Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 6 of 345
Found at i:1897103 original size:18 final size:18
Alignment explanation
Indices: 1897080--1897117 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1897070 AATATTTAAT
1897080 TAAATTTTTAAAGTTATC
1 TAAATTTTTAAAGTTATC
1897098 TAAATTTTTAAAGTTATC
1 TAAATTTTTAAAGTTATC
1897116 TA
1 TA
1897118 TGTGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
TAAATTTTTAAAGTTATC
Found at i:1902927 original size:18 final size:18
Alignment explanation
Indices: 1902901--1902966 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
1902891 AAAAACAATT
1902901 TAATAATAATAATAACTA
1 TAATAATAATAATAACTA
* *
1902919 TAATTATAATAATAGCTA
1 TAATAATAATAATAACTA
* *
1902937 TCATAATATTAAT-A-TA
1 TAATAATAATAATAACTA
*
1902953 -AATAACAATAATAA
1 TAATAATAATAATAA
1902967 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
15 9 0.24
16 3 0.08
18 26 0.68
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAACTA
Found at i:1903962 original size:20 final size:22
Alignment explanation
Indices: 1903937--1903979 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
1903927 AAATTGAACA
1903937 TCGTGACGGC-C-GCCGGTTAT
1 TCGTGACGGCACTGCCGGTTAT
1903957 TCGTGACGGCACTGCCGGTTAT
1 TCGTGACGGCACTGCCGGTTAT
1903979 T
1 T
1903980 GGCAACGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.12, C:0.28, G:0.33, T:0.28
Consensus pattern (22 bp):
TCGTGACGGCACTGCCGGTTAT
Found at i:1907580 original size:23 final size:23
Alignment explanation
Indices: 1907553--1907597 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1907543 ATGATAACTT
1907553 AGCTTAAAGTTTGGCACGTGTTC
1 AGCTTAAAGTTTGGCACGTGTTC
* * *
1907576 AGCTTGAGGTTTGGTACGTGTT
1 AGCTTAAAGTTTGGCACGTGTT
1907598 TATATTCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.31, T:0.38
Consensus pattern (23 bp):
AGCTTAAAGTTTGGCACGTGTTC
Found at i:1909327 original size:13 final size:14
Alignment explanation
Indices: 1909300--1909329 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1909290 AAAAAATGAT
1909300 ATTAATGCTAATTA
1 ATTAATGCTAATTA
1909314 ATTAATGC-AATTA
1 ATTAATGCTAATTA
1909327 ATT
1 ATT
1909330 TTTTTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTAATGCTAATTA
Found at i:1910223 original size:12 final size:12
Alignment explanation
Indices: 1910206--1910230 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1910196 GGTGTTCATT
1910206 CGGTTAACCGAC
1 CGGTTAACCGAC
1910218 CGGTTAACCGAC
1 CGGTTAACCGAC
1910230 C
1 C
1910231 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:1910405 original size:9 final size:9
Alignment explanation
Indices: 1910391--1910442 Score: 86
Period size: 9 Copynumber: 5.8 Consensus size: 9
1910381 TTTGGTTAAA
1910391 AATTACCCG
1 AATTACCCG
*
1910400 AATTACCTG
1 AATTACCCG
1910409 AATTACCCG
1 AATTACCCG
1910418 AATTACCCG
1 AATTACCCG
*
1910427 AATTAACCG
1 AATTACCCG
1910436 AATTACC
1 AATTACC
1910443 GAAAAATACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:1911131 original size:21 final size:22
Alignment explanation
Indices: 1911107--1911154 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1911097 AAATTACATG
* *
1911107 CCCAAACCTGA-ACTACCCTAA
1 CCCAAACCTAATACTACACTAA
*
1911128 CCCAAACCTAATATTACACTAA
1 CCCAAACCTAATACTACACTAA
1911150 CCCAA
1 CCCAA
1911155 GCCCAAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.17
Consensus pattern (22 bp):
CCCAAACCTAATACTACACTAA
Found at i:1912683 original size:12 final size:11
Alignment explanation
Indices: 1912659--1912751 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 11
1912649 TACTTTTTTA
1912659 TATTATTTCAT
1 TATTATTTCAT
1912670 TATTATTATCAT
1 TATTATT-TCAT
1912682 TATTA--TCAT
1 TATTATTTCAT
* *
1912691 ATAGTATTATTAAT
1 -TATTA-T-TTCAT
*
1912705 TAAATATTTC-T
1 T-ATTATTTCAT
1912716 TATTATTTC-T
1 TATTATTTCAT
1912726 TATTATTGTCAT
1 TATTATT-TCAT
* *
1912738 T-TCATCTCAT
1 TATTATTTCAT
1912748 TATT
1 TATT
1912752 CATGTGGTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
9 4 0.06
10 24 0.38
11 15 0.23
12 13 0.20
13 2 0.03
14 6 0.09
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (11 bp):
TATTATTTCAT
Found at i:1918167 original size:21 final size:21
Alignment explanation
Indices: 1918143--1918186 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1918133 TAGATAAATA
* *
1918143 TTATGAATCTTTTTTTATTTT
1 TTATGAAGCTTTTTTAATTTT
1918164 TTATGAAGCTTTTTTAATTTT
1 TTATGAAGCTTTTTTAATTTT
