Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 1 of 25
Found at i:329 original size:110 final size:113
Alignment explanation
Indices: 118--330 Score: 294
Period size: 113 Copynumber: 1.9 Consensus size: 113
108 ACAAAAAACT
* *
118 AATCATTATATAGTAAAATTGAAAACTAAAAAATATTATTTAATTAATTTATTAATTTTAAGTTT
1 AATCATTATATAATAAAATTGAAAACTAAAAAATATTATTTAATTAATATATTAATTTTAAGTTT
183 AGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
66 AGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
* * *
231 AATCATTATTTAATAGAATTGAAAACTAAAAATTATT-TTTAATTAATATATT-ATTTATAAGTT
1 AATCATTATATAATAAAATTGAAAACTAAAAAATATTATTTAATTAATATATTAATTT-TAAGTT
* *
294 ATA-AATAAGGAT-T-AAATATAATTTT-TATAATTAGTTA
65 -TAGAAGAAAGATATAAAATATAATTTTATA-AATTAGTTA
331 AATTATTGTT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
109 2 0.02
110 21 0.23
111 5 0.06
112 27 0.30
113 35 0.39
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (113 bp):
AATCATTATATAATAAAATTGAAAACTAAAAAATATTATTTAATTAATATATTAATTTTAAGTTT
AGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
Found at i:880 original size:48 final size:48
Alignment explanation
Indices: 733--882 Score: 187
Period size: 48 Copynumber: 3.1 Consensus size: 48
723 TTTGCTCAAC
* * *
733 AAATTAATTTGCTGCATGTATAGGAGAAAGGTG-ATGAATACATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGG-GAATGAATACATTTAAT
* * *
781 AAAGTAATTTGGTTCATGTATAGGAGAGA-AGAGATGAATATATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGA-ATGAATACATTTAAT
* * *
829 AAATTAATTTGGTTCATGTATGGGAGAGAGGGAATGTATACATATAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
877 AAATTA
1 AAATTA
883 TTTTAATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.01
48 84 0.97
49 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (48 bp):
AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
Found at i:1692 original size:3 final size:3
Alignment explanation
Indices: 1684--1710 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1674 AAATAAAGAA
1684 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1711 GATCCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13167 original size:33 final size:33
Alignment explanation
Indices: 13107--13175 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
13097 CCATTAGAAG
* *
13107 CAATGTATCGATACAATTCATCATGTATTAATA
1 CAATGTATCGATACAATTCACCATGTATCAATA
*
13140 CAATGTATCGATACAATGT-ACCTTGTATCAATA
1 CAATGTATCGATACAAT-TCACCATGTATCAATA
13173 CAA
1 CAA
13176 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATGTATCAATA
Found at i:17673 original size:16 final size:15
Alignment explanation
Indices: 17637--17666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17627 TTCGAGATTT
*
17637 CAAAAAAATATTAAA
1 CAAAAAAAAATTAAA
17652 CAAAAAAAAATTAAA
1 CAAAAAAAAATTAAA
17667 ATAAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAAAAAAAATTAAA
Found at i:17843 original size:22 final size:22
Alignment explanation
Indices: 17815--17891 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
17805 TTTCACGTAA
17815 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
17837 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
17858 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
17880 CATTTCATGCAT
1 CATTTCATGCAT
17892 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:17843 original size:43 final size:43
Alignment explanation
Indices: 17789--17912 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
17779 CATTGCATGC
*
17789 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
17832 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
17875 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
17913 TGCACTTCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 9 0.12
43 67 0.88
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:17863 original size:21 final size:21
Alignment explanation
Indices: 17794--17867 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
17784 CATGCATTTT
*
17794 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
17815 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
17833 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
17858 CATTTCATGC
1 CATTTCATGC
17868 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:17913 original size:5 final size:5
Alignment explanation
Indices: 17900--17998 Score: 117
Period size: 5 Copynumber: 19.8 Consensus size: 5
17890 ATTTCAAAAA
* * * * * *
17900 CATTT CATTG CATTG CACTT CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
* * *
17950 CATTT CATTT CATTT CATTT CATTT CATTG CATTG CATTT CATTA CATT
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATT
17999 GCTTTCATGC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 83 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (5 bp):
CATTT
Found at i:17923 original size:15 final size:15
Alignment explanation
Indices: 17900--18010 Score: 111
Period size: 15 Copynumber: 7.5 Consensus size: 15
17890 ATTTCAAAAA
* *
17900 CATTTCATTGCATTG
1 CATTGCATTGCATTT
*
17915 CACTT-CATTTCATTT
1 CA-TTGCATTGCATTT
* *
17930 CATTGCATTTCATTG
1 CATTGCATTGCATTT
*
17945 CATTGCATTTCATTT
1 CATTGCATTGCATTT
* *
17960 CATTTCATTTCATTT
1 CATTGCATTGCATTT
17975 CATTGCATTGCATTT
1 CATTGCATTGCATTT
*
17990 CATTACATTGC-TTT
1 CATTGCATTGCATTT
18004 CA-TGCAT
1 CATTGCAT
18011 GAAATGGCCG
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
13 4 0.05
14 7 0.08
15 72 0.85
16 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.50
Consensus pattern (15 bp):
CATTGCATTGCATTT
Found at i:27825 original size:38 final size:38
Alignment explanation
Indices: 27781--27910 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 38
27771 AGCGACCTAT
27781 CAAAGAGCAATGGTCACCATGTTTCACGACCTAATGCA
1 CAAAGAGCAATGGTCACCATGTTTCACGACCTAATGCA
* * *
27819 CAAAGAGATAGAAATATATGTAGATGA-CATATT-CACGACCTAATGCA
1 C-AA-AG--AG---CA-ATG--G-TCACCATGTTTCACGACCTAATGCA
*
27866 CAAAGAGCAATGGTCACCCTGTTTCACGACCTAATGCA
1 CAAAGAGCAATGGTCACCATGTTTCACGACCTAATGCA
27904 CAAAGAG
1 CAAAGAG
27911 ATAGAAATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
36 2 0.03
37 5 0.07
38 22 0.31
39 5 0.07
40 3 0.04
42 2 0.03
43 2 0.03
45 3 0.04
46 5 0.07
47 15 0.21
48 6 0.08
49 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (38 bp):
CAAAGAGCAATGGTCACCATGTTTCACGACCTAATGCA
Found at i:31618 original size:42 final size:42
Alignment explanation
Indices: 31567--32371 Score: 795
Period size: 42 Copynumber: 18.8 Consensus size: 42
31557 TTTTGTTTTC
31567 CCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
*
31608 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* *
31650 CCCTT-AGTCTACCTGTTGGCTTTGACCCTGGAGACTTTGGAGACTTTCCTAT
1 -CCTTCAGTCTGCCTGTCGGCTTTGA-CC------C--TGGAGACTTTCCT-T
* * *
31702 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGAC-TGCC-T
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * *
31743 CATTTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATC
1 C-CTT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* *
31788 CCTT-AGTCTGCCTGTCGGCTTTGACCCTAGAGATTTTCCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * * * **
31829 CCTTTAGTCTGCTTGTCGGCTTTGTCCCTGAAGACTTTTCAA
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * *
31871 CCCTCAATCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * * * * *
31914 CCCTAAGTCTGCCTATCGGCTTCGTCCTTAGAGACTTT-CTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * *
31955 TCTCTCAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTT
1 CCT-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * *
31999 CCCTAAGTCTGCCTGTCGGCTTTGGCCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
32041 CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
*
32083 CCCTT-AGTCGGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
*
32125 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
*
32167 CCTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTAT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-T
* * *
32210 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGAC-TGCC-T
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * *
32251 CATTTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATC
1 C-CTT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * *
32296 CCTT-AGTCTACCTGTCGGTTTTGACCTTGGAGACTTTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * * *
32338 CCCTAAGTCTGCCCGTTGGCTTTGACCCGGGAGA
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA
32372 GTATTTTCTT
Statistics
Matches: 633, Mismatches: 98, Indels: 64
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.00
41 26 0.04
42 414 0.65
43 101 0.16
44 50 0.08
45 2 0.00
46 1 0.00
49 1 0.00
51 12 0.02
52 7 0.01
53 17 0.03
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (42 bp):
CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
Found at i:31718 original size:53 final size:51
Alignment explanation
Indices: 31636--31738 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 51
31626 GCTTTGACCC
* **
31636 TGGAGACTTTTCTTCCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTT
1 TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
* *
31687 TGGAGACTTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACT
1 TGGAGACTTTCCT-TCCCTT-AGTCTACCTGTCAGCTTTGACCCTGGAGACT
31739 GCCTCATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 12 0.27
52 6 0.13
53 27 0.60
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (51 bp):
TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
Found at i:32062 original size:254 final size:254
Alignment explanation
Indices: 31564--32371 Score: 1084
Period size: 254 Copynumber: 3.1 Consensus size: 254
31554 CTTTTTTGTT
31564 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
* * * *
31629 TTGACCCTGGAGACTTTTCTTCCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTTTGGAGAC
66 TTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACTTT---G-C
31694 TTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCT
127 TTT-C--T--CTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCT
*
31759 GTCGGCTTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGATTT
187 GTCGGCTTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTT
31824 TCC
252 TCC
* * * * * ** * * *
31827 TTCCTTTAGTCTGCTTGTCGGCTTTGTCCCTGAAGACTTTTCAACCCTCAATCTACCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
* * * *
31892 TTGACCCTGGAGACTTTTCTTTCCCTAAGTCTGCCTATCGGCTTCGTCCTTAGAGACTTT-CTTT
66 TTGACCCTGGAGACTTTTC-TTCCCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTGCTTT
* * * ** *
31956 CTC-TCAGTCTACCTGTCGGCTTTGACCCTGGAGACT-TTTC-TTTCCCTAAGTCTGCCTGTCGG
130 CTCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTT---AAAGTCTGCCTGTCGG
* * *
32018 CTTTGGCCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
192 CTTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTTTCC
*
32081 TTCCCTTAGTCGGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
* * * *
32146 TTGACCCTGGAGACTTTTCTTCCTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATC
66 TTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTGCTTTC
*
32211 CCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTT
131 TCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTT
* * * *
32276 GACCCTGGAGACTTTTCATCCCTTAGTCTACCTGTCGGTTTTGACCTTGGAGACTTTTCT
196 GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA-TTTTCC
* * * *
32336 TTCCCTAAGTCTGCCCGTTGGCTTTGACCCGGGAGA
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA
32372 GTATTTTCTT
Statistics
Matches: 471, Mismatches: 65, Indels: 26
0.84 0.12 0.05
Matches are distributed among these distances:
251 3 0.01
252 2 0.00
253 64 0.14
254 220 0.47
255 65 0.14
256 3 0.01
257 3 0.01
258 1 0.00
259 4 0.01
263 74 0.16
264 32 0.07
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (254 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
TTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTGCTTTC
TCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTT
GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTTTCC
Found at i:32857 original size:43 final size:43
Alignment explanation
Indices: 32806--32929 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
32796 CATTGCATGC
*
32806 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
32849 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
32892 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
32930 TGCACTTCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 9 0.12
43 67 0.88
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:32860 original size:22 final size:22
Alignment explanation
Indices: 32832--32908 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
32822 TTTCACGTAA
32832 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
32854 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
32875 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
32897 CATTTCATGCAT
1 CATTTCATGCAT
32909 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:32880 original size:21 final size:21
Alignment explanation
Indices: 32811--32884 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
32801 CATGCATTTT
*
32811 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
32832 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
32850 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
32875 CATTTCATGC
1 CATTTCATGC
32885 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:32930 original size:5 final size:5
Alignment explanation
Indices: 32917--33007 Score: 85
Period size: 5 Copynumber: 18.2 Consensus size: 5
32907 ATTTCAAAAA
* * * *
32917 CATTT CATTG CATTG CACTT- CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTG CATTG CATTG CA-TTG CATTG CATTG CATTG CATTG CATTG CATTG
* * * * *
32967 CATTT CATTT CATTT CATTG CATTG CATTT CATTA CATTG C
1 CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG C
33008 TTTCATGCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
4 2 0.03
5 71 0.95
6 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (5 bp):
CATTG
Found at i:32940 original size:10 final size:10
Alignment explanation
Indices: 32917--33005 Score: 97
Period size: 10 Copynumber: 8.9 Consensus size: 10
32907 ATTTCAAAAA
* *
32917 CATTTCATTG
1 CATTGCATTT
*
32927 CATTGCACTT
1 CATTGCATTT
*
32937 CATTTCATTT
1 CATTGCATTT
32947 CATTGCATTT
1 CATTGCATTT
*
32957 CATTGCATTG
1 CATTGCATTT
*
32967 CATTTCATTT
1 CATTGCATTT
* *
32977 CATTTCATTG
1 CATTGCATTT
32987 CATTGCATTT
1 CATTGCATTT
*
32997 CATTACATT
1 CATTGCATT
33006 GCTTTCATGC
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 66 1.00
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.49
Consensus pattern (10 bp):
CATTGCATTT
Found at i:32940 original size:20 final size:20
Alignment explanation
Indices: 32917--33007 Score: 137
Period size: 20 Copynumber: 4.5 Consensus size: 20
32907 ATTTCAAAAA
*
32917 CATTTCATTGCATTGCACTT
1 CATTTCATTGCATTGCATTT
*
32937 CATTTCATTTCATTGCATTT
1 CATTTCATTGCATTGCATTT
* *
32957 CATTGCATTGCATTTCATTT
1 CATTTCATTGCATTGCATTT
32977 CATTTCATTGCATTGCATTT
1 CATTTCATTGCATTGCATTT
*
32997 CATTACATTGC
1 CATTTCATTGC
33008 TTTCATGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (20 bp):
CATTTCATTGCATTGCATTT
Found at i:38270 original size:111 final size:115
Alignment explanation
Indices: 38060--38274 Score: 307
Period size: 113 Copynumber: 1.9 Consensus size: 115
38050 ACAAAAAACT
* *
38060 AATCATTATATAGTAAAATTGAAAACTAAAAAAATATTATTTAATTAATTTATTAATTTTAAGTT
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTTTAAGTT
38125 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
66 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
* * *
38175 AATCATTATTTAATAGAATTGAAAACT-AAAAATTATT-TTTAATTAATATATT-ATTTATAAGT
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTT-TAAGT
* *
38237 TATA-AATAAGGAT-T-AAATATAATTTTATAAATTAGTTA
65 T-TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTA
38275 AATTATTGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
111 24 0.26
112 5 0.05
113 27 0.30
114 11 0.12
115 24 0.26
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (115 bp):
AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTTTAAGTT
TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
Found at i:38824 original size:48 final size:48
Alignment explanation
Indices: 38677--38826 Score: 187
Period size: 48 Copynumber: 3.1 Consensus size: 48
38667 TTTGCTCAAC
* * *
38677 AAATTAATTTGCTGCATGTATAGGAGAAAGGTG-ATGAATACATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGG-GAATGAATACATTTAAT
* * *
38725 AAAGTAATTTGGTTCATGTATAGGAGAGA-AGAGATGAATATATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGA-ATGAATACATTTAAT
* * *
38773 AAATTAATTTGGTTCATGTATGGGAGAGAGGGAATGTATACATATAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
38821 AAATTA
1 AAATTA
38827 TTTTAATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.01
48 84 0.97
49 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (48 bp):
AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
Found at i:39636 original size:3 final size:3
Alignment explanation
Indices: 39628--39654 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39618 AAATAAAGAA
39628 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
39655 GATCCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56274 original size:1 final size:1
Alignment explanation
Indices: 56268--56357 Score: 81
Period size: 1 Copynumber: 90.0 Consensus size: 1
56258 TGGCAATTGG
* * ** * * * **
56268 AAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
56333 AAAGAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
56358 GTGAAGATTT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.88, C:0.06, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:56314 original size:33 final size:33
Alignment explanation
Indices: 56268--56357 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
56258 TGGCAATTGG
56268 AAAA-AAAAAAAAAACAAAACAAAAAAAAAGGA
1 AAAAGAAAAAAAAAACAAAACAAAAAAAAAGGA
56300 AAAAGAAAAAAAAAACAAAAC-AAAAAAAAGGA
1 AAAAGAAAAAAAAAACAAAACAAAAAAAAAGGA
56332 AAAAGAAAAAAAAAACAAAA-AAAAAA
1 AAAAGAAAAAAAAAACAAAACAAAAAA
56358 GTGAAGATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
32 40 0.71
33 16 0.29
ACGTcount: A:0.88, C:0.06, G:0.07, T:0.00
Consensus pattern (33 bp):
AAAAGAAAAAAAAAACAAAACAAAAAAAAAGGA
Found at i:61274 original size:33 final size:33
Alignment explanation
Indices: 61214--61282 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
61204 CCATTAGAAG
* *
61214 CAATGTATCGATACAATTCATCATGTATTAATA
1 CAATGTATCGATACAATTCACCATGTATCAATA
*
61247 CAATGTATCGATACAATGT-ACCTTGTATCAATA
1 CAATGTATCGATACAAT-TCACCATGTATCAATA
61280 CAA
1 CAA
61283 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATGTATCAATA
Found at i:65782 original size:32 final size:33
Alignment explanation
Indices: 65746--65809 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
65736 GAGATTTCAA
*
65746 AAAAATATTA-AACAAAAAAAAT-AAATTAAAAT
1 AAAAATATTATAA-AAAAAAAATGAAATAAAAAT
* *
65778 AAAAATTTTATAAAAAAATAATGAAATAAAAA
1 AAAAATATTATAAAAAAAAAATGAAATAAAAA
65810 GAAGAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (33 bp):
AAAAATATTATAAAAAAAAAATGAAATAAAAAT
Found at i:65950 original size:43 final size:43
Alignment explanation
Indices: 65899--66022 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
65889 CATTGCATGC
*
65899 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
65942 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
65985 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
66023 TGCACTTCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 9 0.12
43 67 0.88
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:65953 original size:22 final size:22
Alignment explanation
Indices: 65925--66001 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
65915 TTTCACGTAA
65925 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
65947 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
65968 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
65990 CATTTCATGCAT
1 CATTTCATGCAT
66002 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:65973 original size:21 final size:21
Alignment explanation
Indices: 65904--65977 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
65894 CATGCATTTT
*
65904 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
65925 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
65943 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
65968 CATTTCATGC
1 CATTTCATGC
65978 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:66023 original size:5 final size:5
Alignment explanation
Indices: 66010--66090 Score: 74
Period size: 5 Copynumber: 16.2 Consensus size: 5
66000 ATTTCAAAAA
* * * * *
66010 CATTT CATTG CATTG CACTT- CATTT CATTT CATTG CATTG CATTT CATTT
1 CATTG CATTG CATTG CA-TTG CATTG CATTG CATTG CATTG CATTG CATTG
* * *
66060 CATTT CATTG CATTG CATTT CATTA CATTG C
1 CATTG CATTG CATTG CATTG CATTG CATTG C
66091 TTTCATGCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
4 2 0.03
5 63 0.94
6 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (5 bp):
CATTG
Found at i:66033 original size:20 final size:20
Alignment explanation
Indices: 66010--66096 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
66000 ATTTCAAAAA
*
66010 CATTTCATTGCATTGCACTT-
1 CATTTCATTTCATTGCA-TTG
66030 CATTTCATTTCATTGCATTG
1 CATTTCATTTCATTGCATTG
*
66050 CATTTCATTTCATTTCATTG
1 CATTTCATTTCATTGCATTG
* *
66070 CATTGCATTTCATTACATTG
1 CATTTCATTTCATTGCATTG
66090 C-TTTCAT
1 CATTTCAT
66097 GCATGAAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
19 7 0.11
