0.84
158 2 0.01
159 4 0.03
160 19 0.12
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (160 bp):
GAACTTTATAGATTGAATTTTTTTGGTCACTCGATCGTTTTCTCTCTAACTAAATGAATGGTATG
GAAAAATTTAATATTAAATAGGCAACGTCAGATTGATATTAAATAACAATTACTAATATTTAATT
TTAAACATGATTTTAACATAAAAAATAAAA
Found at i:971505 original size:25 final size:26
Alignment explanation
Indices: 971470--971518 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
971460 TATAGGTTAG
971470 TTGAGGCACAA-TCTT-AGACACAACT
1 TTGAGGCACAACT-TTGAGACACAACT
*
971495 TTGAGGGACAACTTTGAGACACAA
1 TTGAGGCACAACTTTGAGACACAA
971519 TTCACAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
TTGAGGCACAACTTTGAGACACAACT
Found at i:971518 original size:13 final size:13
Alignment explanation
Indices: 971485--971518 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
971475 GCACAATCTT
971485 AGACACAACTTTG
1 AGACACAACTTTG
**
971498 AGGGACAACTTTG
1 AGACACAACTTTG
971511 AGACACAA
1 AGACACAA
971519 TTCACAAAGT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:976726 original size:262 final size:262
Alignment explanation
Indices: 976261--976781 Score: 963
Period size: 262 Copynumber: 2.0 Consensus size: 262
976251 CATGATAATA
*
976261 TTGTTGGTGTTCAAAGATCCCAAATTCTATAGTTTGTGTTTATATAAGGGATCATGAAATTAATG
1 TTGTTGGTGTTCAAAGATCCCAAATTATATAGTTTGTGTTTATATAAGGGATCATGAAATTAATG
976326 ATGGATCTTGATGTTTGTGAGGTAGTTGATTCATATTCAAGCATGTATGATGATTAGAACATGTT
66 ATGGATCTTGATGTTTGTGAGGTAGTTGATTCATATTCAAGCATGTATGATGATTAGAACATGTT
* * *
976391 TAATCTTTTTAGAACTTGTTCTTTAAATTTTGACCATGGATTGTTTAAGTGAGAAAAATTATGGA
131 TAATCTTTCTAGAACTTGTTATTTAAATTTCGACCATGGATTGTTTAAGTGAGAAAAATTATGGA
* *
976456 AAAATTATATAAGGGTTGGAAATGATGAAGGAAGTATTCTACAAGTCTTAGAAAAATTTGAGGAA
196 AAAATTATATAAGGGTTGGAAATGATGAAGGAAATATTCTACAAGTCTTAAAAAAATTTGAGGAA
976521 TC
261 TC
976523 TTGTTGGTGTTCAAAGATCCCAAATTATATAGTTAT-TGTTTATATAAGGGATCATGAAATTAAT
1 TTGTTGGTGTTCAAAGATCCCAAATTATATAGTT-TGTGTTTATATAAGGGATCATGAAATTAAT
976587 GATGGATCTTGATGTTTGTGAGGTAGTTGATTCATATTCAAGCATGTATGATGATTAGAACATGT
65 GATGGATCTTGATGTTTGTGAGGTAGTTGATTCATATTCAAGCATGTATGATGATTAGAACATGT
*
976652 TTAATCTTTCTAGAACTTGTTATTTAAATTTCGGCCATGGATTGTTTAAGTGAGAAAAATTATGG
130 TTAATCTTTCTAGAACTTGTTATTTAAATTTCGACCATGGATTGTTTAAGTGAGAAAAATTATGG
976717 AAAAATTATATAAGGGTTGGAAATGATGAAGGAAATATTCTACAAGTCTTAAAAAAATTTGAGGA
195 AAAAATTATATAAGGGTTGGAAATGATGAAGGAAATATTCTACAAGTCTTAAAAAAATTTGAGGA
976782 CCATTTTGTA
Statistics
Matches: 251, Mismatches: 7, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
262 250 1.00
263 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.37
Consensus pattern (262 bp):
TTGTTGGTGTTCAAAGATCCCAAATTATATAGTTTGTGTTTATATAAGGGATCATGAAATTAATG
ATGGATCTTGATGTTTGTGAGGTAGTTGATTCATATTCAAGCATGTATGATGATTAGAACATGTT
TAATCTTTCTAGAACTTGTTATTTAAATTTCGACCATGGATTGTTTAAGTGAGAAAAATTATGGA
AAAATTATATAAGGGTTGGAAATGATGAAGGAAATATTCTACAAGTCTTAAAAAAATTTGAGGAA
TC
Found at i:977620 original size:39 final size:39
Alignment explanation
Indices: 977540--977698 Score: 255
Period size: 40 Copynumber: 4.0 Consensus size: 39
977530 CAGGTTTATA
977540 ATACACTTCGGTGTATATGGTGGGCAACGACCTTATGTGT
1 ATACACTTCGGTGTATATGGTGGGC-ACGACCTTATGTGT
*
977580 ATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
1 ATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
* * *
977619 ATACACTTCAGTGTATATGGTGAGCACGACTTTATGTGT
1 ATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
*
977658 AATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGT
1 -ATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
977698 A
1 A
977699 GCACTACGGT
Statistics
Matches: 109, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
39 50 0.46
40 59 0.54
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (39 bp):
ATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
Found at i:977640 original size:79 final size:79
Alignment explanation
Indices: 977540--977698 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
977530 CAGGTTTATA
* * *
977540 ATACACTTCGGTGTATATGGTGGGCAACGACCTTATGTGT-ATACACTTTGGTGTATATGGTGGG
1 ATACACTTCAGTGTATATGGTGAGC-ACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGG
977604 CACGACCTTATGTGT
65 CACGACCTTATGTGT
*
977619 ATACACTTCAGTGTATATGGTGAGCACGACTTTATGTGTAATACACTTCGGTGTATATGGTGGGC
1 ATACACTTCAGTGTATATGGTGAGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGC
*
977684 ATGACCTTATGTGT
