Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 132 of 295
Found at i:40432854 original size:21 final size:23
Alignment explanation
Indices: 40432828--40432870 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40432818 ATACTTCTTG
*
40432828 TATATT-TCT-ATGTATATACTT
1 TATATTGTCTCATGTACATACTT
40432849 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
40432871 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:40433207 original size:16 final size:15
Alignment explanation
Indices: 40433183--40433217 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40433173 TAATTATTAT
40433183 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
40433199 TATTTTAATATTTTA
1 TATTCTAATATTTTA
40433214 TATT
1 TATT
40433218 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:40436751 original size:25 final size:25
Alignment explanation
Indices: 40436717--40436765 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
40436707 AGATGCAACT
40436717 TAACAAGCAAATGCCTCTAAAATAG
1 TAACAAGCAAATGCCTCTAAAATAG
40436742 TAACAAGCAAATGCCTCTAAAATA
1 TAACAAGCAAATGCCTCTAAAATA
40436766 AAAATTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (25 bp):
TAACAAGCAAATGCCTCTAAAATAG
Found at i:40451673 original size:75 final size:72
Alignment explanation
Indices: 40451534--40451954 Score: 592
Period size: 75 Copynumber: 5.8 Consensus size: 72
40451524 NNNNNNNNTG
* *
40451534 GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGA
1 GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGA
40451599 GCCTCAA
66 GCCTCAA
* * * * * **
40451606 GACACGTTGAGGTATTTTTAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGT
1 GACACGCTGAGGTAATTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAAATGAGT
*
40451671 TGAGCCTCAG
63 TGAGCCTCAA
*
40451681 GACACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAAATCAACTCATATTGCGAGAAATGAGTTG
1 GACACGCTGAGGTAATTTCAATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAAATGAGTTG
*
40451746 AGCCTCAG
65 AGCCTCAA
*
40451754 GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGA
1 GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGA
40451819 GCCTCAA
66 GCCTCAA
* * * **
40451826 GACATGCTGAGGTATTTTCAATTTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 GACACGCTGAGGTAATTTCAA-TTTCTG-TTTTC-AAAAATCAACTCATATTGCGAGAAATGAGT
**
40451891 TGAGCCTCGG
63 TGAGCCTCAA
40451901 GACACGCTGAGGTAATTTCAATTTCTGTTTTC-AAAATCAACTCATATTGCGAGA
1 GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGA
40451955 GGTGATTGAG
Statistics
Matches: 310, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
71 22 0.07
72 83 0.27
73 80 0.26
74 11 0.04
75 114 0.37
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (72 bp):
GACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGA
GCCTCAA
Found at i:40451904 original size:147 final size:145
Alignment explanation
Indices: 40451534--40451954 Score: 605
Period size: 147 Copynumber: 2.9 Consensus size: 145
40451524 NNNNNNNNTG
* *
40451534 GACACGCTGAGGTAATTTCAATTTCTG-TTTTC-AAAATTCAACTCATATTGCAAGAAATGAGTT
1 GACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTT
* * * * * *
40451597 GAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGA
66 GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGT-TTTC---AAAATCAACTCATATTGCGA
** *
40451662 GAGGTGAGTTGAGCCTCAG
127 GAAATGAGTTGAGCCTCAA
*
40451681 GACACGCTGAGGTAATTTCAATTTCTGTTGTT-AAAAAATCAACTCATATTGCGAGAAATGAGTT
1 GACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTT
40451745 GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAA
66 GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAA
40451810 ATGAGTTGAGCCTCAA
130 ATGAGTTGAGCCTCAA
* * * **
40451826 GACATGCTGAGGTATTTTCAATTTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 GACACGCTGAGGTAATTTCAA-TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGT
*
40451891 TGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGA
65 TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGA
40451955 GGTGATTGAG
Statistics
Matches: 250, Mismatches: 19, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
144 4 0.02
145 50 0.20
146 27 0.11
147 105 0.42
148 64 0.26
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (145 bp):
GACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTT
GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAA
TGAGTTGAGCCTCAA
Found at i:40451915 original size:220 final size:218
Alignment explanation
Indices: 40451533--40451954 Score: 738
Period size: 220 Copynumber: 1.9 Consensus size: 218
40451523 NNNNNNNNNT
40451533 GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTG
1 GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTG
* *
40451598 AGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAG
66 AGCCTCAAGACACGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAG
40451663 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAAATCAACTCAT
131 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTT-TT-AAAAATCAACTCAT
40451728 ATTGCGAGAAATGAGTTGAGCCTCA
194 ATTGCGAGAAATGAGTTGAGCCTCA
*
40451753 GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
1 GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTG
* * *
40451818 AGCCTCAAGACATGCTGAGGTATTTTCAATTTTTTGTTTTTC-AAAAAATCAACTCATATTGCGA
66 AGCCTCAAGACACGCTGAGGTATTTTCAA-TTTTTGTCTTTCAAAAAAATCAACTCATACTGCGA
* *
40451882 GAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATCAACTCATA
130 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTAAAAATCAACTCATA
40451947 TTGCGAGA
195 TTGCGAGA
40451955 GGTGATTGAG
Statistics
Matches: 193, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
218 22 0.11
219 2 0.01
220 158 0.82
221 11 0.06
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (218 bp):
GGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTG
AGCCTCAAGACACGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAG
AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTAAAAATCAACTCATAT
TGCGAGAAATGAGTTGAGCCTCA
Found at i:40452855 original size:25 final size:25
Alignment explanation
Indices: 40452823--40452898 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
40452813 CCTCCCCAAA
40452823 AAAAAACCTAACCCAAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAG
***
40452848 AAAAAACCTAACCCCCCAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAG
40452873 AAAAAACCTAACCCCCAAAAAAAAAA
1 AAAAAACCTAA--CCCAAAAAAAAAA
40452899 CCAATAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 33 0.77
27 10 0.23
ACGTcount: A:0.67, C:0.26, G:0.03, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCAAAAAAAAAAG
Found at i:40453153 original size:13 final size:13
Alignment explanation
Indices: 40453135--40453159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40453125 TATTTTACTT
40453135 TTTTTTATTTTTA
1 TTTTTTATTTTTA
40453148 TTTTTTATTTTT
1 TTTTTTATTTTT
40453160 TTCCTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:40453167 original size:16 final size:15
Alignment explanation
Indices: 40453123--40453170 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
40453113 TTTTATCTTC
*
40453123 TTTATTTTACTTTTT
1 TTTATTTTTCTTTTT
*
40453138 TTTATTTTTATTTTT
1 TTTATTTTTCTTTTT
40453153 TATT-TTTTTCCTTTTT
1 T-TTATTTTT-CTTTTT
40453169 TT
1 TT
40453171 GAATCTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTTTCTTTTT
Found at i:40453505 original size:24 final size:24
Alignment explanation
Indices: 40453450--40453505 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
40453440 AATCATGTTA
*
40453450 TATATGTAATATTGTTATCACTAT
1 TATATTTAATATTGTTATCACTAT
* *
40453474 TATTTTTATATATTGTTATTA-TAT
1 TATATTTA-ATATTGTTATCACTAT
40453498 TATATTTA
1 TATATTTA
40453506 GCTATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (24 bp):
TATATTTAATATTGTTATCACTAT
Found at i:40453749 original size:21 final size:23
Alignment explanation
Indices: 40453723--40453765 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40453713 ATACTTCTTG
*
40453723 TATATT-TCT-ATGTATATACTT
1 TATATTGTCTCATGTACATACTT
40453744 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
40453766 CCGAATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:40453918 original size:21 final size:21
Alignment explanation
Indices: 40453894--40453936 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40453884 TATATATACC
*
40453894 TTTTTGTGTATATAA-TATTA
1 TTTTTGTATATATAATTATTA
*
40453914 TTTTTGTATATTTAATTATTA
1 TTTTTGTATATATAATTATTA
40453935 TT
1 TT
40453937 CTAAAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTGTATATATAATTATTA
Found at i:40454099 original size:16 final size:15
Alignment explanation
Indices: 40454075--40454109 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40454065 TAATTATTAT
40454075 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
40454091 TATTTTAATATTTTA