20 54 0.89
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (20 bp):
CATTTCATTTCATTGCATTG
Found at i:66038 original size:25 final size:25
Alignment explanation
Indices: 66010--66088 Score: 140
Period size: 25 Copynumber: 3.2 Consensus size: 25
66000 ATTTCAAAAA
*
66010 CATTTCATTGCATTGCACTTCATTT
1 CATTTCATTGCATTGCATTTCATTT
66035 CATTTCATTGCATTGCATTTCATTT
1 CATTTCATTGCATTGCATTTCATTT
*
66060 CATTTCATTGCATTGCATTTCATTA
1 CATTTCATTGCATTGCATTTCATTT
66085 CATT
1 CATT
66089 GCTTTCATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (25 bp):
CATTTCATTGCATTGCATTTCATTT
Found at i:66073 original size:15 final size:15
Alignment explanation
Indices: 66030--66096 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
66020 CATTGCACTT
66030 CATTTCATTTCATTG
1 CATTTCATTTCATTG
* *
66045 CATTGCATTTCATTT
1 CATTTCATTTCATTG
*
66060 CATTTCATTGCATTG
1 CATTTCATTTCATTG
*
66075 CATTTCATTACATTG
1 CATTTCATTTCATTG
66090 C-TTTCAT
1 CATTTCAT
66097 GCATGAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
14 6 0.13
15 40 0.87
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (15 bp):
CATTTCATTTCATTG
Found at i:66088 original size:10 final size:10
Alignment explanation
Indices: 66010--66088 Score: 86
Period size: 10 Copynumber: 7.9 Consensus size: 10
66000 ATTTCAAAAA
*
66010 CATTTCATTG
1 CATTTCATTT
* *
66020 CATTGCACTT
1 CATTTCATTT
66030 CATTTCATTT
1 CATTTCATTT
* *
66040 CATTGCATTG
1 CATTTCATTT
66050 CATTTCATTT
1 CATTTCATTT
*
66060 CATTTCATTG
1 CATTTCATTT
*
66070 CATTGCATTT
1 CATTTCATTT
*
66080 CATTACATT
1 CATTTCATT
66089 GCTTTCATGC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 56 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (10 bp):
CATTTCATTT
Found at i:70808 original size:186 final size:186
Alignment explanation
Indices: 70494--70867 Score: 721
Period size: 186 Copynumber: 2.0 Consensus size: 186
70484 AATTTTCAAA
*
70494 ACTAGACCATGATGTTGCCAAAGCAAAAATAAAGATTATTTTGATTTTTTGGGTTTCTTGGGGTT
1 ACTAGACCATGATGTTGCCAAAGCAAAAATAAAGATTATTTTGATTTTTTGGGTTTCTTGGGGTC
70559 GAACTTGAGCCAAGGACATTCGAACATTTGTGACATAGGGAAAATAGTGACATAAGCATCATGAG
66 GAACTTGAGCCAAGGACATTCGAACATTTGTGACATAGGGAAAATAGTGACATAAGCATCATGAG
70624 TTTGTTCCGTAATCCTGCAATGGTTTGGGACAATGAAACAACCTAGTGACTATGCC
131 TTTGTTCCGTAATCCTGCAATGGTTTGGGACAATGAAACAACCTAGTGACTATGCC
*
70680 ACTAGACCATGCTGTTGCCAAAGCAAAAATAAAGATTATTTTGATTTTTTGGGTTTCTTGGGGTC
1 ACTAGACCATGATGTTGCCAAAGCAAAAATAAAGATTATTTTGATTTTTTGGGTTTCTTGGGGTC
*
70745 GAACTTGAGCCAAGGACATTTGAACATTTGTGACATAGGGAAAATAGTGACATAAGCATCATGAG
66 GAACTTGAGCCAAGGACATTCGAACATTTGTGACATAGGGAAAATAGTGACATAAGCATCATGAG
70810 TTTGTTCCGTAATCCTGCAATGGTTTGGGACAATGAAACAACCTAGTGACTATGCC
131 TTTGTTCCGTAATCCTGCAATGGTTTGGGACAATGAAACAACCTAGTGACTATGCC
70866 AC
1 AC
70868 AAATAAACGT
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (186 bp):
ACTAGACCATGATGTTGCCAAAGCAAAAATAAAGATTATTTTGATTTTTTGGGTTTCTTGGGGTC
GAACTTGAGCCAAGGACATTCGAACATTTGTGACATAGGGAAAATAGTGACATAAGCATCATGAG
TTTGTTCCGTAATCCTGCAATGGTTTGGGACAATGAAACAACCTAGTGACTATGCC
Found at i:72141 original size:67 final size:67
Alignment explanation
Indices: 72056--72181 Score: 164
Period size: 67 Copynumber: 1.9 Consensus size: 67
72046 CTTCAGATAC
* * * * * * *
72056 TATGCTTAGTTGCACTTATTTCCATTGGTTC-AGCCATGCAGAGTAGTGGTGCAAGAACTTTAGG
1 TATGCTTAGCTACACTTATTCCCATTAGTTCTA-CCATGCAAACTAGTGGTGCAAAAACTTTAGG
72120 TAT
65 TAT
*
72123 TATGCTTAGCTACTCTTATTCCCATTAGTTCTACCATGCAAACTAGTGGTGCAAAAACT
1 TATGCTTAGCTACACTTATTCCCATTAGTTCTACCATGCAAACTAGTGGTGCAAAAACT
72182 CCAAGTACTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
67 49 0.98
68 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (67 bp):
TATGCTTAGCTACACTTATTCCCATTAGTTCTACCATGCAAACTAGTGGTGCAAAAACTTTAGGT
AT
Found at i:72194 original size:67 final size:67
Alignment explanation
Indices: 72053--72195 Score: 162
Period size: 67 Copynumber: 2.1 Consensus size: 67
72043 CAACTTCAGA
* * * * * * * **
72053 TACTATGCTTAGTTGCACTTATTTCCATTGGTTCAGCCATGCAGAGTAGTGGTGCAAGAACTTTA
1 TACTATGCTTAGCTACACTTATTCCCATTAGTTCAGCCATGCAAACTAGTGGTGCAAAAACTCCA
*
72118 GG
66 AG
* *
72120 TATTATGCTTAGCTACTCTTATTCCCATTAGTTCTA-CCATGCAAACTAGTGGTGCAAAAACTCC
1 TACTATGCTTAGCTACACTTATTCCCATTAGTTC-AGCCATGCAAACTAGTGGTGCAAAAACTCC
72184 AAG
65 AAG
72187 TACTATGCT
1 TACTATGCT
72196 CAACTGTTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
67 61 0.98
68 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (67 bp):
TACTATGCTTAGCTACACTTATTCCCATTAGTTCAGCCATGCAAACTAGTGGTGCAAAAACTCCA
AG
Found at i:73497 original size:76 final size:76
Alignment explanation
Indices: 73371--73524 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
73361 TTCTAGTTTG
73371 ATTAGCTTAAAGAGGCCTTGTTTTACTTTGTGTTTGGCTTAGGAAAGTAACAAGTCACAATTGCC
1 ATTAGCTTAAAGAGGCCTTGTTTTACTTTGTGTTTGGCTTAGGAAAGTAACAAGTCACAATTGCC
73436 TTGCAAAATAT
66 TTGCAAAATAT
* *
73447 ATTAGCTTAAAGAGGCCTTGTTTTACTTTGTGTTTAGG-TTGGGAAAGTAACAGGTCACAATTGC
1 ATTAGCTTAAAGAGGCCTTGTTTTACTTTGTGTTT-GGCTTAGGAAAGTAACAAGTCACAATTGC
* *
73511 TTTGCAACATAT
65 CTTGCAAAATAT
73523 AT
1 AT
73525 AACTCATGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 71 0.97
77 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (76 bp):
ATTAGCTTAAAGAGGCCTTGTTTTACTTTGTGTTTGGCTTAGGAAAGTAACAAGTCACAATTGCC
TTGCAAAATAT
Found at i:73906 original size:44 final size:44
Alignment explanation
Indices: 73840--73933 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 44
73830 GCTTACTAGT
73840 TTTTTTTTTCTGTTAAGGTAAATTTAACTTGAGATGCTAGATCC
1 TTTTTTTTTCTGTTAAGGTAAATTTAACTTGAGATGCTAGATCC
73884 TTCTTTTTTT-TGTTAAGGTAAATTTAACTTGAGATGCTAGATCC
1 TT-TTTTTTTCTGTTAAGGTAAATTTAACTTGAGATGCTAGATCC
73928 TTTTTT
1 TTTTTT
73934 CTTTAGGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 4 0.08
44 38 0.78
45 7 0.14
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (44 bp):
TTTTTTTTTCTGTTAAGGTAAATTTAACTTGAGATGCTAGATCC
Found at i:79597 original size:14 final size:14
Alignment explanation
Indices: 79574--79611 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
79564 AAGTTATTAA
79574 ATTAAATTTAAGTT
1 ATTAAATTTAAGTT
*
79588 ATTAACTTTAAGTT
1 ATTAAATTTAAGTT
79602 ATTAAATTTA
1 ATTAAATTTA
79612 CACATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
ATTAAATTTAAGTT
Found at i:79838 original size:20 final size:20
Alignment explanation
Indices: 79783--79854 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
79773 TGCTATGTAA
*
79783 GTATCGATACTACATGGATT
1 GTATCGATACCACATGGATT
* * * *
79803 GTATTGACACTACATGGGTT
1 GTATCGATACCACATGGATT
*
79823 GTATCGATACCGCATGGATAT
1 GTATCGATACCACATGGAT-T
*
79844 TTATCGATACC
1 GTATCGATACC
79855 TTAAGGCCCT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
GTATCGATACCACATGGATT
Found at i:81719 original size:155 final size:154
Alignment explanation
Indices: 81445--81994 Score: 634
Period size: 155 Copynumber: 3.6 Consensus size: 154
81435 GTACCTTTGG
** * * * ** * * *
81445 CATAAAAGCGGACCTGGTAATAACCTAAGACTCGGTTCTAAAAAATTACAAAAATACCCCTATGG
1 CATAAAAGCGGACCCAGTGACAACCTAGGACTCAATTTTAAAAAATTACGAAAATACCCCTAAGG
* ** * *
81510 GATACTTTCGACTTAGAAGTGCCCAATACCTTTAAAGGACTTAAAAAAGATTATAGAGGGGATGA
66 GATACTTTCGACTTAGAAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAAAGGGGATGA
* *
81575 ACCTATCCTCAATACTCACCTTAAA
131 ACCTATCCTAAATAC-CACCTTCAA
* * * * *
81600 CATAAAAGCGGGCCCGGTGACAACCTAGGACTCAATTTTAGAAAATTATGAAAATACCCCCAAGG
1 CATAAAAGCGGACCCAGTGACAACCTAGGACTCAATTTTAAAAAATTACGAAAATACCCCTAAGG
* * * * * * *
81665 GACACCTTCAACTTAAAAGTGCCTGATACCCCTAAAGGACTTAAAAAGGATTATAAAGTGAATGA
66 GATACTTTCGACTTAGAAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAAAGGGGATGA
* *
81730 ACCTATCTTAAATACCCACCTTCAT
131 ACCTATCCTAAATA-CCACCTTCAA
* * * * * *
81755 CATAAAAGCGAACCCAGTGATAACTTATGACTCGATTTTAAAAAATTACGAAAATACCCCTAGGG
1 CATAAAAGCGGACCCAGTGACAACCTAGGACTCAATTTTAAAAAATTACGAAAATACCCCTAAGG
*
81820 GATACTTTCGACTTAGAAGTGCCTAATACCCCTAAAGGGCTTAAAAAGGATTATAAAGGGGATGA
66 GATACTTTCGACTTAGAAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAAAGGGGATGA
*
81885 ACCTATCCTAAATACCTACCTTCGA
131 ACCTATCCTAAATACC-ACCTTCAA
* * * * * *
81910 CATAAAAGAGGACCCAGTGACAACCTAGGACTTAATTTTTAAAAATTACGATAAT-GCCCTTAGA
1 CATAAAAGCGGACCCAGTGACAACCTAGGACTCAATTTTAAAAAATTACGAAAATACCCCTAAG-
* *
81974 GGATACCTTCGACATAGAAGT
65 GGATACTTTCGACTTAGAAGT
81995 AACCGACACC
Statistics
Matches: 327, Mismatches: 65, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
154 7 0.02
155 319 0.98
156 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (154 bp):
CATAAAAGCGGACCCAGTGACAACCTAGGACTCAATTTTAAAAAATTACGAAAATACCCCTAAGG
GATACTTTCGACTTAGAAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAAAGGGGATGA
ACCTATCCTAAATACCACCTTCAA
Found at i:82264 original size:134 final size:134
Alignment explanation
Indices: 82120--82490 Score: 514
Period size: 135 Copynumber: 2.8 Consensus size: 134
82110 TCGAAAATTT
* * *
82120 CATTTCGTACCTTAATAGAAAACTAAAAAGATACAGAAAGTTTAAAAGTTTCTATACCCCTACAA
1 CATTTCGTACCTTAATGGAGAACTGAAAAGATACAGAAAGTTTAAAAGTTTCTATACCCCTACAA
82185 AAAACC-TAAGAATATCAAAAATCTTGAAAAATTAAGATAATA-TTTTTTATTTAATTTTAAAAA
66 AAAACCATAAGAATATCAAAAATCTTGAAAAATTAAGATAATATTTTTTTATTTAATTTT--AAA
82248 AAAATC
129 AAAATC
* * *
82254 CATTTCGTACCTTAATGGCGAACTGAAAAGATACATAAAGTTTTAAAAGTTTCTGTACCCCTACA
1 CATTTCGTACCTTAATGGAGAACTGAAAAGATACAGAAAG-TTTAAAAGTTTCTATACCCCTACA
* * *
82319 AAAAACCTTAGGAATATCAGAAATCTTGAAAAATTAAGATAATATTTTTTTATTTAATTTTAAAA
65 AAAAACCATAAGAATATCAAAAATCTTGAAAAATTAAGATAATATTTTTTTATTTAATTTTAAAA
82384 AAATC
130 AAATC
* * * ** * * *
82389 TATTTCATACCTTAATGGAGAACTGGAAAGATA-AGAAAAGTTTTGAAGACTTCTATATCCCTTC
1 CATTTCGTACCTTAATGGAGAACTGAAAAGATACAG-AAAGTTTAAAAG-TTTCTATACCCCTAC
*
82453 AAAAAACCATAAGAATATTAAAAATCTTGAAAAATTAA
64 AAAAAACCATAAGAATATCAAAAATCTTGAAAAATTAA
82491 AATATTAATC
Statistics
Matches: 209, Mismatches: 23, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
134 42 0.20
135 117 0.56
136 34 0.16
137 16 0.08
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (134 bp):
CATTTCGTACCTTAATGGAGAACTGAAAAGATACAGAAAGTTTAAAAGTTTCTATACCCCTACAA
AAAACCATAAGAATATCAAAAATCTTGAAAAATTAAGATAATATTTTTTTATTTAATTTTAAAAA
AATC
Found at i:82541 original size:16 final size:16
Alignment explanation
Indices: 82520--82552 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
82510 GATAAAATAA
82520 TATTTATTTACTATTT
1 TATTTATTTACTATTT
*
82536 TATTTATTTTCTATTT
1 TATTTATTTACTATTT
82552 T
1 T
82553 TCTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTATTTACTATTT
Found at i:83182 original size:11 final size:10
Alignment explanation
Indices: 83162--83209 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
83152 AAACAAATTC
83162 TCTCTTTTTTT
1 TCTC-TTTTTT
83173 TCTCTATTTTCT
1 TCTCT-TTTT-T
83185 T-TCTTTTTT
1 TCTCTTTTTT
83194 TCTCTTTTTT
1 TCTCTTTTTT
*
83204 TTTCTT
1 TCTCTT