66 ACGACCTTATGTGT
977698 A
1 A
977699 GCACTACGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
78 13 0.18
79 61 0.82
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (79 bp):
ATACACTTCAGTGTATATGGTGAGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGC
ACGACCTTATGTGT
Found at i:977867 original size:25 final size:25
Alignment explanation
Indices: 977838--977912 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
977828 ATGGCAAGTA
977838 TATGGGTAAAATAAGCTTACGAGCT
1 TATGGGTAAAATAAGCTTACGAGCT
* *
977863 TAT-GG-AACAA-ATG-GTA--AG-T
1 TATGGGTAA-AATAAGCTTACGAGCT
977882 ATATGGGTAAAATAAGCTTACGAGCT
1 -TATGGGTAAAATAAGCTTACGAGCT
977908 TATGG
1 TATGG
977913 AACAAATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 4 0.11
22 6 0.16
23 6 0.16
24 4 0.11
25 10 0.27
26 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.28
Consensus pattern (25 bp):
TATGGGTAAAATAAGCTTACGAGCT
Found at i:977891 original size:45 final size:45
Alignment explanation
Indices: 977802--977973 Score: 265
Period size: 45 Copynumber: 3.8 Consensus size: 45
977792 ATAACCATGC
* * * *
977802 AAATAAGCTTATGATCTTATGGAA-TAATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGGTA
977846 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGGTA
*
977891 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGCTA
1 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGGTA
* * *
977936 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTAT
1 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTAT
977974 GTTGATAAGA
Statistics
Matches: 119, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 22 0.18
45 97 0.82
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATGGGTA
Found at i:980512 original size:14 final size:14
Alignment explanation
Indices: 980493--980522 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
980483 GTTTAGTTTG
*
980493 TAATTTTTTTTATT
1 TAATTTTCTTTATT
980507 TAATTTTCTTTATT
1 TAATTTTCTTTATT
980521 TA
1 TA
980523 TCAGCAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (14 bp):
TAATTTTCTTTATT
Found at i:980630 original size:13 final size:13
Alignment explanation
Indices: 980589--980637 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
980579 ATGTTTTTAA
980589 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
*
980603 GATTGT-ATCGTTTG
1 TATT-TAAT-GTTTG
980617 TATTTAATGTTTG
1 TATTTAATGTTTG
980630 TATTTAAT
1 TATTTAAT
980638 TATTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 15 0.50
14 14 0.47
15 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.59
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:984058 original size:13 final size:13
Alignment explanation
Indices: 984040--984065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
984030 TCTACTTAGC
984040 TTGATAAAAGGAA
1 TTGATAAAAGGAA
984053 TTGATAAAAGGAA
1 TTGATAAAAGGAA
984066 GAATGTGTAA
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:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TTGATAAAAGGAA
Found at i:991234 original size:19 final size:21
Alignment explanation
Indices: 991196--991239 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
991186 TAGAATTTCG
*
991196 ATTAGGATTTTAATAATTTATT
1 ATTAGGATTTTAAT-ATTTACT
991218 ATTAGGATTTT-AT-TTTACT
1 ATTAGGATTTTAATATTTACT
991237 ATT
1 ATT
991240 TATTAGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
21 2 0.10
22 11 0.52
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
ATTAGGATTTTAATATTTACT
Found at i:995146 original size:63 final size:63
Alignment explanation
Indices: 995061--995219 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 63
995051 TTTATGCTAG
* * * ** *
995061 GTGTATCGATGCTCATGAAGTGCATCGATGCATTAATTTAAA-AGAAAACATCGAATG-CTATCT
1 GTGTATCGATGCACAGGTAGTGCATCGATGCACCAACTTAAATA-AAAACATCGAATGAC-ATCT
** * *
995124 GTGTATCGATGCACAGGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATGACATTT
1 GTGTATCGATGCACAGGTAGTGCATCGATGCACCAACTTAAATAAAAACATCGAATGACATCT
* *
995187 GTGTACCGATGCATAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAGGTAGTGCATCGATGCAC
995220 ACATTAAGGA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 80 0.98
64 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCACAGGTAGTGCATCGATGCACCAACTTAAATAAAAACATCGAATGACATCT
Found at i:995237 original size:24 final size:22
Alignment explanation
