Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 82 of 171
Found at i:27425157 original size:41 final size:41
Alignment explanation
Indices: 27425111--27425201 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
27425101 AAGAGTATTT
27425111 GCGGTGTTTATGGGAAAAACACCGCAAAAGGTTAAGCAAAA
1 GCGGTGTTTATGGGAAAAACACCGCAAAAGGTTAAGCAAAA
* * * * * *
27425152 GCGGTGTTAATGGGAAAAACGCTGCTAAAGGTTAAGTAATA
1 GCGGTGTTTATGGGAAAAACACCGCAAAAGGTTAAGCAAAA
27425193 GCGGTGTTT
1 GCGGTGTTT
27425202 TCTCATAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (41 bp):
GCGGTGTTTATGGGAAAAACACCGCAAAAGGTTAAGCAAAA
Found at i:27425678 original size:25 final size:25
Alignment explanation
Indices: 27425644--27425693 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27425634 CTATAGAGAG
27425644 GTGCTAATTAATTTGCAAAGTTTTC
1 GTGCTAATTAATTTGCAAAGTTTTC
27425669 GTGCTAATTAATTTGCAAAGTTTTC
1 GTGCTAATTAATTTGCAAAGTTTTC
27425694 ATTCATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (25 bp):
GTGCTAATTAATTTGCAAAGTTTTC
Found at i:27429083 original size:43 final size:42
Alignment explanation
Indices: 27429022--27429152 Score: 174
Period size: 43 Copynumber: 3.1 Consensus size: 42
27429012 TCTATTATTA
*
27429022 TTAGCGGAGTTTGTGGGAAAAACGCCACTAAAGAACATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAACGCCACTAAAG-ACATGTTCT
* *
27429065 TTAGCGGCTTTTGTGGGAAAAATGCCACTAAAGACAATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAACGCCACTAAAGAC-ATGTTCT
* * *
27429108 TTAGCGGCGTTTGCT-GGAAAAGCGCCGCTAAAGACATATTCT
1 TTAGCGGCGTTTG-TGGGAAAAACGCCACTAAAGACATGTTCT
27429150 TTA
1 TTA
27429153 CCTTTTTCTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
42 11 0.14
43 66 0.85
44 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGGAAAAACGCCACTAAAGACATGTTCT
Found at i:27431977 original size:66 final size:66
Alignment explanation
Indices: 27431828--27431978 Score: 169
Period size: 66 Copynumber: 2.3 Consensus size: 66
27431818 GTTCAAGAAC
* * * * * *
27431828 TTGAGAAGACCTGATATCTCGTACAGAAGCTTGGGAAGACTCGATATCTCATTCAAGATCTTGGG
1 TTGAGAAGACCTGATATCTCATACAGAAGCTTGGGAAGACACAATAACCCATTCAAGAGCTTGGG
27431893 A
66 A
* * * * * *
27431894 TTGAAAAGGCCTAATATCTCCAT-CAGAAGCTTGGGAAGACACAATAACCCGTTTAGGAGCTTGG
1 TTGAGAAGACCTGATATCT-CATACAGAAGCTTGGGAAGACACAATAACCCATTCAAGAGCTTGG
27431958 GA
65 GA
*
27431960 TTGAGAAGACTTGATATCT
1 TTGAGAAGACCTGATATCT
27431979 GGTTCAAGAG
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
66 66 0.97
67 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (66 bp):
TTGAGAAGACCTGATATCTCATACAGAAGCTTGGGAAGACACAATAACCCATTCAAGAGCTTGGG
A
Found at i:27442862 original size:89 final size:89
Alignment explanation
Indices: 27442762--27442933 Score: 265
Period size: 89 Copynumber: 1.9 Consensus size: 89
27442752 TAAAAAGGAT
27442762 TGTCGAAACGTTTTATTTTTCAGGAAAAACAAACAAGCCTAGAACAATATTTTAAAATTAAAAAA
1 TGTCGAAACGTTTTATTTTTCAGGAAAAACAAACAAGCCTAGAACAATATTTTAAAATT-AAAAA
27442827 TTAT-AAAAAAGGGAGTCATCAAGC
65 TTATAAAAAAAGGGAGTCATCAAGC
* * * * * *
27442851 TGTCGAAACGTTTTATTTTTCGGGAAAAACAAACAAGTCTCGAACAGTATTTTAAAGTTGAAAAT
1 TGTCGAAACGTTTTATTTTTCAGGAAAAACAAACAAGCCTAGAACAATATTTTAAAATTAAAAAT
27442916 TATAAAAAAAAGGGAGTC
66 TAT-AAAAAAAGGGAGTC
27442934 GCCATCAATC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
88 8 0.11
89 54 0.72
90 13 0.17
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (89 bp):
TGTCGAAACGTTTTATTTTTCAGGAAAAACAAACAAGCCTAGAACAATATTTTAAAATTAAAAAT
TATAAAAAAAGGGAGTCATCAAGC
Found at i:27444098 original size:57 final size:58
Alignment explanation
Indices: 27443972--27444241 Score: 207
Period size: 57 Copynumber: 4.7 Consensus size: 58
27443962 TCAAAAATGG
* * * * * * *
27443972 AATTTTT-AAAAAATCAGGGTCAAAAATGGAGTTTTTGGAAGTTTAGGGGTAAAGTCAC
1 AATTTTTGGAAAAATCAGGGTC-AAAATGAAATTTTTGGAAGTTTGGGGGTAAAATGAT
**
27444030 AA-TTTAAGAAAAATCA-GGTCAAAAATGAAATTTTTGGAAGTTTGGGGGT-AAATGAT
1 AATTTTTGGAAAAATCAGGGTC-AAAATGAAATTTTTGGAAGTTTGGGGGTAAAATGAT
* * ** *
27444086 AATTTTTGGAAAAA-CTAGGGTCAAAAT-AGAGTTTTGGAAGTTT-ATGGTCAAAATGGT
1 AATTTTTGGAAAAATC-AGGGTCAAAATGAAATTTTTGGAAGTTTGGGGGT-AAAATGAT
* * * *
27444143 AATTTTTGGAAAAATC-GAGGTTAAAATGTAAATTTTAGAAAGTTTAGGGGCTAAAATG-T
1 AATTTTTGGAAAAATCAG-GGTCAAAATG-AAATTTTTGGAAGTTT-GGGGGTAAAATGAT
* * * *
27444202 AATTTTCGGAAAATTTAGGGATCAAAATGTAATTTTTGGA
1 AATTTTTGGAAAAATCAGGG-TCAAAATGAAATTTTTGGA
27444242 CAGATCGAGG
Statistics
Matches: 168, Mismatches: 30, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
55 3 0.02
56 22 0.13
57 76 0.45
58 15 0.09
59 36 0.21
60 14 0.08
61 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
AATTTTTGGAAAAATCAGGGTCAAAATGAAATTTTTGGAAGTTTGGGGGTAAAATGAT
Found at i:27444173 original size:29 final size:29
Alignment explanation
Indices: 27444135--27444251 Score: 74
Period size: 30 Copynumber: 3.9 Consensus size: 29
27444125 GTTTATGGTC
27444135 AAAATGGTAATTTTTGGAAAAATCGAGGTT
1 AAAAT-GTAATTTTTGGAAAAATCGAGGTT
* * ** * * *
27444165 AAAATGTAAATTTTAGAAAGTTTAGGGGCT
1 AAAATGTAATTTTTGGAAA-AATCGAGGTT
* ** *
27444195 AAAATGTAATTTTCGG-AAAATTTAGGGATC
1 AAAATGTAATTTTTGGAAAAATCGA-GG-TT
* *
27444225 AAAATGTAATTTTTGGACAGATCGAGG
1 AAAATGTAATTTTTGGAAAAATCGAGG
27444252 ACCTTTAGGG
Statistics
Matches: 61, Mismatches: 22, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
28 1 0.02
29 16 0.26
30 40 0.66
31 4 0.07
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.32
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAAATCGAGGTT
Found at i:27444198 original size:30 final size:30
Alignment explanation
Indices: 27444164--27444238 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
27444154 AAATCGAGGT
* *
27444164 TAAAATGTAAATTTT-AGAAAGTTTAGGGGC
1 TAAAATGTAAATTTTCAGAAAATTTA-GGGA
*
27444194 TAAAATGT-AATTTTCGGAAAATTTAGGGA
1 TAAAATGTAAATTTTCAGAAAATTTAGGGA
*
27444223 TCAAAATGTAATTTTT
1 T-AAAATGTAAATTTT
27444239 GGACAGATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 10 0.26
30 23 0.61
31 5 0.13
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (30 bp):
TAAAATGTAAATTTTCAGAAAATTTAGGGA
Found at i:27445364 original size:3 final size:3
Alignment explanation
Indices: 27445351--27445392 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
27445341 CTTTCCATTT
* * *
27445351 TTA TT- TTA TTA TTA ATA TTA TTA ATA TTA TTA ATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27445393 AAATTAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:27445371 original size:9 final size:9
Alignment explanation
Indices: 27445357--27445391 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
27445347 ATTTTTATTT
27445357 TATTATTAA
1 TATTATTAA
27445366 TATTATTAA
1 TATTATTAA
27445375 TATTATTAA
1 TATTATTAA
27445384 TATTATTA
1 TATTATTA
27445392 TAAATTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:27446112 original size:6 final size:6
Alignment explanation
Indices: 27446096--27446171 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
27446086 GTATTTGAAC
* * * * *
27446096 TTTAAA ATTAAA TTTAAA GTTAAG TTTAAA -AT-CA TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* **
27446143 -GTAAA TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
27446172 ACCAATCTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
4 1 0.02
5 6 0.12
6 39 0.78
7 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:27446113 original size:12 final size:12
Alignment explanation
Indices: 27446096--27446172 Score: 61
Period size: 12 Copynumber: 6.6 Consensus size: 12
27446086 GTATTTGAAC
27446096 TTTAAAATTAAA
1 TTTAAAATTAAA
* *
27446108 TTTAAAGTTAAG
1 TTTAAAATTAAA
*
27446120 TTTAAAA-T-CA
1 TTTAAAATTAAA
*
27446130 TTTCAAATTTAAA
1 TTT-AAAATTAAA
* *
27446143 -GTAAATTTAAA
1 TTTAAAATTAAA
*
27446154 TTTAAAAATAAA
1 TTTAAAATTAAA
27446166 TTTAAAA
1 TTTAAAA
27446173 CCAATCTAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 3 0.06
11 13 0.26
12 33 0.66
13 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:27446165 original size:18 final size:17
Alignment explanation
Indices: 27446096--27446171 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 17
27446086 GTATTTGAAC
* *
27446096 TTTAAAATTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
27446114 GTTAAGTTTAAAAT-CA
1 TTTAAATTTAAAATAAA
*
27446130 TTTCAAATTTAAAGTAAA
1 TTT-AAATTTAAAATAAA
27446148 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
27446166 TTTAAA
1 TTTAAA
27446172 ACCAATCTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 3 0.07
17 16 0.36
18 26 0.58
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:27446188 original size:46 final size:46
Alignment explanation
Indices: 27446098--27446188 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 46
27446088 ATTTGAACTT
** * * * *
27446098 TAAAATTAAATTTAAAGTTAAGTTTAAAATCATTTCAAATTTAAAG
1 TAAAATTAAATTTAAAAATAAATTTAAAACCATCTCAAACTTAAAG
*
27446144 TAAATTTAAATTTAAAAATAAATTTAAAACCAATCT-AAACTTAAA
1 TAAAATTAAATTTAAAAATAAATTTAAAACC-ATCTCAAACTTAAA
27446189 ATCAAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
46 34 0.92
47 3 0.08
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (46 bp):
TAAAATTAAATTTAAAAATAAATTTAAAACCATCTCAAACTTAAAG
Found at i:27448879 original size:31 final size:31
Alignment explanation
Indices: 27448836--27448895 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
27448826 AATCTGGGAG
*
27448836 TGAAAAGAATATAAAACAAACATGGAGGGGC
1 TGAAAAGAATATAAAACAAACACGGAGGGGC
*
27448867 TGAATAGAATATAAAACAAACACGGAGGG
1 TGAAAAGAATATAAAACAAACACGGAGGG
27448896 ACTAGAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.10, G:0.25, T:0.13
Consensus pattern (31 bp):
TGAAAAGAATATAAAACAAACACGGAGGGGC
Found at i:27449811 original size:42 final size:41
Alignment explanation
Indices: 27449763--27449902 Score: 106
Period size: 40 Copynumber: 3.3 Consensus size: 41
27449753 AACCACCGCT
27449763 AAAGGTAAAGAGCAATAATGGCGTTTATGGGAAAACGCCGTA
1 AAAGGTAAAGAGCAATAA-GGCGTTTATGGGAAAACGCCGTA
* * * * *
27449805 AAAGGT-AA-AGCAATAGAGACGTTT-TTGCAGAAATGCCGTT
1 AAAGGTAAAGAGCAATA-AGGCGTTTATGGGA-AAACGCCGTA
* * * * *
27449845 AAAGGTAAAGAGTATTAGCGGCGTTTATGGGAAAAACACCGCA
1 AAAGGTAAAGAGCAATA-AGGCGTTTATGGG-AAAACGCCGTA
*
27449888 AAAGGTTAAGCAGCA
1 AAAGGTAAAG-AGCA
27449903 GCGGTCTTTA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
39 3 0.04
40 27 0.36
41 5 0.07
42 18 0.24
43 17 0.23
44 4 0.05
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (41 bp):
AAAGGTAAAGAGCAATAAGGCGTTTATGGGAAAACGCCGTA
Found at i:27453855 original size:44 final size:43
Alignment explanation
Indices: 27453769--27453930 Score: 168
Period size: 43 Copynumber: 3.7 Consensus size: 43
27453759 TCTGTCAATG
*
27453769 TTAGCGGAGTTTGTGAGAAAAACGCCACTAAAGA-ACATGTTCT
1 TTAGCGGCGTTTGTGAGAAAAACGCCACTAAAGACA-ATGTTCT
* * * **
27453812 CTAGTGGCGTTTGTGAGAAAAATGTCTGCTAAAGACAATGTTCT
1 TTAGCGGCGTTTGTGAGAAAAACG-CCACTAAAGACAATGTTCT
* * *
27453856 TTAGCGGAGTTTATG-GTAAAAACGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGAG-AAAAACGCCACTAAAGACAATGTTCT
* *
27453899 TTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAA
1 TTAGCGGCGTTTG-TGAGAAAAACGCCACTAAA
27453931 CACCACGTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
43 61 0.63
44 35 0.36
45 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAGAAAAACGCCACTAAAGACAATGTTCT
Found at i:27453941 original size:43 final size:43
Alignment explanation
Indices: 27453851--27453947 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
27453841 TAAAGACAAT
* *
27453851 GTTCTTTAGCGGAGTTTATGGTAAAAACGCCACTAAAGACCAT
1 GTTCTTTAGCGGAGTTTATGGTAAAAACGCCACTAAACACCAC
* * * *