83210 CCAAAAGCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 2 0.06
10 18 0.55
11 11 0.33
12 2 0.06
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TCTCTTTTTT
Found at i:83193 original size:21 final size:20
Alignment explanation
Indices: 83167--83209 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
83157 AATTCTCTCT
83167 TTTTTTTCTCTATTTTCTTTC
1 TTTTTTTCTCT-TTTTCTTTC
*
83188 TTTTTTTCTCTTTTTTTTTC
1 TTTTTTTCTCTTTTTCTTTC
83208 TT
1 TT
83210 CCAAAAGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTCTCTTTTTCTTTC
Found at i:83836 original size:165 final size:165
Alignment explanation
Indices: 83616--84128 Score: 583
Period size: 165 Copynumber: 3.1 Consensus size: 165
83606 ATTTATGGAA
* * ** *
83616 TAGAAAACTCAGTTTTTTGGGAAATAAAGAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATA
1 TAGAAAACTCCGTATTTCAGGAAATAAGGAAATTTCAAAG-AAAAATTCAAAACTCATGAAAATA
* *
83681 AATGAATTTTTAAAAAATGATCTAATTTAAATTAAATAATAATATTTGATGAAA-TTGAAAAATT
65 AATGAATTTTTGAAAAATGAT-TAATTTGAATTAAATAATAATATTTGATGAAATTTGAAAAATT
*
83745 AAAAACAAAAAAAATCTCCCTGAAAACATTTACAAAG
129 AAAAACAAGAAAAATCTCCCTGAAAACATTTACAAAG
* * *
83782 TAAAAAACTCCGTATTT-AGGAAATAGGGAAATTTCAAAGAAAAATTTTAAAACTCATGAAAATA
1 TAGAAAACTCCGTATTTCAGGAAATAAGGAAATTTCAAAGAAAAA-TTCAAAACTCATGAAAATA
* * * *
83846 AATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTCAT-AAATTTTAAAAATT
65 AATGAATTTTTGAAAAATGA-TTAATTTGAATTAAATAATAATATTTGATGAAATTTGAAAAATT
**
83910 AAAAACCAAGAAAAAT-TCCCCCAAAAACATTTACAAAG
129 AAAAA-CAAGAAAAATCT-CCCTGAAAACATTTACAAAG
* * * ** * * *
83948 TAGAAAACTCTGTATTTCA-AAAATAAGAAAATTTCAAA-AAAAA-AGAAAAATGAATGAAAATG
1 TAGAAAACTCCGTATTTCAGGAAATAAGGAAATTTCAAAGAAAAATTCAAAACT-CATGAAAATA
* * * * *
84010 AATAAATTTTTGAAAACTGATTTATTATGAATTAAATAATAAAATTTGATGAAATTTGAAATATT
65 AATGAATTTTTGAAAAATGATTAATT-TGAATTAAATAATAATATTTGATGAAATTTGAAAAATT
* * *
84075 TAAACCAAGAAAAATC-CTCCTGAAAATATTTACAAAG
129 AAAAACAAGAAAAATCTC-CCTGAAAACATTTACAAAG
*
84112 TAGAAAACTCCATATTT
1 TAGAAAACTCCGTATTT
84129 TGCAAACAAA
Statistics
Matches: 295, Mismatches: 41, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
163 10 0.03
164 96 0.33
165 115 0.39
166 73 0.25
167 1 0.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (165 bp):
TAGAAAACTCCGTATTTCAGGAAATAAGGAAATTTCAAAGAAAAATTCAAAACTCATGAAAATAA
ATGAATTTTTGAAAAATGATTAATTTGAATTAAATAATAATATTTGATGAAATTTGAAAAATTAA
AAACAAGAAAAATCTCCCTGAAAACATTTACAAAG
Found at i:83993 original size:18 final size:17
Alignment explanation
Indices: 83961--83996 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
83951 AAAACTCTGT
*
83961 ATTTCAAAAATAAGAAA
1 ATTTCAAAAAAAAGAAA
83978 ATTTCAAAAAAAAAGAAA
1 ATTTC-AAAAAAAAGAAA
83996 A
1 A
83997 ATGAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (17 bp):
ATTTCAAAAAAAAGAAA
Found at i:84041 original size:164 final size:165
Alignment explanation
Indices: 83637--84128 Score: 561
Period size: 164 Copynumber: 3.0 Consensus size: 165
83627 GTTTTTTGGG
** * * *
83637 AAATAA-AGAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTAAAAAATGA
1 AAATAAGA-AAATTTCAAAG-AAAAATAGAAAAATAATGAAAATAAATGAATTTTTGAAAAATGA
* * *
83701 TCTAATT-TAAATTAAATAATAATATTTGATGAAA-TTGAAAAATTAAAAA-CAAAAAAAATCTC
64 T-TTATTATGAATTAAATAATAATATTTGATGAAATTTGAAAAATTAAAAACCAAGAAAAATC-C
* *
83763 CCTGAAAACATTTACAAAGTAAAAAACTCCGTATTTAGG
127 CCTGAAAACATTTACAAAGTAGAAAACTCCGTATTTAGA
* * ** * * *
83802 AAATAGGGAAATTTCAAAGAAAAATTTTAAAACTCATGAAAATAAATGAATTTTTGAAAATTGAT
1 AAATAAGAAAATTTCAAAGAAAAA-TAGAAAAATAATGAAAATAAATGAATTTTTGAAAAATGAT
* * *
83867 TTAATATGAATTAAATAATAATATTTCAT-AAATTTTAAAAATTAAAAACCAAGAAAAATTCCCC
65 TTATTATGAATTAAATAATAATATTTGATGAAATTTGAAAAATTAAAAACCAAGAAAAA-TCCCC
** *
83931 CAAAAACATTTACAAAGTAGAAAACTCTGTATTTCA-A
129 TGAAAACATTTACAAAGTAGAAAACTCCGTATTT-AGA
* * *
83968 AAATAAGAAAATTTCAAA-AAAAA-AGAAAAATGAATGAAAATGAATAAATTTTTGAAAACTGAT
1 AAATAAGAAAATTTCAAAGAAAAATAGAAAAAT-AATGAAAATAAATGAATTTTTGAAAAATGAT
* * *
84031 TTATTATGAATTAAATAATAAAATTTGATGAAATTTGAAATATT-TAAACCAAGAAAAATCCTCC
65 TTATTATGAATTAAATAATAATATTTGATGAAATTTGAAAAATTAAAAACCAAGAAAAATCC-CC
* *
84095 TGAAAATATTTACAAAGTAGAAAACTCCATATTT
129 TGAAAACATTTACAAAGTAGAAAACTCCGTATTT
84129 TGCAAACAAA
Statistics
Matches: 281, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
163 8 0.03
164 108 0.38
165 105 0.37
166 57 0.20
167 3 0.01
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (165 bp):
AAATAAGAAAATTTCAAAGAAAAATAGAAAAATAATGAAAATAAATGAATTTTTGAAAAATGATT
TATTATGAATTAAATAATAATATTTGATGAAATTTGAAAAATTAAAAACCAAGAAAAATCCCCTG
AAAACATTTACAAAGTAGAAAACTCCGTATTTAGA
Found at i:85231 original size:42 final size:41
Alignment explanation
Indices: 85185--85324 Score: 104
Period size: 42 Copynumber: 3.3 Consensus size: 41
85175 TAGCCAGGGC
*
85185 TAAACCGACAAGTGAACAAAAGATACAAAAGTTAACCGGGAT
1 TAAACCGACAAGTAAACAAAAGATA-AAAAGTTAACCGGGAT
* ** * * * *
85227 TAAACCAACAAGCCAACAAAGGATAAAAGAATTTACCCGAGG-C
1 TAAACCGACAAGTAAACAAAAGAT-AAA-AAGTTAACCG-GGAT
* * *
85270 TAAGCCGACAAGTAAACAACAA-ATAACAAGGTTAACCTGGAT
1 TAAACCGACAAGTAAACAA-AAGATAA-AAAGTTAACCGGGAT
*
85312 TAAACCGATAAGT
1 TAAACCGACAAGT
85325 CAATCAATTA
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
41 2 0.03
42 41 0.56
43 27 0.37
44 3 0.04
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (41 bp):
TAAACCGACAAGTAAACAAAAGATAAAAAGTTAACCGGGAT
Found at i:85504 original size:35 final size:35
Alignment explanation
Indices: 85487--86134 Score: 615
Period size: 35 Copynumber: 18.7 Consensus size: 35
85477 CCATATACAA
* * *
85487 CCAAACAATGATGAAAAGAGTTTGACTAAATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * *
85522 CAAAACGATGATGAAAAGAGCTTGACCAGAAATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * *
85557 CCAAACGATGATGAAAAAAGTTTAACTAGATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * * *
85592 CCAAACGCTGATGAAAAGAGCTTGATCAGATACAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
*
85627 CCAAACAATGATGAAAAGAGTTTGACCAGATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * * *
85662 CTAAACGATGATGAAAAG-TTTTAACCAGACACAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
*
85696 CCAAACCATGATGAAAAGAGTTTGACCAGATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * * *
85731 CTAAACGCTGATGAAAAGATTTTGACTAGATATAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* *
85766 CCAAACAATGATGAAAAGAGTTTGACCAAATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * * * *
85801 CTAAACAATGATG-AAA-AGTTTAACCAGACACAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* *
85834 CCAAACCATGATGAAAAGAGTTTGACCAGATATAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * * *
85869 CTAAATGATGATGAAAAGTGCTTGACTAGATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * *
85904 CTAAACGATGATG--AAGAGCTTAACTAGATATAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * ** *
85937 CCAAACGATGATGAAAAGTGCTTGACCAGATGCAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * ** *
85972 CCAAATGACT-ATGAAAAGATTTTGACCAGATGGAA
1 CCAAACGA-TGATGAAAAGAGTTTGACCAGATATAG
* * **
86007 CCAAACAATGATGCAAAGAGTTTGACCAGATGCAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * *
86042 CCAAATGATGATGAAAAGAGTTTGACCGGATACAG
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* * * ** *
86077 CCAAACGATAATAAAAAAAGTTTGACCAGATGCAA
1 CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
* *
86112 CCAAATGATGATGAAAATAGTTT
1 CCAAACGATGATGAAAAGAGTTT
86135 TTTTTGGTAA
Statistics
Matches: 500, Mismatches: 106, Indels: 14
0.81 0.17 0.02
Matches are distributed among these distances:
33 53 0.11
34 35 0.07
35 411 0.82
36 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (35 bp):
CCAAACGATGATGAAAAGAGTTTGACCAGATATAG
Found at i:85894 original size:138 final size:138
Alignment explanation
Indices: 85481--86134 Score: 641
Period size: 138 Copynumber: 4.7 Consensus size: 138
85471 GTTTAACCAT
* * * *
85481 ATACAACCAAACAATGATGAAAAGAGTTTGACTAAATATAGCAAAACGATGATGAAAAGAGCTTG
1 ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGATG-AAA-AGTTTA
* * * * * * * * *
85546 ACCAGAAATAGCCAAACGATGATGAAAAAAGTTTAACTAGATATAGCCAAACGCTGATGAAAAGA
64 ACCAGACACAACCAAACCATGATGAAAAGAGTTTGACCAGATATAACCAAACGATGATGAAAAGA
85611 GCTTGA-TCAG
129 GCTTGACT-AG
*
85621 ATACAACCAAACAATGATGAAAAGAGTTTGACCAGATATAGCTAAACGATGATGAAAAGTTTTAA
1 ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGATGAAAAG-TTTAA
* * * * *
85686 CCAGACACAGCCAAACCATGATGAAAAGAGTTTGACCAGATATAGCTAAACGCTGATGAAAAGAT
65 CCAGACACAACCAAACCATGATGAAAAGAGTTTGACCAGATATAACCAAACGATGATGAAAAGAG
*
85751 TTTGACTAG
130 CTTGACTAG
* *
85760 ATATAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACAATGATGAAAAGTTTAAC
1 ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGATGAAAAGTTTAAC
* * *
85825 CAGACACAACCAAACCATGATGAAAAGAGTTTGACCAGATATAACTAAATGATGATGAAAAGTGC
66 CAGACACAACCAAACCATGATGAAAAGAGTTTGACCAGATATAACCAAACGATGATGAAAAGAGC
85890 TTGACTAG
131 TTGACTAG
* * * * * * * * * *
85898 ATATAGCTAAACGATGATG--AAGAGCTTAACTAGATATAGCCAAACGATGATGAAAAGTGCTTG
1 ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGATGAAAAGT--TTA
** ** * ** * *
85961 ACCAGATGCAACCAAATGACT-ATGAAAAGATTTTGACCAGATGGAACCAAACAATGATGCAAAG
64 ACCAGACACAACCAAACCA-TGATGAAAAGAGTTTGACCAGATATAACCAAACGATGATGAAAAG
* *
86025 AGTTTGACCAG
128 AGCTTGACTAG
* * ** ** * * * * *
86036 ATGCAGCCAAATGATGATGAAAAGAGTTTGACCGGATACAGCCAAACGATAATAAAAAAAGTTTG
1 ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGAT--GAAAAGTTTA
** ** *
86101 ACCAGATGCAACCAAATGATGATGAAAATAGTTT
64 ACCAGACACAACCAAACCATGATGAAAAGAGTTT
86135 TTTTTGGTAA
Statistics
Matches: 443, Mismatches: 61, Indels: 20
0.85 0.12 0.04
Matches are distributed among these distances:
136 33 0.07
138 166 0.37
139 127 0.29
140 111 0.25
142 6 0.01
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (138 bp):
ATACAACCAAACAATGATGAAAAGAGTTTGACCAAATATAGCTAAACGATGATGAAAAGTTTAAC
CAGACACAACCAAACCATGATGAAAAGAGTTTGACCAGATATAACCAAACGATGATGAAAAGAGC
TTGACTAG
Found at i:96675 original size:20 final size:20
Alignment explanation
Indices: 96650--96725 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
96640 TAAAAAGACT
*
96650 GAATGTATCGATACATTGAA
1 GAATGTATCGATACATTGTA
96670 GAATGTATCGATACATTCGTA
1 GAATGTATCGATACATT-GTA
* * *
96691 -CATGTATCGATACATTTTT
1 GAATGTATCGATACATTGTA
*
96710 CAATGTATCGATACAT
1 GAATGTATCGATACAT
96726 CTGGGTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.94
21 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
GAATGTATCGATACATTGTA
Found at i:97417 original size:20 final size:20
Alignment explanation
Indices: 97392--97446 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
97382 ATTTACCTAT
97392 ATGTATCGATACATTAAATA
1 ATGTATCGATACATTAAATA
*
97412 ATGTATCGATAGATTAAATA
1 ATGTATCGATACATTAAATA
97432 ATGTATCGATACATT
1 ATGTATCGATACATT
97447 TGGGTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTAAATA
Found at i:97530 original size:21 final size:21
Alignment explanation
Indices: 97504--97559 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
97494 AGGGTGGTTT
97504 TGTATCGATACATTTCAAC-CA
1 TGTATCGATACATTTC-ACTCA
*
97525 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACTCA
97545 TGTATCGATACATTT
1 TGTATCGATACATTT
97560 ACTGTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
21 14 0.44
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACTCA
Found at i:97547 original size:20 final size:20
Alignment explanation
Indices: 97504--97577 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
97494 AGGGTGGTTT
*
97504 TGTATCGATACATTTCAAC-CA
1 TGTATCGATACA-TTC-ACTTA
97525 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
* *
97545 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTCACT-TA
*
97566 TATATCGATACA
1 TGTATCGATACA
97578 AATTGTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.04
20 21 0.45
21 24 0.51
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:97573 original size:21 final size:20
Alignment explanation
Indices: 97527--97577 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
97517 TTCAACCATG
*
97527 TATCGATACATTCACTTATG
1 TATCGATACATTCACTTATA
* *
97547 TATCGATACATTTACTGTTTA
1 TATCGATACATTCACT-TATA
97568 TATCGATACA
1 TATCGATACA
97578 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACATTCACTTATA
Found at i:100168 original size:79 final size:75
Alignment explanation
Indices: 100081--100326 Score: 221
Period size: 78 Copynumber: 3.1 Consensus size: 75
100071 GAAAACGCGA
*
100081 TTGGAGTATCCCATCAAAAGTGATGGAGTTGGAGTATCTCCGTTAATGAAAAATCGATATTCTTG
1 TTGGAGTATCCCATCAAAA-TGATGGAGTTGGAGTATCTCC--AAATGAAAAATCGATATT-TTG
100146 AAATAAAAATAGGG
62 AAATAAAAATAGGG
* * * * * * **
100160 TTGCAGTATCTTC-TCGAAAATGATGGGGTTAGAATATCT-CAAGATGAAAATTTTAATATTTTT
1 TTGGAGTATC-CCATC-AAAATGATGGAGTTGGAGTATCTCCAA-ATGAAAA-ATCGATA-TTTT
*
100223 GAAATAAAAATGGGG
61 GAAATAAAAATAGGG
* **
100238 TTGGAGTATCCCATTGAAAAT-AACGAGGTTGGAGTAT-TCCCAAAATGAAAAATCGATATTTTG
1 TTGGAGTATCCCA-TCAAAATGATGGA-GTTGGAGTATCT-CC-AAATGAAAAATCGATATTTTG
100301 AAAGTAAAAATAGGG
62 AAA-TAAAAATAGGG
100316 TTGGAGTATCC
1 TTGGAGTATCC
100327 TCTCGGAATT
Statistics
Matches: 133, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
76 1 0.01
77 19 0.14
78 68 0.51
79 38 0.29
80 7 0.05
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (75 bp):
TTGGAGTATCCCATCAAAATGATGGAGTTGGAGTATCTCCAAATGAAAAATCGATATTTTGAAAT
AAAAATAGGG
Found at i:100345 original size:78 final size:77
Alignment explanation
Indices: 100125--100352 Score: 235
Period size: 78 Copynumber: 2.9 Consensus size: 77
100115 TATCTCCGTT
* * * *
100125 AATGAAAAATCGATATTCTTGAAATAAAAATAGGGTTGCAGTATCTTCTCGAAAATGATGGGGTT
1 AATGAAAAATCGATATT-TTGAAATAAAAATAGGGTTGGAGTATCCTCTCGAAAATAATGAGGTT
* * *
100190 AGAATA-TCTCAA
65 GGAGTATTCCCAA
* * ** * * *
100202 GATGAAAATTTTAATATTTTTGAAATAAAAATGGGGTTGGAGTATCC-CATTGAAAATAACGAGG
1 AATGAAAA-ATCGATA-TTTTGAAATAAAAATAGGGTTGGAGTATCCTC-TCGAAAATAATGAGG
100266 TTGGAGTATTCCCAA
63 TTGGAGTATTCCCAA
* * * *
100281 AATGAAAAATCGATATTTTGAAAGTAAAAATAGGGTTGGAGTATCCTCTCGGAATTTATAAGGTT
1 AATGAAAAATCGATATTTTGAAA-TAAAAATAGGGTTGGAGTATCCTCTCGAAAATAATGAGGTT
100346 GGAGTAT
65 GGAGTAT
100353 CCCCTACGAT
Statistics
Matches: 120, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
77 16 0.13
78 89 0.74
79 15 0.12
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (77 bp):
AATGAAAAATCGATATTTTGAAATAAAAATAGGGTTGGAGTATCCTCTCGAAAATAATGAGGTTG
GAGTATTCCCAA
Found at i:102843 original size:21 final size:19
Alignment explanation
Indices: 102816--102891 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 19
102806 GCATGGTAGT
102816 TTTGTATCGATACATTTTAC
1 TTTGTATCGATACA-TTTAC
* *
102836 GCTTGTATCGATACATTCAC
1 -TTTGTATCGATACATTTAC
102856 TTATGTATCGATACATTTAC
1 TT-TGTATCGATACATTTAC
102876 TATTTGTATCGATACA
1 --TTTGTATCGATACA
102892 AATTGTAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.02
20 20 0.42
21 25 0.52
22 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (19 bp):
TTTGTATCGATACATTTAC
Found at i:102864 original size:20 final size:21
Alignment explanation
Indices: 102839--102891 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
102829 ATTTTACGCT
102839 TGTATCGATACATTCACT-TA
1 TGTATCGATACATTCACTATA
* *
102859 TGTATCGATACATTTACTATT
1 TGTATCGATACATTCACTATA
102880 TGTATCGATACA
1 TGTATCGATACA
102892 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCACTATA
Found at i:107408 original size:155 final size:154
Alignment explanation
Indices: 107145--107554 Score: 463
Period size: 155 Copynumber: 2.6 Consensus size: 154
107135 ATGCACCTTC
* * * * *
107145 GGCATAAAAGCGAACCCAGTGACAATCTAAAACTCAATTCTAAAATATTACGAAGATA-TCCTTA
1 GGCATAAAAGCGAACCC-GTGACAACCTAAGACTCAATTTTAAAAAATTACGAAAATACTCC-TA
* * * *
107209 GGGGATATCTTCGACTTAGAAGTGTCTGATACCCCTAAAGGAC-TTAAAAAGGATTATAAAG-GA
64 GGGGATACCTTCGACTTAGAAGTGTCCGATACCCCTAAAAGACTTTAAAAA-GAATATAAAGTG-
*
107272 GATGAACCTATCTTAAATACCCA-CATTT
127 GATGAACCTATCCTAAATACCCATC-TTT
* * * * *
107300 GGCATAAAAGCAAACCTCGTGGCAACCCAAGACTCGATTTTAAAAAATTATGAAAATACTCCTAG
1 GGCATAAAAGCGAACC-CGTGACAACCTAAGACTCAATTTTAAAAAATTACGAAAATACTCCTAG
* * *
107365 GGGATACCTTCAACTTAGAAGTGTCCGATATCGCTAAAAGACTTTAAAAAGAATATAAAGTGGAT
65 GGGATACCTTCGACTTAGAAGTGTCCGATACCCCTAAAAGACTTTAAAAAGAATATAAAGTGGAT
* *
107430 GAGCGTATCCTAAATACCCATCTTT
130 GAACCTATCCTAAATACCCATCTTT
* * * *
107455 GGCATAAAAACGAACCAAGTGACAACCTAGGACTCAATTTTTAAAAATTACGAAAATAC-CTCTA
1 GGCATAAAAGCGAACC-CGTGACAACCTAAGACTCAATTTTAAAAAATTACGAAAATACTC-CTA
* *
107519 GGAGATACCTTCGACTTAAAAGTG-CCTGATACCCCT
64 GGGGATACCTTCGACTTAGAAGTGTCC-GATACCCCT
107555 GAATGGCTTG
Statistics
Matches: 213, Mismatches: 35, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
154 3 0.01
155 197 0.92
156 13 0.06
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (154 bp):
GGCATAAAAGCGAACCCGTGACAACCTAAGACTCAATTTTAAAAAATTACGAAAATACTCCTAGG
GGATACCTTCGACTTAGAAGTGTCCGATACCCCTAAAAGACTTTAAAAAGAATATAAAGTGGATG
AACCTATCCTAAATACCCATCTTT
Found at i:107916 original size:142 final size:141
Alignment explanation
Indices: 107659--107929 Score: 391
Period size: 142 Copynumber: 1.9 Consensus size: 141
107649 TGCAAATCTC
* * ** **
107659 GAAAATTTCATTTTTTACCTTAATGGAGAACCAAAAATTATACGAAAAGTTTTGAAAGTTTCTAT
1 GAAAATTTCATATTGTACCTTAATGGAGAACCAAAAA-TATAAAAAAAGTTTTGAAAACTTCTAT
*
107724 ACCCCTACAGAAAACCCTAAGAATATCAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAA
65 ACCCCTACAGAAAACCCTAAGAATATCAAAAATCTTGAAAAATTAAGATAATAA-TTTTATTTAA
107789 CCTTTTTAGTTTT
129 CCTTTTTAGTTTT
* *
107802 GAAAATTTGATATTGTACCTTAATGGAGAATCGAAAAA-ATAAAAAAAGTTTTGAAAACTTCTAT
1 GAAAATTTCATATTGTACCTTAATGGAGAA-CCAAAAATATAAAAAAAGTTTTGAAAACTTCTAT
** * *
107866 ACCCCTACAGAAAACTGTAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTATTTAA
65 ACCCCTACAGAAAACCCTAAGAATATCAAAAATCTTGAAAAATTAAGATAATAATTTTATTTAA
107930 TGATAAAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
141 10 0.09
142 71 0.62
143 27 0.24
144 6 0.05
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (141 bp):
GAAAATTTCATATTGTACCTTAATGGAGAACCAAAAATATAAAAAAAGTTTTGAAAACTTCTATA
CCCCTACAGAAAACCCTAAGAATATCAAAAATCTTGAAAAATTAAGATAATAATTTTATTTAACC
TTTTTAGTTTT
Found at i:107982 original size:16 final size:15
Alignment explanation
Indices: 107941--107982 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
107931 GATAAAATAA
107941 TATTTATTTATTATTT
1 TATTTATTT-TTATTT
107957 TATTTATTTTATATTT
1 TATTTATTTT-TATTT
107973 T-TTTATTTTT
1 TATTTATTTTT
107983 GAAAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 9 0.36
16 15 0.60
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:109415 original size:18 final size:21
Alignment explanation
Indices: 109380--109426 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
109370 AAAACTCATG
109380 AAAATAA-ATAAATTTTTAA-
1 AAAATAATATAAATTTTTAAT
109399 AAAATAATAT-AA-TTTTAAT
1 AAAATAATATAAATTTTTAAT
*
109418 TAAATAATA
1 AAAATAATA
109427 ATCTTTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAATATAAATTTTTAAT
Found at i:109527 original size:165 final size:164
Alignment explanation
Indices: 109349--109813 Score: 558
Period size: 165 Copynumber: 2.8 Consensus size: 164
109339 TGAAAACTGA
* * * * *
109349 AAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAAAAAATAATATAATTT
1 AAAATTTCAAAGAAAAAA-TCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATAT
* * * * **
109414 TAATTAAATAATAATCTTTTATGAAATTTAAAAATTAAAAACC-AGGAAAATC-CTCTCGAAAAC
65 AAATTAAATAATAATATTTGATGAATTTTAAAAATT-AAAACCAAAAAAAATCTCTC-CGAAAAC
*
109477 ATTTACGGAGTAAAAAACTTCGTATTT-AGGAAATAGG
128 ATTTACGGAGTAAAAAACTTCGTATTTCA-GAAATAAG
* * * *
109514 GAAATTCCAAAGAAAAAAATCAAAACTCATGAAAATAAATGAATTTTTGAAAACTTATTTGATAT
1 AAAATTTCAAAG-AAAAAATCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATAT
* *
109579 AAATTAAGTAATTATATTTGATGAATTTTAAAAATTAAAACCAAAAAAAATCTCTCCGAAAACAT
65 AAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAACCAAAAAAAATCTCTCCGAAAACAT
** *
109644 TTTTGGAGTAGAAAACTTCGTATTTCAGAAATAAG
130 TTACGGAGTAAAAAACTTCGTATTTCAGAAATAAG
* * * *
109679 AAAATTTTAAGGAAAAAATGAAAATCTCATGAAAATAAATGAATTTTTGAAAACTGATTTAATAT
1 AAAATTTCAAAGAAAAAATCAAAA-CTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATAT
* * * * * * *
109744 GAATTAAATAATAATATTTGGTGAATTTTAAAAATTTGACACCAAGAAAAATCTCCCCGAAGACA
65 AAATTAAATAATAATATTTGATGAATTTTAAAAA-TTAAAACCAAAAAAAATCTCTCCGAAAACA
109809 TTTAC
129 TTTAC
109814 AAAATAGAAA
Statistics
Matches: 255, Mismatches: 39, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
164 17 0.07
165 200 0.78
166 38 0.15
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (164 bp):
AAAATTTCAAAGAAAAAATCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATATA
AATTAAATAATAATATTTGATGAATTTTAAAAATTAAAACCAAAAAAAATCTCTCCGAAAACATT
TACGGAGTAAAAAACTTCGTATTTCAGAAATAAG
Found at i:109881 original size:165 final size:163
Alignment explanation
Indices: 109270--109938 Score: 483
Period size: 165 Copynumber: 4.0 Consensus size: 163
109260 CCATATCAAA
* * * * * * *** *
109270 TGAATTTTAAAAATTTAAACCAAGAAGAATCCCCCCGAATATATTTATGGAATAGAAAACTCGAC
1 TGAATTTTAAAAATTAAAACCAAAAAAAATCTCCCCGAAAACATTTACAAAATAGAAAACTCCA-
* * * * * * *
109335 TTTTTGA-AAACTGAA-AAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTA
65 TATTTCAGAAAC--AAGAAAATTCCAAGAAAAAA-CCAAAACTCATGAAAATAAATGAATTTTTG
* * * * * * **
109398 AAAAATAATATAATTTTAATTAAATAATAATCTTTTA
127 AAAACTGATTTAATATGAATTAAATAATAATATTTGG
* ** * ** * * *
109435 TGAAATTTAAAAATTAAAAACC-AGGAAAATC-CTCTCGAAAACATTTACGGAGTAAAAAACTTC
1 TGAATTTTAAAAATT-AAAACCAAAAAAAATCTC-CCCGAAAACATTTACAAAATAGAAAACTCC
* * * * *
109498 GTATTT-AGGAAATAGGGAAATTCCAAAGAAAAAAATCAAAACTCATGAAAATAAATGAATTTTT