Indices: 995205--995262 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 22
995195 ATGCATAGGT
995205 AGTGCATCGATGCACACAT-TAAGG
1 AGTGCATCGATGCACAC-TGT-A-G
995229 AGTGCATCGAT--ACACTGTAG
1 AGTGCATCGATGCACACTGTAG
995249 AGTGCATCGATGCA
1 AGTGCATCGATGCA
995263 TACCCTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 12 0.39
21 2 0.06
22 6 0.19
24 11 0.35
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (22 bp):
AGTGCATCGATGCACACTGTAG
Found at i:995598 original size:31 final size:30
Alignment explanation
Indices: 995562--995632 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
995552 ATTATATGAA
995562 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTAT-GAAAATGAAATGT
* *
995593 TTATGTGATAAAGGTATGTAAATGATATGT
1 TTATGTGATAAAGGTATGAAAATGAAATGT
* *
995623 CTATGCGATA
1 TTATGTGATA
995633 TAAATTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
TTATGTGATAAAGGTATGAAAATGAAATGT
Found at i:995856 original size:24 final size:24
Alignment explanation
Indices: 995828--995907 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 24
995818 ATATATGGTC
995828 CTTCGGGACAAATTCTACGCGGTCA
1 CTTCGGGACAAATTCTACGCGG-CA
*
995853 -TTCGGGATAAATTTCTACGCGGCA
1 CTTCGGGACAAA-TTCTACGCGGCA
*
995877 CTTCGGTG-CAAAACTCTACGCGGCA
1 CTTCGG-GAC-AAATTCTACGCGGCA
995902 CTTCGG
1 CTTCGG
995908 TGCAATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 12 0.25
25 32 0.67
26 4 0.08
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (24 bp):
CTTCGGGACAAATTCTACGCGGCA
Found at i:1002862 original size:21 final size:22
Alignment explanation
Indices: 1002838--1002882 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1002828 CCTTATCATG
*
1002838 TTTTTATTTAATTTATA-AAAA
1 TTTTAATTTAATTTATAGAAAA
* *
1002859 TTTTAATTTTATTTTTAGAAAA
1 TTTTAATTTAATTTATAGAAAA
1002881 TT
1 TT
1002883 ATATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATTTAATTTATAGAAAA
Found at i:1004247 original size:2 final size:2
Alignment explanation
Indices: 1004234--1004278 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1004224 TAATAATAAA
*
1004234 AT AT AT AC 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
1004276 AT A
1 AT A
1004279 AATAGTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1006190 original size:105 final size:105
Alignment explanation
Indices: 1005903--1006649 Score: 1318
Period size: 105 Copynumber: 7.1 Consensus size: 105
1005893 ATATCCTTCG
* *
1005903 TTGGCTCTGAAATTGAGAAATATGTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1 TTGGCTCTGAAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* *
1005968 GCGTTGTTTGGAGTCCAATATGCTTCGTTGTGAAGTTGAAA
65 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1006009 TTGGCTCTG-AATTGGAGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
1 TTGGCTCTGAAATT-GAG-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
1006073 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
64 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
1006115 TTGGCTCTG-AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1 TTGGCTCTGAAATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* *
1006179 GCGTTGCCTGGAGTCTAATATCCTTCGTTGTGAAGTTGAAA
65 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
1006220 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCATCATGAAGTTGAACTTG
1 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1006285 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
1006325 TTGGCTCTGAAATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1006390 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
1006430 TTGGCTCTGAAATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTG
1 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1006495 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
1006535 TTGGCTCTGAAATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1006600 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1006640 TTGGCTCTGA
1 TTGGCTCTGA
1006650 GTAAAACCTG
Statistics
Matches: 619, Mismatches: 19, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
105 503 0.81
106 109 0.18
107 7 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
Found at i:1007796 original size:16 final size:17
Alignment explanation
Indices: 1007773--1007812 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1007763 TCTTTGCATG
1007773 TGCTTTTTGTCCCTTTT
1 TGCTTTTTGTCCCTTTT
* *
1007790 T-CTTTTTGTTCTTTTT