1918185 TT
1 TT
1918187 TAAAGTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (21 bp):
TTATGAAGCTTTTTTAATTTT
Found at i:1928942 original size:16 final size:16
Alignment explanation
Indices: 1928923--1928964 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1928913 AAATGGCATG
1928923 AACTCAAAATAACCTA
1 AACTCAAAATAACCTA
* *
1928939 AACT-AGAAATGATCTA
1 AACTCA-AAATAACCTA
1928955 AACTCAAAAT
1 AACTCAAAAT
1928965 TCATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (16 bp):
AACTCAAAATAACCTA
Found at i:1931926 original size:16 final size:16
Alignment explanation
Indices: 1931913--1931943 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1931903 CATATTTGAT
1931913 TTATTTTGAGTTTGTG
1 TTATTTTGAGTTTGTG
*
1931929 TTGTTTTGAGTTTGT
1 TTATTTTGAGTTTGT
1931944 ATAAATCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.65
Consensus pattern (16 bp):
TTATTTTGAGTTTGTG
Found at i:1932097 original size:22 final size:22
Alignment explanation
Indices: 1932050--1932093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1932040 TATGATCAAA
* *
1932050 TCAAATTGAATTAAGTTTAATT
1 TCAAATGGAATGAAGTTTAATT
1932072 TCAAATGGAATGAA-TTTAATT
1 TCAAATGGAATGAAGTTTAATT
1932093 T
1 T
1932094 TCAAGTCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (22 bp):
TCAAATGGAATGAAGTTTAATT
Found at i:1932854 original size:31 final size:31
Alignment explanation
Indices: 1932816--1932882 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1932806 ATTATAAAAT
* *
1932816 AGTTATTGAATTATTCGAAAGATTTCATTTA
1 AGTTATTGAACTATTCAAAAGATTTCATTTA
* *
1932847 AGTTATTGAACTATTCAAAAGCTTTTATTTA
1 AGTTATTGAACTATTCAAAAGATTTCATTTA
1932878 AGTTA
1 AGTTA
1932883 CTTGGTTGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (31 bp):
AGTTATTGAACTATTCAAAAGATTTCATTTA
Found at i:1933841 original size:24 final size:24
Alignment explanation
Indices: 1933809--1933856 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1933799 ACCAAGCAAA
1933809 ACCAAAGTGCTTTGGGAAAAATGG
1 ACCAAAGTGCTTTGGGAAAAATGG
1933833 ACCAAAGTGCTTTGGGAAAAATGG
1 ACCAAAGTGCTTTGGGAAAAATGG
1933857 GTTTTAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (24 bp):
ACCAAAGTGCTTTGGGAAAAATGG
Found at i:1938742 original size:25 final size:26
Alignment explanation
Indices: 1938697--1938751 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
1938687 ATCTAATATT
* *
1938697 TATAAAATATCATATTTTATAGCAAA
1 TATAAAAAATCATATTTTATAGAAAA
* *
1938723 TATAAAAAAT-ATGTTTTATATAAAA
1 TATAAAAAATCATATTTTATAGAAAA
1938748 TATA
1 TATA
1938752 TGAAATCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
TATAAAAAATCATATTTTATAGAAAA
Found at i:1941646 original size:30 final size:31
Alignment explanation
Indices: 1941601--1941665 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
1941591 AAAACTTTTT
1941601 TTTGTTAATTTTTGTTATTATTTTAAAGATA
1 TTTGTTAATTTTTGTTATTATTTTAAAGATA
*
1941632 TTTGTTAA-TTTTGTTATTATTTTAGAGATA
1 TTTGTTAATTTTTGTTATTATTTTAAAGATA
1941662 TTTG
1 TTTG
1941666 CTTGTTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (31 bp):
TTTGTTAATTTTTGTTATTATTTTAAAGATA
Found at i:1941819 original size:12 final size:12
Alignment explanation
Indices: 1941789--1941821 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1941779 TATATATTTT
1941789 AAAATT-ATATA
1 AAAATTAATATA
1941800 AAAA-TAATATA
1 AAAATTAATATA
1941811 AAAATTAATAT
1 AAAATTAATAT
1941822 GGGTGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:1945213 original size:45 final size:45
Alignment explanation
Indices: 1945137--1945244 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 45
1945127 TTTCGCCTGT
1945137 TAGGCTCG-AGGCCCG-ATATCAGTTCACCGGCATTATAGCCTAC
1 TAGGCTCGAAGGCCCGAATATCAGTTCACCGGCATTATAGCCTAC
** *
1945180 TAGGCTCGAAGGCCCGAATAGT-A-TCTCACCGGCATTATAGTTTGC
1 TAGGCTCGAAGGCCCGAATA-TCAGT-TCACCGGCATTATAGCCTAC
* *
1945225 TAAGCTCAAAGGCCCGAATA
1 TAGGCTCGAAGGCCCGAATA
1945245 ATCAAGTCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
43 8 0.14
44 8 0.14
45 39 0.70
46 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (45 bp):
TAGGCTCGAAGGCCCGAATATCAGTTCACCGGCATTATAGCCTAC
Found at i:1945622 original size:43 final size:43
Alignment explanation
Indices: 1945575--1945685 Score: 204
Period size: 43 Copynumber: 2.6 Consensus size: 43
1945565 CGGCATTACG
1945575 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA
* *