64 ATATTTCA-GAAACAAGAAAATTCC-AAG-AAAAAACCAAAACTCATGAAAATAAATGAATTTTT
* * * * * *
109562 GAAAACTTATTTGATATAAATTAAGTAATTATATTTGA
126 GAAAACTGATTTAATATGAATTAAATAATAATATTTGG
* **** * * *
109600 TGAATTTTAAAAATTAAAACCAAAAAAAATCTCTCCGAAAACATTTTTGGAGTAGAAAACTTCGT
1 TGAATTTTAAAAATTAAAACCAAAAAAAATCTCCCCGAAAACATTTACAAAATAGAAAACTCCAT
* ** **
109665 ATTTCAGAAATAAGAAAATTTTAAGGAAAAAATGAAAATCTCATGAAAATAAATGAATTTTTGAA
66 ATTTCAGAAACAAGAAAATTCCAA-GAAAAAACCAAAA-CTCATGAAAATAAATGAATTTTTGAA
109730 AACTGATTTAATATGAATTAAATAATAATATTTGG
129 AACTGATTTAATATGAATTAAATAATAATATTTGG
* * * *
109765 TGAATTTTAAAAATTTGACACCAAGAAAAATCTCCCCGAAGACATTTACAAAATAGAAAACTCCA
1 TGAATTTTAAAAA-TTAAAACCAAAAAAAATCTCCCCGAAAACATTTACAAAATAGAAAACTCCA
* * * *
109830 TATTT-TGCAAACAAGAGGAATTCCAA-AAGAGAACCAATAACTCAT-AAAATAAAAGAAATTTT
65 TATTTCAG-AAACAAGA-AAATTCCAAGAA-AAAACCAA-AACTCATGAAAATAAATG-AATTTT
* * *
109892 TTAAAACTGATTTAATTATG-ATTAAATGATAATATTTAG
125 TGAAAACTGATTTAA-TATGAATTAAATAATAATATTTGG
*
109931 CGAATTTT
1 TGAATTTT
109939 TATGTTCAAA
Statistics
Matches: 410, Mismatches: 75, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
163 2 0.00
164 29 0.07
165 249 0.61
166 118 0.29
167 12 0.03
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (163 bp):
TGAATTTTAAAAATTAAAACCAAAAAAAATCTCCCCGAAAACATTTACAAAATAGAAAACTCCAT
ATTTCAGAAACAAGAAAATTCCAAGAAAAAACCAAAACTCATGAAAATAAATGAATTTTTGAAAA
CTGATTTAATATGAATTAAATAATAATATTTGG
Found at i:109881 original size:330 final size:331
Alignment explanation
Indices: 109269--109904 Score: 698
Period size: 330 Copynumber: 1.9 Consensus size: 331
109259 ACCATATCAA
* * * * *
109269 ATGAATTTTAAAAATTTAAACCAAGAAGAATCCCCCCGAATATATTTATGGAATAGAAAACTCGA
1 ATGAATTTTAAAAATTAAAACCAAAAAAAATCCCCCCGAAAACATTTATGGAATAGAAAACTCGA
** *
109334 CTTTTTGAAAACTGAAAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAA
66 CTTTCAGAAAACAGAAAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAA
* * * * *
109399 AAAATAATATAATTTTAATTAAATAATAATCTTTTATGAAATTTAAAAATTAAAAACCAGGAAAA
131 AAAATAATATAATATGAATTAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAGAAAAA
* ** * * * * *
109464 TCCTCTCGAAAACATTTACGGAGTAAAAAACTTCGTATTTAGGAAATAGGGAAATTCCAAAGAAA
196 TCCTCCCGAAAACATTTACAAAATAAAAAACTCCATATTTAGCAAAAAGGGAAATTCCAAAGAAA
* * *
109529 AAAATCAAAACTCATGAAAATAAATG-AATTTTTGAAAACTTATTTGATATAAATTAAGTAATTA
261 AAAACCAAAACTCATGAAAATAAAAGAAATTTTTGAAAACTGATTTGATATAAATTAAGTAATTA
109593 TATTTG
326 TATTTG
* * * *
109599 ATGAATTTTAAAAATTAAAACCAAAAAAAATCTCTCCGAAAACATTTTTGGAGTAGAAAACTTCG
1 ATGAATTTTAAAAATTAAAACCAAAAAAAATCCCCCCGAAAACATTTATGGAATAGAAAAC-TCG
* * * *
109664 TA-TTTCAGAAATA-AG-AAAATTTTAAGGAAAAAA-TGAAAATCTCATGAAAATAAATGAATTT
65 -ACTTTCAGAAA-ACAGAAAAATTTCAAAGAAAAAATTCAAAA-CTCATGAAAATAAATAAATTT
* * * * * * ** *
109725 TTGAAAACTGATTTAATATGAATTAAATAATAATATTTGGTGAATTTTAAAAATTTGACACCAAG
127 TTAAAAAATAATATAATATGAATTAAATAATAATATTTGATGAAATTTAAAAATTAAAAACC-AG
* * *
109790 AAAAAT-CTCCCCGAAGACATTTACAAAATAGAAAACTCCATATTTTGCAAACAAGAGG-AATTC
191 AAAAATCCT-CCCGAAAACATTTACAAAATAAAAAACTCCATATTTAGCAAA-AAG-GGAAATTC
* * *
109853 C-AA-AAGAGAACCAATAACTCAT-AAAATAAAAGAAATTTTTTAAAACTGATTT
253 CAAAGAAAAAAACCAA-AACTCATGAAAATAAAAGAAATTTTTGAAAACTGATTT
109905 AATTATGATT
Statistics
Matches: 249, Mismatches: 47, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
329 5 0.02
330 156 0.63
331 76 0.31
332 10 0.04
333 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (331 bp):
ATGAATTTTAAAAATTAAAACCAAAAAAAATCCCCCCGAAAACATTTATGGAATAGAAAACTCGA
CTTTCAGAAAACAGAAAAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAA
AAAATAATATAATATGAATTAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAGAAAAA
TCCTCCCGAAAACATTTACAAAATAAAAAACTCCATATTTAGCAAAAAGGGAAATTCCAAAGAAA
AAAACCAAAACTCATGAAAATAAAAGAAATTTTTGAAAACTGATTTGATATAAATTAAGTAATTA
TATTTG
Found at i:111733 original size:22 final size:22
Alignment explanation
Indices: 111690--111735 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
111680 TTATATTTTT
*
111690 ATTTGCACAACTGATAAAAAAA
1 ATTTGCACAACTAATAAAAAAA
* * *
111712 ATTTGTACAACTAATTACAAAA
1 ATTTGCACAACTAATAAAAAAA
111734 AT
1 AT
111736 GAGATATAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (22 bp):
ATTTGCACAACTAATAAAAAAA
Found at i:112999 original size:95 final size:95
Alignment explanation
Indices: 112836--113025 Score: 353
Period size: 95 Copynumber: 2.0 Consensus size: 95
112826 TAGGAAGGAG
*
112836 GACATGACCCTCCAAAGATACTCCAAATACATGGAAAACCTTAGAAAACATTGAACATATTCGTG
1 GACATGACCCTCCAAAGATACTCCAAATACATGAAAAACCTTAGAAAACATTGAACATATTCGTG
*
112901 TCAAGCACATACCAGTATTCGACACTCACA
66 TCAAGCACATACCAGTATTCAACACTCACA
*
112931 GACATGACCCTCTAAAGATACTCCAAATACATGAAAAACCTTAGAAAACATTGAACATATTCGTG
1 GACATGACCCTCCAAAGATACTCCAAATACATGAAAAACCTTAGAAAACATTGAACATATTCGTG
112996 TCAAGCACATACCAGTATTCAACACTCACA
66 TCAAGCACATACCAGTATTCAACACTCACA
113026 CCTGAGTCCG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.22
Consensus pattern (95 bp):
GACATGACCCTCCAAAGATACTCCAAATACATGAAAAACCTTAGAAAACATTGAACATATTCGTG
TCAAGCACATACCAGTATTCAACACTCACA
Found at i:117777 original size:13 final size:13
Alignment explanation
Indices: 117747--117784 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
117737 GCTTGGATTG
*
117747 GAAAAAGTGTGTT
1 GAAAAAGTGTGGT
*
117760 TAAAAAGTGTGGT
1 GAAAAAGTGTGGT
117773 GAAAAA-TGTGGT
1 GAAAAAGTGTGGT
117785 TCAAGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (13 bp):
GAAAAAGTGTGGT
Found at i:119522 original size:2 final size:2
Alignment explanation
Indices: 119515--119556 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
119505 CAAAATTCCA
119515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119556 A
1 A
119557 AAGCTAACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120453 original size:22 final size:22
Alignment explanation
Indices: 120428--120481 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
120418 ATATTTATAG
120428 TTTAATTTAAATAAA-AATAATT
1 TTTAA-TTAAATAAATAATAATT
*
120450 TTTAATTATATAAATAATAA-T
1 TTTAATTAAATAAATAATAATT
*
120471 TTTAATAAAAT
1 TTTAATTAAAT
120482 TAATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATTAAATAAATAATAATT
Found at i:121681 original size:13 final size:13
Alignment explanation
Indices: 121663--121688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
121653 CAATTTTTTG
121663 TGTATCGATACAT
1 TGTATCGATACAT
121676 TGTATCGATACAT
1 TGTATCGATACAT
121689 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:121685 original size:33 final size:33
Alignment explanation
Indices: 121643--121707 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
121633 TACAAGCCAA
* *
121643 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
121676 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
121708 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:121812 original size:20 final size:20
Alignment explanation
Indices: 121760--121814 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
121750 CATATTTTTG
*
121760 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
121780 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
121800 ATGTATCGATACTTT
1 ATGTATCGATACTTT
121815 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:122655 original size:20 final size:22
Alignment explanation
Indices: 122619--122658 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
122609 GATTAAAATT
122619 CAAAGTACAATGCAAATAAACA
1 CAAAGTACAATGCAAATAAACA
122641 CAAAGT-CAA-GCAAATAAA
1 CAAAGTACAATGCAAATAAA
122659 TTAAACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.12
Consensus pattern (22 bp):
CAAAGTACAATGCAAATAAACA
Found at i:124259 original size:13 final size:13
Alignment explanation
Indices: 124241--124279 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
124231 ATAATCCCCC
* *
124241 TGTATCGATATAG
1 TGTATCGATACAA
124254 TGTATCGATACAA
1 TGTATCGATACAA
124267 TGTATCGATACAA
1 TGTATCGATACAA
124280 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:130474 original size:13 final size:13
Alignment explanation
Indices: 130456--130481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
130446 CAATTTTTTG
130456 TGTATCGATACAT
1 TGTATCGATACAT
130469 TGTATCGATACAT
1 TGTATCGATACAT
130482 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:130478 original size:33 final size:33
Alignment explanation
Indices: 130436--130500 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
130426 TACAAGCCAA
* *
130436 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
130469 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
130501 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:130605 original size:20 final size:20
Alignment explanation
Indices: 130553--130607 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
130543 CATATTTTTG
*
130553 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
130573 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
130593 ATGTATCGATACTTT
1 ATGTATCGATACTTT
130608 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:132022 original size:20 final size:20
Alignment explanation
Indices: 131997--132048 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
131987 TCCCATTACT
131997 ATGTATCGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
132017 ATGTATCGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
132037 ATGTATCGATAC
1 ATGTATCGATAC
132049 ATGCATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTTCATA
Found at i:132991 original size:71 final size:73
Alignment explanation
Indices: 132916--133104 Score: 221
Period size: 71 Copynumber: 2.6 Consensus size: 73
132906 TAAAGGTGTT
* *
132916 ATTTATTTTTATTTATAGAAATTTAAATTTATTTTTTATTTGATTATGTGAGTTTAAA-TTTTT-
1 ATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTATTTGATTATGTAAGTTTAAATTTTTTA
132979 A-GAGTATA
66 ATGA-TATA
* * * *
132987 ATTTATTTTGATTTGTAAAAATTTAAATGTATTTTTT-TGT-ATTATGTAAGTTTAAATTTTTTA
1 ATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTATTTGATTATGTAAGTTTAAATTTTTTA
*
133050 ATGATGTA
66 ATGATATA
* *
133058 ATTTA-TTTT-TTTATAAAAATTTAGGATTTATTTTTTGACTTGATTAT
1 ATTTATTTTTATTTATAAAAATTTA-AATTTATTTTTT-ATTTGATTAT
133105 AGAATTGAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
69 28 0.29
70 20 0.20
71 42 0.43
72 3 0.03
73 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.58
Consensus pattern (73 bp):
ATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTATTTGATTATGTAAGTTTAAATTTTTTA
ATGATATA
Found at i:135632 original size:165 final size:167
Alignment explanation
Indices: 135346--135658 Score: 391
Period size: 165 Copynumber: 1.9 Consensus size: 167
135336 ATTCACATTA
* * * ***
135346 AATCAGTTTTGAAAGATTCTTTTTATTTTATAAATTTTTTATTTTTTTCTTAAAATTTTTCTATT
1 AATCAGTTTTGAAAAATTCTATTTATTTTATAAATTTTTCATTTTTTTCTTAAAATTCCCCTATT
* ** * *