1 TGCTTTTTGTCCCTTTT
1007806 TGCTTTT
1 TGCTTTT
1007813 GTTTTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.72
Consensus pattern (17 bp):
TGCTTTTTGTCCCTTTT
Found at i:1007819 original size:13 final size:14
Alignment explanation
Indices: 1007798--1007833 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1007788 TTTCTTTTTG
1007798 TTCTTTTTTGCTT-
1 TTCTTTTTTGCTTC
*
1007811 TTGTTTTTTGCTTC
1 TTCTTTTTTGCTTC
1007825 TTCTTTTTT
1 TTCTTTTTT
1007834 TTTTGCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (14 bp):
TTCTTTTTTGCTTC
Found at i:1011591 original size:2 final size:2
Alignment explanation
Indices: 1011584--1011648 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1011574 TAATAATAAA
1011584 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
1011626 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1011649 GTAATAAGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1013984 original size:22 final size:22
Alignment explanation
Indices: 1013959--1014013 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1013949 TCAGGAGTTA
* *
1013959 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1013981 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1014003 CAGGAGTTATA
1 CAGGAGTTATA
1014014 ACAGCTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1019168 original size:2 final size:2
Alignment explanation
Indices: 1019163--1019189 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1019153 TATACTTTTG
1019163 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1019190 CTTACACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1019566 original size:5 final size:5
Alignment explanation
Indices: 1019556--1019594 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
1019546 GTCCGTCCGT
*
1019556 CTCGG CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1019595 TGGTCGTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.03, C:0.41, G:0.38, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:1019603 original size:6 final size:6
Alignment explanation
Indices: 1019592--1019622 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1019582 TCGGCTCGGC
1019592 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1019623 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1020707 original size:24 final size:25
Alignment explanation
Indices: 1020670--1020716 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1020660 CTATTCTTTC
*
1020670 GCTTCAATTAAGC-TCGAATTTTAG
1 GCTTCAATCAAGCTTCGAATTTTAG
* *
1020694 GCTTCAATCGAGCTTCTAATTTT
1 GCTTCAATCAAGCTTCGAATTTT
1020717 TTTTTTGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (25 bp):
GCTTCAATCAAGCTTCGAATTTTAG
Found at i:1020968 original size:30 final size:30
Alignment explanation
Indices: 1020932--1020996 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1020922 AGTGAACCGG
* *
1020932 CGGTTCACACCGATTTTACCGGTTTTTAGC
1 CGGTTCACACCGATTTTACCGGTTCTCAGC
* *
1020962 CGGTTCACCCCGGTTTTACCGGTTCTCAGC
1 CGGTTCACACCGATTTTACCGGTTCTCAGC
1020992 CGGTT
1 CGGTT
1020997 TTACCAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (30 bp):
CGGTTCACACCGATTTTACCGGTTCTCAGC
Found at i:1023337 original size:29 final size:29
Alignment explanation
Indices: 1023302--1023364 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
1023292 ATGAAATTAT
* * *
1023302 AAAAATTAGGGGTTCTAATTATAAATATA
1 AAAAATTAAGGGCTCTAATTATAAATACA
1023331 AAAAATTAAGGGCTCTAATTATAAATACA
1 AAAAATTAAGGGCTCTAATTATAAATACA
1023360 AAAAA
1 AAAAA
1023365 CTGAGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (29 bp):
AAAAATTAAGGGCTCTAATTATAAATACA
Found at i:1026194 original size:2 final size:2
Alignment explanation
Indices: 1026189--1026262 Score: 89
Period size: 2 Copynumber: 36.5 Consensus size: 2
1026179 TAGTAATTAA
*
1026189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AGT AG A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
1026230 AGT AT CAT AT AT GT AT AT AT AT AT AT AT AT AT A
1 A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1026263 AACAATAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.03
2 57 0.89
3 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1027401 original size:33 final size:33
Alignment explanation
Indices: 1027354--1027424 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1027344 ATTTCAAGCA
* *
1027354 GCTTTATCTATAGGCATGTATGAGTTTACTCAT
