Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003502.1 Hibiscus syriacus cultivar Beakdansim tig00007400_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 95175
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1817 original size:17 final size:18
Alignment explanation
Indices: 1779--1822 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1769 TTTCTGAGAG
* *
1779 ATTGAAATCTGTGAAGGA
1 ATTGGAATCTGTCAAGGA
1797 ATTGGAATCTGTCAA-GA
1 ATTGGAATCTGTCAAGGA
1814 ATTGGAATC
1 ATTGGAATC
1823 CAATTCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (18 bp):
ATTGGAATCTGTCAAGGA
Found at i:2848 original size:243 final size:244
Alignment explanation
Indices: 2199--2971 Score: 921
Period size: 243 Copynumber: 3.1 Consensus size: 244
2189 CCCCCGACTA
*
2199 AAATAAAGTTTCACCCGACCCGACCCGAATATATGAA-T-GAAACCCGACCCGACCTAAATAATA
1 AAATAAAGTTTCACCCGACCCGACCCGAATATA--AATTAGAAACTCGACCCG----AAATAAT-
* * *
2262 AAAAAATTATTTTTATTCAAT-AAAACTGTGACTTAATTTAAAAAAAAATATATAGAGAGAGGGT
59 AAAAAATTATTTTTATTCAATAAAAACAGTGACTTAA-TT--GAAAAAATATA-ATAGAG-GGGT
* *
2326 ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTTTTTGGGTTGGGTCGGGTCGGG
119 ATTATTGTAATTATTCCT-AATATATAAGGTAAAATTATA--TATAT---TT---TCGGGTC-GG
* * * *
2391 TATTTTTCACCCT-AATCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAAACCCGACCTG
174 TATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTT-AAAAAAA-CCGACCCG
2455 A-CCGACC
237 ACCCGACC
* * * * *
2462 AAA-AAATTTTCACTC--CCCGACCCAAATAT-GATTAGAAA-TCCGACCTGACCCGAATAATAA
1 AAATAAAGTTTCACCCGACCCGACCCGAATATAAATTAGAAACT-CGACCCGA----AATAATAA
** * *
2522 AAAAAAATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAATAT-ATAGAGAGGTATTATTG
61 AAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATAATAGAGGGGTATTATTG
*
2586 TAATTATTCCTAA-ATATAAGGTAAAATTATATATATTTTCGGGTCAGGTTTTTTTCACCCTAAA
126 TAATTATTCCTAATATATAAGGTAAAATTATATATATTTTCGGGTC-GGTATTTTTCACCCTAAA
*
2650 CCCGAACTCGA-CCGACCCGAATATCACACTTAAAAAAACCAACCCGACCCGACC
190 CCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCCGACC
2704 AAATAAAGTTTCACCCGACCCGACCCGAATATAAATTAGAAACTCGACCCGAAATAAT-AAAAAT
1 AAATAAAGTTTCACCCGACCCGACCCGAATATAAATTAGAAACTCGACCCGAAATAATAAAAAAT
2768 TA-TTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATAATAGAGGGGTATTATTGTAAT
66 TATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAA-TATAATAGAGGGGTATTATTGTAAT
2832 TATTCCTAATATATAAGGTAAAATTATATATATTTTCGGGTCGGTATTTTTCACCCTAAACCCGA
130 TATTCCTAATATATAAGGTAAAATTATATATATTTTCGGGTCGGTATTTTTCACCCTAAACCCGA
* *
2897 ATTCGACCCGACCCG-ATATCACACTTAAAAAAACTGACCCGACCCCGACC
195 ACTCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCGA-CCCGACC
* *
2947 AAATAAAGTTCCACCTGACCCGACC
1 AAATAAAGTTTCACCCGACCCGACC
2972 AAATAAAGTT
Statistics
Matches: 453, Mismatches: 37, Indels: 60
0.82 0.07 0.11
Matches are distributed among these distances:
240 35 0.08
241 16 0.04
242 103 0.23
243 121 0.27
244 10 0.02
245 13 0.03
246 17 0.04
247 1 0.00
249 3 0.01
251 18 0.04
252 2 0.00
253 21 0.05
254 5 0.01
255 1 0.00
256 8 0.02
257 1 0.00
258 22 0.05
259 30 0.07
260 13 0.03
262 10 0.02
263 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (244 bp):
AAATAAAGTTTCACCCGACCCGACCCGAATATAAATTAGAAACTCGACCCGAAATAATAAAAAAT
TATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATAATAGAGGGGTATTATTGTAATT
ATTCCTAATATATAAGGTAAAATTATATATATTTTCGGGTCGGTATTTTTCACCCTAAACCCGAA
CTCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCCGACC
Found at i:2969 original size:25 final size:26
Alignment explanation
Indices: 2933--2997 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
2923 AAAAAAACTG
2933 ACCCGACCCCGACCAAATAAAG-TTCC
1 ACCCGA-CCCGACCAAATAAAGTTTCC
* *
2959 ACCTGACCCGACCAAATAAAGTTTTC
1 ACCCGACCCGACCAAATAAAGTTTCC
2985 ACCCGACCCGACC
1 ACCCGACCCGACC
2998 CGAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.32, C:0.42, G:0.12, T:0.14
Consensus pattern (26 bp):
ACCCGACCCGACCAAATAAAGTTTCC
Found at i:3432 original size:3 final size:3
Alignment explanation
Indices: 3426--3464 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
3416 GAATAATAAT
* *
3426 TTA TTA TTA TTA TTA TTG TTA TTGT TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT
3465 TTCTATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6227 original size:41 final size:41
Alignment explanation
Indices: 6176--6280 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 41
6166 CTCAAAAGAT
*
6176 TGACAAATGACCTAAGGATTTAAACATCATGCTCGAAAAAC
1 TGACAGATGACCTAAGGATTTAAACATCATGCTCGAAAAAC
* *
6217 TGATAGATGACCTAAGGATTTAAACATCATGCTCGAAAGAC
1 TGACAGATGACCTAAGGATTTAAACATCATGCTCGAAAAAC
*
6258 TGACATATGACCCTAAGGATTTA
1 TGACAGATGA-CCTAAGGATTTA
6281 CAATTTGGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 46 0.79
42 12 0.21
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (41 bp):
TGACAGATGACCTAAGGATTTAAACATCATGCTCGAAAAAC
Found at i:6754 original size:258 final size:248
Alignment explanation
Indices: 6221--6835 Score: 858
Period size: 258 Copynumber: 2.4 Consensus size: 248
6211 AAAAACTGAT
* * *
6221 AGATGA-CCTAAGGATTTAAACATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAT
1 AGATGACCCTAAGGTTTTAAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAA
* * ** *
6285 TTGGGAAATAATTTACTAGGTAAGAAACTTTGGAAATTGCTTTTTTACTTTTCAAGAATTTCATT
66 TTGGGAAATAATTTACTGGGTAAGAAACTTTGAAAACCGCTTTCTTACTTTTCAAGAATTTCATT
* * *
6350 TTCTTGAACATTAAATGAGAAACTTTGAAAAGCGCTTTCCCATTTTCATGTGTAAAGATCCTACC
131 ATCTTGAACATTAAACGAGAAACTTTGAAAAGCGCTTTCCCATTTTCATGTGTAAACATCCTACC
* *
6415 CAAAGGTCTGACGGATGGCCCTAAGAACTTATCATCTTGCTTAAAAGACTAAC
196 CAAAGGTCTGACGGATGGCCCTAAGAACTTATCATCTTACTCAAAAGACTAAC
* * * * *
6468 AAATGACCATAAGGTTTTAAGTATCATGCTCGAAAGACTGACAGATTACCCTAAGGATTTACAAA
1 AGATGACCCTAAGGTTTTAAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAA
* *
6533 TTGGGAAATAA-TTACTGGGTAAGAAACTTTGAAAACCGCTTTCTTATTTTTTACA-AATTTCAT
66 TTGGGAAATAATTTACTGGGTAAGAAACTTTGAAAACCGCTTTCTTACTTTTCA-AGAATTTCAT
*
6596 TATCTTGAACATTAAACGAGAAACTTTGAAAATCGCTTTCCCATTTTCATGTGAAAATCATGTGT
130 TATCTTGAACATTAAACGAGAAACTTTGAAAAGCGCTTTCCCA---T--T-T-----TCATGTGT
* * *
6661 AAACATCCTACCCAAAGGTTTGACGGATGGCCCTAAGGACTTATCATCTTACTCAAAATACTAAC
184 AAACATCCTACCCAAAGGTCTGACGGATGGCCCTAAGAACTTATCATCTTACTCAAAAGACTAAC
*
6726 AGATGACCCTAAAGTTTTAAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAA
1 AGATGACCCTAAGGTTTTAAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAA
*
6791 TTTGGGAAATAATTTATTGGGTAAGAAACTTTGAAAACCGCTTTC
66 -TTGGGAAATAATTTACTGGGTAAGAAACTTTGAAAACCGCTTTC
6836 CCATTTTCAT
Statistics
Matches: 322, Mismatches: 31, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
247 88 0.27
248 63 0.20
250 1 0.00
252 1 0.00
253 1 0.00
258 126 0.39
259 11 0.03
260 31 0.10
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (248 bp):
AGATGACCCTAAGGTTTTAAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAA
TTGGGAAATAATTTACTGGGTAAGAAACTTTGAAAACCGCTTTCTTACTTTTCAAGAATTTCATT
ATCTTGAACATTAAACGAGAAACTTTGAAAAGCGCTTTCCCATTTTCATGTGTAAACATCCTACC
CAAAGGTCTGACGGATGGCCCTAAGAACTTATCATCTTACTCAAAAGACTAAC
Found at i:6926 original size:40 final size:41
Alignment explanation
Indices: 6871--6980 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 41
6861 AAACATCCTA
* * * *
6871 CTCAAAGGTCTAACAGATGACCCTAAGACTT-ATCATCTTG
1 CTCAAAAGACTAACAGATGACCCTAAGACTTAAGCATCATG
**
6911 CTCAAAAGACTAACAGATGACCCTAAGGTTTTAAGCATCATG
1 CTCAAAAGACTAACAGATGACCCTAA-GACTTAAGCATCATG
** *
6953 CTTGAAAGACTGACAGATGACCCTAAGA
1 CTCAAAAGACTAACAGATGACCCTAAGA
6981 ATTTACAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 24 0.41
41 4 0.07
42 30 0.52
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
CTCAAAAGACTAACAGATGACCCTAAGACTTAAGCATCATG
Found at i:6975 original size:199 final size:200
Alignment explanation
Indices: 6614--7031 Score: 694
Period size: 199 Copynumber: 2.1 Consensus size: 200
6604 ACATTAAACG
6614 AGAAACTTTGAAAATCGCTTTCCCATTTTCATGTGAAAATCATGTGTAAACATCCTACCCAAAGG
1 AGAAACTTTGAAAATCGCTTTCCCATTTTCATGTGAAAATCATGTGTAAACATCCTACCCAAAGG
* * * * *
6679 TTTGACGGATGGCCCTAAGGACTTATCATCTTACTCAAAATACTAACAGATGACCCTAAAGTTTT
66 TCTAACAGATGACCCTAAGGACTTATCATCTTACTCAAAAGACTAACAGATGACCCTAAAGTTTT
* * * *
6744 AAGCATCATGCTCGAAAGACTGACATATGACCCTAAGGATTTACAAATTTGGGAAATAATTTATT
131 AAGCATCATGCTCGAAAGACTGACAGATGACCCTAAGAATTTACAAATTTGGGAAATAATTAACT
6809 GGGTA
196 GGGTA
* *
6814 AGAAACTTTGAAAACCGCTTTCCCATTTTCATGTGAAAATCATGTGTAAACATCCTACTCAAAGG
1 AGAAACTTTGAAAATCGCTTTCCCATTTTCATGTGAAAATCATGTGTAAACATCCTACCCAAAGG
* *
6879 TCTAACAGATGACCCTAA-GACTTATCATCTTGCTCAAAAGACTAACAGATGACCCTAAGGTTTT
66 TCTAACAGATGACCCTAAGGACTTATCATCTTACTCAAAAGACTAACAGATGACCCTAAAGTTTT
*
6943 AAGCATCATGCTTGAAAGACTGACAGATGACCCTAAGAATTTACAAATTTGGGAAATAATTAACT
131 AAGCATCATGCTCGAAAGACTGACAGATGACCCTAAGAATTTACAAATTTGGGAAATAATTAACT
7008 GGGTA
196 GGGTA
*
7013 ATAAACTTTGAAAATCGCT
1 AGAAACTTTGAAAATCGCT
7032 CTCTTACTTT
Statistics
Matches: 202, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
199 125 0.62
200 77 0.38
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (200 bp):
AGAAACTTTGAAAATCGCTTTCCCATTTTCATGTGAAAATCATGTGTAAACATCCTACCCAAAGG
TCTAACAGATGACCCTAAGGACTTATCATCTTACTCAAAAGACTAACAGATGACCCTAAAGTTTT
AAGCATCATGCTCGAAAGACTGACAGATGACCCTAAGAATTTACAAATTTGGGAAATAATTAACT
GGGTA
Found at i:8563 original size:37 final size:37
Alignment explanation
Indices: 8512--8594 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
8502 TATGTCTGAA
* *
8512 CCCCAACATTTTTCATGCTGATGTGCGCGTTCAAAATG
1 CCCC-ACATTTTTCATACTGATGTGAGCGTTCAAAATG
8550 CCCCACATTTTTCATACTGATGTGAGCGTTCAAAATG
1 CCCCACATTTTTCATACTGATGTGAGCGTTCAAAATG
8587 CCCCACAT
1 CCCCACAT
8595 GGATCATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
37 39 0.91
38 4 0.09
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (37 bp):
CCCCACATTTTTCATACTGATGTGAGCGTTCAAAATG
Found at i:18120 original size:29 final size:29
Alignment explanation
Indices: 18088--18155 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
18078 CTTCGAGTCG
*
18088 ATTCAAATTTAAGAAATTCGAGTCGAGTT
1 ATTCGAATTTAAGAAATTCGAGTCGAGTT
18117 ATTCGAATTTAAGAAATTCGAGTCGAGTT
1 ATTCGAATTTAAGAAATTCGAGTCGAGTT
18146 ATTCGAATTT
1 ATTCGAATTT
18156 TTATATTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (29 bp):