1945618 CCTGCTAGGCACGAAGGTCCGAATACACATCACCGGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA
1945661 CCTGCTAGGCACGAAGGCCCGAATA
1 CCTGCTAGGCACGAAGGCCCGAATA
1945686 TAATACCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.11
Consensus pattern (43 bp):
CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA
Found at i:1945726 original size:38 final size:38
Alignment explanation
Indices: 1945678--1945841 Score: 202
Period size: 38 Copynumber: 4.3 Consensus size: 38
1945668 GGCACGAAGG
* * * *
1945678 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
1945716 CCCAGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** * **
1945754 CCCGGATATTTTACCAGCACGAAGCCTACAGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGC-GGGATTTAA
*
1945793 GCCCGGATATAATACTAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
1945832 CTCGGATATA
1 CCCGGATATA
1945842 CATCGATAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
38 67 0.63
39 14 0.13
40 25 0.24
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:1951647 original size:73 final size:74
Alignment explanation
Indices: 1951554--1951702 Score: 169
Period size: 72 Copynumber: 2.0 Consensus size: 74
1951544 GACTAAAAAC
*
1951554 ATTATTATAAAACTTCTTTATACT-CACAAATACTTTAAAAAAATCCATAACCACAAAATATAAA
1 ATTATTATAAAACGTCTTTATA-TGCACAAATAC-TTAAAAAAATCCATAACCACAAAATATAAA
*
1951618 AAGAATCCCAA
64 AAAAATCCCAA
* * ** * * * *
1951629 ATTA-TATAAAA-GTCTTTATATGCGCAACTACTTATGAAAATTCATAACCACCATATTTAAAAA
1 ATTATTATAAAACGTCTTTATATGCACAAATACTTAAAAAAATCCATAACCACAAAATATAAAAA
1951692 AAATCCCAA
66 AAATCCCAA
1951701 AT
1 AT
1951703 ATTTTAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
72 37 0.59
73 15 0.24
74 7 0.11
75 4 0.06
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (74 bp):
ATTATTATAAAACGTCTTTATATGCACAAATACTTAAAAAAATCCATAACCACAAAATATAAAAA
AAATCCCAA
Found at i:1957376 original size:26 final size:26
Alignment explanation
Indices: 1957341--1957391 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1957331 CTTTGGCATC
1957341 TTGCTAAGCTTGCAGCTTGCACATTT
1 TTGCTAAGCTTGCAGCTTGCACATTT
*
1957367 TTGCTGAGCTTGCAGCTTGCACATT
1 TTGCTAAGCTTGCAGCTTGCACATT
1957392 GGAAAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
TTGCTAAGCTTGCAGCTTGCACATTT
Found at i:1963582 original size:69 final size:69
Alignment explanation
Indices: 1963488--1963622 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
1963478 TTTGGATATT
1963488 ATTTAAAGATTTTTAACATCTCTAGATTTGAGAGTTGAGACCAATCCTTACTGATAATATATATA
1 ATTTAAAGATTTTTAACATCTCTAGATTTGAGAGTTGAGACCAATCCTTACTGATAATATATATA
1963553 TGCG
66 TGCG
1963557 ATTTCAAA-ATTTTTAACATCTCTAGATTTGAGAGTTGAGACCAATCCTTACTGATAATATATAT
1 ATTT-AAAGATTTTTAACATCTCTAGATTTGAGAGTTGAGACCAATCCTTACTGATAATATATAT
1963621 AT
65 AT
1963623 ATATATATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 62 0.95
70 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (69 bp):
ATTTAAAGATTTTTAACATCTCTAGATTTGAGAGTTGAGACCAATCCTTACTGATAATATATATA
TGCG
Found at i:1970601 original size:21 final size:21
Alignment explanation
Indices: 1970575--1970615 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1970565 AGACGAGCAA
* *
1970575 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1970596 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1970616 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1973277 original size:6 final size:6
Alignment explanation
Indices: 1973266--1973301 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1973256 ACTTCAGTCA
1973266 AAGCAT AAGCAT AAGCAT AAGCAT AAGCAT AAGCAT
1 AAGCAT AAGCAT AAGCAT AAGCAT AAGCAT AAGCAT
1973302 GAAATAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
AAGCAT
Found at i:1975857 original size:11 final size:11
Alignment explanation
Indices: 1975841--1975865 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1975831 TTGCAGGGAC
1975841 TCATAATTGAA
1 TCATAATTGAA
1975852 TCATAATTGAA
1 TCATAATTGAA
1975863 TCA
1 TCA
1975866 ACTAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (11 bp):
TCATAATTGAA
Found at i:1982154 original size:6 final size:6
Alignment explanation
Indices: 1982145--1982178 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1982135 TTTTTTAAAA
1982145 TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
1982179 AAATTAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:1982157 original size:18 final size:19
Alignment explanation