1 TATTCTAATATTTTA
40454106 TATT
1 TATT
40454110 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:40455967 original size:17 final size:17
Alignment explanation
Indices: 40455936--40455972 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
40455926 TTAAAATAAA
40455936 AATAAAAATCTTAAAAC
1 AATAAAAATCTTAAAAC
*
40455953 AATAATAAATCTAAAAAC
1 AATAA-AAATCTTAAAAC
40455971 AA
1 AA
40455973 AGTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAAATCTTAAAAC
Found at i:40456117 original size:7 final size:7
Alignment explanation
Indices: 40456105--40456134 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40456095 AAATTATAAA
40456105 AATTATT
1 AATTATT
40456112 AATTATT
1 AATTATT
40456119 AATTATT
1 AATTATT
*
40456126 AGTTATT
1 AATTATT
40456133 AA
1 AA
40456135 AAATTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
AATTATT
Found at i:40456139 original size:17 final size:17
Alignment explanation
Indices: 40456096--40456139 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
40456086 AATTATAAAA
40456096 AATTA-TAAAAATTATT
1 AATTATTAAAAATTATT
40456112 AATTATT---AATTATT
1 AATTATTAAAAATTATT
*
40456126 AGTTATTAAAAATT
1 AATTATTAAAAATT
40456140 CTAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTATTAAAAATTATT
Found at i:40465837 original size:9 final size:9
Alignment explanation
Indices: 40465815--40465858 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
40465805 TGACATGTAC
40465815 AATTAAAAA
1 AATTAAAAA
40465824 CAATTAAAAA
1 -AATTAAAAA
40465834 AATTAAAAA
1 AATTAAAAA
*
40465843 AA-CAAAAA
1 AATTAAAAA
40465851 AATTAAAA
1 AATTAAAA
40465859 TACAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.48
10 9 0.29
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (9 bp):
AATTAAAAA
Found at i:40465869 original size:17 final size:17
Alignment explanation
Indices: 40465815--40465868 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
40465805 TGACATGTAC
*
40465815 AATTAAAAACAATTAAAAA
1 AATTAAAAA-AA-CAAAAA
40465834 AATTAAAAAAACAAAAA
1 AATTAAAAAAACAAAAA
*
40465851 AATT-AAAATACAAAAA
1 AATTAAAAAAACAAAAA
40465867 AA
1 AA
40465869 AAACACTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
18 2 0.06
19 9 0.27
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AATTAAAAAAACAAAAA
Found at i:40465982 original size:3 final size:3
Alignment explanation
Indices: 40465976--40466024 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
40465966 CCGACTCCTC
*
40465976 CTT CTT C-T CTT CTTT CTT -TT CTT CTT CTC CTT CTTT CTT -TT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
40466020 CTT CT
1 CTT CT
40466025 CTTTCTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:40465998 original size:12 final size:12
Alignment explanation
Indices: 40465977--40466028 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
40465967 CGACTCCTCC
*
40465977 TTCTTCTCTTCT
1 TTCTTTTCTTCT
40465989 TTCTTTTCTTC-
1 TTCTTTTCTTCT
*
40466000 TTC--TCCTTCT
1 TTCTTTTCTTCT
40466010 TTCTTTTCTTCT
1 TTCTTTTCTTCT
40466022 TCTCTTT
1 T-TCTTT
40466029 CTTTATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 17 0.52
13 5 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:40465999 original size:17 final size:17
Alignment explanation
Indices: 40465977--40466032 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
40465967 CGACTCCTCC
40465977 TTCTTCTCTTCTTTCTTTT
1 TTCTTCTCTTCTTTC--TT
40465996 CTTCTTCTCCTTCTTTCTT
1 -TTCTTCT-CTTCTTTCTT
40466015 TTCTTCT-TCTCTTTCTT
1 TTCTTCTCT-TCTTTCTT
40466032 T
1 T
40466033 ATTTTCCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 7 0.21
19 2 0.06
20 7 0.21
21 8 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTCTCTTCTTTCTT
Found at i:40466010 original size:21 final size:21
Alignment explanation
Indices: 40465976--40466065 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
40465966 CCGACTCCTC
40465976 CTTCTTCT-CTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
40465996 CTTCTTCTCCTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
40466017 CTTCTTCTCTTTCTTTATTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
40466038 CCTCTTCTCCTTATTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
40466059 CTTCTTC
1 CTTCTTC
40466066 CCGAAATGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 8 0.13
21 54 0.87
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTCTTCTCCTTCTTTCTTTT
Found at i:40466029 original size:12 final size:12
Alignment explanation
Indices: 40465976--40466031 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 12
40465966 CCGACTCCTC
40465976 CTTCTTCTC-TT
1 CTTCTTCTCTTT
40465987 C-T-TTCT-TTT
1 CTTCTTCTCTTT
*
40465996 CTTCTTCTCCTT
1 CTTCTTCTCTTT
40466008 C-T-TTCT-TTT
1 CTTCTTCTCTTT
40466017 CTTCTTCTCTTT
1 CTTCTTCTCTTT
40466029 CTT
1 CTT
40466032 TATTTTCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
9 10 0.28
10 7 0.19
11 10 0.28
12 9 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTCTTCTCTTT
Found at i:40466219 original size:20 final size:20
Alignment explanation
Indices: 40466194--40466243 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
40466184 ACCACCAATC
40466194 CAGCTTTTTTTTTTCAAATT
1 CAGCTTTTTTTTTTCAAATT
**
40466214 CAGC-TTTTTTTTTCAGTTT
1 CAGCTTTTTTTTTTCAAATT
40466233 CAGCTTTTTTT
1 CAGCTTTTTTT
40466244 CAGCTACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.14, C:0.16, G:0.08, T:0.62
Consensus pattern (20 bp):
CAGCTTTTTTTTTTCAAATT
Found at i:40467159 original size:20 final size:20
Alignment explanation
Indices: 40467134--40467201 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
40467124 TTTAAGATAC
40467134 AACAATTATTACTATTTTTT
1 AACAATTATTACTATTTTTT
* *
40467154 AACAATCTTTTA-TAATTTTT
1 AACAAT-TATTACTATTTTTT
* * *
40467174 AATAATT-CTACGATTTTTT
1 AACAATTATTACTATTTTTT
40467193 -ACAA-TATTA
1 AACAATTATTA
40467202 TACAATTTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 7 0.19
20 18 0.49
21 4 0.11
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (20 bp):
AACAATTATTACTATTTTTT
Found at i:40468272 original size:27 final size:27
Alignment explanation
Indices: 40468224--40468275 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40468214 CGATATCATA
*
40468224 AATAGTTTGACGAGACATTAAACATGG
1 AATAGTTTGACGAGACACTAAACATGG
* * *
40468251 AATAGTTTGATGGGACGCTAAACAT
1 AATAGTTTGACGAGACACTAAACAT
40468276 CATCTAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (27 bp):
AATAGTTTGACGAGACACTAAACATGG
Found at i:40469058 original size:30 final size:29
Alignment explanation
Indices: 40469024--40469089 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
40469014 CCCAGCCACC
40469024 CCCAATCC-AGATAAAAATTTATAAACCCAA
1 CCCAATCCGA-ATAAAAATTTAT-AACCCAA
*
40469054 CCCAATTCGAATAAAAATTTATAACCCAA
1 CCCAATCCGAATAAAAATTTATAACCCAA
*
40469083 TCCAATC
1 CCCAATC
40469090 TAAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.38
30 19 0.59
31 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (29 bp):
CCCAATCCGAATAAAAATTTATAACCCAA
Found at i:40471374 original size:54 final size:54
Alignment explanation
Indices: 40471315--40471423 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
40471305 TTAGTGAAAC
*
40471315 TGTGAAATTGGTTTGAAATTAAGATGATTCATGTTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
40471369 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
40471423 T
1 T
40471424 ATTTGATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (54 bp):
TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
Found at i:40471415 original size:27 final size:26
Alignment explanation
Indices: 40471331--40471421 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 26
40471321 ATTGGTTTGA
*
40471331 AATTAAGATGATTCATGTTATTATATG
1 AATTAA-ATGATTCATGATATTATATG
* * * * *
40471358 AATTAAATGAGT-GTGAAATTGGTTTG
1 AATTAAATGATTCATGATATT-ATATG
*
40471384 AAATTAAGATGATTCATGCTATTATATG
1 -AATTAA-ATGATTCATGATATTATATG
40471412 AATTAAATGA
1 AATTAAATGA
40471422 GTATTTGATT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
25 5 0.10
26 12 0.25
27 18 0.38
28 8 0.17
29 5 0.10
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (26 bp):
AATTAAATGATTCATGATATTATATG
Found at i:40472054 original size:26 final size:30
Alignment explanation
Indices: 40471998--40472054 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
40471988 TAAATTGATT
**
40471998 AAATGTTGATTGATTATGTGAATGACACTG
1 AAATGTTGATTGATTATGTGAACAACACTG
40472028 AAATGTTGATT-A-TATGT-AACAAC-CTG
1 AAATGTTGATTGATTATGTGAACAACACTG
40472054 A
1 A
40472055 TTTTGGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 5 0.20
29 1 0.04
30 11 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (30 bp):
AAATGTTGATTGATTATGTGAACAACACTG
Found at i:40472171 original size:38 final size:38
Alignment explanation
Indices: 40472118--40472190 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