ATTCGAATTTAAGAAATTCGAGTCGAGTT
Found at i:22915 original size:13 final size:13
Alignment explanation
Indices: 22897--22924 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22887 TGGATAAGAG
22897 CAGCAATGAAGCA
1 CAGCAATGAAGCA
22910 CAGCAATGAAGCA
1 CAGCAATGAAGCA
22923 CA
1 CA
22925 CATGCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.07
Consensus pattern (13 bp):
CAGCAATGAAGCA
Found at i:23323 original size:55 final size:55
Alignment explanation
Indices: 23306--23943 Score: 769
Period size: 55 Copynumber: 11.7 Consensus size: 55
23296 AGTCCGTTCT
* *
23306 CTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAAT-GTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCC
* * * *
23357 CCATTCCTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAATCGTGTCTGCTCC
* * * * *
23409 CTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * *
23464 CTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * * * * *
23519 CTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * * *
23574 CTATTGCTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* *
23629 CTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTGTCTGCTCT
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* *
23684 CTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* *
23739 CTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* * * *
23794 CTATTTCTTCAGATAGTATAAGACTCGAACAATCTTCAACAGTCGTGTCTACTCC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* *
23849 CTATTTCTTCATAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGT-TCGCTCC
1 CTATTCCTTC--AGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCC
* * *
23906 CTCTTTCTTTCAG-GCAGTAT-AGAACTCGAATAATCTTC
1 CT-ATTCCTTCAGAG-AGTATAAG-ACTCGAACAATCTTC
23944 TTACGGGGTT
Statistics
Matches: 518, Mismatches: 56, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
51 35 0.07
52 34 0.07
55 372 0.72
56 31 0.06
57 41 0.08
58 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
Found at i:24007 original size:54 final size:51
Alignment explanation
Indices: 23894--24050 Score: 174
Period size: 54 Copynumber: 3.0 Consensus size: 51
23884 CTTCAACAAT
* * *
23894 CGGGTTCGCTCCCTCTTTCTTTCAGGCAGTATAGAACTCGAATAATCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTCT-AGGAAGTAT-GAACTCGAATAATATTCTTA
*
23947 CGGGGTTCACTCCCTCTTTCTCTAGGAAGTATGGAACTCGAA-AATATTCTTCAAA
1 C-GGGTTCGCTCCCTCTTTCTCTAGGAAGTAT-GAACTCGAATAATATTCTT---A
* * *
24002 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTA-GAACTCGAATGATAATCTT
1 CGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGAACTCGAATAATATTCTT
24051 CCTACGAGAC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
52 17 0.19
53 25 0.28
54 46 0.51
55 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (51 bp):
CGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGAACTCGAATAATATTCTTA
Found at i:24080 original size:52 final size:52
Alignment explanation
Indices: 24024--25087 Score: 1867
Period size: 52 Copynumber: 20.5 Consensus size: 52
24014 CTCTTTCTCT
* ** * *
24024 AGGGAGTAGAACTCGAATGATAATCTTCCTACGAGACTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24076 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* *
24128 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* * *
24180 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24232 AGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24284 AAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* *
24336 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
24388 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24440 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* *
24492 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24544 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* *
24596 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
24648 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24700 AGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
*
24752 AAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* **
24804 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
24856 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
24908 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
* **
24960 AGGGACTAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
25012 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
1 AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
25064 AGGGACTAGAACTCGAACAATAAT
1 AGGGACTAGAACTCGAACAATAAT
25088 ATCCAACGAT
Statistics
Matches: 963, Mismatches: 49, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 963 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (52 bp):
AGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTC
Found at i:25155 original size:55 final size:55
Alignment explanation
Indices: 25091--25365 Score: 473
Period size: 55 Copynumber: 5.0 Consensus size: 55
25081 CAATAATATC
25091 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
* *
25146 CAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTT
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
*
25201 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTT
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
* * *
25254 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTT
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
25309 CAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 CAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
25365 C
1 C
25366 TTTTGCTTCA
Statistics
Matches: 205, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
53 48 0.23
54 4 0.02
55 113 0.55
56 40 0.20
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
Found at i:25289 original size:108 final size:110
Alignment explanation
Indices: 25091--25365 Score: 491
Period size: 108 Copynumber: 2.5 Consensus size: 110
25081 CAATAATATC
25091 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
25156 GTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTT
66 GTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTT
* *
25201 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATCAATCGC
1 CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* *
25264 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTT
66 GTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTT
25309 CAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 CAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
25366 TTTTGCTTCA
Statistics
Matches: 157, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
108 75 0.48
109 29 0.18
110 44 0.28
111 9 0.06
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (110 bp):
CAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
GTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTT
Found at i:26689 original size:9 final size:8
Alignment explanation
Indices: 26671--26747 Score: 65
Period size: 9 Copynumber: 9.8 Consensus size: 8
26661 TTTCTTCTTC
26671 TTTTTT-A
1 TTTTTTCA
26678 TTTTTTCCA
1 TTTTTT-CA
26687 TTTTTTC-
1 TTTTTTCA
26694 TATTTTTC-
1 T-TTTTTCA
*
26702 -TATTTCA
1 TTTTTTCA
26709 TTTTTTCA
1 TTTTTTCA
*
26717 TTTTTTTTA
1 -TTTTTTCA
26726 TTTTTTTCA
1 -TTTTTTCA
26735 -TTTTTCA
1 TTTTTTCA
26742 TTTTTT
1 TTTTTT
26748 TTATCTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
6 5 0.08
7 14 0.24
8 18 0.31
9 22 0.37
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:26712 original size:31 final size:30
Alignment explanation
Indices: 26668--26730 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
26658 TTTTTTCTTC
* *
26668 TTCTTTTTTATTTTTTCCATTTTTTCTATTT
1 TTCTATTTCATTTTTT-CATTTTTTCTATTT
*
26699 TTCTATTTCATTTTTTCATTTTTTTTATTT
1 TTCTATTTCATTTTTTCATTTTTTCTATTT
26729 TT
1 TT
26731 TTCATTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (30 bp):
TTCTATTTCATTTTTTCATTTTTTCTATTT
Found at i:26714 original size:39 final size:38
Alignment explanation
Indices: 26671--26744 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
26661 TTTCTTCTTC
26671 TTTTTT-ATTTTTTCCA-TTTTTTCTATTTTTCTATTTCA
1 TTTTTTCATTTTTTCCATTTTTTTC-ATTTTTC-ATTTCA
**
26709 TTTTTTCATTTTTTTTATTTTTTTCATTTTTCATTT
1 TTTTTTCATTTTTTCCATTTTTTTCATTTTTCATTT
26745 TTTTTATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 10 0.31
39 15 0.47
40 7 0.22
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (38 bp):
TTTTTTCATTTTTTCCATTTTTTTCATTTTTCATTTCA
Found at i:26724 original size:25 final size:25
Alignment explanation
Indices: 26696--26753 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
26686 ATTTTTTCTA
26696 TTTT-TCTATTTCATTTTTTCATTTT
1 TTTTATCTATTTCA-TTTTTCATTTT
* *
26721 TTTTATTTTTTTCATTTTTCATTTT
1 TTTTATCTATTTCATTTTTCATTTT
26746 TTTTATCT
1 TTTTATCT
26754 TTAAGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTATCTATTTCATTTTTCATTTT
Found at i:27886 original size:3 final size:3
Alignment explanation
Indices: 27872--27906 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
27862 GTACCAAGGC
27872 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT C
27907 AATACTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:35305 original size:13 final size:13
Alignment explanation
Indices: 35287--35314 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35277 TGGATAAGAG
35287 CAGCAATGAAGCA
1 CAGCAATGAAGCA
35300 CAGCAATGAAGCA
1 CAGCAATGAAGCA
35313 CA
1 CA
35315 CATGCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.07
Consensus pattern (13 bp):
CAGCAATGAAGCA
Found at i:35414 original size:3 final size:3
Alignment explanation
Indices: 35396--35448 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
35386 GCCAATGTAA
* * *
35396 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAC AAT AAT AAC AAT -AT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35441 AATT AAT A
1 AA-T AAT A
35449 TTTATAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35653 original size:27 final size:28
Alignment explanation
Indices: 35623--35736 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 28
35613 TAAAAATAAG
* *
35623 TTTATTATTTTTATATTTAT-AATTAAA
1 TTTAATATTTTTATATTTTTAAATTAAA
* *
35650 TTTAATA-TTTTATATTATTAAATTTAA
1 TTTAATATTTTTATATTTTTAAATTAAA
* *
35677 TTTAATATTTTT-CA----T--ACTAAA
1 TTTAATATTTTTATATTTTTAAATTAAA
35698 TTTAATATTTTTATATTTTTAAATTAAA
1 TTTAATATTTTTATATTTTTAAATTAAA
35726 TTTAATATTTT