Indices: 1982130--1982180 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1982120 TTGGATTATT
*
1982130 TTTTATTTTTTAA-AATAA
1 TTTTAATTTTTAATAATAA
**
1982148 TTTTAA-TTTTAATTTTAA
1 TTTTAATTTTTAATAATAA
1982166 TTTTAA-TTTTAATAA
1 TTTTAATTTTTAATAA
1982181 ATTAGAGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATTTTTAATAATAA
Found at i:2015721 original size:69 final size:69
Alignment explanation
Indices: 2015547--2015721 Score: 217
Period size: 70 Copynumber: 2.5 Consensus size: 69
2015537 CTTTCCAAGG
* ** *
2015547 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
2015612 TTTT
66 TTTT
* ** * *
2015616 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTT-
2015681 TGTTTT
64 TGTTTT
** *
2015687 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2015722 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
69 31 0.34
70 55 0.60
71 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
TTTT
Found at i:2015865 original size:76 final size:75
Alignment explanation
Indices: 2015739--2016078 Score: 463
Period size: 76 Copynumber: 4.5 Consensus size: 75
2015729 TTTGTTTTTC
*
2015739 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
2015804 GTTGTTAAAAA
66 GTT-TTAAAAA
**
2015815 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
2015880 GTTTT---CA
66 GTTTTAAAAA
* * ** * * *
2015887 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
2015952 GTTTTCAAAAA
66 GTTTT-AAAAA
* * *
2015963 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
*
2016027 TCTGTTTTTAAAA
63 TCTGTTTTAAAAA
*
2016040 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
2016079 ATTACACACT
Statistics
Matches: 237, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
72 66 0.28
75 3 0.01
76 100 0.42
77 39 0.16
78 29 0.12
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAAA
Found at i:2015993 original size:148 final size:148
Alignment explanation
Indices: 2015725--2016073 Score: 479
Period size: 148 Copynumber: 2.3 Consensus size: 148
2015715 TAAGCCTTTT
* * *
2015725 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
2015790 TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
66 TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GG
2015855 -ACACGCTGAGGTAATTTC
130 TACACGCTGAGGTAATTTC
* ** *
2015873 AATTTCTG-TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTGTTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
* * **
2015937 GTATTTTCAATTTCTGTT-TTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCG
65 GTAATTTCAATTTCTGTTGTT-AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCG
* *
2016001 GTTCACATGCTGAGGTATTTTC
129 G-T-ACACGCTGAGGTAATTTC
*
2016023 AATTTCTGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AATTTCTGTTTTT---CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
2016074 TTCAGATTAC
Statistics
Matches: 175, Mismatches: 17, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
147 13 0.07
148 103 0.59
150 24 0.14
151 4 0.02
153 27 0.15
154 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (148 bp):
AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGT
ACACGCTGAGGTAATTTC
Found at i:2016529 original size:71 final size:72
Alignment explanation
Indices: 2016355--2017025 Score: 391
Period size: 71 Copynumber: 8.8 Consensus size: 72
2016345 TTCAATTTTC
* *
2016355 TTTTAATTTATGTTTA-AAAAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCA--AGACGC
1 TTTTAATTTATGTTCATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
2016416 TGAGGTAA
65 TGAGGTAA
* * ** *
2016424 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTATGTTCATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
**
2016489 TGAGGTGG
65 TGAGGTAA
* *
2016497 TTTTAATTTATGTTCATAAAAAAT-ACTCATATTGCAAGAGGTGAGTTGAGCCT--GGCTCAACG
1 TTTTAATTTATGTTCATAAAAAATAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-AC-ACG
2016559 CTGAGGT-A
64 CTGAGGTAA
* * *
2016567 TTTTCAATTTCTGTTTTAATTTCTGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTT-AATTTATG-------TTC---ATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCC
*
2016632 TCGGGACACGCTGAGGTAA
54 TCAGGACACGCTGAGGTAA
* * * *
2016651 TTTCAATTTCTGTT-TTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACA
1 TTTTAATTTATGTTCATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
*
2016715 TGCTGAGGTTTTCAA
62 CGCTGAGG---T-AA
* *
2016730 TTTCTGTTTCAATTTCTGTT-TTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ----T-TTT-AATTTATGTTCAT-AA--AAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTC
2016794 AGGACACGCTGAGGTAA
56 AGGACACGCTGAGGTAA
* * * * * * ** *
2016811 TTTCAATTTCTGTT-TTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCA-GACACGT
1 TTTTAATTTATGTTCATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
2016874 TGAGGT-A
65 TGAGGTAA
* * *
2016881 TTTTCAATTTCTGTTTTCAAAAAAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTT-AATTTATG--TTC------ATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
2016946 -GGTTCACATGCTGAGGT-A
56 AGG---ACACGCTGAGGTAA
* ** ** *
2016964 TTTTCAATTTCTGTTTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTTT-AATTTATG---TTCATAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
2017026 ATTACACACT
Statistics
Matches: 497, Mismatches: 51, Indels: 98
0.77 0.08 0.15
Matches are distributed among these distances:
69 15 0.03
70 32 0.06
71 80 0.16
72 75 0.15
73 32 0.06
74 1 0.00
75 22 0.04
76 4 0.01
77 1 0.00
78 39 0.08
79 3 0.01
80 36 0.07
81 9 0.02
82 1 0.00
83 71 0.14
84 11 0.02
85 24 0.05
86 2 0.00
88 39 0.08
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (72 bp):
TTTTAATTTATGTTCATAAAAAATAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTAA
Found at i:2016643 original size:83 final size:81
Alignment explanation
Indices: 2016521--2017020 Score: 437
Period size: 83 Copynumber: 6.3 Consensus size: 81
2016511 CATAAAAAAT
* *
2016521 ACTCATATTGCAAGAGGTGAGTTGAGCCT-GGCTCAACGCTGAGGTATTTTCAATTTCTGTTTTA
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCAC-ACGCTGAGGTATTTTCAATTTCTGTTTTA
2016585 ATTTCTGTTTCAAAAATCA
65 ATTT-T-TTTCAAAAATCA
* *
2016604 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTT-A
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTATTTTCAATTTCTGTTTTAA
*
2016668 --------AAAATTCA
66 TTTTTTTCAAAAATCA
*
2016676 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGG--TTTTCAATTTCTGTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG--CACACGCTGAGGTATTTTCAATTTCTGTTT
* *
2016739 CAATTTCTGTTTTAAAAAAAAATCA
63 TAA-TT-T-TTTT---CAAAAATCA
*
2016764 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTTCTG-----
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACACGCTGAGGTATTTTCAATTTCTGTTTTA
*
2016823 ----TTTTCAAAATTCA
65 ATTTTTTTCAAAAATCA
* ** * *
2016836 ACTTATATTGCGAGAAATGAGTTGAGCCTCAG-ACACGTTGAGGTATTTTCAATTTCTGTTTTCA
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTATTTTCAATTTCTGTTTT-A
*******
2016900 A-AAAAAAAAAAAATCA
65 ATTTTTTTCAAAAATCA
* *
2016916 ACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTG-TTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACGCTGAGGTATTTTCAATTTCTGTTTT
2016980 --TTTTTTT--AAAATCA
64 AATTTTTTTCAAAAATCA
2016994 ACTCATATTGCGAGAGGTGAGTTGAGC
1 ACTCATATTGCGAGAGGTGAGTTGAGC
2017021 TTCAGATTAC
Statistics
Matches: 345, Mismatches: 38, Indels: 73
0.76 0.08 0.16
Matches are distributed among these distances:
71 25 0.07
72 71 0.21
73 17 0.05
74 1 0.00
75 14 0.04
78 33 0.10
80 36 0.10
82 4 0.01
83 79 0.23
84 3 0.01
85 10 0.03
87 12 0.03
88 40 0.12
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (81 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTATTTTCAATTTCTGTTTTAA
TTTTTTTCAAAAATCA
Found at i:2016700 original size:72 final size:71
Alignment explanation
Indices: 2016584--2017020 Score: 399
Period size: 72 Copynumber: 5.7 Consensus size: 71
2016574 TTTCTGTTTT
*
2016584 AATTTCTGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
1 AATTTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
2016649 AATTTC
66 AATTTC
* *
2016655 AATTTCTGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTG
1 AATTTCTGTTTTAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG--GACACGCTG
2016720 AGGTTTTCAATTTCTGTTTC
62 AGG---T-AA------TTTC
*
2016740 AATTTCTGTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
1 AATTTCTGTTTTAAA----AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTG
2016805 AGGTAATTTC
62 AGGTAATTTC
* * ** * *
2016815 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTTGAGG
1 AATTTCTGTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGG
*
2016879 TATTTTC
65 TAATTTC
* *
2016886 AATTTCTGTTTTCAAAAAAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTC
1 AATTTCTGTTTT----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--G
* *
2016951 ACATGCTGAGGTATTTTC
54 ACACGCTGAGGTAATTTC
*