1 GCTTTATCTATAGGCACGTACGAGTTTACTCAT
* *
1027387 GCTTTATCTGTAGGCGCGTACGAGTTTACTCAT
1 GCTTTATCTATAGGCACGTACGAGTTTACTCAT
1027420 G-TTTA
1 GCTTTA
1027425 AAACCGAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (33 bp):
GCTTTATCTATAGGCACGTACGAGTTTACTCAT
Found at i:1033625 original size:20 final size:20
Alignment explanation
Indices: 1033578--1033633 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 20
1033568 AACTCAGTTT
1033578 TCAAATTCGCAACGCGATTC
1 TCAAATTCGCAACGCGATTC
1033598 TCCAAATTCGCAACGCGATTC
1 T-CAAATTCGCAACGCGATTC
*
1033619 TCAAATTCGTAACGC
1 TCAAATTCGCAACGC
1033634 TAATTACCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATTC
Found at i:1033672 original size:99 final size:99
Alignment explanation
Indices: 1033501--1033691 Score: 321
Period size: 99 Copynumber: 1.9 Consensus size: 99
1033491 AAATAACCAA
*
1033501 CAAATTCGCAACGCGAGCTCCAATTTCGCAACGCTAATTACCGATATAAGTAAACACAACTATTC
1 CAAATTCGCAACGCGAGCTCCAAATTCGCAACGCTAATTACCGATATAAGTAAACACAACTATTC
1033566 GCAACTCAGTTTTCAAATTCGCAACGCGATTCTC
66 GCAACTCAGTTTTCAAATTCGCAACGCGATTCTC
* * *
1033600 CAAATTCGCAACGCGA-TTCTCAAATTCGTAACGCTAATTACCGATATAGGTAAACACAACTATT
1 CAAATTCGCAACGCGAGCTC-CAAATTCGCAACGCTAATTACCGATATAAGTAAACACAACTATT
*
1033664 TGCAACTCAGTTTTCAAATTCGCAACGC
65 CGCAACTCAGTTTTCAAATTCGCAACGC
1033692 TAATTGCCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
98 2 0.02
99 84 0.98
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (99 bp):
CAAATTCGCAACGCGAGCTCCAAATTCGCAACGCTAATTACCGATATAAGTAAACACAACTATTC
GCAACTCAGTTTTCAAATTCGCAACGCGATTCTC
Found at i:1033738 original size:57 final size:58
Alignment explanation
Indices: 1033619--1033747 Score: 206
Period size: 57 Copynumber: 2.2 Consensus size: 58
1033609 AACGCGATTC
* * **
1033619 TCAAATTCGTAACGCTAATTACCGATATAGGTAAACACAACTATTTGCAACTCAGTTT
1 TCAAATTCGCAACGCTAATTACCGATATAGATAAACACAACTATTCACAACTCAGTTT
*
1033677 TCAAATTCGCAACGCTAATTGCCGATATAGAT-AACACAACTATTCACAACTCAGTTT
1 TCAAATTCGCAACGCTAATTACCGATATAGATAAACACAACTATTCACAACTCAGTTT
1033734 TCAAATTCGCAACG
1 TCAAATTCGCAACG
1033748 AGATTTTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
57 37 0.56
58 29 0.44
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (58 bp):
TCAAATTCGCAACGCTAATTACCGATATAGATAAACACAACTATTCACAACTCAGTTT
Found at i:1034148 original size:20 final size:20
Alignment explanation
Indices: 1034125--1034202 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
1034115 CGAAAACGAA
*
1034125 AATCGCATTGCGAATTTGAG
1 AATCGCGTTGCGAATTTGAG
*
1034145 AATCACGTTGCGAATTTG-G
1 AATCGCGTTGCGAATTTGAG
* *
1034164 AAACTGTGTTGCGAAATTTGAG
1 AATC-GCGTTGCG-AATTTGAG
1034186 -ATCGCGTTGCGAATTTG
1 AATCGCGTTGCGAATTTG
1034203 TTGGTTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 10 0.21
20 29 0.60
21 8 0.17
22 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (20 bp):
AATCGCGTTGCGAATTTGAG
Found at i:1037405 original size:16 final size:16
Alignment explanation
Indices: 1037384--1037415 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1037374 AAGGAACCAG
1037384 AGATTATTTCAAGGCC
1 AGATTATTTCAAGGCC
1037400 AGATTATTTCAAGGCC
1 AGATTATTTCAAGGCC
1037416 GTATCCGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
AGATTATTTCAAGGCC
Found at i:1040958 original size:3 final size:3
Alignment explanation
Indices: 1040950--1040999 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1040940 TACACCTTCG
* *
1040950 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1040998 AA
1 AA
1041000 GAGTTAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1044235 original size:2 final size:2
Alignment explanation
Indices: 1044228--1044289 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1044218 TATCAAGAAT
1044228 TA TA TA TA TA TA -A 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
1044269 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1044290 CTTATATGGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1046865 original size:19 final size:19
Alignment explanation
Indices: 1046843--1046880 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1046833 CAAAACTTCA
*
1046843 TTTGTTTTCAACATCAAAT
1 TTTGCTTTCAACATCAAAT
1046862 TTTGCTTTCAACATCAAAT
1 TTTGCTTTCAACATCAAAT
1046881 CATTTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTGCTTTCAACATCAAAT
Found at i:1047368 original size:11 final size:11
Alignment explanation