40472108 AAGAATTTTA
40472118 TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
1 TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
*
40472156 TTATTATTTTGGAGTTATAGCATGTTTATATTAGT
1 TTATTATTTTAGAGTTATAGCATGTTTATATTAGT
40472191 GCATGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (38 bp):
TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
Found at i:40472203 original size:38 final size:38
Alignment explanation
Indices: 40472123--40472205 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
40472113 TTTTATTATT
* ** * **
40472123 ATTTTAGAGTTATAGCATGTTTATATTAGTATTTTATT
1 ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
*
40472161 ATTTTGGAGTTATAGCATGTTTATATTAGTGCATGAAA
1 ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
40472199 ATTTTGG
1 ATTTTGG
40472206 TGAAGTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (38 bp):
ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
Found at i:40473401 original size:48 final size:48
Alignment explanation
Indices: 40473294--40473459 Score: 162
Period size: 48 Copynumber: 3.5 Consensus size: 48
40473284 TTTGTGTGCT
* * *
40473294 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--AG-TA-TGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCC-TCGAGATATTCA-AGCC
*
40473340 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTCAAGCC
* * ** * * *
40473388 AGTTTAAGACATGTTTACTACATGCATCGGCCTCGCGATATACAAGCT
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTCAAGCC
*
40473436 AGTGTAAGACCTGTCT-GAGACATG
1 AGTGTAAGACATGTCTAG-GACATG
40473460 GCGTCAGCTT
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 30 0.30
47 2 0.02
48 64 0.65
49 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTCAAGCC
Found at i:40473541 original size:49 final size:49
Alignment explanation
Indices: 40473479--40473604 Score: 182
Period size: 49 Copynumber: 2.6 Consensus size: 49
40473469 TGTGGTTTAT
* *
40473479 CAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CTATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCAATAGATGAAAGC
* * *
40473528 CAGTGTAAAACCTGTCTGGGACATGGCATCGGCCTCAATATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
40473577 CAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
40473605 GTTGGTATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
48 1 0.01
49 53 0.77
50 15 0.22
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
Found at i:40480531 original size:120 final size:120
Alignment explanation
Indices: 40480395--40481261 Score: 1540
Period size: 120 Copynumber: 7.2 Consensus size: 120
40480385 TATATTTAGA
* * * * *
40480395 AAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 AAAA-TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGT
* *
40480460 AAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
* * * *
40480516 AAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
1 AAAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGT
* * *
40480580 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
*
40480636 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
*
40480701 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT
66 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
40480756 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
*
40480821 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT
66 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
40480876 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
40480941 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
40480996 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
40481061 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
40481116 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
40481181 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
40481236 AAAATATATTTAATAATAATTATGTT
1 AAAATATATTTAATAATAATTATGTT
40481262 TAAATATGAT
Statistics
Matches: 730, Mismatches: 13, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
119 5 0.01
120 719 0.98
121 6 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
Found at i:40480998 original size:18 final size:17
Alignment explanation
Indices: 40480970--40481004 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40480960 ATTATTAAGA
*
40480970 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40480987 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40481005 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40481118 original size:18 final size:17
Alignment explanation
Indices: 40481090--40481124 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40481080 ATTATTAAGA
*
40481090 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40481107 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40481125 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40481238 original size:18 final size:17
Alignment explanation
Indices: 40481210--40481244 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40481200 ATTATTAAGA
*
40481210 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40481227 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40481245 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40481458 original size:44 final size:45
Alignment explanation
Indices: 40481409--40481499 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40481399 ACCTCTATTC
* * *
40481409 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
40481453 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
40481498 CA
1 CA
40481500 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:40481501 original size:16 final size:16
Alignment explanation
Indices: 40481480--40481548 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
40481470 GATTAGCTAT
40481480 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40481496 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
40481513 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40481529 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40481545 TACA
1 TACA
40481549 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40481522 original size:33 final size:32
Alignment explanation
Indices: 40481480--40481548 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
40481470 GATTAGCTAT
40481480 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
40481513 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
40481545 TACA
1 TACA
40481549 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:40482370 original size:12 final size:12
Alignment explanation
Indices: 40482353--40482381 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40482343 AGTGTATCCA
40482353 AGGGTGAAAGTG
1 AGGGTGAAAGTG
40482365 AGGGTGAAAGTG
1 AGGGTGAAAGTG
40482377 AGGGT
1 AGGGT
40482382 TCAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.52, T:0.17
Consensus pattern (12 bp):
AGGGTGAAAGTG
Found at i:40488844 original size:5 final size:5
Alignment explanation
Indices: 40488836--40488887 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
40488826 TGAAATTTTC
*
40488836 TCGAA TCGAA TC-AA GT-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA
1 TCGAA TCGAA TCGAA -TCGA-A TCGAA -TCGAA TCGAA TCGAA TCGAA
40488882 TCGAA T
1 TCGAA T
40488888 ATATTTGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
4 2 0.05
5 32 0.78
6 7 0.17
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:40489433 original size:15 final size:15
Alignment explanation
Indices: 40489398--40489456 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
40489388 AAGAGTGAGA
**
40489398 AGTAAAATTTTAGAA
1 AGTAAAATTTTAGGG
40489413 AGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
* *
40489428 A-TTAAATTTAAGGG
1 AGTAAAATTTTAGGG
*
40489442 GGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
40489457 GAAAATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (15 bp):
AGTAAAATTTTAGGG
Found at i:40495872 original size:93 final size:93
Alignment explanation
Indices: 40495708--40495880 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
40495698 CGCCCATAAG
* *
40495708 CGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40495773 ACGAGTTCAGATGCCTAGTTACATTTCA
66 ACGAGTTCAGATGCCTAGTTACATTTCA
* *
40495801 CGAACTCGGACTCAACTCAATGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
* *
40495865 AATGAGTTCGGATGCC
65 AACGAGTTCAGATGCC
40495881 CAAATATCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATTTCA
Found at i:40495876 original size:46 final size:47
Alignment explanation
Indices: 40495701--40495873 Score: 169
Period size: 46 Copynumber: 3.7 Consensus size: 47
40495691 TGTAACCCGC
* *
40495701 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGGACATTCGCAT
* * * *
40495747 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAG--GAC-A-TTCGCAT
* * *