27453894 GTTCTTTAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAACACCAC
1 GTTCTTTAGCGGAGTTT-ATGGTAAAAACGCCACTAAACACCAC
*
27453937 GTTCTATAGCG
1 GTTCTTTAGCG
27453948 ACATTTTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 43 0.93
44 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
GTTCTTTAGCGGAGTTTATGGTAAAAACGCCACTAAACACCAC
Found at i:27462056 original size:45 final size:45
Alignment explanation
Indices: 27462006--27462096 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
27461996 TCCAATATAC
27462006 AAAAAAAAAGAC-ACTAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
1 AAAAAAAAA-ACTA-TAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
27462052 AAAAAAAAAACTATAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
1 AAAAAAAAAACTATAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
27462097 GGAGTTTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 34 0.77
46 10 0.23
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (45 bp):
AAAAAAAAAACTATAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
Found at i:27462154 original size:40 final size:40
Alignment explanation
Indices: 27462109--27462231 Score: 138
Period size: 40 Copynumber: 3.0 Consensus size: 40
27462099 AGTTTGGATC
** *
27462109 AAAAACGTCGCAAAAGGTAAAGCAATGGCGATGTTTTTGG
1 AAAAACGTCGCAAAAGGTAAAGCAATAACGACGTTTTTGG
* * * * *
27462149 AAAAACGCCGCTAAAGGTAAAGAGCAATAATGGCGTTTATGG
1 AAAAACGTCGCAAAAGGT-AA-AGCAATAACGACGTTTTTGG
* *
27462191 GAAAACATCGCAAAAGGTAAAGCAATAACGACGTTTTTGG
1 AAAAACGTCGCAAAAGGTAAAGCAATAACGACGTTTTTGG
27462231 A
1 A
27462232 GAAATACCGT
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
40 33 0.51
41 4 0.06
42 28 0.43
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (40 bp):
AAAAACGTCGCAAAAGGTAAAGCAATAACGACGTTTTTGG
Found at i:27462196 original size:42 final size:42
Alignment explanation
Indices: 27462141--27462291 Score: 137
Period size: 42 Copynumber: 3.6 Consensus size: 42
27462131 CAATGGCGAT
* * * *
27462141 GTTTTTGGAAAAACGCCGCTAAAGGTAAAGAGCAATAATGGC
1 GTTTATGGGAAAACACCGCAAAAGGTAAAGAGCAATAATGGC
* * *
27462183 GTTTATGGGAAAACATCGCAAAAGGT-AA-AGCAATAACGAC
1 GTTTATGGGAAAACACCGCAAAAGGTAAAGAGCAATAATGGC
* * ** * * *
27462223 GTTT-TTGGAGAAATACCGTTAAAGGTAAAGAGTATTAGTGGC
1 GTTTATGGGA-AAACACCGCAAAAGGTAAAGAGCAATAATGGC
27462265 GTTTATGGGAAAAACACCGCAAAAGGT
1 GTTTATGGG-AAAACACCGCAAAAGGT
27462292 TAAGCAGTAG
Statistics
Matches: 83, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
39 4 0.05
40 26 0.31
41 4 0.05
42 32 0.39
43 16 0.19
44 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (42 bp):
GTTTATGGGAAAACACCGCAAAAGGTAAAGAGCAATAATGGC
Found at i:27462247 original size:40 final size:39
Alignment explanation
Indices: 27462121--27462252 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 39
27462111 AAACGTCGCA
** *
27462121 AAAGGTAAAGCAATGGCGATGTTTTTGGA-AAAACGCCGCT
1 AAAGGTAAAGCAATAACGACGTTTTTGGAGAAAA--CCGCT
* * * *
27462161 AAAGGTAAAGAGCAATAATGGCGTTTATGG-GAAAACATCGCA
1 AAAGGT-AA-AGCAATAACGACGTTTTTGGAGAAAAC--CGCT
*
27462203 AAAGGTAAAGCAATAACGACGTTTTTGGAGAAATACCGTT
1 AAAGGTAAAGCAATAACGACGTTTTTGGAGAAA-ACCGCT
27462243 AAAGGTAAAG
1 AAAGGTAAAG
27462253 AGTATTAGTG
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
40 36 0.49
41 8 0.11
42 29 0.40
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (39 bp):
AAAGGTAAAGCAATAACGACGTTTTTGGAGAAAACCGCT
Found at i:27462331 original size:41 final size:41
Alignment explanation
Indices: 27462265--27462350 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
27462255 TATTAGTGGC
* *
27462265 GTTTATGGGAAAAACACCGCAAAAGGTTAAGCAGTAGCGGT
1 GTTTATGGGAAAAACACCACAAAAGGTTAAGCAATAGCGGT
** * * *
27462306 GTTTATGGGAAAAATGCCACTAAAGGTTAAGTAATAGTGGT
1 GTTTATGGGAAAAACACCACAAAAGGTTAAGCAATAGCGGT
27462347 GTTT
1 GTTT
27462351 TCTCATAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (41 bp):
GTTTATGGGAAAAACACCACAAAAGGTTAAGCAATAGCGGT
Found at i:27462344 original size:82 final size:82
Alignment explanation
Indices: 27462117--27462350 Score: 274
Period size: 82 Copynumber: 2.9 Consensus size: 82
27462107 TCAAAAACGT
* * * *
27462117 CGCAAAAGGTAAAGCAATGGCGATGTTTTTGGAAAAACGCCGCTAAAGGTAAAGAGCAATAATGG
1 CGCAAAAGGTAAAGCAATAGCGATGTTTTTGGAAAAATGCCGCTAAAGGTAAAGAGTAATAGTGG
*
27462182 CGTTTATGGGAAAACAT
66 CGTTTATGGGAAAACAC
* * * * * *
27462199 CGCAAAAGGTAAAGCAATAACGACGTTTTTGGAGAAATACCGTTAAAGGTAAAGAGTATTAGTGG
1 CGCAAAAGGTAAAGCAATAGCGATGTTTTTGGAAAAATGCCGCTAAAGGTAAAGAGTAATAGTGG
27462264 CGTTTATGGGAAAAACAC
66 CGTTTATGGG-AAAACAC
* * * * * *
27462282 CGCAAAAGGTTAAGCAGTAGCGGTGTTTATGGGAAAAATGCCACTAAAGGT-TA-AGTAATAGTG
1 CGCAAAAGGTAAAGCAATAGCGATGTTT-TTGGAAAAATGCCGCTAAAGGTAAAGAGTAATAGTG
*
27462345 GTGTTT
65 GCGTTT
27462351 TCTCATAAAT
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
82 79 0.63
83 30 0.24
84 17 0.13
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.24
Consensus pattern (82 bp):
CGCAAAAGGTAAAGCAATAGCGATGTTTTTGGAAAAATGCCGCTAAAGGTAAAGAGTAATAGTGG
CGTTTATGGGAAAACAC
Found at i:27470338 original size:16 final size:17
Alignment explanation
Indices: 27470300--27470348 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 17
27470290 GAGTAAAGAG
*
27470300 GTATATGATGATATATAT
1 GTATATGATGA-ACATAT
*
27470318 ATATATGATGAACA-AT
1 GTATATGATGAACATAT
27470334 GTATATG-TGAA-ATAT
1 GTATATGATGAACATAT
27470349 TATGTGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.04
15 6 0.22
16 8 0.30
17 2 0.07
18 10 0.37
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (17 bp):
GTATATGATGAACATAT
Found at i:27470573 original size:23 final size:23
Alignment explanation
Indices: 27470545--27470705 Score: 135
Period size: 23 Copynumber: 7.3 Consensus size: 23
27470535 ACACTAGCGC
27470545 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
27470568 TCTCTCTGTTTAGCACTGTCTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
27470591 TCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
27470614 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
27470637 GCTCTCTG-TTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
27470659 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
27470675 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
27470698 GCTCTCTG
1 GCTCTCTG
27470706 TTGCCCAACA
Statistics
Matches: 116, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
16 11 0.09
18 3 0.03
20 3 0.03
22 17 0.15
23 81 0.70
24 1 0.01
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:27470697 original size:39 final size:38
Alignment explanation
Indices: 27470628--27470701 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
27470618 TCTGATTAGC
* *
27470628 ACTTCGTGTGCTCTCTGTTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGTTAGCACTGTGTGTGCTCAGT
*
27470666 ACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTC
1 ACTTCGTGTACTCTCTG-TTAGCACTGTGTGTGCTC
27470702 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 15 0.47
39 17 0.53
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (38 bp):
ACTTCGTGTACTCTCTGTTAGCACTGTGTGTGCTCAGT
Found at i:27471208 original size:22 final size:22
Alignment explanation
Indices: 27471180--27471223 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27471170 TATGCTTGTA
27471180 ATGCTTACTAAGCCTTCACCGG
1 ATGCTTACTAAGCCTTCACCGG
27471202 ATGCTTACTAAGCCTTCACCGG
1 ATGCTTACTAAGCCTTCACCGG
27471224 CTTAACGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (22 bp):
ATGCTTACTAAGCCTTCACCGG
Found at i:27473098 original size:23 final size:22
Alignment explanation
Indices: 27473066--27473145 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 22
27473056 GCTGGGGAAA
*
27473066 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
27473088 CCAGTAGGCACACGCAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* *
27473111 CAGTAGGCACACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
27473134 CAGTAGGCACAC
1 CAGTAGGCACAC
27473146 GAAGTGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:27473121 original size:45 final size:46
Alignment explanation
Indices: 27473062--27473164 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 46
27473052 AAGTGCTGGG
* *
27473062 GAAACAGTAAGCACACACAGTGC-AATCCAGTAGGCACACGCAGTGC
1 GAAACAGTAAGCACACACAGCGCAAAT-CAGTAGGCACACGAAGTGC
* * *
27473108 -AATCAGTAGGCACACATAGCGCAAATCAGTAGGCACACGAAGTGC
1 GAAACAGTAAGCACACACAGCGCAAATCAGTAGGCACACGAAGTGC
27473153 GAAACAGTAAGC
1 GAAACAGTAAGC
27473165 GTGCTAGCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
45 36 0.75
46 12 0.25
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGCGCAAATCAGTAGGCACACGAAGTGC
Found at i:27473160 original size:23 final size:22
Alignment explanation
Indices: 27473063--27473161 Score: 101
Period size: 23 Copynumber: 4.4 Consensus size: 22
27473053 AGTGCTGGGG
*
27473063 AAACAGTAAGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
* *
27473085 AATCCAGTAGGCACACGCAGTGC
1 AA-ACAGTAGGCACACACAGTGC
* * *
27473108 AATCAGTAGGCACACATAGCGC
1 AAACAGTAGGCACACACAGTGC
27473130 AAATCAGTAGGCACACGA-AGTGC
1 AAA-CAGTAGGCACAC-ACAGTGC
27473153 GAAACAGTA
1 -AAACAGTA
27473162 AGCGTGCTAG
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
22 20 0.31
23 40 0.62
24 4 0.06
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:27483986 original size:14 final size:15
Alignment explanation
Indices: 27483962--27483990 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27483952 TATGCGAAAA
27483962 TATTATTATTTTGAT
1 TATTATTATTTTGAT
27483977 TATT-TTATTTTGAT
1 TATTATTATTTTGAT
27483991 AAAATACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TATTATTATTTTGAT
Found at i:27487388 original size:17 final size:17
Alignment explanation
Indices: 27487366--27487404 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27487356 CTCCACCTTG
* *
27487366 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
27487383 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
27487400 ACAAG
1 ACAAG
27487405 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:27491887 original size:89 final size:89
Alignment explanation
Indices: 27491784--27491951 Score: 257
Period size: 89 Copynumber: 1.9 Consensus size: 89
27491774 AAGGATTGTC
27491784 GAAAAGTTTTATTTTTCAGGAAAAACAAACAAGTCTAGAACAATATTTTAAAATAAAAAAATTAT
1 GAAAAGTTTTATTTTTCAGGAAAAACAAACAAGTCTAGAACAATATTTTAAAAT-AAAAAATTAT
27491849 -AAAAAAGGGAGTCACCAAGCTGTT
65 AAAAAAAGGGAGTCACCAAGCTGTT
* * * * **
27491873 GAAACGTTTTATTTTTCGGGAAAAACAAACAAGTCTCGAACAATATTTTAAAGTCGAAAATTATA
1 GAAAAGTTTTATTTTTCAGGAAAAACAAACAAGTCTAGAACAATATTTTAAAATAAAAAATTAT-
27491938 AAAAAAAGGGAGTC
65 AAAAAAAGGGAGTC
27491952 GCTACCAATC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
88 8 0.11
89 50 0.70
90 13 0.18
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.27
Consensus pattern (89 bp):
GAAAAGTTTTATTTTTCAGGAAAAACAAACAAGTCTAGAACAATATTTTAAAATAAAAAATTATA
AAAAAAGGGAGTCACCAAGCTGTT
Found at i:27492993 original size:29 final size:29
Alignment explanation
Indices: 27492961--27493029 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
27492951 GTAAAACGAT
* * *
27492961 AATTTTGGATAATTTGAGGTCAAAAATGG
1 AATTTTGGAAAAATCGAGGTCAAAAATGG
* *
27492990 AATTTTTGAAAAATCGGGGTCAAAAATGG
1 AATTTTGGAAAAATCGAGGTCAAAAATGG
* *
27493019 AGTTTTTGAAA
1 AATTTTGGAAA
27493030 GTTTAGGGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
AATTTTGGAAAAATCGAGGTCAAAAATGG
Found at i:27493197 original size:30 final size:29
Alignment explanation
Indices: 27493077--27493199 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 29
27493067 CAAAATAGAG