135411 TTCGAAATAAAGAGTTTTCTACTCCGTAAATATTTTTGAGGATATTTTTCTCGATTTATAATTTT
66 TTCGAAATAAAGAATTTTCTACTCCGTAAATATTTTCAAGGAGATTTTTCTCGATTTAAAATTTT
135476 TAAAA-TTAATCAAATATCATCACTTAATATATAATG
131 TAAAATTTAATCAAATATCATCACTTAATATATAATG
* * *
135512 AATCAGTTTTGAAAAATTC-ATTTATTTTCATGAGTTTTTCATTTTTTTCTTTAAA-TCCCCTAT
1 AATCAGTTTTGAAAAATTCTATTTATTTT-ATAAATTTTTCATTTTTTTCTTAAAATTCCCCTAT
* * * * * *
135575 TTTTGAAA-AATTGAATTTTTTACTTCGTAAATGTTTTCAAGGGGATTTTTCTCGATTTAAAATT
65 TTTCGAAATAA-AGAATTTTCTACTCCGTAAATATTTTCAAGGAGATTTTTCTCGATTTAAAATT
*
135639 TTTAAAATTTGATCAAATAT
129 TTTAAAATTTAATCAAATAT
135659 TGTTATTAAA
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
164 2 0.02
165 70 0.57
166 51 0.41
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (167 bp):
AATCAGTTTTGAAAAATTCTATTTATTTTATAAATTTTTCATTTTTTTCTTAAAATTCCCCTATT
TTCGAAATAAAGAATTTTCTACTCCGTAAATATTTTCAAGGAGATTTTTCTCGATTTAAAATTTT
TAAAATTTAATCAAATATCATCACTTAATATATAATG
Found at i:136065 original size:12 final size:14
Alignment explanation
Indices: 136048--136079 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
136038 TAATGGAGAT
136048 AAAAATCAA-G-AA
1 AAAAATCAAGGTAA
136060 AAAAATCAAGGTAA
1 AAAAATCAAGGTAA
136074 AAAAAT
1 AAAAAT
136080 TAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAATCAAGGTAA
Found at i:136636 original size:20 final size:21
Alignment explanation
Indices: 136611--136663 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
136601 ATCGATACAT
**
136611 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
136631 TGTATCGATACATGAAAAGAA
1 TGTATCGATACATGAAAAGAA
136652 TGTATCGATACA
1 TGTATCGATACA
136664 GGTCATTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:136733 original size:13 final size:13
Alignment explanation
Indices: 136715--136740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
136705 ACACACAATA
136715 TGTATCGATACAT
1 TGTATCGATACAT
136728 TGTATCGATACAT
1 TGTATCGATACAT
136741 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:136756 original size:33 final size:32
Alignment explanation
Indices: 136695--136762 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
136685 GTAGCCAAAT
*
136695 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
136727 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
136760 TTG
1 TTG
136763 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:138361 original size:3 final size:3
Alignment explanation
Indices: 138346--138376 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
138336 AACCATCAAG
*
138346 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
138377 GTGACTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:142893 original size:13 final size:13
Alignment explanation
Indices: 142875--142939 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
142865 ACAGCATTCT
142875 TTGTATCGATACA
1 TTGTATCGATACA
142888 TTGTATCGATACA
1 TTGTATCGATACA
*
142901 CTGTATCGATACA
1 TTGTATCGATACA
142914 TTGTATCGATACA
1 TTGTATCGATACA
*
142927 CTGTATCGATACA
1 TTGTATCGATACA
142940 AAAGGTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:142912 original size:26 final size:26
Alignment explanation
Indices: 142876--142939 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
142866 CAGCATTCTT
142876 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
142902 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
142928 TGTATCGATACA
1 TGTATCGATACA
142940 AAAGGTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAC
Found at i:143408 original size:21 final size:21
Alignment explanation
Indices: 143375--143427 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
143365 CCTCTAAGCA
* *
143375 GCACCCACCAGGTCGCGACCTG
1 GCACCC-CCAGGTCGCAACCGG
*
143397 GCACCCCCAGGTCTCAACCGG
1 GCACCCCCAGGTCGCAACCGG
143418 GCAGCCCCCA
1 GCA-CCCCCA
143428 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.19, C:0.49, G:0.25, T:0.08
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:145499 original size:13 final size:13
Alignment explanation
Indices: 145481--145505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
145471 AGATTGCACA
145481 GTATCGATACATT
1 GTATCGATACATT
145494 GTATCGATACAT
1 GTATCGATACAT
145506 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:145518 original size:20 final size:21
Alignment explanation
Indices: 145493--145545 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
145483 ATCGATACAT
**
145493 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
* *
145513 TGTATCAATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
145534 TGTATCGATACA
1 TGTATCGATACA
145546 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:145615 original size:13 final size:13
Alignment explanation
Indices: 145597--145622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
145587 ACACACAATA
145597 TGTATCGATACAT
1 TGTATCGATACAT
145610 TGTATCGATACAT
1 TGTATCGATACAT
145623 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:145638 original size:33 final size:32
Alignment explanation
Indices: 145577--145644 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
145567 GTAGCCAAAT
*
145577 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
145609 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
145642 TTG
1 TTG
145645 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:150820 original size:21 final size:22
Alignment explanation
Indices: 150795--150849 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
150785 TAATCAATAC
*
150795 TCAATAAATAATT-AGATAAAT
1 TCAATAAATAATTAAAATAAAT
150816 TCAATATAA-AATTAAAATAAAT
1 TCAATA-AATAATTAAAATAAAT
*
150838 T-AATAATTAATT
1 TCAATAAATAATT
150850 GAACTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 18 0.62
22 10 0.34
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TCAATAAATAATTAAAATAAAT
Found at i:153063 original size:33 final size:32
Alignment explanation
Indices: 153026--153090 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
153016 TACCACTGTT
153026 TGTATCAATACATG-GCACATTGTATCGATACAA
1 TGTATCAATACATGAG-A-ATTGTATCGATACAA
*
153059 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCAATACATGA-GAATTGTATCGATACA
153091 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCAATACATGAGAATTGTATCGATACAA
Found at i:153064 original size:13 final size:13
Alignment explanation
Indices: 153046--153070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153036 CATGGCACAT
153046 TGTATCGATACAA
1 TGTATCGATACAA
153059 TGTATCGATACA
1 TGTATCGATACA
153071 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:154689 original size:3 final size:3
Alignment explanation
Indices: 154670--154703 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
154660 AACCATTAAA
* *
154670 GAT GAT GAA GAT AAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
154704 GTGACTCGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:159375 original size:21 final size:22
Alignment explanation
Indices: 159351--159400 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
159341 ATCAAATCTT
* *
159351 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
159372 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
159394 --TCAAAAT
1 CTTCAAAAT
159401 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:164985 original size:166 final size:165
Alignment explanation
Indices: 164799--165221 Score: 485
Period size: 166 Copynumber: 2.6 Consensus size: 165
164789 TATGCATCAT
* * * *
164799 GCATTAGTCTTATCAACTTCTTCCATATAAGA-AGGAATCTAATTCTCA-TCAGCAATCTATGCA
1 GCATTAGTCTTATCAACTTCTTTCATATAA-ATA-AAATCTAATTCCCATTAAG-AATCTATGCA
* *** * * ** *
164862 TTAATCGTATTTATTTCAAATTAGAATTTATGCATTAGTCACATCTTTCGAATTTCAATCCATGC
63 TTAATCATATTTATCAAAAAATAAAATCCATGCATTAGTCACATCTTTCGAACTTCAATCCATGC
* *
164927 ATTAGTCTATTCATTGCAGTTTGATATTTACAATCCAC
128 ATTAGTCTATTCATTGCAATTTAATATTTACAATCCAC
* *
164965 GCATTAGTCTTATCAACTTCTTTCATATCAAATAAAATCTGATTCCCATTAAGAATCTATGTATT
1 GCATTAGTCTTATCAACTTCTTTCATAT-AAATAAAATCTAATTCCCATTAAGAATCTATGCATT
* * * * *
165030 TATTATATTTATCAAAAAATAAAATCCATGTATTAGTCCCATCTTTTGAACTTCAATCCATGCAT
65 AATCATATTTATCAAAAAATAAAATCCATGCATTAGTCACATCTTTCGAACTTCAATCCATGCAT
* *
165095 TAGTCTATTCTTTGCAATTTAATATTTACAATCTAC
130 TAGTCTATTCATTGCAATTTAATATTTACAATCCAC
* * * * *
165131 GGATTAATCTTATCAACTTTTTTCATATAAA-AAAAT-TGATTCCCATTAAGAATCTATGCATTT
1 GCATTAGTCTTATCAACTTCTTTCATATAAATAAAATCTAATTCCCATTAAGAATCTATGCATTA
* ** *
165194 ATCATAATTATTGAAAAACAAAATCCAT
66 ATCATATTTATCAAAAAATAAAATCCAT
165222 ATATCGGTCT
Statistics
Matches: 221, Mismatches: 33, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
163 49 0.22
164 5 0.02
165 3 0.01
166 158 0.71
167 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (165 bp):
GCATTAGTCTTATCAACTTCTTTCATATAAATAAAATCTAATTCCCATTAAGAATCTATGCATTA
ATCATATTTATCAAAAAATAAAATCCATGCATTAGTCACATCTTTCGAACTTCAATCCATGCATT
AGTCTATTCATTGCAATTTAATATTTACAATCCAC
Found at i:166305 original size:32 final size:34
Alignment explanation
Indices: 166269--166333 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
166259 ATGGAAAACC
166269 CAAAGTTGAATTGC-AAATTCAA-TAAAAAAAAT
1 CAAAGTTGAATTGCAAAATTCAATTAAAAAAAAT
* * *
166301 CAAAGTTTACTTGCAAAATTCAATTAAATAAAA
1 CAAAGTTGAATTGCAAAATTCAATTAAAAAAAA
166334 GTAAAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 12 0.43
33 8 0.29
34 8 0.29
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.28
Consensus pattern (34 bp):
CAAAGTTGAATTGCAAAATTCAATTAAAAAAAAT
Found at i:167865 original size:78 final size:78
Alignment explanation
Indices: 167726--167908 Score: 194
Period size: 78 Copynumber: 2.3 Consensus size: 78
167716 AAAAATGCAA
* * *
167726 TATTACTTAGATAACTCTAATGGACATATTTCAACATAGAAGTTCCCAAATCACCTTAGAGA-TT
1 TATTACCTAAATAACTCCAATGGACATATTTCAACATAGAAGTTCCCAAATCACCTTAGAGACTT
167790 CAATTTTAAGGTAC
66 -AATTTTAAGGTAC
* ** * *
167804 TATTGCCTAAATAACTCCAATGGACATATTTCAACAT-GAAAGTTTTCACATGATCC-TAGAGAC
1 TATTACCTAAATAACTCCAATGGACATATTTCAACATAG-AAGTTCCCAAATCA-CCTTAGAGAC
** *
167867 TTGGTTTTAAGGTAT
64 TTAATTTTAAGGTAC
*
167882 TATTACCTAAAT-ACCCCTAATGGACAT
1 TATTACCTAAATAACTCC-AATGGACAT
167909 GCACTGACAT
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
77 5 0.06
78 79 0.90
79 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (78 bp):
TATTACCTAAATAACTCCAATGGACATATTTCAACATAGAAGTTCCCAAATCACCTTAGAGACTT
AATTTTAAGGTAC
Found at i:168239 original size:59 final size:59
Alignment explanation
Indices: 168165--168308 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 59
168155 CCCCTATATT
* * ** * *
168165 ATGAAAATTGCAAAATGGTCCTTAGATTATATAAAATAATTTACATGAA-CCTAAAATGC
1 ATGAAAATTGCAAAATGGTCCCTAGATTATAAAAAATAACCTAAAT-AACCCTAAAATAC
*
168224 ATGAAAATTGCAAAATGGTCCCTAAATTATAAAAAATAACCTAAATAACCCTAAAATAC
1 ATGAAAATTGCAAAATGGTCCCTAGATTATAAAAAATAACCTAAATAACCCTAAAATAC
* * *
168283 ATGGAGATTGCTAAATGGTCCCTAGA