40495797 --TTCA-CGAACTCGGACTCAACTCAATGAGTTC-GGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGGACATTCGCAT
* *
40495840 CCATAAGTGAACTCGGACTCAACTCAATGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
40495874 GGATGCCCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.58
47 25 0.24
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGGACATTCGCAT
Found at i:40500198 original size:55 final size:55
Alignment explanation
Indices: 40500076--40500205 Score: 136
Period size: 55 Copynumber: 2.4 Consensus size: 55
40500066 TGCGACATAG
* * * * *
40500076 CCGTGGTCAAACCTGTCAAAACAACACGGGCGTTAGACACGCCCGTGTGGAAGAA
1 CCGTGGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
* * * * * * *
40500131 CTGTGGGT-GAACCTGTTAAAATAGCAAGGGCGTGCGACACGCCCGTGTCTAACAC
1 CCGT-GGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
40500186 CCGTGGTCGAACCTGTCAAA
1 CCGTGGTCGAACCTGTCAAA
40500206 TTAACACGGG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
54 3 0.05
55 53 0.90
56 3 0.05
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
Found at i:40510315 original size:19 final size:19
Alignment explanation
Indices: 40510277--40510334 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
40510267 TCTTTATATA
* *
40510277 TTATAAAT-TTTGGAATTT
1 TTATAAATATTTTGTATTT
40510295 TTATAAATATTTTGTATTT
1 TTATAAATATTTTGTATTT
40510314 TTGA-AAATTATTTT-TATTT
1 TT-ATAAA-TATTTTGTATTT
40510333 TT
1 TT
40510335 TGTAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 8 0.23
19 20 0.57
20 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATAAATATTTTGTATTT
Found at i:40510315 original size:20 final size:19
Alignment explanation
Indices: 40510292--40510335 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
40510282 AATTTTGGAA
40510292 TTTTTATAAA-TATTTTGTAT
1 TTTTTA-AAATTATTTT-TAT
*
40510312 TTTTGAAAATTATTTTTAT
1 TTTTTAAAATTATTTTTAT
40510331 TTTTT
1 TTTTT
40510336 GTAATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTAAAATTATTTTTAT
Found at i:40510341 original size:19 final size:19
Alignment explanation
Indices: 40510291--40510341 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
40510281 AAATTTTGGA
* *
40510291 ATTTTTATAAATATTTTGT
1 ATTTTTGTAATTATTTTGT
*
40510310 ATTTTTGAAAATTATTTT-T
1 ATTTTTG-TAATTATTTTGT
40510329 ATTTTTTGTAATT
1 A-TTTTTGTAATT
40510342 TATGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
ATTTTTGTAATTATTTTGT
Found at i:40514453 original size:18 final size:18
Alignment explanation
Indices: 40514417--40514462 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
40514407 ATTCGAAAAA
40514417 AATTCGAGTTAACTTAAAT
1 AATTCGA-TTAACTTAAAT
40514436 AATTCGATTAA-TTCAAAT
1 AATTCGATTAACTT-AAAT
*
40514454 AACTCGATT
1 AATTCGATT
40514463 CGTTTAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (18 bp):
AATTCGATTAACTTAAAT
Found at i:40521394 original size:19 final size:18
Alignment explanation
Indices: 40521364--40521413 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40521354 ATATGAATTG
*
40521364 AAAAATAAATATTCACATAT
1 AAAAAT-AATATTCAC-TAA
* *
40521384 AAAAATTATATTTACTAA
1 AAAAATAATATTCACTAA
40521402 AAAAATAATATT
1 AAAAATAATATT
40521414 TACAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 7 0.27
20 6 0.23
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATAATATTCACTAA
Found at i:40521863 original size:16 final size:16
Alignment explanation
Indices: 40521839--40521869 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40521829 ATATATCGAT
40521839 AAATATAAAAAAATTA
1 AAATATAAAAAAATTA
*
40521855 AAATTTAAAAAAATT
1 AAATATAAAAAAATT
40521870 CAACCCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAAAAAAATTA
Found at i:40523739 original size:11 final size:11
Alignment explanation
Indices: 40523725--40523758 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40523715 TTTCTCTTAT
*
40523725 TCTTCTTTTTC
1 TCTTCTTCTTC
*
40523736 TCTTCTTCTCC
1 TCTTCTTCTTC
40523747 TCTTCTTCTTC
1 TCTTCTTCTTC
40523758 T
1 T
40523759 TCGACTGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:40531854 original size:21 final size:22
Alignment explanation
Indices: 40531830--40531884 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
40531820 TAAAGTAACT
40531830 ATTTATTATATATTACATA-AA
1 ATTTATTATATATTACATATAA
* *
40531851 ATTTCATTTATATTTTACATATAT
1 ATTT-A-TTATATATTACATATAA
40531875 ATTT-TTATAT
1 ATTTATTATAT
40531885 GCATGCGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 13 0.45
24 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTATTATATATTACATATAA
Found at i:40537825 original size:3 final size:3
Alignment explanation
Indices: 40537817--40537861 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
40537807 CAAGGTGATT
* *
40537817 TTC TTC TTC TTC TTC GTC TTC TTC TTC TTC TTC ATC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40537862 CACCTCCTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:40542306 original size:12 final size:12
Alignment explanation
Indices: 40542289--40542314 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40542279 GCTAACGAAA
40542289 TAACCAGACAGT
1 TAACCAGACAGT
40542301 TAACCAGACAGT
1 TAACCAGACAGT
40542313 TA
1 TA
40542315 CACATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (12 bp):
TAACCAGACAGT
Found at i:40549730 original size:18 final size:17
Alignment explanation
Indices: 40549690--40549723 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40549680 ATGTGTACAA
*
40549690 ATAATATATATATGTAT
1 ATAATATATATATGAAT
40549707 ATAATA-ATATATGAAT
1 ATAATATATATATGAAT
40549723 A
1 A
40549724 CTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATAATATATATATGAAT
Found at i:40550802 original size:40 final size:40
Alignment explanation
Indices: 40550680--40550817 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
40550670 ACCTCGAGTC
*
40550680 GATGAGACACTGGGTGTCAATTTATTACTTC-AGATATAT-T
1 GATGAGACACTGAGTGTCAATTTATTACTTCGA-AT-TATCT
* * ** * *
40550720 CGATGAGGCACTGAGTGCCAA---ATTACTTCGGTTTAGCC
1 -GATGAGACACTGAGTGTCAATTTATTACTTCGAATTATCT
*
40550758 GATGAGACACTGAATGTCAATTTATTACTTCGAATTATCT
1 GATGAGACACTGAGTGTCAATTTATTACTTCGAATTATCT
* *
40550798 GATGAGGCACTGGGTGTCAA
1 GATGAGACACTGAGTGTCAA
40550818 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
37 19 0.25
38 9 0.12
40 30 0.40
41 17 0.23
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (40 bp):
GATGAGACACTGAGTGTCAATTTATTACTTCGAATTATCT
Found at i:40554399 original size:43 final size:43
Alignment explanation
Indices: 40554349--40554435 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
40554339 TCATATTTGA
40554349 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
* * * *
40554392 TTTCTCATCTCATATTCATTTCTCATCTTTGCCCTTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
40554435 T
1 T
40554436 AATCATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.02, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:40564763 original size:19 final size:20
Alignment explanation
Indices: 40564726--40564764 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40564716 TTAACAACCA
40564726 TAAAATAAAAATGATCAAAT
1 TAAAATAAAAATGATCAAAT
*
40564746 TAAAATATAAAT-ATCAAAT
1 TAAAATAAAAATGATCAAAT
40564765 ATGTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAATAAAAATGATCAAAT
Found at i:40569203 original size:19 final size:19
Alignment explanation
Indices: 40569179--40569215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40569169 TTTTATTAAT
*
40569179 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
40569198 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
40569216 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:40572618 original size:7 final size:7
Alignment explanation
Indices: 40572606--40572678 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
40572596 AATATATTTT
40572606 AGAATTG
1 AGAATTG
40572613 AGAATTG
1 AGAATTG
40572620 AGAATTG
1 AGAATTG
* *
40572627 AAAATTA
1 AGAATTG
*
40572634 AGAATTA
1 AGAATTG
*
40572641 AGGATT-
1 AGAATTG
*
40572647 ACGAATTT
1 A-GAATTG
40572655 AGAATTG
1 AGAATTG
*
40572662 AGGATTG
1 AGAATTG
*
40572669 AGTATTG
1 AGAATTG
40572676 AGA
1 AGA
40572679 TAAAAAGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 1 0.02
7 53 0.96
8 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.25, T:0.30
Consensus pattern (7 bp):
AGAATTG
Found at i:40573190 original size:65 final size:65
Alignment explanation
Indices: 40573119--40573301 Score: 224
Period size: 65 Copynumber: 2.8 Consensus size: 65
40573109 TATAAGATAA
* * * * * * *
40573119 ATAATTTGTGTATTTATATTTGGTATTTAAATATCTAATTGAATTATAATCATATTTGTTTTAAT
1 ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATAATTATTTTAAT
* * * *
40573184 ATAATTTGTATATTTATAACTCATATTTAAATATTTTATTAAATTATAATAATAATTATTTTAAT
1 ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATAATTATTTTAAT
* * *