27493077 TTTTGG-AAGTTTAGGGGT--AAATGGTAAT
1 TTTTGGAAAGTTTA-GGGTCAAAAT-GTAAT
* ** *
27493105 TTTTGGAAAATCGA-GGTTAAAATGTAAAT
1 TTTTGGAAAGTTTAGGGTCAAAATGT-AAT
* *
27493134 TTTAGG-AAGTTTAGGGGCTAAAATGTAAT
1 TTTTGGAAAGTTTAGGGTC-AAAATGTAAT
27493163 TTTTGGAAAGTTTAGGGATCAAAATGTAAT
1 TTTTGGAAAGTTTAGGG-TCAAAATGTAAT
27493193 TTTTGGA
1 TTTTGGA
27493200 CAGATCGAGG
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.04
28 12 0.16
29 26 0.34
30 34 0.45
31 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTCAAAATGTAAT
Found at i:27494302 original size:3 final size:3
Alignment explanation
Indices: 27494294--27494346 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
27494284 TTTTCCATTG
* * * * *
27494294 TTA TTA TTA ATA CTTT TTA TTA TTA ATA TTA TTA ATA TTA TTA ATA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27494340 TTA TTA T
1 TTA TTA T
27494347 AAATTAATGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
3 38 0.97
4 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:27494325 original size:9 final size:9
Alignment explanation
Indices: 27494295--27494345 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
27494285 TTTCCATTGT
27494295 TATTATTAA
1 TATTATTAA
27494304 TACTT-TT--
1 TA-TTATTAA
27494311 TATTATTAA
1 TATTATTAA
27494320 TATTATTAA
1 TATTATTAA
27494329 TATTATTAA
1 TATTATTAA
27494338 TATTATTA
1 TATTATTA
27494346 TAAATTAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 2 0.05
7 4 0.11
9 30 0.79
10 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:27494362 original size:34 final size:34
Alignment explanation
Indices: 27494295--27494362 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
27494285 TTTCCATTGT
* * *
27494295 TATTATTAATACTTTTTATTATTAATATTATTAA
1 TATTATTAATACTTATTATAATTAATATAATTAA
*
27494329 TATTATTAATA-TTATTATAAATTAATGTAATTAA
1 TATTATTAATACTTATTAT-AATTAATATAATTAA
27494363 AACGTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
TATTATTAATACTTATTATAATTAATATAATTAA
Found at i:27495152 original size:40 final size:40
Alignment explanation
Indices: 27495046--27495153 Score: 96
Period size: 42 Copynumber: 2.6 Consensus size: 40
27495036 AAAACGTTGC
* *
27495046 AAAAGGTAAAGCAATGGCGACATATTTGGAAAACCACCGCT
1 AAAAGGTAAAGCAATAGCGACGT-TTTGGAAAACCACCGCT
** * *
27495087 -AAAGGTAAAGAGCAATAATGGCGTTTATGGGAAAA-CGCCG-T
1 AAAAGGT-AA-AGCAATAGCGACGTTT-T-GGAAAACCACCGCT
27495128 AAAAGGTAAAGCAATAGCGACGTTTT
1 AAAAGGTAAAGCAATAGCGACGTTTT
27495154 TTCAGAAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
39 1 0.02
40 19 0.36
41 7 0.13
42 20 0.38
43 6 0.11
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (40 bp):
AAAAGGTAAAGCAATAGCGACGTTTTGGAAAACCACCGCT
Found at i:27498801 original size:66 final size:66
Alignment explanation
Indices: 27498680--27498804 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
27498670 CTTAAAGCGG
* * **
27498680 AGGCAGCAGTGAGAGAAGCAGAGGCTCAAAGAAAATATGATGAACTTTAACTACAACTTGAAGCT
1 AGGCAGCAGTGAGAGAAGCAGAGGCTCAAAGAAAATAGGACGAACTGCAACTACAACTTGAAGCT
27498745 A
66 A
* * * **
27498746 AGGCAGCAGTGA-AGGAAGTAGAGTCTCAAAGAAAGTAGGACGAACTGCAGTTACAACTT
1 AGGCAGCAGTGAGA-GAAGCAGAGGCTCAAAGAAAATAGGACGAACTGCAACTACAACTT
27498805 CAAAATATGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 48 0.98
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (66 bp):
AGGCAGCAGTGAGAGAAGCAGAGGCTCAAAGAAAATAGGACGAACTGCAACTACAACTTGAAGCT
A
Found at i:27499127 original size:43 final size:43
Alignment explanation
Indices: 27499078--27499220 Score: 153
Period size: 43 Copynumber: 3.3 Consensus size: 43
27499068 TGTTAGCAGA
* * *
27499078 GTTTGTGGGAAAAACGCCACTAGAGAACATGTTCTCTAGTGGC
1 GTTTGTGGGAAAAACGCCACTAAAGAACATGTTCTTTAGCGGC
* * * **
27499121 TTTTGTGAGAAAAATGTCTGCTAAAG-ACAATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAACG-CCACTAAAGAAC-ATGTTCTTTAGCGGC
* * *
27499165 GTTTATGGTAAAAACGCCACTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAACGCCACTAAAGAACATGTTCTTTAGCGGC
*
27499208 GTTTGTTGGAAAA
1 GTTTGTGGGAAAA
27499221 GCGCTGTTAA
Statistics
Matches: 78, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
43 47 0.60
44 31 0.40
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCACTAAAGAACATGTTCTTTAGCGGC
Found at i:27502620 original size:30 final size:30
Alignment explanation
Indices: 27502584--27502649 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
27502574 CTTACGAGGA
27502584 CGTTCAGGAACTT-GAGAAGAC-CTGATATCT
1 CGTTCAGGAACTTAG-GAAGACTC-GATATCT
*
27502614 CGTTCAGGAGCTTAGGAAGACTCGATATCT
1 CGTTCAGGAACTTAGGAAGACTCGATATCT
*
27502644 CATTCA
1 CGTTCA
27502650 AGATTTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (30 bp):
CGTTCAGGAACTTAGGAAGACTCGATATCT
Found at i:27502755 original size:36 final size:36
Alignment explanation
Indices: 27502595--27502762 Score: 101
Period size: 36 Copynumber: 5.0 Consensus size: 36
27502585 GTTCAGGAAC
27502595 TTGAGAAGACCTGATATCTCGTTCAGGAGCTT---A
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
* * **
27502628 --G-GAAGA-CTCGATATCTCATTCAAGATTTTGGGA
1 TTGAGAAGACCT-GATATCTCGTTCAGGAGCTTGGGA
* * * ** *
27502661 TTGAAAAGGCCTAATATCTCCATCAGAAGCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
* * * *
27502697 ---AG-ACA-C-GATAACGCGTTTAGGAGCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
*
27502727 TTGAGAAGACTTGATATCTCGTTCAGGAGCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
27502763 AGATCTGATA
Statistics
Matches: 93, Mismatches: 28, Indels: 25
0.64 0.19 0.17
Matches are distributed among these distances:
29 2 0.02
30 38 0.41
31 2 0.02
32 1 0.01
33 4 0.04
34 2 0.02
35 1 0.01
36 41 0.44
37 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (36 bp):
TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
Found at i:27507416 original size:47 final size:47
Alignment explanation
Indices: 27507364--27507457 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
27507354 CCAATATACA
* *
27507364 AAAAAAAAGACGCTATAGCAAAACAGGTTTTTAGTGACATTTTTAGT
1 AAAAAAAAGACACTATAGCAAAACAGGTTTTTAGCGACATTTTTAGT
*
27507411 AAAAAAAAGACACTATAGCAAAACAGGTTTTTAGCGACGTTTTTAGT
1 AAAAAAAAGACACTATAGCAAAACAGGTTTTTAGCGACATTTTTAGT
27507458 GGAGTTTGGA
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:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (47 bp):
AAAAAAAAGACACTATAGCAAAACAGGTTTTTAGCGACATTTTTAGT
Found at i:27507607 original size:82 final size:83
Alignment explanation
Indices: 27507480--27507658 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 83
27507470 GAAAACGTCT
** * * *
27507480 CAAAAGGTAAAGCAATGGCGATGTTTTTGGAAAAACGCCGCTAAAGGTAAAGAGCAATAATGGCA
1 CAAAAGGTAAAGCAATAACGACGTTTTTGGAAAAACACCGCTAAAGGTAAAGAGCAATAACGGCA
*
27507545 TTTAT-GGGAAAACACCG
66 TTTATAGGAAAAACACCG
* * * * * * *
27507562 CAAAAGGTAAAGCAATAACGACGTTTTTGGAGAAATACCGTTAAAGGTAAAGAGTATTAGCGGCG
1 CAAAAGGTAAAGCAATAACGACGTTTTTGGAAAAACACCGCTAAAGGTAAAGAGCAATAACGGCA
27507627 TTTATAGGAAAAACACCG
66 TTTATAGGAAAAACACCG
*
27507645 CAAAAGGTTAAGCA
1 CAAAAGGTAAAGCA
27507659 GTAGCGGTGT
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
82 58 0.71
83 24 0.29
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (83 bp):
CAAAAGGTAAAGCAATAACGACGTTTTTGGAAAAACACCGCTAAAGGTAAAGAGCAATAACGGCA
TTTATAGGAAAAACACCG
Found at i:27507665 original size:41 final size:40
Alignment explanation
Indices: 27507480--27507674 Score: 131
Period size: 40 Copynumber: 4.8 Consensus size: 40
27507470 GAAAACGTCT
* * ** * *
27507480 CAAAAGGTAAAGCAATGGCGATGTTTTTGGAAAAACGCCG
1 CAAAAGGTAAAGCAGTAGCGGCGTTTATGGAAAAACACCG
* * ** * *
27507520 CTAAAGGTAAAGAGCAATAATGGCATTTATGGGAAAACACCG
1 CAAAAGGT-AA-AGCAGTAGCGGCGTTTATGGAAAAACACCG
* * * * * *
27507562 CAAAAGGTAAAGCAATAACGACGTTTTTGGAGAAATACCG
1 CAAAAGGTAAAGCAGTAGCGGCGTTTATGGAAAAACACCG
**
27507602 TTAAAGGTAAAG-AGTATTAGCGGCGTTTATAGGAAAAACACCG
1 CAAAAGGTAAAGCAG---TAGCGGCGTTTAT-GGAAAAACACCG
* *
27507645 CAAAAGGTTAAGCAGTAGCGGTGTTTATGG
1 CAAAAGGTAAAGCAGTAGCGGCGTTTATGG
27507675 GGAAAATGCC
Statistics
Matches: 118, Mismatches: 30, Indels: 14
0.73 0.19 0.09
Matches are distributed among these distances:
39 1 0.01
40 42 0.36
41 16 0.14
42 38 0.32
43 19 0.16
44 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (40 bp):
CAAAAGGTAAAGCAGTAGCGGCGTTTATGGAAAAACACCG
Found at i:27513854 original size:15 final size:17
Alignment explanation
Indices: 27513828--27513862 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
27513818 TTAATGTAAT
27513828 TAAGGTAAATAT-TCAA
1 TAAGGTAAATATATCAA
27513844 TAAGG-AAATATATCAA
1 TAAGGTAAATATATCAA
27513860 TAA
1 TAA
27513863 TTTGATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
TAAGGTAAATATATCAA
Found at i:27514477 original size:21 final size:21
Alignment explanation
Indices: 27514452--27514493 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
27514442 CTAGTTTGTC
*
27514452 TCAATTGTTACTCACGTAAAA
1 TCAATTGTTACTCACGAAAAA
*
27514473 TCAATTGTTACTGACGAAAAA
1 TCAATTGTTACTCACGAAAAA
27514494 AAAAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (21 bp):
TCAATTGTTACTCACGAAAAA
Found at i:27521797 original size:42 final size:42
Alignment explanation
Indices: 27521739--27521921 Score: 189
Period size: 42 Copynumber: 4.5 Consensus size: 42
27521729 TTTGGATCGG
** *
27521739 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGTGTTTATAGGA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
* * *
27521781 AAACGTCGCAAGAGGT-AA-AGCAATAGCGGCATTT-T-TGA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
* * *
27521819 AGAA--ACGCAAAAGGTAAAGAGCTATAGCGGCGTTTATGGGA
1 A-AACGCCGCAAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
** * *
27521860 AAATACCACTAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
*
27521902 AAACGTCGCAAAAGGTAAAG
1 AAACGCCGCAAAAGGTAAAG
27521922 CAATAGTGGC
Statistics
Matches: 114, Mismatches: 20, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
37 9 0.08
38 5 0.04
39 17 0.15
40 17 0.15
41 5 0.04
42 61 0.54
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.17
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCATTTATGGGA
Found at i:27521876 original size:79 final size:81
Alignment explanation
Indices: 27521745--27521895 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 81
27521735 TCGGAAACGC
* ** *
27521745 CGCAAAAGGTAAAGAGCAATAGCGGTGTTTATAGGAAAACGTCGCAAGAGGT-AA-AGCAATAGC
1 CGCAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAAACACCACAAGAGGTAAAGAGCAATAGC
27521808 GGCATTTTTGAAGAAA
66 GGCATTTTTGAAGAAA
* * *
27521824 CGCAAAAGGTAAAGAGCTATAGCGGCGTTTATGGGAAAATACCACTAA-AGGTAAAGAGCAATAG
1 CGCAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAAACACCAC-AAGAGGTAAAGAGCAATAG
27521888 CGGCATTT
65 CGGCATTT
27521896 ATGGGAAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 42 0.68
80 4 0.06
81 16 0.26
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (81 bp):
CGCAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAAACACCACAAGAGGTAAAGAGCAATAGC
GGCATTTTTGAAGAAA
Found at i:27522163 original size:40 final size:40
Alignment explanation
Indices: 27521738--27522166 Score: 154
Period size: 40 Copynumber: 10.5 Consensus size: 40
27521728 GTTTGGATCG
* * *
27521738 GAAACGCCGCAAAAGGTAAAGAGCAATAGCGGTGTTTAT-AG
1 GAAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTTTGAA
* * *
27521779 GAAAACGTCGCAAGAGGTAAAGCAATAGCGGCATTTTTGAA
1 G-AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTGAA
* * *
27521820 GAAA---CGCAAAAGGTAAAGAGCTATAGCGGCGTTTATG-G
1 GAAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTTTGAA
** * * * * *
27521858 GAAAATACCACTAAAGGTAAAGAGCAATAGCGGCATTTATG-G