Indices: 1047352--1047380 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1047342 ATCTTATTTT
1047352 TTTTCTTCTTC
1 TTTTCTTCTTC
1047363 TTTTCTTCTTC
1 TTTTCTTCTTC
1047374 -TTTCTTC
1 TTTTCTTC
1047381 CTTTGGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTCTTCTTC
Found at i:1048857 original size:20 final size:20
Alignment explanation
Indices: 1048832--1048881 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1048822 CAATATGTAA
*
1048832 TATCGGTACTGCCATAATAG
1 TATCGGTACTACCATAATAG
*
1048852 TATCGGTACTACCATGATAG
1 TATCGGTACTACCATAATAG
*
1048872 TATCGATACT
1 TATCGGTACT
1048882 TCTCTTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (20 bp):
TATCGGTACTACCATAATAG
Found at i:1052945 original size:36 final size:36
Alignment explanation
Indices: 1052905--1053019 Score: 203
Period size: 36 Copynumber: 3.2 Consensus size: 36
1052895 TGCTACCTTC
1052905 GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
1 GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
1052941 GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
1 GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
* * *
1052977 GGCTTCGATTTCGCAGAAGCAGAGGTAGCAGCTTTA
1 GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
1053013 GGCTTCG
1 GGCTTCG
1053020 CGGCGGAGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (36 bp):
GGCTTCGATTTCACAGTAGCAGAGGTGGCAGCTTTA
Found at i:1054058 original size:28 final size:27
Alignment explanation
Indices: 1054022--1054074 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
1054012 ATAAGTATAA
*
1054022 ATATGATTAAAAGGAACAACTTTCAAAT
1 ATATAATTAAAAGGAACAA-TTTCAAAT
1054050 ATATAATTAAAAGGAACAATTTCAA
1 ATATAATTAAAAGGAACAATTTCAA
1054075 TTTAACATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (27 bp):
ATATAATTAAAAGGAACAATTTCAAAT
Found at i:1057867 original size:21 final size:21
Alignment explanation
Indices: 1057843--1057896 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1057833 TTATAAAGAA
*
1057843 AGTATCGATACTTCAAAAGGC
1 AGTATTGATACTTCAAAAGGC
*
1057864 AGTATTGATACTTTAAAAGGC
1 AGTATTGATACTTCAAAAGGC
1057885 AGTATTGATACT
1 AGTATTGATACT
1057897 CCTCCTTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTATTGATACTTCAAAAGGC
Found at i:1064229 original size:3 final size:3
Alignment explanation
Indices: 1064221--1064262 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1064211 TAGAGAAAAG
1064221 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1064263 TGATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1067983 original size:14 final size:15
Alignment explanation
Indices: 1067952--1067989 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1067942 TAAATTTTGA
1067952 TTTTATGAATAGTAT
1 TTTTATGAATAGTAT
1067967 TTTTATG-ATA-TAT
1 TTTTATGAATAGTAT
1067980 TTTTAT-AATA
1 TTTTATGAATA
1067990 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.55
14 3 0.14
15 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (15 bp):
TTTTATGAATAGTAT
Found at i:1068912 original size:3 final size:3
Alignment explanation
Indices: 1068902--1068930 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1068892 TTATTACAAA
1068902 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1068931 TAATTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1069006 original size:2 final size:2
Alignment explanation
Indices: 1068999--1069040 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1068989 TTCACTTATT
1068999 TA TA TA 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
1069041 CTCATTCACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1069163 original size:20 final size:20
Alignment explanation
Indices: 1069138--1069178 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1069128 AATTAAATTC
*
1069138 ATGTTAGATCATAATTTTTA
1 ATGTTAGATCATAAATTTTA
1069158 ATGTTAGATCATAAATTTTA
1 ATGTTAGATCATAAATTTTA
1069178 A
1 A
1069179 GAAAGTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTTAGATCATAAATTTTA
Found at i:1070109 original size:20 final size:20
Alignment explanation
Indices: 1070084--1070150 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
1070074 TTTTCCGAAT
*
1070084 TCGCAACGCGAATATATAAA
1 TCGCAACGCGAATATGTAAA
*** *
1070104 TCGCAATATGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
* *
1070124 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATATGTAAA
1070144 TCGCAAC