40573249 ATAATTTGTAG-ATTTGTAATTGACATTAAAATATTTTATTGAATTATAATAAT
1 ATAATTTGT-GTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAAT
40573302 TTTAATAAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 99 1.00
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (65 bp):
ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATAATTATTTTAAT
Found at i:40573299 original size:18 final size:20
Alignment explanation
Indices: 40573267--40573305 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40573257 TAGATTTGTA
40573267 ATTGACATTAAAAT-ATTTT
1 ATTGACATTAAAATAATTTT
*
40573286 ATTGA-ATTATAATAATTTT
1 ATTGACATTAAAATAATTTT
40573305 A
1 A
40573306 ATAAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTGACATTAAAATAATTTT
Found at i:40575487 original size:160 final size:159
Alignment explanation
Indices: 40575216--40575520 Score: 452
Period size: 160 Copynumber: 1.9 Consensus size: 159
40575206 CAAAAATTGA
* *
40575216 TTACAATGCTTTTTTTTTCTTTGAACAAAATTTGTTCATTCATTTTTTTTTTGTATTTCATTTGT
1 TTACAATGCTTTTTTTTTCTTT-AACAAAATCTATTCATTCATTTTTTTTTTGTATTTCATTTGT
* * * *
40575281 ATTTTTCACTATCTACTAACATTTATATAATGGAAAAATTGCTACTTTAAGCT-TTACATCAAAT
65 ATTTGTCACCATCTACTAACATTCATATAATGGAAAAATAGCTACTTTAAG-TGTTACATCAAAT
40575345 ACCAATTACAATTTCTCTAGCGATGGAACTT
129 ACCAATTACAATTTCTCTAGCGATGGAACTT
40575376 TTACAATGCTTCTTTTTTTC-TTATACAAAATCTATTCATTCATTTTTTTTTTGTATTTCATTTG
1 TTACAATGCTT-TTTTTTTCTTTA-ACAAAATCTATTCATTCATTTTTTTTTTGTATTTCATTTG
* * * * * *
40575440 TATTTGTCGCCGTTTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACGTCAAGT
64 TATTTGTCACCATCTACTAACATTCATATAATGGAAAAATAGCTACTTTAAGTGTTACATCAAAT
40575505 ACCAATTACAATTTCT
129 ACCAATTACAATTTCT
40575521 TTGCCGATTG
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
159 2 0.02
160 120 0.92
161 8 0.06
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (159 bp):
TTACAATGCTTTTTTTTTCTTTAACAAAATCTATTCATTCATTTTTTTTTTGTATTTCATTTGTA
TTTGTCACCATCTACTAACATTCATATAATGGAAAAATAGCTACTTTAAGTGTTACATCAAATAC
CAATTACAATTTCTCTAGCGATGGAACTT
Found at i:40576662 original size:17 final size:17
Alignment explanation
Indices: 40576634--40576678 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
40576624 AACGGGGACT
*
40576634 AAATTGAAAGTGCAATA
1 AAATTTAAAGTGCAATA
*
40576651 AATTTTAAAGTGCAATA
1 AAATTTAAAGTGCAATA
40576668 AAATTTAAAGT
1 AAATTTAAAGT
40576679 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (17 bp):
AAATTTAAAGTGCAATA
Found at i:40578481 original size:188 final size:187
Alignment explanation
Indices: 40578214--40578670 Score: 504
Period size: 188 Copynumber: 2.4 Consensus size: 187
40578204 TCCACTATAG
* * * ** *
40578214 CTTCAAGGATATAAGATTTGTAATTTCATCTTGTTCCATTGCAACTTCAGGGAGATAAGATTCAC
1 CTTCAGGGGTATAAGATTTATAGCTTCATCTTGTT-CATTGCAACTTCAGGGAGATAAGATTCGC
* ** * * * *
40578279 CATTATAACTTCAATCCAACCCACTGTAACTCCAGGGGTATATAATTTGTAGCTTTATTTTTACT
65 CATTATAGCTTCAATCCAACCCACTACAACTCCAAGGGTATACAATTTATAACTTTA-TTTTACT
* * ** * *
40578344 CCA-TGCAACTTTAGGGAGATAAGATTCACTATGGTGGCTTCAAT-TAAATCCGTTGCAA
129 CCACTACAACTTCAGGGAGATAAGATTCACTATGGTAACTTCAATCT-AACCCATTGCAA
* * * *
40578402 CTTCAGGGGTATAAGATTTATAGCTTCATCTTGCTTCACTGCATCTTTAGGGAGATAAAATTCGC
1 CTTCAGGGGTATAAGATTTATAGCTTCATCTTG-TTCATTGCAACTTCAGGGAGATAAGATTCGC
*** *
40578467 CATTATAGCTTCAATTTGACCCACTACAACTTCAAGGGTATACAATTTATAACTTTATTTTACTC
65 CATTATAGCTTCAATCCAACCCACTACAACTCCAAGGGTATACAATTTATAACTTTATTTTACTC
* * *
40578532 CACTACAACTTCAGGGAGATAAGATTCGCTATGGTAACTTTAATCTGACCCATTGCAA
130 CACTACAACTTCAGGGAGATAAGATTCACTATGGTAACTTCAATCTAACCCATTGCAA
* * * * * * *
40578590 CTTTAGGGGTATACGGTTTATAGCTTTATCTTGGTCCATTGCAACTTCAGAGAGATAAGATTTGC
1 CTTCAGGGGTATAAGATTTATAGCTTCATCTT-GTTCATTGCAACTTCAGGGAGATAAGATTCGC
* *
40578655 CATTTTAGTTTCAATC
65 CATTATAGCTTCAATC
40578671 TATTCCACTA
Statistics
Matches: 221, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
187 10 0.05
188 207 0.94
189 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (187 bp):
CTTCAGGGGTATAAGATTTATAGCTTCATCTTGTTCATTGCAACTTCAGGGAGATAAGATTCGCC
ATTATAGCTTCAATCCAACCCACTACAACTCCAAGGGTATACAATTTATAACTTTATTTTACTCC
ACTACAACTTCAGGGAGATAAGATTCACTATGGTAACTTCAATCTAACCCATTGCAA
Found at i:40578671 original size:94 final size:94
Alignment explanation
Indices: 40578241--40578839 Score: 337
Period size: 94 Copynumber: 6.4 Consensus size: 94
40578231 TTGTAATTTC
* * * * ** ** * *
40578241 ATCTTGTTCCATTGCAACTTCAGGGAGATAAGATTCACCATTATAACTTCAATCCAACCCACTGT
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAGTTTCAATCTGACCCATTGC
* ** *
40578306 AACTCCAGGGGTATATAATTTGTAGCTTT
66 AACTTCAGGGGTATACGATTTATAGCTTT
* * * * * ** * * * * *
40578335 ATTTTTACTCCA-TGCAACTTTAGGGAGATAAGATTCACTATGGTGGCTTCAAT-TAAATCCGTT
1 A-TCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAGTTTCAATCT-GACCCATT
* *
40578398 GCAACTTCAGGGGTATAAGATTTATAGCTTC
64 GCAACTTCAGGGGTATACGATTTATAGCTTT
* * * * * * * * *
40578429 ATCTTGCTTCACTGCATCTTTAGGGAGATAAAATTCGCCATTATAGCTTCAATTTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAGTTTCAATCTGACCCATTGC
* * *
40578494 AACTTCAAGGGTATACAATTTATAACTTT
66 AACTTCAGGGGTATACGATTTATAGCTTT
* * * * * * *
40578523 ATTTTACTCCACTACAACTTCAGGGAGATAAGATTCGCTATGGTAACTTT-AATCTGACCCATTG
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCAT-TTTAGTTTCAATCTGACCCATTG
* *
40578587 CAACTTTAGGGGTATACGGTTTATAGCTTT
65 CAACTTCAGGGGTATACGATTTATAGCTTT
* * * * * * *
40578617 ATCTTGGTCCATTGCAACTTCAGAGAGATAAGATTTGCCATTTTAGTTTCAATCT-ATTCCACTA
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAGTTTCAATCTGA-CCCATTG
* * * * * * *
40578681 AAACTTTAAGGATATAAGGTTTGTAGCTTT
65 CAACTTCAGGGGTATACGATTTATAGCTTT
* * * ** * * * * * * * *
40578711 GTCTTGCTCTACTGCAACTTTAGATATATAAGACTCGCAATTGT-GATTTCATTCCGACCTACTG
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAG-TTTCAATCTGACCCATTG
* * * * * *
40578775 TAACATCAAGGGTATAGGAATTGTAGCTTT
65 CAACTTCAGGGGTATACGATTTATAGCTTT
* * *
40578805 AATC-TGATCCACTGCAACTCCAGGGATATAAGATT
1 -ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
40578840 TGTAGCTTCA
Statistics
Matches: 385, Mismatches: 110, Indels: 20
0.75 0.21 0.04
Matches are distributed among these distances:
93 14 0.04
94 357 0.93
95 14 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (94 bp):
ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTAGTTTCAATCTGACCCATTGC
AACTTCAGGGGTATACGATTTATAGCTTT
Found at i:40578911 original size:94 final size:94
Alignment explanation
Indices: 40578801--40579003 Score: 291
Period size: 94 Copynumber: 2.2 Consensus size: 94
40578791 GGAATTGTAG
* *
40578801 CTTTAATCTGATCCACTGCAACTCCAGGGATATAAGATTTGTAGCTTCAT-CTTACACCACTACA
1 CTTTAATCTGACCCACTGCAACTCCAGGGAGATAAGATTTGTAGCTTCATCCTT-CACCACTACA
* *
40578865 ACTTCAGGGAGATAAGATTCGCTACGGTAA
65 ACTTCAAGGAGATAAAATTCGCTACGGTAA
* * * * *
40578895 CTTTAATCAGACCCACTGCAACTTCAGTGAGATAAGATTTGTAGCTTCATCCTTCTCCACTGCAA
1 CTTTAATCTGACCCACTGCAACTCCAGGGAGATAAGATTTGTAGCTTCATCCTTCACCACTACAA
*
40578960 CTTCAAGGAGATAAAATTCGCTATGGTAA
66 CTTCAAGGAGATAAAATTCGCTACGGTAA
*
40578989 CTTCAATCTGACCCA
1 CTTTAATCTGACCCA
40579004 TTGTAACTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 93 0.97
95 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (94 bp):
CTTTAATCTGACCCACTGCAACTCCAGGGAGATAAGATTTGTAGCTTCATCCTTCACCACTACAA
CTTCAAGGAGATAAAATTCGCTACGGTAA
Found at i:40578971 original size:44 final size:44
Alignment explanation
Indices: 40578812--40578973 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 44
40578802 TTTAATCTGA
* * *
40578812 TCCACTGCAACTCCAGGGATATAAGATTTGTAGCTTCAT-CTTAC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCATCCTT-C
* * * * * ***
40578856 ACCACTACAACTTCAGGGAGATAAGATTCGCTACGGTAACTTTAATCAGAC
1 TCCACTGCAACTTCAAGGAGATAAGATT---T---GTAGC-TTCATCCTTC
40578907 -CCACTGCAACTTC-AGTGAGATAAGATTTGTAGCTTCATCCTTC
1 TCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCTTCATCCTTC
40578950 TCCACTGCAACTTCAAGGAGATAA
1 TCCACTGCAACTTCAAGGAGATAA
40578974 AATTCGCTAT
Statistics
Matches: 91, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
43 6 0.07
44 48 0.53
45 2 0.02
47 2 0.02
49 1 0.01
50 27 0.30
51 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
TCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCATCCTTC
Found at i:40581197 original size:19 final size:19
Alignment explanation
Indices: 40581169--40581205 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40581159 CTCGACACAC
* *
40581169 TCTTGGATTTCATGAAATT
1 TCTTGCATTTAATGAAATT
40581188 TCTTGCATTTAATGAAAT
1 TCTTGCATTTAATGAAAT
40581206 GTAGTGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (19 bp):
TCTTGCATTTAATGAAATT
Found at i:40582614 original size:38 final size:38
Alignment explanation
Indices: 40582548--40582620 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
40582538 ACCAGTTTGG
*