1 G-AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTTTGAA
* * *
27521900 GAAAACGTCGCAAAAGGTAAAGCAATAGTGGCGTTTTTGGA
1 G-AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTGAA
* * ** * * * ** * ***
27521941 GAAACGCTGCTATTGCTTAACCTTTAACGGCGTTTTCCCCCA
1 GAAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTT--TGAA
* * **
27521983 TAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCA
1 GAAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTGAA
* * * *** *
27522023 TAAACGCAGCAAAAGGTAAAGCAATAACGATATTTTTCCCAA
1 GAAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTT--GAA
* * * * ** * *
27522065 -AAACGCAGCTAGAGGCAAAGAGCAATAGCGGTATTTAT-AG
1 GAAACGCCGCAAAAGG-TAA-AGCAATAGCGGCGTTTTTGAA
*** * *
27522105 GAAAACATTGCAAGAGGTAAAGCAATAGCGACGTTTTTGAA
1 G-AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTGAA
27522146 GAAACGCCGCAAAAGGTAAAG
1 GAAACGCCGCAAAAGGTAAAG
27522167 AGCTATAGTG
Statistics
Matches: 290, Mismatches: 80, Indels: 37
0.71 0.20 0.09
Matches are distributed among these distances:
37 9 0.03
38 3 0.01
39 19 0.07
40 122 0.42
41 25 0.09
42 97 0.33
43 15 0.05
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (40 bp):
GAAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTGAA
Found at i:27525663 original size:14 final size:14
Alignment explanation
Indices: 27525644--27525683 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
27525634 CGTGATATCG
*
27525644 AAAGAAGTTGCTC-A
1 AAAGAAGTTAC-CGA
27525658 AAAGAAGTTACCGA
1 AAAGAAGTTACCGA
27525672 AAAGAAGTTACC
1 AAAGAAGTTACC
27525684 CTAGAGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (14 bp):
AAAGAAGTTACCGA
Found at i:27531580 original size:43 final size:43
Alignment explanation
Indices: 27531505--27531598 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
27531495 TCTGTTAATG
* *
27531505 TTAGCGGCATTTGTGGGAAAAACGCCATTAAAGAACATGTT-T
1 TTAGCGGCATTTGTAGGAAAAACGCCACTAAAGAACATGTTCT
* * ** *
27531547 TATAGCGTCATTTGTAGGAAAAATGCTGCTAAAGACCATGTTCT
1 T-TAGCGGCATTTGTAGGAAAAACGCCACTAAAGAACATGTTCT
27531591 TTAGCGGC
1 TTAGCGGC
27531599 GCATGTAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
42 1 0.02
43 39 0.93
44 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (43 bp):
TTAGCGGCATTTGTAGGAAAAACGCCACTAAAGAACATGTTCT
Found at i:27534576 original size:30 final size:30
Alignment explanation
Indices: 27534535--27534593 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
27534525 GGAACTTGAG
* *
27534535 AAGACTTGATATCTCATTCAGGAGCTTGGA
1 AAGACTCGATATCTCATTCAAGAGCTTGGA
*
27534565 AAGACTCGATATCTCATTCAAGATCTTGG
1 AAGACTCGATATCTCATTCAAGAGCTTGG
27534594 GATTGAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (30 bp):
AAGACTCGATATCTCATTCAAGAGCTTGGA
Found at i:27534695 original size:66 final size:66
Alignment explanation
Indices: 27534530--27534700 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 66
27534520 ATTTAGGAAC
* * * * * * *
27534530 TTGAGAAGACTTGATATCTCATTCAGGAGCTTGGAAAGACTCGATATCTCATTCAAGATCTTGGG
1 TTGAGAAGACTTGATATCTCATTCAGGAACTTGGGAAGACACGATAGCGCATTCAAGAGCTTAGG
27534595 A
66 A
* * * * * * *
27534596 TTGAAAAGGCCTGATATCTCCA-TCA-AAAGCTTGGGAAGACACGATAGCGCGTTTAGGAGCTTA
1 TTGAGAAGACTTGATATCT-CATTCAGGAA-CTTGGGAAGACACGATAGCGCATTCAAGAGCTTA
27534659 GGA
64 GGA
27534662 TTGAGAAGACTTGATATCTCATTCAGGAACTTGGGAAGA
1 TTGAGAAGACTTGATATCTCATTCAGGAACTTGGGAAGA
27534701 TCTAATATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
65 3 0.04
66 76 0.92
67 4 0.05
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (66 bp):
TTGAGAAGACTTGATATCTCATTCAGGAACTTGGGAAGACACGATAGCGCATTCAAGAGCTTAGG
A
Found at i:27540271 original size:158 final size:158
Alignment explanation
Indices: 27539978--27540310 Score: 438
Period size: 158 Copynumber: 2.1 Consensus size: 158
27539968 TGTTAAAGTT
*
27539978 ACAGCTTGTGTGAGCATTACATGTTATATGAGTGCTGGTCTTACATGTCCTACAAATGGCTGAAG
1 ACAGCTTGTGTGAGCATTACAGGTTATATGAGTGCTGGTCTTACATGTCCTACAAATGGCTGAAG
* * * * *
27540043 TCCTACATTGGTTGCGGATTATTCACAGCTCGTGTAAGCAGCATCGCGTAGCCTAACATCTCGAC
66 TCCGACATTGATTGCGAATTATCCACAGCTCGTGTAAGCAGCATCGCGTAGCCCAACATCTCGAC
27540108 CCACAGCTCGTGTGAGCAGGCCCATTTC
131 CCACAGCTCGTGTGAGCAGGCCCATTTC
* **
27540136 ACAGCTTGTGTGAGCATTACAGGTTATAT-AGGTGCTGGTCTTAGATGT-CTCACTGATGGCT-A
1 ACAGCTTGTGTGAGCATTACAGGTTATATGA-GTGCTGGTCTTACATGTCCT-ACAAATGGCTGA
* * * ** * * * *
27540198 AGGTCCGACATTTATTGTGAATTCTCCATTGCTTGTGTGAGCAGCATCGTGTAGCCCCACATCTC
64 A-GTCCGACATTGATTGCGAATTATCCACAGCTCGTGTAAGCAGCATCGCGTAGCCCAACATCTC
* *
27540263 GACTCACAGCTTGTGTGAGCAGGCCCATTTC
128 GACCCACAGCTCGTGTGAGCAGGCCCATTTC
27540294 ACAGCTTGTGTGAGCAT
1 ACAGCTTGTGTGAGCAT
27540311 ATATGATTAC
Statistics
Matches: 152, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
157 5 0.03
158 147 0.97
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (158 bp):
ACAGCTTGTGTGAGCATTACAGGTTATATGAGTGCTGGTCTTACATGTCCTACAAATGGCTGAAG
TCCGACATTGATTGCGAATTATCCACAGCTCGTGTAAGCAGCATCGCGTAGCCCAACATCTCGAC
CCACAGCTCGTGTGAGCAGGCCCATTTC
Found at i:27543216 original size:186 final size:186
Alignment explanation
Indices: 27542940--27543299 Score: 630
Period size: 186 Copynumber: 1.9 Consensus size: 186
27542930 TAAAATTACC
* *
27542940 TAAAAATTTTAGCTAATTTGAATAGAAATCTGAATACAAACCTGTTGTTACTTATATGAGAGGTA
1 TAAAAATTTTAGCTAATTTGAACAGAAATCTGAATACAAAACTGTTGTTACTTATATGAGAGGTA
27543005 CATGACCATAAATTTGAGACACTTTTATATGCACTAAGTAACATAAAAGATTTTGTCAGATGTGT
66 CATGACCATAAATTTGAGACACTTTTATATGCACTAAGTAACATAAAAGATTTTGTCAGATGTGT
* *
27543070 TACATGAGTATGTTATTAAAGAAATGAACTCTTTTAGGCCAAAAAGCCATAATAAA
131 TACATGAGTATGTTACTAAAGAAACGAACTCTTTTAGGCCAAAAAGCCATAATAAA
* * *
27543126 TAAAAATTTTAGCTAATTTGAACAGAGATCTGAATGCAAAACTGTTGTTACTTATTTGAGAGGTA
1 TAAAAATTTTAGCTAATTTGAACAGAAATCTGAATACAAAACTGTTGTTACTTATATGAGAGGTA
* *
27543191 GATGACCATAAATTTGAGACACTTTTATATGCACTAAGTAACATAAAAGATTTTGTCAGATGTTT
66 CATGACCATAAATTTGAGACACTTTTATATGCACTAAGTAACATAAAAGATTTTGTCAGATGTGT
*
27543256 TACATGAGTATGTTACTAAAGAAACGAACTCTTTTAGGCTAAAA
131 TACATGAGTATGTTACTAAAGAAACGAACTCTTTTAGGCCAAAA
27543300 TGTCATAGTT
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
186 164 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (186 bp):
TAAAAATTTTAGCTAATTTGAACAGAAATCTGAATACAAAACTGTTGTTACTTATATGAGAGGTA
CATGACCATAAATTTGAGACACTTTTATATGCACTAAGTAACATAAAAGATTTTGTCAGATGTGT
TACATGAGTATGTTACTAAAGAAACGAACTCTTTTAGGCCAAAAAGCCATAATAAA
Found at i:27556819 original size:17 final size:18
Alignment explanation
Indices: 27556768--27556819 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
27556758 TAAGAATATT
27556768 ATTTTTATATTTTT-ATG
1 ATTTTTATATTTTTAATG
*
27556785 CTTTTTATATAATTTTAATG
1 ATTTTTATAT--TTTTAATG
27556805 ATTTTTA-ATTTTTAA
1 ATTTTTATATTTTTAA
27556820 AAAATAGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 15 0.50
19 6 0.20
20 9 0.30
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTATATTTTTAATG
Found at i:27556916 original size:9 final size:9
Alignment explanation
Indices: 27556876--27556919 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
27556866 TTTTAAAAAA
27556876 ATAAAAAGT
1 ATAAAAAGT
*
27556885 ATTAAAAGT
1 ATAAAAAGT
27556894 ATTAAATAAGT
1 A-TAAA-AAGT
*
27556905 ATAAAAATT
1 ATAAAAAGT
27556914 ATAAAA
1 ATAAAA
27556920 CTATATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 18 0.60
10 7 0.23
11 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (9 bp):
ATAAAAAGT
Found at i:27562936 original size:33 final size:31
Alignment explanation
Indices: 27562885--27562986 Score: 97
Period size: 33 Copynumber: 3.3 Consensus size: 31
27562875 AGCATTTAAT
**
27562885 TAATTTTTTTAAAATTTAAAAAATACTTTATA
1 TAATTTTTTTAATTTTTAAAAAATA-TTTATA
*
27562917 TATATTTTTTTAATTTTTAAATAAT-TTTA-A
1 TA-ATTTTTTTAATTTTTAAAAAATATTTATA
*
27562947 TGA--TTTTTAATTTTTAAAAAATAGTTCT-TA
1 TAATTTTTTTAATTTTTAAAAAATA-TT-TATA
27562977 TAATTTTTTT
1 TAATTTTTTT
27562987 TATATCTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 18 0.32
29 3 0.05
30 6 0.11
31 4 0.07
32 7 0.12
33 19 0.33
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (31 bp):
TAATTTTTTTAATTTTTAAAAAATATTTATA
Found at i:27567911 original size:11 final size:11
Alignment explanation
Indices: 27567891--27567955 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
27567881 AGCCTGTACC
*
27567891 AAATTCATTTT
1 AAATTTATTTT
27567902 AAATTTATTTT
1 AAATTTATTTT
*
27567913 AAGATTAATTTT
1 AA-ATTTATTTT
* *
27567925 -ATTTTAAAGTTT
1 AAATTT--ATTTT
27567937 AAATTTATTTT
1 AAATTTATTTT
27567948 CAAATTTA
1 -AAATTTA
27567956 AAATTATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
10 2 0.05
11 17 0.40
12 19 0.45
13 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
AAATTTATTTT
Found at i:27567925 original size:17 final size:18
Alignment explanation
Indices: 27567900--27567977 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
27567890 CAAATTCATT
27567900 TTAAATTTATTTT-AAGA
1 TTAAATTTATTTTAAAGA
* *
27567917 TTAATTTTATTTTAAAGT
1 TTAAATTTATTTTAAAGA
*
27567935 TTAAATTTATTTTCAAA-T
1 TTAAATTTATTTT-AAAGA
* * *
27567953 TTAAAATTATTATAAA-T
1 TTAAATTTATTTTAAAGA
27567970 TTAAATTT
1 TTAAATTT
27567978 CAATGTCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
17 23 0.43
18 27 0.51
19 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (18 bp):
TTAAATTTATTTTAAAGA
Found at i:27567938 original size:35 final size:35
Alignment explanation
Indices: 27567899--27567977 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
27567889 CCAAATTCAT
** *
27567899 TTTAAATTTATTTT-AAGA-TTAATTTTATTTTAAA
1 TTTAAATTTATTTTCAA-ATTTAAAATTATTATAAA
27567933 GTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 -TTTAAATTTATTTTCAAATTTAAAATTATTATAAA
27567969 TTTAAATTT
1 TTTAAATTT
27567978 CAATGTCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 24 0.62
36 15 0.38
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTCAAATTTAAAATTATTATAAA
Found at i:27567943 original size:18 final size:17
Alignment explanation
Indices: 27567899--27567977 Score: 97
Period size: 17 Copynumber: 4.5 Consensus size: 17
27567889 CCAAATTCAT
27567899 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
27567917 -TTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
27567933 GTTTAAATTTATTTTCAAA
1 -TTTAAATTTATTTT-AAA
* *
27567952 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
27567969 TTTAAATTT
1 TTTAAATTT
27567978 CAATGTCCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.02
17 25 0.47
18 24 0.45
19 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:27569022 original size:18 final size:18
Alignment explanation
Indices: 27568986--27569023 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27568976 TAAATTTTTG
*
27568986 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
*
27569004 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCAAAT
27569022 AA
1 AA
27569024 AACTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:27570956 original size:28 final size:29
Alignment explanation
Indices: 27570913--27571229 Score: 288
Period size: 28 Copynumber: 11.0 Consensus size: 29
27570903 TTAAAAACAA
* *
27570913 AATTTTTGGACA--TTCGAGGT-AAAATGG
1 AATTTTTGGA-AGTTTCGGGGTAAAAATGT
27570940 AATTTTTGGAAGTTTCGGGGTCAAAAATGT
1 AATTTTTGGAAGTTTCGGGGT-AAAAATGT
*
27570970 AATTTTTGGAAGTTTAGGGG-AAAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
* * *
27570998 AATTTTTGAAAGTTT-GGGGGATAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
*** * * *
27571026 AATTTTCAAAAGTTTTGGGATCAAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
*