2016969 AATTTCTGTTTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AATTTCTG-----TTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
2017021 TTCAGATTAC
Statistics
Matches: 307, Mismatches: 23, Indels: 65
0.78 0.06 0.16
Matches are distributed among these distances:
71 45 0.15
72 64 0.21
73 2 0.01
75 26 0.08
76 3 0.01
78 34 0.11
79 2 0.01
80 35 0.11
81 2 0.01
82 1 0.00
83 24 0.08
85 29 0.09
87 1 0.00
88 37 0.12
89 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (71 bp):
AATTTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
AATTTC
Found at i:2016741 original size:12 final size:12
Alignment explanation
Indices: 2016724--2016750 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2016714 ATGCTGAGGT
2016724 TTTCAATTTCTG
1 TTTCAATTTCTG
2016736 TTTCAATTTCTG
1 TTTCAATTTCTG
2016748 TTT
1 TTT
2016751 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTCAATTTCTG
Found at i:2016787 original size:160 final size:160
Alignment explanation
Indices: 2016442--2017025 Score: 688
Period size: 160 Copynumber: 3.7 Consensus size: 160
2016432 TTTGTTTGTC
** * *
2016442 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTTTTAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * *
2016507 TGTTCATAAAAAAT--ACTCATATTGCAAGAGGTGAGTTGAGCCT--GGCTCA-ACGCTGAGGTA
66 TGTT-TTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACACGCTGAGG-A
* *
2016567 TTTTCAATTTCTGTTTTAATTTCTGTTT---C
129 TTTTCAATTTCTGTTTCAATTTCTGTTTAAAA
*
2016596 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
2016661 TGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGG-TT
66 TGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACACGCTGAGGATT
2016725 TTCAATTTCTGTTTCAATTTCTGTTTTAAAA
131 TTCAATTTCTGTTTCAATTTCTG-TTTAAAA
2016756 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * ** *
2016821 TGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCA-G---ACACGTTGAGGTAT
66 TGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACACGCTGAGG-AT
***
2016882 TTTCAATTTCTGTTTTCAA------AAAAAAA
130 TTTCAATTTCTG-TTTCAATTTCTGTTTAAAA
* * *
2016908 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAAT
* *
2016972 TTCTGTTTTTTTTTTAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
63 TTCTG-----TTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
2017026 ATTACACACT
Statistics
Matches: 380, Mismatches: 29, Indels: 37
0.85 0.07 0.08
Matches are distributed among these distances:
151 2 0.01
152 41 0.11
153 7 0.02
154 88 0.23
155 28 0.07
156 33 0.09
157 9 0.02
158 51 0.13
159 15 0.04
160 106 0.28
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (160 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACACGCTGAGGATT
TTCAATTTCTGTTTCAATTTCTGTTTAAAA
Found at i:2016829 original size:88 final size:83
Alignment explanation
Indices: 2016651--2016825 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 83
2016641 GCTGAGGTAA
* *
2016651 TTTCAATTTCTGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACAT
1 TTTCAATTTCTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--CACAC
2016716 GCTGAGGTTTTCAATTTCTG
64 GCTGAGGTTTTCAATTTCTG
2016736 TTTCAATTTCTGTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACA
1 TTTCAATTTCTGTTTT---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACA
2016800 CGCTGAGGTAATTTCAATTTCTG
63 CGCTGAGGT--TTTCAATTTCTG
2016823 TTT
1 TTT
2016826 TCAAAATTCA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
85 27 0.33
87 15 0.18
88 41 0.49
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (83 bp):
TTTCAATTTCTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGC
TGAGGTTTTCAATTTCTG
Found at i:2017562 original size:75 final size:74
Alignment explanation
Indices: 2017330--2017698 Score: 421
Period size: 73 Copynumber: 5.0 Consensus size: 74
2017320 ATGTTTCAAA
* * * *
2017330 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT---CAAGACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACGCTGAGGTATTTTCAATTT
*
2017392 TTGTTTGTC
66 CTGTTTGTC
* *
2017401 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTGGTTTT-AAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCCACACGCTGAGGT-ATTTTCAAT
* ** *
2017463 TTATGTTCATA
64 TTCTGTTTGTC
* * * *
2017474 AAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACACGCTGAGGTATTTTCAATT
*
2017539 TCTGTTTTTC
65 TCTGTTTGTC
* * *
2017549 AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GACACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACGCTGAGGTATTTTCAATTT
2017613 CTGTTTGTC
66 CTGTTTGTC
* * * * *
2017622 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCTTTTTAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACACGCTGAGGTATTTTCAATT
2017687 TCTGCTTT-TC
65 TCTG-TTTGTC
2017697 AA
1 AA
2017699 TTTCTGTTTT
Statistics
Matches: 253, Mismatches: 33, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
71 35 0.14
72 2 0.01
73 123 0.49
74 7 0.03
75 83 0.33
76 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (74 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACGCTGAGGTATTTTCAATTT
CTGTTTGTC
Found at i:2017576 original size:148 final size:148
Alignment explanation
Indices: 2017311--2017698 Score: 505
Period size: 148 Copynumber: 2.6 Consensus size: 148
2017301 ATTTTCATTT
* * * * *
2017311 TTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-T--C-AAGA
1 TTTTAATTTATG-TTCATAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACA
* * *
2017372 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
65 CGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
**
2017437 TCAGGACACGCTGAGGTGG
130 TCAGGACACGCTGAGGTAA
* *
2017456 TTTTAATTTATGTTCATAAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACAC
1 TTTTAATTTATGTTCATAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACAC
* *
2017521 GCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCT
66 GCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
*
2017586 CGGGACACGCTGAGGTAA
131 CAGGACACGCTGAGGTAA
* * ** * * * *
2017604 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACAT
1 TTTTAATTTATGTTCATAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACAC
* * *
2017669 GCTGAGGTCTTTTTAATTTCTGCTTTTCAA
66 GCTGAGGTATTTTCAATTTCTGTTTTTCAA
2017699 TTTCTGTTTT
Statistics
Matches: 211, Mismatches: 28, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
144 37 0.18
145 13 0.06
147 1 0.00
148 160 0.76
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (148 bp):
TTTTAATTTATGTTCATAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACAC
GCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
CAGGACACGCTGAGGTAA
Found at i:2017661 original size:73 final size:73
Alignment explanation
Indices: 2017330--2017661 Score: 425
Period size: 73 Copynumber: 4.5 Consensus size: 73
2017320 ATGTTTCAAA
* * * *
2017330 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC--AAGACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
2017393 TGTTTGTC
66 TGTTTGTC
* * ** * *
2017401 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTTTTAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
** *
2017466 TGTTCATA
66 TGTTTGTC
* * * * * *
2017474 AAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGCTGAGGTAATTTCAATT
*
2017539 TCTGTTTTTC
64 TCTGTTTGTC
*
2017549 AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
2017614 TGTTTGTC
66 TGTTTGTC
* *
2017622 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
2017662 CTCACATGCT
Statistics
Matches: 223, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
71 36 0.16
73 127 0.57
75 60 0.27
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
TGTTTGTC
Found at i:2017709 original size:14 final size:14
Alignment explanation
Indices: 2017678--2017728 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2017668 TGCTGAGGTC
2017678 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
2017691 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
2017705 TTTTTTTCAATTTATA
1 --TTTTTCAATTTCTG
2017721 TTTTTCAA
1 TTTTTCAA
2017729 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
16 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:2017724 original size:16 final size:16
Alignment explanation
Indices: 2017692--2017725 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2017682 TAATTTCTGC
* *
2017692 TTTTCAATTTCTGTTT
1 TTTTCAATTTATATTT
2017708 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
2017724 TT
1 TT
2017726 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:2017898 original size:77 final size:76
Alignment explanation
Indices: 2017800--2018051 Score: 382
Period size: 77 Copynumber: 3.3 Consensus size: 76
2017790 AAATCTACTT
*
2017800 TTGCGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAG
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAA-
2017865 AATCAACTCATA
65 AATCAACTCATA
* *