1 TTTAATATTTT
35737 AAAATAAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
21 16 0.23
22 1 0.01
23 1 0.01
26 11 0.16
27 20 0.29
28 20 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTAATATTTTTATATTTTTAAATTAAA
Found at i:35758 original size:19 final size:19
Alignment explanation
Indices: 35717--35760 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35707 TTTATATTTT
* * * *
35717 TAAATTAAATTTAATATTT
1 TAAAATAAATATAAAATTA
35736 TAAAATAAATATAAAATTA
1 TAAAATAAATATAAAATTA
35755 TAAAAT
1 TAAAAT
35761 TAAGTATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATAAATATAAAATTA
Found at i:35782 original size:21 final size:20
Alignment explanation
Indices: 35758--35796 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35748 AAAATTATAA
35758 AATTAAGTATGAAAAATATTG
1 AATTAAGT-TGAAAAATATTG
* *
35779 AATTTAGTTTAAAAATAT
1 AATTAAGTTGAAAAATAT
35797 AAAATAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
AATTAAGTTGAAAAATATTG
Found at i:35876 original size:24 final size:24
Alignment explanation
Indices: 35847--35896 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35837 TAAATACGAT
*
35847 TTATAATATATT-TAATCTATTTAA
1 TTATAAAATATTAT-ATCTATTTAA
*
35871 TTATAAAATATTATATTTATTTAA
1 TTATAAAATATTATATCTATTTAA
35895 TT
1 TT
35897 TAGTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATAAAATATTATATCTATTTAA
Found at i:53577 original size:33 final size:33
Alignment explanation
Indices: 53540--53606 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53530 AAGCTGTGTT
53540 CGGGGGTGCACGCGTGTCGGAGGTCGAATCAGC
1 CGGGGGTGCACGCGTGTCGGAGGTCGAATCAGC
53573 CGGGGGTGCACGCGTGTCGGAGGTCGAATCAGC
1 CGGGGGTGCACGCGTGTCGGAGGTCGAATCAGC
53606 C
1 C
53607 AGTTTGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (33 bp):
CGGGGGTGCACGCGTGTCGGAGGTCGAATCAGC
Found at i:53675 original size:3 final size:3
Alignment explanation
Indices: 53654--53721 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
53644 CCATATTGAT
* * *
53654 TTA TTA TATA ATA TAA TTA TTA TTA TTA TTA TTA -TA TTA TT- TAA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
53698 ATA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
53722 ATATATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 5 0.09
3 47 0.87
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:53709 original size:24 final size:26
Alignment explanation
Indices: 53677--53729 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
53667 TAATTATTAT
53677 TATTATTATTA-TATTATT-TAAATA
1 TATTATTATTATTATTATTATAAATA
*
53701 TATTATTATTATTATTATTATATATA
1 TATTATTATTATTATTATTATAAATA
53727 TAT
1 TAT
53730 ATATATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.42
25 7 0.27
26 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATTATTATTATTATTATAAATA
Found at i:66421 original size:10 final size:10
Alignment explanation
Indices: 66402--66440 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
66392 TGCTTGAAGA
66402 AAAAAAAAAG
1 AAAAAAAAAG
*
66412 AAAAAGAAAG
1 AAAAAAAAAG
66422 AAAAAAAAGAG
1 AAAAAAAA-AG
66433 AAAAAAAA
1 AAAAAAAA
66441 GGGGGGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:66424 original size:21 final size:20
Alignment explanation
Indices: 66398--66441 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
66388 ATTATGCTTG
66398 AAGAAAAAAAAAAGAAAAAGA
1 AAGAAAAAAAAAAGAAAAA-A
*
66419 AAGAAAAAAAAGAGAAAAAA
1 AAGAAAAAAAAAAGAAAAAA
66439 AAG
1 AAG
66442 GGGGGGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAAAGAAAAAA
Found at i:66441 original size:11 final size:11
Alignment explanation
Indices: 66399--66441 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
66389 TTATGCTTGA
*
66399 AGAAAAAAAAA
1 AGAAAAAAAAG
*
66410 AGAAAAAGAA-
1 AGAAAAAAAAG
66420 AGAAAAAAAAG
1 AGAAAAAAAAG
66431 AGAAAAAAAAG
1 AGAAAAAAAAG
66442 GGGGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:67738 original size:83 final size:83
Alignment explanation
Indices: 67599--67845 Score: 451
Period size: 83 Copynumber: 3.0 Consensus size: 83
67589 CAATGTACTC
*
67599 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
67664 TGGAAGATGAATTTGCCG
66 TGGAAGATGAATTTGCCA
67682 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
67747 TAGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
67765 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAAT
67829 TTGGAAGATGAATTTGC
65 TTGGAAGATGAATTTGC
67846 TCATAGTAGA
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
82 4 0.03
83 155 0.97
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TGGAAGATGAATTTGCCA
Found at i:68845 original size:113 final size:113
Alignment explanation
Indices: 68661--70133 Score: 1356
Period size: 113 Copynumber: 12.9 Consensus size: 113
68651 TGGATTGACA
68661 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
68726 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCC
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
68774 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
68839 AGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
*
68887 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
68952 AGAATTTGTTCAACCTTTTG-CTCAAATCCAACATTTGATGGATCATCT