27571055 AATTTTTGGAAGTTTAGGGGTAAAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
**
27571084 AATTTTTGGAAGTTTCAAGGTCAAAAATGT
1 AATTTTTGGAAGTTTCGGGGT-AAAAATGT
** * *
27571114 AATTTTTAAAAGTTT-TGGGTCAAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
* * *
27571142 AATTTTTAGAAGTTTTAGGGTTAAAAATGT
1 AATTTTTGGAAG-TTTCGGGGTAAAAATGT
* * **
27571172 ATTTTTTGAAAGTTT-GGGGGCAAAATGT
1 AATTTTTGGAAGTTTCGGGGTAAAAATGT
**
27571200 AATTTTTGGAAGTTTTAAGGGTAAAAATGT
1 AATTTTTGGAAG-TTTCGGGGTAAAAATGT
27571230 TTGGAAGTTT
Statistics
Matches: 239, Mismatches: 40, Indels: 19
0.80 0.13 0.06
Matches are distributed among these distances:
26 1 0.00
27 14 0.06
28 87 0.36
29 62 0.26
30 75 0.31
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAGTTTCGGGGTAAAAATGT
Found at i:27571011 original size:58 final size:57
Alignment explanation
Indices: 27570933--27571229 Score: 307
Period size: 58 Copynumber: 5.1 Consensus size: 57
27570923 CATTCGAGGT
* *
27570933 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGA
1 AAAATGTAATTTTTGAAAGTTT-GGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGA
* * *** *
27570991 AAAATGTAATTTTTGAAAGTTTGGGG-GATAAATGTAATTTTCAAAAGTTT-TGGGA
1 AAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGA
* **
27571046 TCAAAATGTAATTTTTGGAAGTTTAGGGGT-AAAAATGTAATTTTTGGAAGTTTCAAGGTCA
1 --AAAATGTAATTTTTGAAAGTTT-GGGGTCAAAAATGTAATTTTTGGAAGTTT--AGGGGA
* * * *
27571107 AAAATGTAATTTTTAAAAGTTTTGGGTC-AAAATGTAATTTTTAGAAGTTTTAGGGTTA
1 AAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATGTAATTTTTGGAAG-TTTAGGG-GA
* * *
27571165 AAAATGTATTTTTTGAAAGTTTGGGGGC-AAAATGTAATTTTTGGAAGTTTTAAGGGTA
1 AAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATGTAATTTTTGGAAG-TTT-AGGGGA
27571223 AAAATGT
1 AAAATGT
27571230 TTGGAAGTTT
Statistics
Matches: 201, Mismatches: 27, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.02
56 19 0.09
57 28 0.14
58 121 0.60
59 27 0.13
61 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGA
Found at i:27571232 original size:25 final size:25
Alignment explanation
Indices: 27571204--27571251 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
27571194 AAATGTAATT
*
27571204 TTTGGAAGTTTTAAGGGTAAAAATG
1 TTTGGAAGTTTTAAGGGGAAAAATG
27571229 TTTGGAAGTTTTAAGGGGAAAAA
1 TTTGGAAGTTTTAAGGGGAAAAA
27571252 AAGTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (25 bp):
TTTGGAAGTTTTAAGGGGAAAAATG
Found at i:27571552 original size:29 final size:31
Alignment explanation
Indices: 27571494--27571562 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
27571484 GGTGAATTCA
27571494 AAAAGT-CAAGGGACCAAATTGAAAAATAATG
1 AAAAGTAC-AGGGACCAAATTGAAAAATAATG
* * *
27571525 AAAATTACAGGG-CCAAATT-AAAATTAATT
1 AAAAGTACAGGGACCAAATTGAAAAATAATG
27571554 AAAAGTACA
1 AAAAGTACA
27571563 AAAGAACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.48
30 7 0.21
31 9 0.27
32 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.20
Consensus pattern (31 bp):
AAAAGTACAGGGACCAAATTGAAAAATAATG
Found at i:27573175 original size:6 final size:6
Alignment explanation
Indices: 27573164--27573201 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
27573154 AATTTAAACC
27573164 AAATTT AAATTT AAATTT AAATTT AGAA--T AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT A-AATTT AAATTT AAA
27573202 ATCAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.07
5 2 0.07
6 23 0.79
7 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:27573197 original size:11 final size:11
Alignment explanation
Indices: 27573169--27573212 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
27573159 AAACCAAATT
*
27573169 TAAATTTAAATT
1 TAAATTTAAA-A
*
27573181 TAAATTTAGAA
1 TAAATTTAAAA
27573192 TAAATTTAAAA
1 TAAATTTAAAA
*
27573203 TCAATTTAAA
1 TAAATTTAAA
27573213 CCAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:27574111 original size:200 final size:200
Alignment explanation
Indices: 27573578--27574487 Score: 1403
Period size: 200 Copynumber: 4.5 Consensus size: 200
27573568 GTTTCGTTGA
*
27573578 CTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATTGAGCGTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATTGAGCGTT
* * *
27573643 GAGTTGGTATACTTCTCTATATCTCATCAGGATGATGACTGCCTCGTTTGTTTCAATTCGCTTCT
66 GAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTCT
*
27573708 CTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTT
131 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTT
27573773 TATTG
196 TATTG
* * *
27573778 CTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGC
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT-GGGTTCGAAGGTTTGCTCGCATTGAGCGT
* *
27573843 TGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTC
65 TGAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTC
*
27573908 TCTGTATCTCATCAGGAAGACGAATTTTGGTCTACTTCTCTGTGTCTCATCA-GAAGCTAACCAT
130 TCTGTATCTCATCAGGAAGACGAA-TTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCAT
27573972 TTTATTG
194 TTTATTG
*
27573979 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCACATTGAGCGTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATTGAGCGTT
* ** *
27574044 GAGTTGGTATTCTTCTCTATATCTCATCAAAAAGATGACCGCCTCACTTGTTTCAATTCGCTTCT
66 GAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTCT
* *
27574109 CTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATTAGGAAGCTAACCATTT
131 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTT
27574174 TATTG
196 TATTG
* * * *
27574179 CTTCGACTTGCTTTTCAATGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATT-AGGCGC
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATTGA-GCGT
* * *
27574243 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTACAATTCGCTTT
65 TGAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTC
* * * * * * *
27574308 TCTGTGTCTTATCCGGAAGACGAATTTGGTCCACTTCTTTATATCTCATCAAGAAGCTAACCATT
130 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATT
27574373 TTATTG
195 TTATTG
* * * *
27574379 CTTCGACCTGCTTTTCTGTGTCTCATCAGGAAGCTGGGTTCG-CGGATTTGCTCGCGTTGAGCGT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGG-TTTGCTCGCATTGAGCGT
** * *
27574443 TGAGTTGGTATTTTTCTCTATATCTTATCAGGAAGATGATCGCCT
65 TGAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCT
27574488 TACTGGTTTG
Statistics
Matches: 648, Mismatches: 56, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
199 28 0.04
200 430 0.66
201 164 0.25
202 26 0.04
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (200 bp):
CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGGTTTGCTCGCATTGAGCGTT
GAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATTCGCTTCT
CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTT
TATTG
Found at i:27585267 original size:28 final size:29
Alignment explanation
Indices: 27585227--27585289 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
27585217 AAACGGGACC
27585227 TTTGG-ATACTCGGGGGC-AAAATGATAAT
1 TTTGGAATACTC-GGGGCAAAAATGATAAT
*
27585255 TTTGGAAT-CTCGGGGCAAAAATGGTAAT
1 TTTGGAATACTCGGGGCAAAAATGATAAT
27585283 TTTGGAA
1 TTTGGAA
27585290 AAATTTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.16
28 25 0.78
29 2 0.06
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.30
Consensus pattern (29 bp):
TTTGGAATACTCGGGGCAAAAATGATAAT
Found at i:27585425 original size:30 final size:30
Alignment explanation
Indices: 27585389--27585835 Score: 205
Period size: 30 Copynumber: 15.5 Consensus size: 30
27585379 ATCTGGGTGT
*
27585389 AAAATGGTAA-TTTTGAAAGTGTCAGGGTCA
1 AAAATGGTAATTTTTGGAAGT-TCAGGGTCA
**
27585419 AAAATGG-AATTTTTGGAAGTTC-GGGGGA
1 AAAATGGTAATTTTTGGAAGTTCAGGGTCA
* * * * *
27585447 AAAAT-ATTATTTTTGAAAGTTTTAGGGTTA
1 AAAATGGTAATTTTTGGAAG-TTCAGGGTCA
27585477 AAAATGG-AATTTTTGGAAGTTCGAGGG-CA
1 AAAATGGTAATTTTTGGAAGTTC-AGGGTCA
* *
27585506 AAAAT-ATAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGTAATTTTTGGAAG-TTCAGGGTCA
* *
27585536 AAAATGG-AATTTATGGAAGTTTAAGGGT--
1 AAAATGGTAATTTTTGGAAG-TTCAGGGTCA
* * *
27585564 AAAAT-GTAATTTTTGAAAGTTCGGGGGCA
1 AAAATGGTAATTTTTGGAAGTTCAGGGTCA
* * * *
27585593 AAAAT-ATAGTTTTTGGAAGATGAGGG-CA
1 AAAATGGTAATTTTTGGAAGTTCAGGGTCA
** *
27585621 AAAAT-GTAATTTTTGGAAGTTTTGGGATTA
1 AAAATGGTAATTTTTGGAAGTTCAGGG-TCA
* *
27585651 AAAAT-GTAATTTTT-TAAGTTTGAGGG--A
1 AAAATGGTAATTTTTGGAAG-TTCAGGGTCA
* ** ** *
27585678 AAAATTGTAATTTTTAAAAGTTTTTGGGT-T
1 AAAATGGTAATTTTTGGAAG-TTCAGGGTCA
* * * *
27585708 AAAAT-ATAATTTTTGAAAGTT-TGGGGC-
1 AAAATGGTAATTTTTGGAAGTTCAGGGTCA
* *
27585735 -AAATTGTAATTTTTGGAAGTTTAGGGGTC-
1 AAAATGGTAATTTTTGGAAGTTCA-GGGTCA
** *
27585764 -AAAT-GTAATTTTTAAAAGTTTAGGGGT-A
1 AAAATGGTAATTTTTGGAAGTTCA-GGGTCA
* ** *
27585792 AAAAT-GTAATTTTTAGAAGTTTTGAGGTTA
1 AAAATGGTAATTTTTGGAAGTTCAG-GGTCA
27585822 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
27585836 TGATAGTTTA
Statistics
Matches: 335, Mismatches: 55, Indels: 54
0.75 0.12 0.12
Matches are distributed among these distances:
26 4 0.01
27 30 0.09
28 90 0.27
29 104 0.31
30 107 0.32
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGTTCAGGGTCA
Found at i:27585451 original size:58 final size:57
Alignment explanation
Indices: 27585389--27585805 Score: 283
Period size: 58 Copynumber: 7.2 Consensus size: 57
27585379 ATCTGGGTGT
27585389 AAAATGGTAA-TTTTGAAAGTGTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGA
1 AAAAT-GTAATTTTTGAAAGT-TCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGA
* * * * *
27585447 AAAATATTATTTTTGAAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGCA
1 AAAATGTAATTTTTGAAAG-TTCAGGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGGA
* * * * *** *
27585506 AAAATATAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTATGGAAGTTTAAGGGT
1 AAAATGTAATTTTTGAAAG-TTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGA
* * ** * * *
27585564 AAAATGTAATTTTTGAAAGTTCGGGGGCAAAAATATAGTTTTTGGAAGAT-GAGGGCA
1 AAAATGTAATTTTTGAAAGTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGGA
* ** * * * * *
27585621 AAAATGTAATTTTTGGAAGTTTTGGGATTAAAAATGTAATTTTT-TAAGTTTGAGGGA
1 AAAATGTAATTTTTGAAAGTTCAGGG-TCAAAAATGGAATTTTTGGAAGTTCGGGGGA
* ** * * * *
27585678 AAAATTGTAATTTTTAAAAGTTTTTGGGTTAAAATAT--AATTTTTGAAAGTT-TGGGGC
1 AAAA-TGTAATTTTTGAAAG-TTCAGGGTCAAAA-ATGGAATTTTTGGAAGTTCGGGGGA
* * * * ** * *
27585735 AAATTGTAATTTTTGGAAGTTTAGGGGTC--AAATGTAATTTTTAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAGTTCA-GGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGGA
27585792 AAAATGTAATTTTT
1 AAAATGTAATTTTT
27585806 AGAAGTTTTG
Statistics
Matches: 287, Mismatches: 57, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
53 2 0.01
54 2 0.01
55 14 0.05
56 19 0.07
57 90 0.31
58 101 0.35
59 59 0.21
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAAGTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGA
Found at i:27585458 original size:28 final size:28
Alignment explanation
Indices: 27585389--27585835 Score: 226
Period size: 28 Copynumber: 15.5 Consensus size: 28
27585379 ATCTGGGTGT
* *
27585389 AAAATGGTAA-TTTTGAAAGTGTCAGGGTCA
1 AAAAT-GTAATTTTTGGAAGT-TC-GGGGCA
* *
27585419 AAAATGGAATTTTTGGAAGTTCGGGGGA
1 AAAATGTAATTTTTGGAAGTTCGGGGCA
* * * * **
27585447 AAAATATTATTTTTGAAAGTTTTAGGGTTA
1 AAAATGTAATTTTTGGAAG--TTCGGGGCA
*
27585477 AAAATGGAATTTTTGGAAGTTCGAGGGCA
1 AAAATGTAATTTTTGGAAGTTCG-GGGCA
* * *
27585506 AAAATATAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGTAATTTTTGGAAG-TTC-GGGGCA
* * ** *
27585536 AAAATGGAATTTATGGAAGTTTAAGGG-T
1 AAAATGTAATTTTTGGAAG-TTCGGGGCA
*
27585564 AAAATGTAATTTTTGAAAGTTCGGGGGCA
1 AAAATGTAATTTTTGGAAGTTC-GGGGCA
* * *
27585593 AAAATATAGTTTTTGGAAGAT-GAGGGCA