40582548 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTAA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTAA
* * *
40582586 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGT
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGCAAAGT
40582621 GGTACCCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTAA
Found at i:40583737 original size:16 final size:17
Alignment explanation
Indices: 40583705--40583738 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40583695 AATCCTTAGT
*
40583705 TTTCTCTTTTATCTTTC
1 TTTCCCTTTTATCTTTC
40583722 TTTCCCTTTT-TCTTTC
1 TTTCCCTTTTATCTTTC
40583738 T
1 T
40583739 CTTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCCTTTTATCTTTC
Found at i:40587510 original size:6 final size:6
Alignment explanation
Indices: 40587499--40587527 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40587489 CATCTTCTTA
40587499 ATCATG ATCATG ATCATG ATCATG ATCAT
1 ATCATG ATCATG ATCATG ATCATG ATCAT
40587528 CATCTTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
ATCATG
Found at i:40587595 original size:24 final size:24
Alignment explanation
Indices: 40587545--40587621 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
40587535 AACTTTTTCG
* *
40587545 TCTTCACCTCAACCCTTGTAC-TGA
1 TCTTCACCTCAACCCTCGT-CTTCA
*
40587569 TCTTCACCTCGACCCTCGTCTTCA
1 TCTTCACCTCAACCCTCGTCTTCA
* * *
40587593 TCTTCATCTCTATCCC-CGTCTTCG
1 TCTTCACCTC-AACCCTCGTCTTCA
40587617 TCTTC
1 TCTTC
40587622 GTCTCCATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.91
25 3 0.07
ACGTcount: A:0.13, C:0.42, G:0.08, T:0.38
Consensus pattern (24 bp):
TCTTCACCTCAACCCTCGTCTTCA
Found at i:40590084 original size:17 final size:18
Alignment explanation
Indices: 40590064--40590097 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40590054 AATGAATTTT
*
40590064 TTTATTGTAT-AAATTAA
1 TTTATTGAATGAAATTAA
40590081 TTTATTGAATGAAATTA
1 TTTATTGAATGAAATTA
40590098 TTAATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTATTGAATGAAATTAA
Found at i:40590506 original size:21 final size:21
Alignment explanation
Indices: 40590468--40590517 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
40590458 GATTTGGGTG
* * *
40590468 GTTCAGCTCTGACGAGCTTTT
1 GTTCAGCTCTCACAAGCTTCT
*
40590489 GTTCAGCTTTCACAAGCTTCT
1 GTTCAGCTCTCACAAGCTTCT
*
40590510 ATTCAGCT
1 GTTCAGCT
40590518 GTTATGAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (21 bp):
GTTCAGCTCTCACAAGCTTCT
Found at i:40593892 original size:20 final size:21
Alignment explanation
Indices: 40593856--40593896 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40593846 CTGCAGTGTT
40593856 AAAAATTTTAAATGTTTCCGA
1 AAAAATTTTAAATGTTTCCGA
*
40593877 AAAAATTTTTAA-GTTTCCGA
1 AAAAATTTTAAATGTTTCCGA
40593897 TTTAGTCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
AAAAATTTTAAATGTTTCCGA
Found at i:40594200 original size:16 final size:17
Alignment explanation
Indices: 40594161--40594195 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40594151 TTATATCGAC
*
40594161 AAAA-TAAAATATTTTA
1 AAAATTAAAAAATTTTA
40594177 AAAATTAAAAAATTTTA
1 AAAATTAAAAAATTTTA
40594194 AA
1 AA
40594196 TTTAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTAAAAAATTTTA
Found at i:40594604 original size:8 final size:8
Alignment explanation
Indices: 40594583--40594631 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
40594573 TAAATAAGAA
40594583 ATAATAATT
1 ATAATAA-T
40594592 ATAATAAT
1 ATAATAAT
40594600 ATAATAAT
1 ATAATAAT
40594608 ATAATAAT
1 ATAATAAT
**
40594616 AT-ATGTT
1 ATAATAAT
40594623 ATAATAAT
1 ATAATAAT
40594631 A
1 A
40594632 ATAGAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
7 5 0.14
8 23 0.66
9 7 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
ATAATAAT
Found at i:40597143 original size:16 final size:18
Alignment explanation
Indices: 40597122--40597156 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
40597112 TAATGTCTAG
40597122 GAAAATTA-TT-AATTGA
1 GAAAATTAGTTCAATTGA
40597138 GAAAATTAGTTCAATTGA
1 GAAAATTAGTTCAATTGA
40597156 G
1 G
40597157 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (18 bp):
GAAAATTAGTTCAATTGA
Found at i:40598758 original size:20 final size:20
Alignment explanation
Indices: 40598733--40598793 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
40598723 ACACGACTGC
40598733 TCCCAAGCCACACGGGCGTG
1 TCCCAAGCCACACGGGCGTG
40598753 TCCCAAGCCACACGGGCGTG
1 TCCCAAGCCACACGGGCGTG
40598773 TCCCAAGCCACACGGGCGTG
1 TCCCAAGCCACACGGGCGTG
40598793 T
1 T
40598794 GCCTCTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (20 bp):
TCCCAAGCCACACGGGCGTG
Found at i:40600570 original size:17 final size:17
Alignment explanation
Indices: 40600548--40600594 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
40600538 TTTTAGAATT
40600548 TTTTTAAAAATTTATAA
1 TTTTTAAAAATTTATAA
*
40600565 TTTTTAAAAATATATAA
1 TTTTTAAAAATTTATAA
**
40600582 AATTTAAAAATTT
1 TTTTTAAAAATTT
40600595 TTTACAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAATTTATAA
Found at i:40600605 original size:26 final size:26
Alignment explanation
Indices: 40600554--40600605 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
40600544 AATTTTTTTA
*
40600554 AAAATTTATAATTTTTAAAAATATAT
1 AAAATTTAAAATTTTTAAAAATATAT
*
40600580 AAAATTTAAAAATTTTTTACAAATAT
1 AAAATTT-AAAA-TTTTTAAAAATAT
40600606 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 3 0.14
28 12 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATTTAAAATTTTTAAAAATATAT
Found at i:40602734 original size:21 final size:20
Alignment explanation
Indices: 40602695--40602734 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40602685 ACATAAATAC
* *
40602695 TAGTTATTATTTAACATATA
1 TAGTTATTAATTAAAATATA
40602715 TAGTTATATAATTAAAATAT
1 TAGTTAT-TAATTAAAATAT
40602735 TTTGTGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TAGTTATTAATTAAAATATA
Found at i:40605224 original size:36 final size:36
Alignment explanation
Indices: 40605184--40605254 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
40605174 AGGAATGAGG
40605184 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
1 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
*
40605220 CAGTCCAAAATCTATTCTCAAATTACGGAATCTTA
1 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTA
40605255 CATTGGAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (36 bp):
CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
Found at i:40613573 original size:22 final size:22
Alignment explanation
Indices: 40613549--40613590 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40613539 ATTATTTTTA
40613549 AAAATCATAAAA-ATTATAAAC
1 AAAATCATAAAATATTATAAAC
* *
40613570 AAAATTATAAAATATTTTAAA
1 AAAATCATAAAATATTATAAA
40613591 ACTATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATCATAAAATATTATAAAC
Found at i:40617347 original size:6 final size:6
Alignment explanation
Indices: 40617336--40617370 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
40617326 AGGGAGCAAC
*
40617336 TTCCTA TTCCTA TACCTA TTCCTA TTCCTA TTCCT
1 TTCCTA TTCCTA TTCCTA TTCCTA TTCCTA TTCCT
40617371 CCCTCATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (6 bp):
TTCCTA
Found at i:40617564 original size:26 final size:26
Alignment explanation
Indices: 40617516--40617569 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
40617506 ATCATCTCTT
* *
40617516 TTCATTACTTTAATGTTATATTAATAA
1 TTCATTACTTTAATATTAAATTAA-AA
40617543 TTCATTA-TTTAATATTAAATTAAAA
1 TTCATTACTTTAATATTAAATTAAAA
40617568 TT
1 TT
40617570 TTTGAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 14 0.56
27 7 0.28
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (26 bp):
TTCATTACTTTAATATTAAATTAAAA
Found at i:40622801 original size:3 final size:3
Alignment explanation
Indices: 40622788--40622848 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
40622778 CATTTAACAG
* * *
40622788 AGA AAA AGA AGA AGA AGA AGA AG- AGA GGA AGA AGA AGG AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
40622835 AAA AGA AGA AGA AG
1 AGA AGA AGA AGA AG
40622849 CAGCAGCAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40623927 original size:9 final size:9
Alignment explanation
Indices: 40623913--40623937 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40623903 AATGTTTAGC
40623913 AGGGCTGGT
1 AGGGCTGGT
40623922 AGGGCTGGT
1 AGGGCTGGT
40623931 AGGGCTG
1 AGGGCTG
40623938 TCAAATTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.56, T:0.20
Consensus pattern (9 bp):
AGGGCTGGT
Found at i:40624373 original size:16 final size:16
Alignment explanation
Indices: 40624337--40624451 Score: 98
Period size: 16 Copynumber: 7.4 Consensus size: 16
40624327 GTTTGGTTCA
* *
40624337 CTGTAATAGAATAGGG
1 CTGTAATTGAATAGAG
*
40624353 ATGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
40624369 CTGTAA-TGAAATAGAG
1 CTGTAATTG-AATAGAG
*
40624385 CTGTAATCT---T-CA-