66 AGAATTTGTTCAACCTTTTGCCT-GAATTCATCACTTGATGGATCATCT
69000 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG-
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*** * * * ** ** * * ** * * *
69064 AGAGCCTATACTA--TTGAGTTTTATTCTCAAAAGGTT-TTGTGA-CATAAT
66 AGAATTTGTTCAACCTTTTGCCTGAAT-TCATCA-CTTGATG-GATCAT-CT
* * *** ** * * * *
69112 ATCTACATCTACATTTGTCA-AA-GATGATAGATTCTCTGATTTGAAGAAGAAAGATCTATTG-G
1 -TTTCCAGAGA-AAGT-TCATAATGA-GA-AGA-ACTC--ATCTGAAGAAGGAAGA---A--GAA
* * *** * * ** * * * * *
69174 GTTTTTACAATTGAAGAA-ATACTCAATTC-ACCAATCTGAAATCAAATAACATAACATTCATGC
53 G--TTCATAA-TG-AGAAGA-A-TTTGTTCAACC-TTTTG-CCT-GAAT-TCATCAC-TTGATGG
*
69237 ATCATAT
107 ATCATCT
* * ** ** **** *** * ** **
69244 TTT--AG-G--TGTTTACAAAAAT-AGGTGCATTTTCATTCATTTTCATCTATGTTGAA-TTTTT
1 TTTCCAGAGAAAG-TT-C-ATAATGAGAAG-A-ACTCA-TC-TGAAGAAGGAAGAAGAAGTTCAT
** ** *
69302 AACT--G--GAA--T-TTCAAAGATTTTAG-CAAAGATTCAAATCTATCATTTGATGGATTGA-C
59 AA-TGAGAAGAATTTGTTC-AACCTTTT-GCCTGA-ATTC--ATC-A-C--TTGATGGA-TCATC
*
69358 A
113 T
69359 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
69424 AGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAGCC
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
69472 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
69537 AGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
*
69585 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
69650 AGAATTTGTTCAACCTTTTG-CTCAAATCCATCA-TATGATGGATCATCT
66 AGAATTTGTTCAACCTTTTGCCT-GAATTCATCACT-TGATGGATCATCT
69698 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
69763 AGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
69811 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
69875 AGAATTTGTTCAACCTTTTG-CTCAAATCCATCATTTGATGGATCATCT
66 AGAATTTGTTCAACCTTTTGCCT-GAATTCATCACTTGATGGATCATCT
69923 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
69988 AGAATTTGTTCAATCTTTTACCTGAATTCATCAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
*
70036 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
70100 AGAACTTGTTCAACTTTTTGCAT-AATTCTATCAC
66 AGAATTTGTTCAACCTTTTGCCTGAATTC-ATCAC
70134 AGAAGGAGAT
Statistics
Matches: 1129, Mismatches: 153, Indels: 157
0.78 0.11 0.11
Matches are distributed among these distances:
110 8 0.01
111 22 0.02
112 203 0.18
113 720 0.64
114 20 0.02
115 24 0.02
116 11 0.01
117 11 0.01
118 22 0.02
119 6 0.01
120 16 0.01
121 4 0.00
122 2 0.00
123 1 0.00
124 5 0.00
125 5 0.00
126 7 0.01
127 13 0.01
128 7 0.01
129 1 0.00
130 2 0.00
131 3 0.00
132 11 0.01
133 5 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
Found at i:69041 original size:226 final size:226
Alignment explanation
Indices: 68642--70120 Score: 1539
Period size: 226 Copynumber: 6.5 Consensus size: 226
68632 ATTCAAATCT
* *
68642 ATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAATTGATGGATT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
68706 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTTGATGGATC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-AAATCCATCATTTGATGGATC
* *
68770 AGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
129 ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
68835 GAGAAGAATTTGTTCAACCTTTTACCTGAATTC
194 GAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
68868 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
68933 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCAACATTTGATGGATCAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAT
68998 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * * * * *
69063 GAGAGCCTATACTATT-GA-GTTTTATTCTCAA--A
196 GA-AG--AAT-TTGTTCAACCTTTTA-CCTGAATTC
**** * ** * * *** * *
69095 AGGTTTTG-TGACATAATATCTACATCTACA-TTTG-TCA-AA-GATGATAGATTCTCTGATTTG
1 ATCAATTGATG-GAT--TATCT-TTTCCAGAGAAAGTTCATAATGA-GA-AGA-ACTC--ATCTG
* * * * *** * * *
69155 AAGAAGAAAGATCTATTG-GGTTTTTACAATTGAAGAA-ATACTCAATTC-ACCAATCTGAAATC
57 AAGAAGGAAGA---A--GAAG--TTCATAA-TG-AGAAGA-A-TTTGTTCAACC-TTTTG--CTC
* * * * * * ** **
69217 AAATAACATAACA-TTCATGCATCATATTTT--AG-G--TGTTTACAAAAAT-AGGTGCATTTTC
108 AAAT-CCAT--CATTTGATGGATCATCTTTTCCAGAGAAAG-TT-C-ATAATGAGAAG-A-ACTC
**** *** * ** ** ** * **
69275 ATTCATTTTCATCTATGTTGAA-TTTTTAACT--G--GAA--T-TTCAAAGATTTTAGCAAAGAT
165 A-TC-TGAAGAAGGAAGAAGAAGTTCATAA-TGAGAAGAATTTGTTC-AACCTTTTACCTGA-AT
69332 TC
225 TC
*
69334 AAATCTATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 --ATC-A--A-TTGATGGATT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
69398 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTGAATTCATCACTTGA
59 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-AAATCCATCATTTGA
* *
69462 TGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
123 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
69527 CATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
188 CATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
69566 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
69631 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATATGATGGATCAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAT
69696 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