1 TCGCAAC
1070151 ACAGAAGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1070164 original size:20 final size:20
Alignment explanation
Indices: 1070141--1070189 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1070131 GCGAATTTGT
*
1070141 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAAAAGTCA
1070161 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
1070181 AATTCGCAA
1 AATTCGCAA
1070190 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:1070370 original size:22 final size:22
Alignment explanation
Indices: 1070337--1070416 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
1070327 TCACTCTCTA
* *
1070337 CGGCGACATCCGTCCCTATCTC
1 CGGCGAAATCCGTCCCCATCTC
* *
1070359 CGACAAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
1070381 CGGCGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
1070403 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
1070417 TATCTCCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.19
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:1070820 original size:19 final size:20
Alignment explanation
Indices: 1070798--1070869 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1070788 ATCGCAATGT
* *
1070798 GATTTT-AGTTTCGCGCTAC
1 GATTTTAAGTTTCGCGTTGC
* *
1070817 GATTTTCATTTTCGCGTTGC
1 GATTTTAAGTTTCGCGTTGC
* * *
1070837 AATTTTTATTTTCGCGTTGC
1 GATTTTAAGTTTCGCGTTGC
1070857 GATTTTAAGTTTC
1 GATTTTAAGTTTC
1070870 AGAAACCACT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 6 0.14
20 38 0.86
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.50
Consensus pattern (20 bp):
GATTTTAAGTTTCGCGTTGC
Found at i:1070831 original size:20 final size:20
Alignment explanation
Indices: 1070806--1070862 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1070796 GTGATTTTAG
* *
1070806 TTTCGCGCTACGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* *
1070826 TTTCGCGTTGCAATTTTTAT
1 TTTCGCGTTGCGATTTTCAT
1070846 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1070863 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.19, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:1072590 original size:21 final size:21
Alignment explanation
Indices: 1072563--1072615 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1072553 GTTAGGGGAG
*
1072563 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * *
1072584 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
1072605 TTACGTGATGA
1 TTACGTGATGA
1072616 AAATGGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.13, G:0.36, T:0.32
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1072671 original size:63 final size:63
Alignment explanation
Indices: 1072604--1072738 Score: 148
Period size: 63 Copynumber: 2.1 Consensus size: 63
1072594 AGGTCGGTAC
* * *
1072604 TTTACGTGATGAAAATGGTGCATGGCGTGATGAGGTA-C-AGTCTTTACGTGGTGAGGTAGAGGT
1 TTTACGTGATGAAAATGGTGCATGACGTGATGAGGTATCTA--CTTTACGTGATGAGGTAGACGT
** * * * * *
1072667 TTTACACGATGACAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGCCGT
1 TTTACGTGATGAAAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGACGT
1072730 TTTACGTGA
1 TTTACGTGA
1072739 GATTGTTACA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
63 56 0.97
64 1 0.02
65 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.33
Consensus pattern (63 bp):
TTTACGTGATGAAAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGACGT
Found at i:1072861 original size:12 final size:12
Alignment explanation
Indices: 1072835--1072876 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1072825 TTTTTCGACA
1072835 TTATTTATTTG-T
1 TTATTTA-TTGAT
1072847 TTATTTATTGAT
1 TTATTTATTGAT
* *
1072859 TTATGTATTAAT
1 TTATTTATTGAT
1072871 TTATTT
1 TTATTT
1072877 TTAGCGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:1073071 original size:21 final size:20
Alignment explanation
Indices: 1073020--1073094 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
1073010 GATTCACCTG
*
1073020 TCATCGTTCAAGAGGCCCCC
1 TCATCGTTCAAGAGGCCCTC
* *
1073040 T-ATCTTTCAAGATGCCACTC
1 TCATCGTTCAAGAGGCC-CTC
1073060 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGG-CCCTC
* *
1073081 TCACCATTCAAGAG
1 TCATCGTTCAAGAG
1073095 CTCGATTCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.29
20 4 0.09
21 26 0.58
22 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:1074599 original size:20 final size:20