1 CTGTAAT-TGAATAGAG
* *
40624397 CTGTAATGGAATAGGG
1 CTGTAATTGAATAGAG
*
40624413 ATGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
*
40624429 CTGTAATGGAATAGAG
1 CTGTAATTGAATAGAG
40624445 CTGTAAT
1 CTGTAAT
40624452 CAATAATTCA
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
12 7 0.09
13 1 0.01
14 2 0.03
15 2 0.03
16 65 0.83
18 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:40624426 original size:60 final size:60
Alignment explanation
Indices: 40624333--40624452 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
40624323 TTACGTTTGG
40624333 TTCACTGTAATAGAATAGGGATGTAATTGAATAGAGCTGTAATGAAATAGAGCTGTAATC
1 TTCACTGTAATAGAATAGGGATGTAATTGAATAGAGCTGTAATGAAATAGAGCTGTAATC
* *
40624393 TTCACTGTAATGGAATAGGGATGTAATTGAATAGAGCTGTAATGGAATAGAGCTGTAATC
1 TTCACTGTAATAGAATAGGGATGTAATTGAATAGAGCTGTAATGAAATAGAGCTGTAATC
40624453 AATAATTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (60 bp):
TTCACTGTAATAGAATAGGGATGTAATTGAATAGAGCTGTAATGAAATAGAGCTGTAATC
Found at i:40624641 original size:25 final size:25
Alignment explanation
Indices: 40624597--40624647 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
40624587 GTTGATAGAT
40624597 GATTATTGTTATTAAA-TTTTAATAA
1 GATTATTGTTA-TAAATTTTTAATAA
40624622 GATTATTGTTA-AATATTTTTTAATAA
1 GATTATTGTTATAA-A-TTTTTAATAA
40624648 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 1 0.04
25 11 0.48
26 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
GATTATTGTTATAAATTTTTAATAA
Found at i:40624708 original size:24 final size:21
Alignment explanation
Indices: 40624687--40624745 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
40624677 TAACATAATT
40624687 ATTATTAAATATAATTTAATAA
1 ATTATT-AATATAATTTAATAA
* *
40624709 AATAAT-ATATAATTTAATAA
1 ATTATTAATATAATTTAATAA
40624729 CATTATTAATATAATTT
1 -ATTATTAATATAATTT
40624746 TTAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
22 13 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAATATAATTTAATAA
Found at i:40624709 original size:55 final size:54
Alignment explanation
Indices: 40624649--40624769 Score: 127
Period size: 57 Copynumber: 2.2 Consensus size: 54
40624639 TTTTAATAAA
* * *
40624649 AATAAAAATAAATAATTTAATCATATT-TTAACATAATTATTATTAAATATAATTT
1 AATAAAAATAAATAATTTAATAACATTATTAACATAATTATTAAT-AATA-AATTT
* * * *
40624704 AATAAAATAATATATAATTTAATAACATTATTAATATAATTTTTAATAATAATTTT
1 AAT-AAA-AATAAATAATTTAATAACATTATTAACATAATTATTAATAATAAATTT
40624760 AATATAAAAT
1 AATA-AAAAT
40624770 TATTATTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
55 7 0.13
56 12 0.22
57 22 0.40
58 14 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (54 bp):
AATAAAAATAAATAATTTAATAACATTATTAACATAATTATTAATAATAAATTT
Found at i:40624748 original size:24 final size:24
Alignment explanation
Indices: 40624721--40624766 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40624711 TAATATATAA
*
40624721 TTTAATAA-CATTATTAATATAATT
1 TTTAATAATAATT-TTAATATAATT
40624745 TTTAATAATAATTTTAATATAA
1 TTTAATAATAATTTTAATATAA
40624767 AATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATAATAATTTTAATATAATT
Found at i:40627250 original size:40 final size:40
Alignment explanation
Indices: 40627206--40627286 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
40627196 TTAGTTATAC
40627206 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
1 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
40627246 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
1 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
40627286 T
1 T
40627287 AGAGTTCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (40 bp):
TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
Found at i:40628964 original size:33 final size:34
Alignment explanation
Indices: 40628900--40628967 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
40628890 GCTCAAATCC
*
40628900 ATCATCTCCTAAATGGGAAACGAACTTGAAAATG
1 ATCATCTCCTAAATAGGAAACGAACTTGAAAATG
*
40628934 ATCATCTCCTGAATAGGAAAC-AACTTGAAAATG
1 ATCATCTCCTAAATAGGAAACGAACTTGAAAATG
40628967 A
1 A
40628968 CACTTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (34 bp):
ATCATCTCCTAAATAGGAAACGAACTTGAAAATG
Found at i:40634528 original size:23 final size:22
Alignment explanation
Indices: 40634502--40634546 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40634492 ATAATTTTCA
40634502 AAAATAGATTATGATTTTTTTTG
1 AAAAT-GATTATGATTTTTTTTG
**
40634525 AAAATTTTTATGATTTTTTTTG
1 AAAATGATTATGATTTTTTTTG
40634547 GATTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (22 bp):
AAAATGATTATGATTTTTTTTG
Found at i:40634535 original size:22 final size:21
Alignment explanation
Indices: 40634510--40634574 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
40634500 CAAAAATAGA
40634510 TTATGATTTTTTTTGAAAATTT
1 TTATGATTTTTTTTG-AAATTT
*
40634532 TTATGATTTTTTTTG-GATTT
1 TTATGATTTTTTTTGAAATTT
40634552 TTAATGATATTTTTTT-AAATTT
1 TT-ATGAT-TTTTTTTGAAATTT
40634574 T
1 T
40634575 CAAGTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 27 0.71
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TTATGATTTTTTTTGAAATTT
Found at i:40634791 original size:20 final size:20
Alignment explanation
Indices: 40634766--40634803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40634756 TATTTAGCCT
40634766 TCTTTTAATTAAAACATTTA
1 TCTTTTAATTAAAACATTTA
**
40634786 TCTTTTTTTTAAAACATT
1 TCTTTTAATTAAAACATT
40634804 CAAAAATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TCTTTTAATTAAAACATTTA
Found at i:40638314 original size:2 final size:2
Alignment explanation
Indices: 40638307--40638346 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40638297 AAATCAAAGT
40638307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40638347 AAAGCCTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40638566 original size:22 final size:22
Alignment explanation
Indices: 40638541--40638583 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40638531 TGTAATAATA
*
40638541 ATATTTTAATTTTAGAATATAT
1 ATATTTTAATTTTAAAATATAT
*
40638563 ATATTTTAGTTTTAAAATATA
1 ATATTTTAATTTTAAAATATA
40638584 ATTACATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
ATATTTTAATTTTAAAATATAT
Found at i:40639140 original size:41 final size:41
Alignment explanation
Indices: 40639093--40639198 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
40639083 AAAAGGTAAG
*
40639093 CAATAGTAGTGTTTTTGGTCCAAACGGCGTAAAA-AGTTGAA
1 CAATAGTAGTGTTTTTGGTCCAAACGCCGTAAAACA-TTGAA
* *
40639134 CAATAGTGACGT-TTTTT-GTCCAAATGCCGTAAAACATTGAG
1 CAATAGT-A-GTGTTTTTGGTCCAAACGCCGTAAAACATTGAA
* *
40639175 CAATAATAGCGTTTTTGGT-CAAAC
1 CAATAGTAGTGTTTTTGGTCCAAAC
40639199 TCCGCGAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 1 0.02
40 10 0.19
41 34 0.63
42 7 0.13
43 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (41 bp):
CAATAGTAGTGTTTTTGGTCCAAACGCCGTAAAACATTGAA
Found at i:40639626 original size:7 final size:7
Alignment explanation
Indices: 40639614--40639761 Score: 80
Period size: 7 Copynumber: 20.7 Consensus size: 7
40639604 ATGACTTTCT
40639614 CTAAACC
1 CTAAACC
40639621 CTAAACC
1 CTAAACC
*
40639628 CTAAAACT
1 CT-AAACC
40639636 CTAAACC
1 CTAAACC
*
40639643 TTAAACC
1 CTAAACC
*
40639650 ATAAACC
1 CTAAACC
*
40639657 ATAAACC
1 CTAAACC
* *
40639664 ATAAACA
1 CTAAACC
*
40639671 CTAAACT
1 CTAAACC
* **
40639678 TTAAATA
1 CTAAACC
* *
40639685 ATAAACA
1 CTAAACC
40639692 CTAAACC
1 CTAAACC
* *
40639699 TTAAAGC
1 CTAAACC
40639706 CTAAACC
1 CTAAACC
*
40639713 ATAAAACC
1 CT-AAACC
*
40639721 ATAAACC
1 CTAAACC
*
40639728 ATAAACC
1 CTAAACC
* *
40639735 ATAAACT
1 CTAAACC
40639742 CTAAAACC
1 CT-AAACC
* *
40639750 TTAAACA
1 CTAAACC
40639757 CTAAA
1 CTAAA
40639762 AACTAAATTT
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
7 95 0.84
8 18 0.16
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:40639661 original size:21 final size:21
Alignment explanation
Indices: 40639616--40639755 Score: 106
Period size: 22 Copynumber: 6.5 Consensus size: 21
40639606 GACTTTCTCT
* * *
40639616 AAACCCTAAACCCTAAAACTCT
1 AAACCATAAACCATAAACCT-T
* *
40639638 AAACCTTAAACCATAAACCAT
1 AAACCATAAACCATAAACCTT
*
40639659 AAACCATAAACAC-TAAACTTT
1 AAACCATAAAC-CATAAACCTT
**
40639680 AAATAATAAA-CACTAAACCTT
1 AAACCATAAACCA-TAAACCTT
*
40639701 AAAGCC-TAAACCATAAAACCAT
1 AAA-CCATAAACCAT-AAACCTT
*
40639723 AAACCATAAACCATAAACTCTA
1 AAACCATAAACCATAAAC-CTT
*
40639745 AAACCTTAAAC
1 AAACCATAAAC
40639756 ACTAAAAACT
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
19 1 0.01
21 46 0.49
22 47 0.50
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.19
Consensus pattern (21 bp):
AAACCATAAACCATAAACCTT
Found at i:40639721 original size:8 final size:7
Alignment explanation
Indices: 40639615--40639740 Score: 98
Period size: 7 Copynumber: 17.7 Consensus size: 7
40639605 TGACTTTCTC
*
40639615 TAAACCC
1 TAAACCA