69761 GAAGAATTTGTTCAACCTTTTACCTGAATTC
196 GAAGAATTTGTTCAACCTTTTACCTGAATTC
69792 ATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
69856 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAT
69921 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
69986 GAAGAATTTGTTCAATCTTTTACCTGAATTC
196 GAAGAATTTGTTCAACCTTTTACCTGAATTC
70017 ATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
70081 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
70121 ATAATTCTAT
Statistics
Matches: 1030, Mismatches: 143, Indels: 161
0.77 0.11 0.12
Matches are distributed among these distances:
225 297 0.29
226 423 0.41
227 25 0.02
228 30 0.03
229 25 0.02
230 20 0.02
231 22 0.02
232 12 0.01
233 19 0.02
234 9 0.01
235 7 0.01
236 5 0.00
237 12 0.01
238 5 0.00
239 9 0.01
240 10 0.01
241 20 0.02
242 17 0.02
243 12 0.01
244 28 0.03
245 19 0.02
246 4 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (226 bp):
ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAT
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:69702 original size:698 final size:698
Alignment explanation
Indices: 68366--69762 Score: 2740
Period size: 698 Copynumber: 2.0 Consensus size: 698
68356 AAGCTTTTCA
68366 AGAGCCTATACTATTGAGTTTTATTCTCAAAAGGTTTTGTGACATAATATCTACATCTACATTTG
1 AGAGCCTATACTATTGAGTTTTATTCTCAAAAGGTTTTGTGACATAATATCTACATCTACATTTG
*
68431 TCAAAGATGATAGATTCTTTGATTTGAAGAAGAAAGATCTATTGGGTTTTTACAATTGAAGAAAT
66 TCAAAGATGATAGATTCTCTGATTTGAAGAAGAAAGATCTATTGGGTTTTTACAATTGAAGAAAT
*
68496 ACTCAATTCACCAATCTGAAATCAAATAACTTAACATTCATGCATCATATTTTAGGTGTTTACAA
131 ACTCAATTCACCAATCTGAAATCAAATAACATAACATTCATGCATCATATTTTAGGTGTTTACAA
68561 AAATAGGTGCATTTTCATTCATTTTCATCTATGTTGAATTTTTAACAGGAATTTCAAAGATTTTA
196 AAATAGGTGCATTTTCATTCATTTTCATCTATGTTGAATTTTTAACAGGAATTTCAAAGATTTTA
68626 GCAAAGATTCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
261 GCAAAGATTCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
*
68691 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCA
326 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCA
68756 TCACTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
391 TCACTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
68821 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATC
456 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATC
68886 TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
521 TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
68951 AAGAATTTGTTCAACCTTTTGCTCAAATCCAACATTTGATGGATCATCTTTTCCAGAGAAAGTTC
586 AAGAATTTGTTCAACCTTTTGCTCAAATCCAACATATGATGGATCATCTTTTCCAGAGAAAGTTC
69016 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
651 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
69064 AGAGCCTATACTATTGAGTTTTATTCTCAAAAGGTTTTGTGACATAATATCTACATCTACATTTG
1 AGAGCCTATACTATTGAGTTTTATTCTCAAAAGGTTTTGTGACATAATATCTACATCTACATTTG
69129 TCAAAGATGATAGATTCTCTGATTTGAAGAAGAAAGATCTATTGGGTTTTTACAATTGAAGAAAT
66 TCAAAGATGATAGATTCTCTGATTTGAAGAAGAAAGATCTATTGGGTTTTTACAATTGAAGAAAT
69194 ACTCAATTCACCAATCTGAAATCAAATAACATAACATTCATGCATCATATTTTAGGTGTTTACAA
131 ACTCAATTCACCAATCTGAAATCAAATAACATAACATTCATGCATCATATTTTAGGTGTTTACAA
*
69259 AAATAGGTGCATTTTCATTCATTTTCATCTATGTTGAATTTTTAACTGGAATTTCAAAGATTTTA
196 AAATAGGTGCATTTTCATTCATTTTCATCTATGTTGAATTTTTAACAGGAATTTCAAAGATTTTA
69324 GCAAAGATTCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
261 GCAAAGATTCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
69389 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCA
326 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCA
69454 TCACTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
391 TCACTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
69519 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATC
456 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATC
69584 TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
521 TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
69649 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATATGATGGATCATCTTTTCCAGAGAAAGTTC
586 AAGAATTTGTTCAACCTTTTGCTCAAATCCAACATATGATGGATCATCTTTTCCAGAGAAAGTTC
69714 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
651 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
69762 A
1 A
69763 AGAATTTGTT
Statistics
Matches: 693, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
698 693 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (698 bp):
AGAGCCTATACTATTGAGTTTTATTCTCAAAAGGTTTTGTGACATAATATCTACATCTACATTTG
TCAAAGATGATAGATTCTCTGATTTGAAGAAGAAAGATCTATTGGGTTTTTACAATTGAAGAAAT
ACTCAATTCACCAATCTGAAATCAAATAACATAACATTCATGCATCATATTTTAGGTGTTTACAA
AAATAGGTGCATTTTCATTCATTTTCATCTATGTTGAATTTTTAACAGGAATTTCAAAGATTTTA
GCAAAGATTCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCA
TCACTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATC
TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCAACATATGATGGATCATCTTTTCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
Found at i:70454 original size:3 final size:3
Alignment explanation
Indices: 70446--70529 Score: 123
Period size: 3 Copynumber: 28.0 Consensus size: 3