Alignment explanation
Indices: 1074576--1074625 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1074566 TCGCGTTGCG
1074576 AAAGTAAAATTCGCAACGCA
1 AAAGTAAAATTCGCAACGCA
*
1074596 AAAGTCAAATTCGCAACGCA
1 AAAGTAAAATTCGCAACGCA
*
1074616 AAAGTTAAAT
1 AAAGTAAAAT
1074626 GTGCGTTGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (20 bp):
AAAGTAAAATTCGCAACGCA
Found at i:1074646 original size:14 final size:15
Alignment explanation
Indices: 1074627--1074655 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1074617 AAGTTAAATG
1074627 TGCGTTGCG-ATTTT
1 TGCGTTGCGAATTTT
1074641 TGCGTTGCGAATTTT
1 TGCGTTGCGAATTTT
1074656 ACTTTCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.10, C:0.14, G:0.28, T:0.48
Consensus pattern (15 bp):
TGCGTTGCGAATTTT
Found at i:1074693 original size:29 final size:29
Alignment explanation
Indices: 1074668--1074740 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
1074658 TTTCGCATTT
*
1074668 CGAATTTGATTTTCGTAACAATCGCAACG
1 CGAATTTGACTTTCGTAACAATCGCAACG
* *
1074697 CGAATTTGACTTTCGTAACTATCTCAACG
1 CGAATTTGACTTTCGTAACAATCGCAACG
*
1074726 TGAATTTGACTTTCG
1 CGAATTTGACTTTCG
1074741 CGTTGCGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (29 bp):
CGAATTTGACTTTCGTAACAATCGCAACG
Found at i:1074976 original size:18 final size:18
Alignment explanation
Indices: 1074953--1074988 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1074943 AAGCCGGTTG
*
1074953 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1074971 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1074989 CCTTTTACTT
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:1077213 original size:24 final size:24
Alignment explanation
Indices: 1077186--1077239 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1077176 CTGTTTCATC
1077186 ATCAAAATAC-GAGTATTGACCAAG
1 ATCAAAAT-CTGAGTATTGACCAAG
* *
1077210 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
1077234 ATCAAA
1 ATCAAA
1077240 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:1078016 original size:14 final size:15
Alignment explanation
Indices: 1077980--1078017 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1077970 GAAATCATTG
1077980 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1077995 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1078010 AAAAATTA
1 AAAAATTA
1078018 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1081380 original size:21 final size:21
Alignment explanation
Indices: 1081354--1081397 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1081344 AGCTGAAGTT
*
1081354 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTACATCGATAC
1081375 ACTGTAGCAGTACATCGATAC
1 ACTGTAGCAGTACATCGATAC
1081396 AC
1 AC
1081398 AATTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATAC
Found at i:1081536 original size:19 final size:20
Alignment explanation
Indices: 1081502--1081541 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1081492 TACTATTTGC
*
1081502 ACATTATCGATACTATTCAT
1 ACATTATAGATACTATTCAT
1081522 ACATTATAG-TACTATTCAT
1 ACATTATAGATACTATTCAT
1081541 A
1 A
1081542 AAAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (20 bp):
ACATTATAGATACTATTCAT
Found at i:1082157 original size:71 final size:71
Alignment explanation
Indices: 1082040--1082176 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 71
1082030 AAAGTAAGAT
* * *
1082040 TAACACTATGTACATTTAAGGGTAAAGTACATGAATGGTCCCCCGATTATAAGGAGTTGTTTTGT
1 TAACACTATGTACATTTAAGGGTAAAGTACATAAATAGTCCCCCGATTATAAGGAGTTATTTTGT
1082105 TGGGTC
66 TGGGTC
* *
1082111 TAACACTATGTACATTTAAGGGTAACA-TACATAAATAGTCCTCCGATTATAGGGAGTTATTTTG
1 TAACACTATGTACATTTAAGGGTAA-AGTACATAAATAGTCCCCCGATTATAAGGAGTTATTTTG
1082175 TT
65 TT
1082177 AAGTCTCTCG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 59 0.98
72 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (71 bp):
TAACACTATGTACATTTAAGGGTAAAGTACATAAATAGTCCCCCGATTATAAGGAGTTATTTTGT
TGGGTC
Found at i:1092509 original size:11 final size:11
Alignment explanation
Indices: 1092495--1092545 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
1092485 TTTACATTAT
1092495 ATTTTTATTGA
1 ATTTTTATTGA
*
1092506 A-TTTTATTTA
1 ATTTTTATTGA
* *
1092516 TTTTTTATT-T
1 ATTTTTATTGA
*
1092526 ATTTTTATTGC
1 ATTTTTATTGA
1092537 ATTTTTATT
1 ATTTTTATT
1092546 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (11 bp):
ATTTTTATTGA
Done.