*
40639622 TAAACCC
1 TAAACCA
40639629 TAAAACTC-
1 T-AAAC-CA
*
40639637 TAAACCT
1 TAAACCA
40639644 TAAACCA
1 TAAACCA
40639651 TAAACCA
1 TAAACCA
40639658 TAAACCA
1 TAAACCA
40639665 TAAA-CA
1 TAAACCA
**
40639671 CTAAACTT
1 -TAAACCA
**
40639679 TAAATAA
1 TAAACCA
40639686 TAAA-CA
1 TAAACCA
*
40639692 CTAAACCT
1 -TAAACCA
40639700 TAAAGCC-
1 TAAA-CCA
40639707 TAAACCA
1 TAAACCA
40639714 TAAAACCA
1 T-AAACCA
40639722 TAAACCA
1 TAAACCA
40639729 TAAACCA
1 TAAACCA
40639736 TAAAC
1 TAAAC
40639741 TCTAAAACCT
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
6 6 0.06
7 79 0.78
8 15 0.15
9 1 0.01
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:40640233 original size:41 final size:41
Alignment explanation
Indices: 40640160--40640238 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
40640150 AATTTTAATT
* * *
40640160 AAGTTGAGCAATAGTGTGTTTTTGGCTTCAAACGCCGCAAA
1 AAGTTGAGCAATAGTGTGTTTTTAGCTCCAAACACCGCAAA
40640201 AAGTTG-GACAATAGTGGTGTTTTTAG-TCCAAACACCGC
1 AAGTTGAG-CAATAGT-GTGTTTTTAGCTCCAAACACCGC
40640239 GAATATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.03
41 23 0.70
42 9 0.27
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
AAGTTGAGCAATAGTGTGTTTTTAGCTCCAAACACCGCAAA
Found at i:40640387 original size:117 final size:117
Alignment explanation
Indices: 40640230--40640751 Score: 665
Period size: 116 Copynumber: 4.5 Consensus size: 117
40640220 TTTTTAGTCC
* * * * * *
40640230 AAACACCGCGAATAT-TTATTAAAAGATTGCAAAACGTTGTCGTCTTTACCTGCGCTTTTAGTGG
1 AAACGCCGCGAATATGTT-TTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTTTTTAGTGG
* *
40640294 CGTTTTTACTAAAACGCCACAAAAGTATATGCGTTAGTGTCGTTTTCAAAAAA
65 CGTTTTTACTAAAACGCCACAAAAGGATATGCGTTAGTGGCGTTTTCAAAAAA
* * *
40640347 AAACGCCACGAATATGTTTTAAGAGTTTGCAAAACATTGTCGTTTTTATTTGCGTTTTTAGTGGC
1 AAACGCCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTTTTTAGTGGC
* * *
40640412 ATTTTTACTAAAACGCCACAAAAGGATATGCGTTAGCGGCGTTTTC-ACAAA
66 GTTTTTACTAAAACGCCACAAAAGGATATGCGTTAGTGGCGTTTTCAAAAAA
* * * * * *
40640463 AAACACCGCGAATATGTTTTACGAGTTTGCAAAATGTTGCCATTTTTATCTGTGTTTTTAGTGGC
1 AAACGCCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTTTTTAGTGGC
* * * *
40640528 GTTTTTACTAAAACCCCGA-AAAAGGATATGCATTAGTGGCATTTTCACAAAA
66 GTTTTTACTAAAACGCC-ACAAAAGGATATGCGTTAGTGGCGTTTTCAAAAAA
* * * *
40640580 AAACGTCGCGAATATGTTTTAAGAGTTTGCAAAATGTTGTC-TTTTTATCTGTGTTTTTAGTGGT
1 AAACGCCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTTTTTAGTGGC
* * * * *
40640644 GTTTTTACTAAAAAGCCGCAAAAGGATATGTGTTAGTGGTGTTTTCACAAAA
66 GTTTTTACTAAAACGCCACAAAAGGATATGCGTTAGTGGCGTTTTCAAAAAA
** * *
40640696 AAACGTTGCGAATATGTTTTAAGAGTTTGCAAAACGTTGCCGTTTTTAGCTGCGTT
1 AAACGCCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTT
40640752 AGTGGCGCTT
Statistics
Matches: 353, Mismatches: 47, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
116 203 0.58
117 148 0.42
118 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (117 bp):
AAACGCCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGTCGTTTTTATCTGCGTTTTTAGTGGC
GTTTTTACTAAAACGCCACAAAAGGATATGCGTTAGTGGCGTTTTCAAAAAA
Found at i:40640596 original size:233 final size:232
Alignment explanation
Indices: 40640230--40640749 Score: 695
Period size: 233 Copynumber: 2.2 Consensus size: 232
40640220 TTTTTAGTCC
* * * *
40640230 AAACACCGCGAATAT-TTATTAAAAGATTGCAAAACGTTGTCGTCTTTACCTGCGCTTTTAGTGG
1 AAACACCGCGAATATGTT-TTAAGAGTTTGCAAAACGTTGCCGTTTTTACCTGCGCTTTTAGTGG
* * * * *
40640294 CGTTTTTACTAAAACGCCACAAAAGTATATGCGTTAGTGTCGTTTTCAAAAAAAAACGCCACGAA
65 CGTTTTTACTAAAACCCCACAAAAGGATATGCATTAGTGGCATTTTCAAAAAAAAACGCCACGAA
*
40640359 TATGTTTTAAGAGTTTGCAAAACATTGTCGTTTTTATTTGCGTTTTTAGTGGCATTTTTACTAAA
130 TATGTTTTAAGAGTTTGCAAAACATTGTC-TTTTTATCTGCGTTTTTAGTGGCATTTTTACTAAA
*
40640424 ACGCCACAAAAGGATATGCGTTAGCGGCGTTTTCACAAA
194 AAGCCACAAAAGGATATGCGTTAGCGGCGTTTTCACAAA
* * * * * *
40640463 AAACACCGCGAATATGTTTTACGAGTTTGCAAAATGTTGCCATTTTTATCTGTGTTTTTAGTGGC
1 AAACACCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGCCGTTTTTACCTGCGCTTTTAGTGGC
* * *
40640528 GTTTTTACTAAAACCCCGA-AAAAGGATATGCATTAGTGGCATTTTCACAAAAAAACGTCGCGAA
66 GTTTTTACTAAAACCCC-ACAAAAGGATATGCATTAGTGGCATTTTCAAAAAAAAACGCCACGAA
** * **
40640592 TATGTTTTAAGAGTTTGCAAAATGTTGTCTTTTTATCTGTGTTTTTAGTGGTGTTTTTACTAAAA
130 TATGTTTTAAGAGTTTGCAAAACATTGTCTTTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAA
* * * *
40640657 AGCCGCAAAAGGATATGTGTTAGTGGTGTTTTCACAAA
195 AGCCACAAAAGGATATGCGTTAGCGGCGTTTTCACAAA
* *
40640695 AAA-ACGTTGCGAATATGTTTTAAGAGTTTGCAAAACGTTGCCGTTTTTAGCTGCG
1 AAACAC--CGCGAATATGTTTTAAGAGTTTGCAAAACGTTGCCGTTTTTACCTGCG
40640750 TTAGTGGCGC
Statistics
Matches: 248, Mismatches: 35, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
231 2 0.01
232 68 0.27
233 175 0.71
234 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (232 bp):
AAACACCGCGAATATGTTTTAAGAGTTTGCAAAACGTTGCCGTTTTTACCTGCGCTTTTAGTGGC
GTTTTTACTAAAACCCCACAAAAGGATATGCATTAGTGGCATTTTCAAAAAAAAACGCCACGAAT
ATGTTTTAAGAGTTTGCAAAACATTGTCTTTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAAA
GCCACAAAAGGATATGCGTTAGCGGCGTTTTCACAAA
Found at i:40644296 original size:43 final size:43
Alignment explanation
Indices: 40644229--40644352 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
40644219 AGCTCGTACA
* * * * *
40644229 ATGCC-ATATCCTAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATATCCCAGACAGGGTCTTACATGTAATCACATAACG
* * * * *
40644271 ATGCTACTATCCCAGACAGGGTCTTATATGAAATCATATAACG
1 ATGCCAATATCCCAGACAGGGTCTTACATGTAATCACATAACG
* *
40644314 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATATCCCAGACAGGGTCTTACATGTAATCACAT
40644353 CTCGGTAATC
Statistics
Matches: 64, Mismatches: 17, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
42 4 0.06
43 60 0.94
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGCCAATATCCCAGACAGGGTCTTACATGTAATCACATAACG
Found at i:40653332 original size:17 final size:18
Alignment explanation
Indices: 40653312--40653347 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40653302 TAATCTTGTT
40653312 TTAATAAATTAATA-GCA
1 TTAATAAATTAATATGCA
*
40653329 TTAATAATTTAATATGCA
1 TTAATAAATTAATATGCA
40653347 T
1 T
40653348 ATATTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAATAAATTAATATGCA
Found at i:40653391 original size:6 final size:6
Alignment explanation
Indices: 40653380--40653404 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40653370 TAACTTTGAG
40653380 TAGAAT TAGAAT TAGAAT TAGAAT T
1 TAGAAT TAGAAT TAGAAT TAGAAT T
40653405 TCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (6 bp):
TAGAAT
Found at i:40666278 original size:13 final size:13
Alignment explanation
Indices: 40666260--40666285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40666250 GCAGTATACC
40666260 TACATACATACAT
1 TACATACATACAT
40666273 TACATACATACAT
1 TACATACATACAT
40666286 GTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TACATACATACAT
Found at i:40675278 original size:14 final size:14
Alignment explanation
Indices: 40675254--40675300 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
40675244 TAAAGGGACC
*
40675254 AAAAATCAAAAGCAA
1 AAAAATGAAAAG-AA
40675269 AAAAA-GAAAAGAA
1 AAAAATGAAAAGAA
40675282 AAGAAATG-AAAGAA
1 AA-AAATGAAAAGAA
40675296 AAAAA
1 AAAAA
40675301 CCCATATCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 7 0.24
14 16 0.55
15 6 0.21
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAATGAAAAGAA
Found at i:40684196 original size:34 final size:35
Alignment explanation
Indices: 40684157--40684227 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
40684147 AAACCAATAG
40684157 AAAACTC-TCTCTAATAAAAACCAATAAAATTATT
1 AAAACTCGTCTCTAATAAAAACCAATAAAATTATT
* *
40684191 AAAACTCTGTCTCTAATAGAAACCAATAGAATTATT
1 AAAACTC-GTCTCTAATAAAAACCAATAAAATTATT
40684227 A
1 A
40684228 TTCCCAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 7 0.21
36 26 0.79
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (35 bp):
AAAACTCGTCTCTAATAAAAACCAATAAAATTATT
Found at i:40684243 original size:22 final size:22
Alignment explanation
Indices: 40684215--40684267 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40684205 AATAGAAACC
*
40684215 AATAGAATTATTATTCCCAAGA-
1 AATAGAATTACTATTCCCAA-AT
*
40684237 AATAGAATTGCTATTCCCAAAT
1 AATAGAATTACTATTCCCAAAT
40684259 AATAGAATT
1 AATAGAATT
40684268 TATACTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (22 bp):
AATAGAATTACTATTCCCAAAT
Found at i:40684661 original size:15 final size:16
Alignment explanation
Indices: 40684624--40684661 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40684614 AAATAGACAT
*
40684624 TATTTTTTAAATTAAT
1 TATTTTTTAAATTAAA
*
40684640 TAATTTTT-AATTAAA
1 TATTTTTTAAATTAAA
40684655 TATTTTT
1 TATTTTT
40684662 CTTAACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTTAAATTAAA
Done.