1 AAAATGTAATTTTTGGAAGTTCG-GGGCA
* **
27585621 AAAATGTAATTTTTGGAAGTTTTGGGATTA
1 AAAATGTAATTTTTGGAAG-TTCGGG-GCA
* *
27585651 AAAATGTAATTTTT-TAAGTTTGAGGG-A
1 AAAATGTAATTTTTGGAAGTTCG-GGGCA
** ** **
27585678 AAAATTGTAATTTTTAAAAGTTTTTGGGTT
1 AAAA-TGTAATTTTTGGAAG-TTCGGGGCA
* * *
27585708 AAAATATAATTTTTGAAAGTTTGGGGC-
1 AAAATGTAATTTTTGGAAGTTCGGGGCA
* *
27585735 AAATTGTAATTTTTGGAAGTTTAGGGGTC-
1 AAAATGTAATTTTTGGAAG-TTCGGGG-CA
** * *
27585764 -AAATGTAATTTTTAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAG-TTCGGGGCA
* * **
27585792 AAAATGTAATTTTTAGAAGTTTTGAGGTTA
1 AAAATGTAATTTTTGGAAG-TTCG-GGGCA
27585822 AAAATGTAATTTTT
1 AAAATGTAATTTTT
27585836 TGATAGTTTA
Statistics
Matches: 332, Mismatches: 63, Indels: 44
0.76 0.14 0.10
Matches are distributed among these distances:
27 24 0.07
28 112 0.34
29 94 0.28
30 102 0.31
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGGGGCA
Found at i:27585479 original size:87 final size:86
Alignment explanation
Indices: 27585389--27585835 Score: 322
Period size: 87 Copynumber: 5.2 Consensus size: 86
27585379 ATCTGGGTGT
** * *
27585389 AAAATGGTAA-TTTTGAAAGTGTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGAAAAATA
1 AAAAT-GTAATTTTTGAAAGT-TCAGGG-CAAAAATATAATTTTTGGAAGTTCGGGGCAAAAATG
* *
27585453 TTATTTTTGAAAGTTTTAGGGTTA
63 TAATTTTTGGAAGTTTTAGGGTTA
* * * *
27585477 AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATATAATTTTTGGAAGTTTCAAGGTCAAAAATG
1 AAAATGTAATTTTTGAAAGTTC-AGGGCAAAAATATAATTTTTGGAAG-TTC-GGGGCAAAAATG
* * *
27585542 GAATTTATGGAAGTTTAAGGG-T-
63 TAATTTTTGGAAGTTTTAGGGTTA
* * *
27585564 AAAATGTAATTTTTGAAAGTTCGGGGGCAAAAATATAGTTTTTGGAAGAT-GAGGGCAAAAATGT
1 AAAATGTAATTTTTGAAAGTTC-AGGGCAAAAATATAATTTTTGGAAGTTCG-GGGCAAAAATGT
27585628 AATTTTTGGAAGTTTT-GGGATTA
64 AATTTTTGGAAGTTTTAGGG-TTA
* * * ** ** ** *
27585651 AAAATGTAATTTTT-TAAGTTTGAGGG-AAAAATTGTAATTTTTAAAAGTTTTTGGGTTAAAATA
1 AAAATGTAATTTTTGAAAG-TTCAGGGCAAAAA-TATAATTTTTGGAAG-TTCGGGGCAAAAATG
* **
27585714 TAATTTTTGAAAG-TTT-GGG-GC
63 TAATTTTTGGAAGTTTTAGGGTTA
* * * *** * ** * *
27585735 AAATTGTAATTTTTGGAAGTTTAGGGGTCAAATGTAATTTTTAAAAGTTTAGGGGTAAAAATGTA
1 AAAATGTAATTTTTGAAAGTTCAGGGCAAAAATATAATTTTTGGAAG-TTCGGGGCAAAAATGTA
*
27585800 ATTTTTAGAAGTTTT-GAGGTTA
65 ATTTTTGGAAGTTTTAG-GGTTA
27585822 AAAATGTAATTTTT
1 AAAATGTAATTTTT
27585836 TGATAGTTTA
Statistics
Matches: 290, Mismatches: 52, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
84 60 0.21
85 39 0.13
86 27 0.09
87 118 0.41
88 22 0.08
89 24 0.08
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (86 bp):
AAAATGTAATTTTTGAAAGTTCAGGGCAAAAATATAATTTTTGGAAGTTCGGGGCAAAAATGTAA
TTTTTGGAAGTTTTAGGGTTA
Found at i:27586122 original size:29 final size:30
Alignment explanation
Indices: 27586063--27586133 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
27586053 TGGTGAATTC
27586063 AAAAAGT-CAAGGGACCAAATTGAAAAATAAT
1 AAAAAGTACAA-GG-CCAAATTGAAAAATAAT
* *
27586094 AAAAATTACAAGGCCAAATT-AAAATTAAT
1 AAAAAGTACAAGGCCAAATTGAAAAATAAT
*
27586123 TAAAAGTACAA
1 AAAAAGTACAA
27586134 AAGGACTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 17 0.49
30 7 0.20
31 8 0.23
32 3 0.09
ACGTcount: A:0.59, C:0.10, G:0.11, T:0.20
Consensus pattern (30 bp):
AAAAAGTACAAGGCCAAATTGAAAAATAAT
Found at i:27587764 original size:12 final size:12
Alignment explanation
Indices: 27587747--27587779 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
27587737 AAACCAAATT
27587747 TAAATTTAAAAA
1 TAAATTTAAAAA
27587759 TAAATTT-AAAA
1 TAAATTTAAAAA
27587770 TAAATTTAAA
1 TAAATTTAAA
27587780 CCAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:27587779 original size:17 final size:17
Alignment explanation
Indices: 27587711--27587768 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
27587701 TAACTTTAAT
* *
27587711 TTTAAGTTTAAAAT-CA
1 TTTAAATTTAAAATAAA
**
27587727 TTTCAAATTTAAACCAAA
1 TTT-AAATTTAAAATAAA
27587745 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
27587763 TTTAAA
1 TTTAAA
27587769 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.09
17 14 0.42
18 16 0.48
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:27587786 original size:29 final size:28
Alignment explanation
Indices: 27587731--27587800 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 28
27587721 AAATCATTTC
** **
27587731 AAATTTAAACCAAATTTAAATTTAAAAAT
1 AAATTTAAAATAAATTTAAA-CCAAAAAT
27587760 AAATTTAAAATAAATTTAAACCAAAAAT
1 AAATTTAAAATAAATTTAAACCAAAAAT
* *
27587788 AAAATAAAAATAA
1 AAATTTAAAATAA
27587801 TGACCCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (28 bp):
AAATTTAAAATAAATTTAAACCAAAAAT
Found at i:27588943 original size:20 final size:19
Alignment explanation
Indices: 27588919--27588969 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
27588909 TAAAAAAAAA
*
27588919 ATAAAAAAGTATCAAAAGT
1 ATAAAAAAGTATAAAAAGT
* *
27588938 ATTAAATAAGTATAAAAATT
1 A-TAAAAAAGTATAAAAAGT
*
27588958 ATAAAAATGTAT
1 ATAAAAAAGTAT
27588970 TTTTAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (19 bp):
ATAAAAAAGTATAAAAAGT
Found at i:27594091 original size:12 final size:12
Alignment explanation
Indices: 27594072--27594108 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
27594062 TCTCATAATT
27594072 AAATACAAATGC
1 AAATACAAATGC
* *
27594084 ATATACAAATTC
1 AAATACAAATGC
27594096 AAATACAAATGC
1 AAATACAAATGC
27594108 A
1 A
27594109 GACGTAGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (12 bp):
AAATACAAATGC
Found at i:27599229 original size:23 final size:23
Alignment explanation
Indices: 27599203--27599346 Score: 168
Period size: 23 Copynumber: 6.2 Consensus size: 23
27599193 ACACTAGCGC
27599203 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
27599226 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
* *
27599249 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
27599272 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
27599297 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
27599320 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
27599343 GCTC
1 GCTC
27599347 AGTACTTTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.04
23 85 0.78
24 1 0.01
25 16 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:27599346 original size:71 final size:69
Alignment explanation
Indices: 27599203--27599335 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 69
27599193 ACACTAGCGC
* * *
27599203 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTTAGCACGTC
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTCTCTGATTAGCACGTC
27599268 TCGT
66 TCGT
*
27599272 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGT-GTGCTCTCTGATTAGCAC
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTC-TCGTGCTCTCTGATTAGCAC
27599336 TTTGTGTGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 8 0.14
71 48 0.84
72 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (69 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTCTCTGATTAGCACGTC
TCGT
Found at i:27599375 original size:39 final size:39
Alignment explanation
Indices: 27599311--27599385 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
27599301 TCCGATTAGC
*
27599311 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
27599350 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
27599386 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:27600706 original size:13 final size:12
Alignment explanation
Indices: 27600675--27600719 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
27600665 TCTTCTCTTC
*
27600675 TTTTTCTCAATT
1 TTTTTTTCAATT
27600687 TTTTTTTCAATT
1 TTTTTTTCAATT
*
27600699 TTTCTTTTCGACTT
1 TTT-TTTTC-AATT
27600713 TTTTTTT
1 TTTTTTT
27600720 TTTTTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.48
13 9 0.31
14 6 0.21
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:27605277 original size:21 final size:22
Alignment explanation
Indices: 27605260--27605386 Score: 112
Period size: 23 Copynumber: 5.5 Consensus size: 22
27605250 CAAAGAGTAC
*
27605260 CAAAGTACTAACAGAGAGCACA
1 CAAAGTGCTAACAGAGAGCACA
* *
27605282 -TAAGTGCTGGGTAACAAAGAGCACA
1 CAAAGTGC----TAACAGAGAGCACA
* *
27605307 CACAGTGCTGAACAGAGAGTACA
1 CAAAGTGCT-AACAGAGAGCACA
*
27605330 CAAAGTACTAATCAGAGAGCACA
1 CAAAGTGCTAA-CAGAGAGCACA
*
27605353 TAAAGTGCTAATCAGAGAGCACA
1 CAAAGTGCTAA-CAGAGAGCACA
*
27605376 CACAGTGCTAA
1 CAAAGTGCTAA
27605387 TAACAGAGAG
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
21 5 0.06
22 3 0.04
23 58 0.69
25 13 0.15
26 5 0.06
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (22 bp):
CAAAGTGCTAACAGAGAGCACA
Found at i:27605296 original size:25 final size:26
Alignment explanation
Indices: 27605268--27605316 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
27605258 ACCAAAGTAC
* *
27605268 TAACAGAGAGCACATA-AGTGCTGGG
1 TAACAAAGAGCACACACAGTGCTGGG
27605293 TAACAAAGAGCACACACAGTGCTG
1 TAACAAAGAGCACACACAGTGCTG
27605317 AACAGAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (26 bp):
TAACAAAGAGCACACACAGTGCTGGG
Found at i:27605325 original size:23 final size:22
Alignment explanation
Indices: 27605267--27605417 Score: 108
Period size: 23 Copynumber: 6.4 Consensus size: 22
27605257 TACCAAAGTA
*
27605267 CTAACAGAGAGCACATA-AGTG
1 CTAACAGAGAGCACACACAGTG
*
27605288 CTGGGTAACAAAGAGCACACACAGTG
1 C----TAACAGAGAGCACACACAGTG
* * *
27605314 CTGAACAGAGAGTACACAAAGTA
1 CT-AACAGAGAGCACACACAGTG
* *
27605337 CTAATCAGAGAGCACATAAAGTG
1 CTAA-CAGAGAGCACACACAGTG
27605360 CTAATCAGAGAGCACACACAGTG
1 CTAA-CAGAGAGCACACACAGTG
*
27605383 CTAATAACAGAGAGCACGAGAC-GTG
1 C---TAACAGAGAGCAC-ACACAGTG
27605408 CTAAACAGAG
1 CT-AACAGAG
27605418 CGCGCGCTAG
Statistics
Matches: 106, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
21 1 0.01
22 4 0.04
23 62 0.58
25 28 0.26
26 11 0.10
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (22 bp):
CTAACAGAGAGCACACACAGTG
Found at i:27605374 original size:69 final size:66
Alignment explanation
Indices: 27605248--27605384 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 66
27605238 ATACGGAACA
27605248 AACAAAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACAAAGAGCACACACAGT
1 AACAAAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGC---GTAACAAAGAGCACACACAGT
27605313 GCTG
63 GCTG
* *
27605317 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACATAAAGTGC-TAATCAGAGAGCACACACAG
1 AACAAAGAGTAC-CAAAGTACTAA-CAGAGAGCACAT-AAGTGCGTAA-CAAAGAGCACACACAG
27605381 TGCT
62 TGCT
27605385 AATAACAGAG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
68 3 0.05
69 30 0.48
70 11 0.18
71 12 0.19
72 6 0.10
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (66 bp):
AACAAAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCGTAACAAAGAGCACACACAGTGCT
G
Found at i:27605408 original size:25 final size:23
Alignment explanation
Indices: 27605299--27605417 Score: 125
Period size: 23 Copynumber: 5.1 Consensus size: 23
27605289 TGGGTAACAA
27605299 AGAGCACACACAGTGCTGAA-CAG
1 AGAGCACACACAGTGCT-AATCAG
* * *
27605322 AGAGTACACAAAGTACTAATCAG
1 AGAGCACACACAGTGCTAATCAG
* *
27605345 AGAGCACATAAAGTGCTAATCAG
1 AGAGCACACACAGTGCTAATCAG
27605368 AGAGCACACACAGTGCTAATAACAG
1 AGAGCACACACAGTGCTAAT--CAG
* *
27605393 AGAGCACGAGAC-GTGCTAAACAG
1 AGAGCAC-ACACAGTGCTAATCAG
27605416 AG
1 AG
27605418 CGCGCGCTAG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.02
23 60 0.73
25 17 0.21
26 3 0.04
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (23 bp):
AGAGCACACACAGTGCTAATCAG
Found at i:27605409 original size:48 final size:45
Alignment explanation
Indices: 27605267--27605417 Score: 126