1 ATGAAAATTGCAAAATGGTCCCTAGA
168309 ATGCATAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 2 0.03
59 71 0.97
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (59 bp):
ATGAAAATTGCAAAATGGTCCCTAGATTATAAAAAATAACCTAAATAACCCTAAAATAC
Found at i:170937 original size:79 final size:79
Alignment explanation
Indices: 170700--171647 Score: 1073
Period size: 79 Copynumber: 12.1 Consensus size: 79
170690 ACTCCCTCAG
** * * * * * *
170700 AAATAACAAGGTTGGAGTAT-CTCGAATGGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTT
1 AAATAACGGGGTTGGAGTATCCCCG-ATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTT
170764 GGAGTATCCCCT--A
65 GGAGTATCCCCTCGA
* * * * * * * * * * *
170777 AAAAAATGGGTTTAGAGTATCCTCGATTGTGGAAAATTGGTATTTTGAAAATAAAA-CTGGGTTA
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTG
170841 GAGTATCCCCTCGA
66 GAGTATCCCCTCGA
* * * * *
170855 AAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATTGATATTTTGGAAATAAAACCAGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTG
170920 GAGTATCCCCTCGA
66 GAGTATCCCCTCGA
* * * *
170934 AAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATT-AGTGTTTTGAAAATAAAACCGAGATT
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGGAAATAAAACCGGGGTT
* * *
170998 GGAGTATCTCTTCGG
65 GGAGTATCCCCTCGA
* * *
171013 AAATAACGGGGTTGGAATATCCTCGATTGTGAAAAATTGGTGGTTTTGGAAATAAAACCGGGGTT
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGAT-GTTTTGGAAATAAAACCGGGGTT
*
171078 GGAGTATCTCCTC-A
65 GGAGTATCCCCTCGA
* * * * * *
171092 GAAA-AACGAGGTAGGTGTATCCCCGATTGTGATAAATT-AGTGTTTTGAAAATAAAACTGGGGT
1 -AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGGAAATAAAACCGGGGT
171155 TGGAGTATCCCCTC-A
64 TGGAGTATCCCCTCGA
* * * *
171170 AAAGTAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGATT
1 AAA-TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTT
171235 GGAGTATCCCCTCGA
65 GGAGTATCCCCTCGA
* *
171250 AAATAACGGGGTTGGAGTATCCCC-ATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTG
171314 GAGTATCCCCTC-A
66 GAGTATCCCCTCGA
* * * **
171327 GAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTT
1 -AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTT
* *
171392 GGAGTATCCCTTCGG
65 GGAGTATCCCCTCGA
** * *
171407 AAATAAAAGGGTTGGAGTAT-CCCGATTGTGAAAAATT-ATTGTTTTAGAAATAAAACCGAGGTT
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGGAAATAAAACCGGGGTT
171470 GGAGTATCCCCTCGA
65 GGAGTATCCCCTCGA
* * * *
171485 AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGCGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTG
*
171550 GAGTATCCTCTC-A
66 GAGTATCCCCTCGA
** * **
171563 GAAATAACGTAGTTGGAGTATCCCCGATTGTGAAAAATT-AGTGTTTTAGAAATAAAATTGGGGT
1 -AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGGAAATAAAACCGGGGT
*
171627 TGGAATAT-CCCTCGA
64 TGGAGTATCCCCTCGA
171642 AAATAA
1 AAATAA
171648 AAACATGAAT
Statistics
Matches: 749, Mismatches: 100, Indels: 43
0.84 0.11 0.05
Matches are distributed among these distances:
76 16 0.02
77 42 0.06
78 240 0.32
79 412 0.55
80 39 0.05
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (79 bp):
AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTG
GAGTATCCCCTCGA
Found at i:171047 original size:157 final size:156
Alignment explanation
Indices: 170700--171647 Score: 1137
Period size: 157 Copynumber: 6.0 Consensus size: 156
170690 ACTCCCTCAG
** * * * *
170700 AAATAACAAGGTTGGAGTAT-CTCGAATGGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTT
1 AAATAACGGGGTTGGAGTATCCTCG-ATTGTGAAAAATTGGTGTTTTGGAAATAAAATCG-GGTT
* * * * * * * *
170764 GGAGTATCCCCT-AAAAAAATGGGTTTAGAGTATCCTCGATTGTGGAAAATTGGTATTTTGAAAA
64 GGAGTATCCCCTCAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAAA
* *
170828 TAAAACTG-GGTTAGAGTATCCCCTCGA
129 TAAAACCGAGGTTGGAGTATCCCCTCGA
* * * * *
170855 AAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATTGATATTTTGGAAATAAAACCAGGGTTG
1 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GGGTTG
*
170920 GAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAAA
65 GAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAAA
* * * *
170985 TAAAACCGAGATTGGAGTATCTCTTCGG
129 TAAAACCGAGGTTGGAGTATCCCCTCGA
* *
171013 AAATAACGGGGTTGGAATATCCTCGATTGTGAAAAATTGGTGGTTTTGGAAATAAAACCGGGGTT
1 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATC-GGGTT
* * * * *
171078 GGAGTATCTCCTCAGAAA-AACGAGGTAGGTGTATCCCCGATTGTGATAAATTAGTGTTTTGAAA
64 GGAGTATCCCCTCA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAA
* *
171142 ATAAAACTGGGGTTGGAGTATCCCCTC-A
128 ATAAAACCGAGGTTGGAGTATCCCCTCGA
171170 AAAGTAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGATT
1 AAA-TAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGG-TT
* *
171235 GGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-ATTGTGAAAAATTGGTGTTTTGGAA
64 GGAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAA
* *
171299 ATAAAATCGGGGTTGGAGTATCCCCTC-A
128 ATAAAACCGAGGTTGGAGTATCCCCTCGA
* * * *
171327 GAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTT
1 -AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAA-TCGGGTT
* * ** *
171392 GGAGTATCCCTTCGGAAATAAAAGGGTTGGAGTAT-CCCGATTGTGAAAAATTATTGTTTT-AGA
64 GGAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGA-A
171455 AATAAAACCGAGGTTGGAGTATCCCCTCGA
127 AATAAAACCGAGGTTGGAGTATCCCCTCGA
* *
171485 AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAA-CTGGCGTT
1 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GG-GTT
* **
171549 GGAGTATCCTCTCAGAAATAACGTAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-AGA
64 GGAGTATCCCCTCA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGA-A
** * *
171613 AATAAAATTGGGGTTGGAATAT-CCCTCGA
127 AATAAAACCGAGGTTGGAGTATCCCCTCGA
171642 AAATAA
1 AAATAA
171648 AAACATGAAT
Statistics
Matches: 695, Mismatches: 78, Indels: 38
0.86 0.10 0.05
Matches are distributed among these distances:
155 62 0.09
156 13 0.02
157 361 0.52
158 223 0.32
159 36 0.05
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (156 bp):
AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGTTGG
AGTATCCCCTCAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAAATA
AAACCGAGGTTGGAGTATCCCCTCGA
Found at i:176740 original size:18 final size:19
Alignment explanation
Indices: 176717--176757 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
176707 AACGAAGTTG
*
176717 AAAAATCTA-AATTAATGA
1 AAAAATCGATAATTAATGA
*
176735 AAAAATCGATAATTATTGA
1 AAAAATCGATAATTAATGA
176754 AAAA
1 AAAA
176758 CAAGATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAAATCGATAATTAATGA
Found at i:182003 original size:19 final size:19
Alignment explanation
Indices: 181979--182015 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
181969 CTTTTATAAA
* *
181979 AATAAATTTTCTCCCTTTT
1 AATAAATTCTCCCCCTTTT
181998 AATAAATTCTCCCCCTTT
1 AATAAATTCTCCCCCTTT
182016 GTGAAAGCTC
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:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAAATTCTCCCCCTTTT
Found at i:188363 original size:3 final size:3
Alignment explanation
Indices: 188357--188391 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
188347 AGTCAACTTT
* *
188357 ATC ATC ATC ATC ATC ATC ATC ATC TTC GTC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
188392 TGATGGTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.31, G:0.03, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:196004 original size:19 final size:19
Alignment explanation
Indices: 195960--196029 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
195950 TACAAGCTAA
* * *
195960 TGTATTGATACATTTTGGG
1 TGTATCGATACATATTGTG
195979 ATGTATCGATACATATTGTG
1 -TGTATCGATACATATTGTG
195999 TGTATCGATACATATTGTG
1 TGTATCGATACATATTGTG
*
196018 TGTATTGATACA
1 TGTATCGATACA
196030 AACAGTTAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 30 0.65
20 16 0.35
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATATTGTG
Found at i:196118 original size:20 final size:21
Alignment explanation
Indices: 196071--196123 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
196061 GCCAATGACC
**
196071 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
196092 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
196112 TGTATCGATACA
1 TGTATCGATACA
196124 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:196129 original size:13 final size:13
Alignment explanation
Indices: 196111--196135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196101 ACATTTGGTC
196111 ATGTATCGATACA
1 ATGTATCGATACA
196124 ATGTATCGATAC
1 ATGTATCGATAC
196136 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:196168 original size:20 final size:20
Alignment explanation
Indices: 196145--196185 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
196135 CTGTGCAATC
196145 TGTATCGATACATTTAAAGG
1 TGTATCGATACATTTAAAGG
* *
196165 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTAAAGG
196185 T
1 T
196186 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAAAGG
Found at i:199489 original size:3 final size:3
Alignment explanation
Indices: 199481--199506 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
199471 AATTTCTTGC
199481 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
199507 TTCCTCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:201150 original size:20 final size:20
Alignment explanation
Indices: 201121--201158 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
201111 GTTGGGCTCA
*
201121 ATGTATCGATACAATTTACC
1 ATGTACCGATACAATTTACC
201141 ATGTACCGATACAATTTA
1 ATGTACCGATACAATTTA
201159 ATTATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTACCGATACAATTTACC
Found at i:201272 original size:33 final size:32
Alignment explanation
Indices: 201216--201277 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
201206 CATTTCATGG
*
201216 TGTATCGATACAAAGAACATGTATCGATATAA
1 TGTATCAATACAAAGAACATGTATCGATATAA
* *
201248 TGTATCAATACTAAGCAATATGTATCGATA
1 TGTATCAATACAAAG-AACATGTATCGATA
201278 CAACTGGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCAATACAAAGAACATGTATCGATATAA
Found at i:203025 original size:15 final size:15
Alignment explanation
Indices: 203005--203042 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
202995 TCCTCTAAGT
203005 AAGAAAAACAAAA-AA
1 AAGAAAAA-AAAAGAA
203020 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
*
203035 ATGAAAAA
1 AAGAAAAA
203043 TGAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:203093 original size:9 final size:9
Alignment explanation
Indices: 203079--203112 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
203069 AAAAAATTGC
203079 AGAAAAAAG
1 AGAAAAAAG
203088 AGAAAAAAG
1 AGAAAAAAG
203097 A-AAAAAAG
1 AGAAAAAAG
203105 AAGAAAAA
1 -AGAAAAA
203113 TGAAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 11 0.48
10 5 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Done.