70436 CCATATTGAT
* * *
70446 TTA TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
70494 TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
70530 AATATATATA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:71013 original size:15 final size:15
Alignment explanation
Indices: 70993--71024 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
70983 AACGCAGCAG
70993 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
71008 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
71023 AA
1 AA
71025 CTTACTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:76703 original size:17 final size:17
Alignment explanation
Indices: 76681--76714 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
76671 TTGATTTTGA
76681 CTAAAAAGTCAAATTTT
1 CTAAAAAGTCAAATTTT
* *
76698 CTAAAATGTCATATTTT
1 CTAAAAAGTCAAATTTT
76715 AGGTTGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
CTAAAAAGTCAAATTTT
Found at i:79201 original size:14 final size:14
Alignment explanation
Indices: 79182--79209 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
79172 TATATCATTC
79182 TATTGTTACTTATA
1 TATTGTTACTTATA
79196 TATTGTTACTTATA
1 TATTGTTACTTATA
79210 GCAATGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTGTTACTTATA
Found at i:80960 original size:19 final size:19
Alignment explanation
Indices: 80936--80993 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
80926 TGAGAAATTG
80936 GCTAA-GTATCGATATCTCT
1 GCTAAGGTATCGATA-CTCT
80955 GCTAAGGGTATCGATACTCT
1 GCTAA-GGTATCGATACTCT
**
80975 TATATAGGTATCGATACTC
1 GCTA-AGGTATCGATACTC
80994 CCTCAAGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.15
20 19 0.56
21 10 0.29
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (19 bp):
GCTAAGGTATCGATACTCT
Found at i:86786 original size:20 final size:20
Alignment explanation
Indices: 86761--86806 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
86751 TACAATGTCA
*
86761 ATACCCTTTCTATA-GTATCG
1 ATACCCTTCCTA-AGGTATCG
86781 ATACCCTTCCTAAGGTATCG
1 ATACCCTTCCTAAGGTATCG
86801 ATACCC
1 ATACCC
86807 CTACAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (20 bp):
ATACCCTTCCTAAGGTATCG
Found at i:87915 original size:14 final size:14
Alignment explanation
Indices: 87896--87928 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
87886 TCGAGATTCG
87896 GGATGTTACAACTA
1 GGATGTTACAACTA
87910 GGATGTTACAACTA
1 GGATGTTACAACTA
87924 GGATG
1 GGATG
87929 ACATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (14 bp):
GGATGTTACAACTA
Found at i:90767 original size:30 final size:30
Alignment explanation
Indices: 90731--90797 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 30
90721 TAAAGATTGG
90731 AAAAGTTTAGGGACCAAA-ATAGTAATTTTC
1 AAAAGTTTAGGGACCAAACATA-TAATTTTC
*
90761 AAAAGTTTAGGGACCAAACATATAATTTTT
1 AAAAGTTTAGGGACCAAACATATAATTTTC
90791 AAAAGTT
1 AAAAGTT
90798 ATGTACTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (30 bp):
AAAAGTTTAGGGACCAAACATATAATTTTC
Found at i:91910 original size:19 final size:20
Alignment explanation
Indices: 91868--91912 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
91858 ACTATGCTGA
* *
91868 AAATTTATGTTAGAGTGTTG
1 AAATTGATGTTAGAATGTTG
91888 AAATTGATGTTAGAATG-TG
1 AAATTGATGTTAGAATGTTG
91907 AAATTG
1 AAATTG
91913 GGTCATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (20 bp):
AAATTGATGTTAGAATGTTG
Found at i:95119 original size:55 final size:55
Alignment explanation
Indices: 95021--95175 Score: 167
Period size: 54 Copynumber: 2.8 Consensus size: 55
95011 ATTTTGACGA
* * * * *
95021 TTTATTTCTTTTATAAAATAGAATAATTGAAGATTATGAAGAAAATAAATTTAATT
1 TTTATTTCTTTTA-AAAATAGAATCATTAAAGATTCTTAAGAAAATAAATTTAAAT
95077 GTTTATTTCTTTTAAAAGATA-AA-CATTAAAGATTCTTAAG-AAATAAATTTAAAT
1 -TTTATTTCTTTTAAAA-ATAGAATCATTAAAGATTCTTAAGAAAATAAATTTAAAT
* * *
95131 TTTATTATTTTTTCAAAATAGAATCATTCAAGATTC-TAA-AAAATA
1 TTTATT-TCTTTTAAAAATAGAATCATTAAAGATTCTTAAGAAAATA
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
53 9 0.11
54 31 0.36
55 24 0.28
56 5 0.06
57 16 0.19
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (55 bp):
TTTATTTCTTTTAAAAATAGAATCATTAAAGATTCTTAAGAAAATAAATTTAAAT
Found at i:95175 original size:54 final size:54
Alignment explanation
Indices: 94960--95175 Score: 163
Period size: 56 Copynumber: 3.9 Consensus size: 54
94950 AAGATATATT
* ** * *
94960 AATGATTTATTTCCTTTACAAAATAGAATTGTTCAAA-ATTTCCAAAAAAT-AATTTT
1 AATG-TTTATTTCTTTTA-AAAATAGAATCATT-AAAGA-TTCTAAAAAATAAATTTA
* * * * *
95016 GACGATTTATTTCTTTTATAAAATAGAATAATTGAAGATTATGAAGAAAATAAATTTA
1 AATG-TTTATTTCTTTTA-AAAATAGAATCATTAAAGATTCT-AA-AAAATAAATTTA
* *
95074 ATTGTTTATTTCTTTTAAAAGATA-AA-CATTAAAGATTCTTAAGAAATAAATTTA
1 AATGTTTATTTCTTTTAAAA-ATAGAATCATTAAAGATTC-TAAAAAATAAATTTA
* * *
95128 AAT-TTTATTATTTTTTCAAAATAGAATCATTCAAGATTCTAAAAAATA
1 AATGTTTATT-TCTTTTAAAAATAGAATCATTAAAGATTCTAAAAAATA
Statistics
Matches: 129, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
53 9 0.07
54 31 0.24
55 26 0.20
56 36 0.28
57 21 0.16
58 6 0.05
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (54 bp):
AATGTTTATTTCTTTTAAAAATAGAATCATTAAAGATTCTAAAAAATAAATTTA
Done.