Period size: 46 Copynumber: 3.2 Consensus size: 45
27605257 TACCAAAGTA
* ** * *
27605267 CTAACAGAGAGCACATAAGTGCTGGGTAACAAAGAGCACACACAGTG
1 CTAACAGAGAGCACACAAGTGCT-AATAACAGAGAGCACAAAC-GTG
* * *
27605314 CTGAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACATAAAGTG
1 CT-AACAGAGAGCACAC-AAGTGCTAATAACAGAGAGCACA-AACGTG
*
27605360 CTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTG
1 CTAA-CAGAGAGCACACA-AGTGCTAATAACAGAGAGCAC-AAACGTG
27605408 CTAAACAGAG
1 CT-AACAGAG
27605418 CGCGCGCTAG
Statistics
Matches: 83, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
45 3 0.04
46 34 0.41
47 3 0.04
48 34 0.41
49 9 0.11
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (45 bp):
CTAACAGAGAGCACACAAGTGCTAATAACAGAGAGCACAAACGTG
Found at i:27612634 original size:23 final size:23
Alignment explanation
Indices: 27612556--27612707 Score: 114
Period size: 23 Copynumber: 6.5 Consensus size: 23
27612546 TATACGGAAC
* *
27612556 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
27612578 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
27612599 GGGTAACATAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
27612625 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
27612648 AATCAGAGAACACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
27612671 AATCAAAGAGCACACACAA-TGCT
1 AAACAGAGAGCACACA-AAGTGCT
27612694 AATAACAGAGAGCA
1 -A-AACAGAGAGCA
27612708 GGAGACATTT
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
21 17 0.17
23 55 0.54
24 3 0.03
25 21 0.21
26 6 0.06
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:27612681 original size:69 final size:67
Alignment explanation
Indices: 27612556--27612705 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 67
27612546 TATACGGAAC
* * * *
27612556 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACATAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAACACAAAAGTGC---GTAACAAAGAGCACACACAA
27612621 TGCT-
63 TGCTA
27612625 AAACAGAGAGTACACAAAGTACTAATCAGAGAACACACAAAGTGC-TAATCAAAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAACACA-AAAGTGCGTAA-CAAAGAGCACACACA
27612689 ATGCTA
62 ATGCTA
27612695 ATAACAGAGAG
1 A-AACAGAGAG
27612706 CAGGAGACAT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
68 3 0.04
69 31 0.44
70 12 0.17
71 19 0.27
72 6 0.08
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAACACAAAAGTGCGTAACAAAGAGCACACACAATGC
TA
Found at i:27616819 original size:18 final size:18
Alignment explanation
Indices: 27616796--27616833 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
27616786 TAATATAGTT
*
27616796 TTATTC-AGTTTATTTGAA
1 TTATTCAAG-TTATTCGAA
27616814 TTATTCAAGTTATTCGAA
1 TTATTCAAGTTATTCGAA
27616832 TT
1 TT
27616834 CGAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (18 bp):
TTATTCAAGTTATTCGAA
Found at i:27620604 original size:13 final size:14
Alignment explanation
Indices: 27620586--27620618 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
27620576 TATATATTTC
27620586 TTTATATAT-AATA
1 TTTATATATAAATA
27620599 TTTATATATCAAATA
1 TTTATATAT-AAATA
27620614 TTTAT
1 TTTAT
27620619 TTCCTCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATATATAAATA
Found at i:27637139 original size:12 final size:12
Alignment explanation
Indices: 27637108--27637166 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
27637098 GTTCACGAAC
* *
27637108 AAGCTCATTTAA
1 AAGCTCGTTTAT
27637120 AAGCTCGTTTAT
1 AAGCTCGTTTAT
*
27637132 AAGTTCGTTTATT
1 AAGCTCGTTTA-T
27637145 AA-CTCGTTTAT
1 AAGCTCGTTTAT
27637156 -AGCTCGTTTAT
1 AAGCTCGTTTAT
27637167 TTATTAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 1 0.02
11 10 0.24
12 27 0.66
13 3 0.07
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:27637150 original size:24 final size:23
Alignment explanation
Indices: 27637123--27637167 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
27637113 CATTTAAAAG
*
27637123 CTCGTTTATAAGTTCGTTTATTAA
1 CTCGTTTAT-AGCTCGTTTATTAA
27637147 CTCGTTTATAGCTCGTTTATT
1 CTCGTTTATAGCTCGTTTATT
27637168 TATTAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (23 bp):
CTCGTTTATAGCTCGTTTATTAA
Found at i:27637316 original size:23 final size:23
Alignment explanation
Indices: 27637260--27637352 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
27637250 TCATTAACAT
* * *
27637260 TGTTCGTGAACGTGTTCAATTATA
1 TGTTTGTGAACATGTTCGATTA-A
** *
27637284 TGTTCATGAACATGTTCGTTTAA
1 TGTTTGTGAACATGTTCGATTAA
*
27637307 TGTTTGTGAACATATTCGATTAA
1 TGTTTGTGAACATGTTCGATTAA
*
27637330 TGTTTGTGAACATGTTAGATTAA
1 TGTTTGTGAACATGTTCGATTAA
27637353 GTTAAATGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
23 41 0.69
24 18 0.31
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (23 bp):
TGTTTGTGAACATGTTCGATTAA
Found at i:27642706 original size:22 final size:21
Alignment explanation
Indices: 27642681--27642736 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
27642671 GAACGGGTTG
27642681 AATTTATTTAAT-AATTATTTTA
1 AATTTATTTAATGAA--ATTTTA
*
27642703 AATTT-TTTTATGAAATTTTA
1 AATTTATTTAATGAAATTTTA
27642723 ATTATTTATTTAAT
1 A--ATTTATTTAAT
27642737 TATTGTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 7 0.25
21 5 0.18
22 11 0.39
23 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTTATTTAATGAAATTTTA
Found at i:27643211 original size:10 final size:10
Alignment explanation
Indices: 27643184--27643231 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
27643174 ATTAATTTTT
27643184 TTAAAAT-T-
1 TTAAAATATA
27643192 TTAAAA-ATA
1 TTAAAATATA
27643201 TTAAAATATA
1 TTAAAATATA
*
27643211 TAAAAATATA
1 TTAAAATATA
*
27643221 ATAAAA-ATA
1 TTAAAATATA
27643230 TT
1 TT
27643232 TTTTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 7 0.21
9 10 0.30
10 16 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATATA
Found at i:27643226 original size:11 final size:10
Alignment explanation
Indices: 27643193--27643230 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
27643183 TTTAAAATTT
27643193 TAAAAATAT-
1 TAAAAATATA
27643202 T-AAAATATA
1 TAAAAATATA
27643211 TAAAAATATAA
1 TAAAAATAT-A
27643222 TAAAAATAT
1 TAAAAATAT
27643231 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 2 0.08
10 7 0.27
11 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAAAATATA
Found at i:27648497 original size:39 final size:40
Alignment explanation
Indices: 27648443--27648522 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
27648433 TATGCACTCA
27648443 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
*
27648482 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
27648522 A
1 A
27648523 CATATCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 28 0.72
40 11 0.28
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:27648538 original size:39 final size:38
Alignment explanation
Indices: 27648447--27648539 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
27648437 CACTCAATGG
* *
27648447 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
27648486 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
* *
27648524 ATATCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
27648540 ACTTGTCTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 4 0.09
39 32 0.68
40 11 0.23
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:27652287 original size:6 final size:6
Alignment explanation
Indices: 27652276--27652301 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27652266 AACAAACTTG
27652276 CCTCTT CCTCTT CCTCTT CCTCTT CC
1 CCTCTT CCTCTT CCTCTT CCTCTT CC
27652302 ATGACTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
CCTCTT
Found at i:27654361 original size:72 final size:71
Alignment explanation
Indices: 27654240--27654376 Score: 211
Period size: 72 Copynumber: 1.9 Consensus size: 71
27654230 ATGCTCCATC
* ** *
27654240 AACTCCTCCTTCAGCTTATCCAAGCTTGTTTGGGAGTCTTACAGGGGTGAGCTGCTGCTGCCTTA
1 AACTCCTCCTTCAGCTTATCCAAGCTTGTTTGGGAGTCTCACAAAGGTGAGCTGCTGCTACCTTA
27654305 CCTTGG
66 CCTTGG
* *
27654311 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCATAAAGGTGAGCTGTTGCTACCTT
1 AACTCCTCCTTCAGCTTAT-CCAAGCTTGTTTGGGAGTCTCACAAAGGTGAGCTGCTGCTACCTT
27654376 A
65 A
27654377 ACAAGTAGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
71 19 0.32
72 40 0.68
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (71 bp):
AACTCCTCCTTCAGCTTATCCAAGCTTGTTTGGGAGTCTCACAAAGGTGAGCTGCTGCTACCTTA
CCTTGG
Found at i:27658045 original size:24 final size:24
Alignment explanation
Indices: 27658013--27658087 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
27658003 CTAGACAAAA
* * *
27658013 TTAGCTCTCACGAGCCTAAAATGG
1 TTAGATCTCACGAGCCCAGAATGG
* * *
27658037 TTAGTTCTCATGAGCCCAGAATAG
1 TTAGATCTCACGAGCCCAGAATGG
*
27658061 TTAGATCTTACGAGCCCAGAATGG
1 TTAGATCTCACGAGCCCAGAATGG
27658085 TTA
1 TTA
27658088 ACCAGTATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
TTAGATCTCACGAGCCCAGAATGG
Found at i:27663000 original size:27 final size:28
Alignment explanation
Indices: 27662965--27663017 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
27662955 TCGTTTGAGC
* *
27662965 TTCTGTTCTTCCTTCTTTTGTTTCTTTT
1 TTCTGTTCTTCATTCTTTTATTTCTTTT
*
27662993 TTCT-TTCTTTATTCTTTTATTTCTT
1 TTCTGTTCTTCATTCTTTTATTTCTT
27663018 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (28 bp):
TTCTGTTCTTCATTCTTTTATTTCTTTT
Found at i:27666839 original size:27 final size:26
Alignment explanation
Indices: 27666793--27667021 Score: 65
Period size: 30 Copynumber: 7.9 Consensus size: 26
27666783 AGGTTTTTTA
27666793 GGGGTAAAATGGTAATTTTGTGAAATT
1 GGGGTAAAATGGTAATTTTG-GAAATT
27666820 GGGGTTAAGAATGG-AA-TTTGGAAAGTTT
1 GGGG-TAA-AATGGTAATTTTGGAAA--TT
* **
27666848 GGGGAATAAAATGATAAATTTTGGCAAAAAC
1 GGGG--TAAAATGGT-AATTTTGG--AAATT
** *
27666879 AAGGTCAAAAAT-GAAATTTTGGAAAGTTT
1 GGGGT--AAAATGGTAATTTTGGAAA--TT
*
27666908 GGGGGTAAAATGGTAATTTTTGAAAGTTTT
1 -GGGGTAAAATGGTAATTTTGGAAA---TT
* *
27666938 GGGGTTAAAAT-ATAATTTTAGAAAAGTTTT
1 GGGG-TAAAATGGTAATTTT-GGAAA---TT
*
27666968 GGGGTCAAAAT-GTAATTATGGAAAAGTTTT
1 GGGGT-AAAATGGTAATTTTGG-AAA---TT
27666998 GGGGTCAAAAT-GTAATTTTGGAAA
1 GGGGT-AAAATGGTAATTTTGGAAA
27667022 AGTTTTGGGG
Statistics
Matches: 159, Mismatches: 22, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.03
27 11 0.07
28 20 0.13
29 44 0.28
30 65 0.41
31 12 0.08
33 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (26 bp):
GGGGTAAAATGGTAATTTTGGAAATT
Found at i:27666939 original size:30 final size:30
Alignment explanation
Indices: 27666881--27667285 Score: 532
Period size: 30 Copynumber: 13.6 Consensus size: 30
27666871 GCAAAAACAA
* *
27666881 GGTCAAAAATGAAATTTTGG-AAAGTTTGGG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTTGG
*
27666911 GGT-AAAATGGTAATTTTTG-AAAGTTTTGG
1 GGTCAAAAT-GTAATTTTGGAAAAGTTTTGG
* * *
27666940 GGTTAAAATATAATTTTAGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
27666970 GGTCAAAATGTAATTATGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
27667000 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
* * * *
27667030 GGTTAAAATGTAATTTTAGAAAACTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
27667060 GGTCAAAATGTAATTTTGGAAAAGTTTT-A
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
27667089 GGTCAAAATGTAATTTTGGAAACA-TTTCGG
1 GGTCAAAATGTAATTTTGGAAA-AGTTTTGG
* *
27667119 GGTCAAAATATAATTATGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
27667149 GGTCAAAATGTAATTTTGGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
* *
27667179 GGTTAAAATGTAATTTTAGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
27667209 GGTCAAAATGTAATTTTGGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
* *
27667239 GGTTAAAATGTAATTTTAGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
** *
27667269 GGTTTAAATATAATTTT
1 GGTCAAAATGTAATTTT
27667286 TAGACAATTT
Statistics
Matches: 332, Mismatches: 37, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.02
29 54 0.16
30 273 0.82
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTTGG
Found at i:27667103 original size:149 final size:149
Alignment explanation
Indices: 27666910--27667283 Score: 583
Period size: 149 Copynumber: 2.5 Consensus size: 149
27666900 GAAAGTTTGG
* * *
27666910 GGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGGTTAAAATATAATTTTAGAAAAGTTTTGGGGT
1 GGGTCAAAAT-GTAATTTTGGAAAAGTTTT-AGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGT
* *
27666973 CAAAATGTAATTATGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAA
64 CAAAATATAATTATGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAA
27667038 TGTAATTTTAGAAAACTTTTA
129 TGTAATTTTAGAAAACTTTTA
* * *
27667059 GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGTCAAAATGTAATTTTGGAAACA-TTTCGGGGTC
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGTTAAAATGTAATTTTAGAAA-AGTTTTGGGGTC
27667123 AAAATATAATTATGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAAT
65 AAAATATAATTATGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAAT
* *
27667188 GTAATTTTAGAAAAGTTTTG
130 GTAATTTTAGAAAACTTTTA
*
27667208 GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTT
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA-GGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTC
*
27667273 TAAATATAATT
65 AAAATATAATT
27667284 TTTAGACAAT
Statistics
Matches: 205, Mismatches: 15, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
149 153 0.75
150 52 0.25
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (149 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTCA
AAATATAATTATGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATG
TAATTTTAGAAAACTTTTA
Found at i:27669140 original size:17 final size:16
Alignment explanation
Indices: 27669118--27669193 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
27669108 TTTAATTTTT
27669118 ATTTAAATTCAAAGTAA
1 ATTTAAATTCAAA-TAA
*
27669135 ATTTAAA-T-AATTAA
1 ATTTAAATTCAAATAA
*
27669149 ATTTAAATTTAAAATAA
1 ATTTAAA-TTCAAATAA
*
27669166 ATTTAAATTTAAATAA
1 ATTTAAATTCAAATAA
*
27669182 ATTTAAAATCAA
1 ATTTAAATTCAA
27669194 TTTAACTCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 20 0.39
17 19 0.37
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (16 bp):
ATTTAAATTCAAATAA
Found at i:27669154 original size:6 final size:6
Alignment explanation
Indices: 27669095--27669188 Score: 70
Period size: 6 Copynumber: 15.8 Consensus size: 6
27669085 TTTTTTAATG
* * ** * *
27669095 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TCAAA- GTAAAT TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
27669143 AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT TTAAA
1 --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
27669189 ATCAATTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
4 4 0.06
5 7 0.10
6 48 0.70
7 4 0.06
8 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:27669205 original size:27 final size:27
Alignment explanation
Indices: 27669152--27669206 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
27669142 TAATTAAATT
*
27669152 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
27669179 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
27669206 T
1 T
27669207 TAAACGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:27669522 original size:65 final size:65
Alignment explanation
Indices: 27669444--27669570 Score: 182
Period size: 65 Copynumber: 2.0 Consensus size: 65
27669434 AAGACTTTGC
* * * ** *
27669444 TATCCAACTTTACTTCAATCTCAAGAGGATGGGAAGAGATTTTGCTCTTACTTCAGTTTCAGTAA
1 TATCCAACTTTACTTCAATCTCAAAAGGATAGGAAAAGACCTTGCTCTTACTTCAATTTCAGTAA
* *
27669509 TATCCAGCTTTACTTCAATTTCAAAAGGATAGGAAAAGACCTTGCTCTTACTTCAATTTCAG
1 TATCCAACTTTACTTCAATCTCAAAAGGATAGGAAAAGACCTTGCTCTTACTTCAATTTCAG
27669571 AGATAAAGAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (65 bp):
TATCCAACTTTACTTCAATCTCAAAAGGATAGGAAAAGACCTTGCTCTTACTTCAATTTCAGTAA
Found at i:27670057 original size:69 final size:68
Alignment explanation
Indices: 27669706--27670998 Score: 2136
Period size: 68 Copynumber: 18.9 Consensus size: 68
27669696 AAGGTCCTGT
* * * *
27669706 TCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27669771 TGC
66 TGC
*
27669774 TCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27669839 TGC
66 TGC
*
27669842 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27669907 TGC
66 TGC
*
27669910 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27669975 TGC
66 TGC
*
27669978 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGATGACA
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670043 TTGC
65 TTGC
* * *
27670047 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670112 TTGC
65 TTGC
* * * * * *
27670116 TCTTACTTTAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTCAAGCGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670181 TTGC
65 TTGC
* *
27670185 TCTTACTTTAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27670250 TGC
66 TGC
*
27670253 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
*
27670318 TTC
66 TGC
27670321 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27670386 TGC
66 TGC
*
27670389 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGATGACA
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670454 TTGC
65 TTGC
* * *
27670458 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670523 TTGC
65 TTGC
* * * * *
27670527 TCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTCAAGCGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670592 TTGC
65 TTGC
*
27670596 TCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27670661 TGC
66 TGC
*
27670664 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27670729 TGC
66 TGC
27670732 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
27670797 TGC
66 TGC
* *
27670800 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGATGTCA
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670865 TTGC
65 TTGC
* * *
27670869 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACA
27670934 TTGC
65 TTGC
* * * *
27670938 TCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTCAAGCGGAT
1 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
27670999 TGGAAATGAT
Statistics
Matches: 1170, Mismatches: 52, Indels: 5
0.95 0.04 0.00
Matches are distributed among these distances:
68 623 0.53
69 547 0.47
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACAT
TGC
Found at i:27670508 original size:411 final size:411
Alignment explanation
Indices: 27669550--27670998 Score: 2549
Period size: 411 Copynumber: 3.5 Consensus size: 411
27669540 GGAAAAGACC
* * * *
27669550 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGCTATCCATCTCTACTTCAATTTCAAGCGAAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAG-G---
** * ** * * * * *
27669615 AGGAAAAGATCCTATTCTTACTTCAATTTCAGAGATAAAGGCGTGCTATCCATCTCTACTTCAAT
62 -GGATGACAT--TGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAAT
* * *
27669680 TTCAAGCGGATAGGAAAAGGTCCTGTTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-AC
124 TTCAAGAGGAT--G---ACGT--TGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAAC
* *
27669744 TCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
182 TTTACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
27669809 CACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTT
247 CACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTT
27669874 ATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGT
312 ATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGT
*
27669939 GTTATCCACTCTACTTCAATTTCAAAGGGATGACA
377 GTTATCCACTCTACTTCAATTTCAAGGGGATGACA
27669974 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
27670039 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
*
27670104 GGATGACGTTGCTCTTACTTTAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
*
27670169 AAGCGGATGACGTTGCTCTTACTTTAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
196 AAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
27670234 TTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTC
261 TTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTC
*
27670299 AATTTCAAGGGGATGACGTTTCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTAC
326 AATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTAC
27670364 TTCAATTTCAAGGGGATGACA
391 TTCAATTTCAAGGGGATGACA
27670385 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
27670450 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
27670515 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
27670580 AAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
196 AAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
27670645 TTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTC
261 TTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTC
27670710 AATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTAC
326 AATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTAC
27670775 TTCAATTTCAAGGGGATGACA
391 TTCAATTTCAAGGGGATGACA
27670796 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
*
27670861 GTCATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
27670926 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
27670991 AAGCGGAT
196 AAGCGGAT
27670999 TGGAAATGAT
Statistics
Matches: 997, Mismatches: 27, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
410 37 0.04
411 837 0.84
412 3 0.00
415 1 0.00
417 56 0.06
419 6 0.01
423 1 0.00
424 56 0.06
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (411 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
GACATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTTTACTTCAATTTC
AAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
TTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTC
AATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTAC
TTCAATTTCAAGGGGATGACA
Found at i:27682889 original size:30 final size:30
Alignment explanation
Indices: 27682816--27683148 Score: 424
Period size: 30 Copynumber: 11.2 Consensus size: 30
27682806 TTAAAAATGA
*
27682816 AATTTTGG-AAAG-TTTGAGGGT-AAAATGGT
1 AATTTTGGAAAAGTTTTG-GGGTCAAAAT-AT
* * * *
27682845 AATTTTTG-AAAGTTTTAGGGTTAATATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * *
27682874 AATTTTAGAAAAGTTTTGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* *
27682904 AATTGTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
*
27682934 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
*
27682964 AATTTTAGAAAAGTTTTGGGGTCAAAATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
*
27682994 AATTTTGGAAAAGTTTT-GGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
*
27683023 AATTTTGGAAAAGTTTCGGGGTCAAAATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* *
27683053 AATTATGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* *
27683083 AATTTTGGAAAAGTTTTAGGGTTAAAATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* **
27683113 AATTTTAGAAAAGTTTTGGGGTTTAAATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
27683143 AATTTT
1 AATTTT
27683149 TGGATAATTT
Statistics
Matches: 272, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
29 50 0.18
30 222 0.82
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTGGGGTCAAAATAT
Done.