2017877 TTGTGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTTTGCTTTTCAAAAA
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTC-AAAA
2017942 AATCAACTCATA
65 AATCAACTCATA
** * **
2017954 TTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGC-ATTTTCAATTTCTGCTTTTC-AAA
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGA-GCTATTTTCAATTTCTGCTTTTCAAAA
2018017 AATCAACTCATA
65 AATCAACTCATA
*
2018029 TTGCGAGATGTGAGTTGAGCCTT
1 TTGCGAGAGGTGAGTTGAGCCTT
2018052 GGGTTTACAT
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
75 36 0.22
77 119 0.74
78 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAA
ATCAACTCATA
Found at i:2018797 original size:30 final size:29
Alignment explanation
Indices: 2018763--2018907 Score: 173
Period size: 30 Copynumber: 4.8 Consensus size: 29
2018753 ACTTTTCTCA
*
2018763 ACTAGCCACACATTTTCCACCACCAACTCC
1 ACTAGCCACAC-TTCTCCACCACCAACTCC
* *
2018793 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCAC-ACTTCTCCACCACCAACTCC
*
2018823 ACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACA-CTTCTCCACCACCAACTCC
** *
2018853 ACTAGCCACACTTGCTCCATTACCTACTCC
1 ACTAGCCACACTT-CTCCACCACCAACTCC
*
2018883 ACTAACCACACTTGCTCCACCACCA
1 ACTAGCCACACTT-CTCCACCACCA
2018908 CTTGTACCTA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
29 3 0.03
30 96 0.96
31 1 0.01
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.21
Consensus pattern (29 bp):
ACTAGCCACACTTCTCCACCACCAACTCC
Found at i:2019499 original size:25 final size:25
Alignment explanation
Indices: 2019471--2019610 Score: 99
Period size: 25 Copynumber: 5.5 Consensus size: 25
2019461 ATATTACGTA
*
2019471 TATATATATTTTATACTATTTTATT
1 TATATATATTTTATACTATATTATT
* * *
2019496 TATATATCTTTAATATTATATTATT
1 TATATATATTTTATACTATATTATT
* *
2019521 TATATATATATTT-TTCTACATGTTATCT
1 TATATATAT-TTTATACT--ATATTAT-T
* *
2019549 TATGTATATTCTTA-ACTATATTATG
1 TATATATATT-TTATACTATATTATT
* *
2019574 TATATAT-TTTTAACACTATATTATG
1 TATATATATTTT-ATACTATATTATT
*
2019599 TACATAT-TTTTA
1 TATATATATTTTA
2019611 ATATTATCAC
Statistics
Matches: 92, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.02
24 4 0.04
25 58 0.63
26 8 0.09
27 7 0.08
28 13 0.14
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (25 bp):
TATATATATTTTATACTATATTATT
Found at i:2019751 original size:16 final size:16
Alignment explanation
Indices: 2019732--2019812 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 16
2019722 ATTTCTATTT
2019732 TATTTT-TTATTTTCAA
1 TATTTTATTATTTT-AA
2019748 TATTAATTATTATTATTCTAA
1 TATT--TTATTA-T-TT-TAA
2019769 TATTTTGA-TATTTTAA
1 TATTTT-ATTATTTTAA
2019785 TATTTTA-TATTTTATA
1 TATTTTATTATTTTA-A
2019801 TATTTTATTATT
1 TATTTTATTATT
2019813 CACATCATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.14
16 21 0.38
17 6 0.11
18 3 0.05
19 7 0.12
20 2 0.04
21 8 0.14
22 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTTATTATTTTAA
Found at i:2019796 original size:7 final size:8
Alignment explanation
Indices: 2019761--2019812 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2019751 TAATTATTAT
*
2019761 TATTCTAA
1 TATTTTAA
*
2019769 TATTTTGA
1 TATTTTAA
2019777 TATTTTAA
1 TATTTTAA
2019785 TATTTT-A
1 TATTTTAA
2019792 TATTTTATA
1 TATTTTA-A
*
2019801 TATTTTAT
1 TATTTTAA
2019809 TATT
1 TATT
2019813 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:2027329 original size:6 final size:6
Alignment explanation
Indices: 2027318--2027352 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2027308 GTCCCACTCG
2027318 ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCA
1 ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCA
2027353 TTTTTCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCAC
Found at i:2028861 original size:38 final size:38
Alignment explanation
Indices: 2028817--2028893 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
2028807 TTTAAGAATC
*
2028817 ACTTTATTTAATGAAGTTTACGAAATGTTATTCGTTTA
1 ACTTTATTTAATGAAGTTTACAAAATGTTATTCGTTTA
* *
2028855 ACTTTATTTAATGAAGTTTACAAAATGTTGTTTGTTTA
1 ACTTTATTTAATGAAGTTTACAAAATGTTATTCGTTTA
2028893 A
1 A
2028894 AATCAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (38 bp):
ACTTTATTTAATGAAGTTTACAAAATGTTATTCGTTTA
Found at i:2029449 original size:15 final size:16
Alignment explanation
Indices: 2029417--2029456 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2029407 AGTCCATGTA
2029417 ATTTCAAGTTCAAATT
1 ATTTCAAGTTCAAATT
*
2029433 ATTTCAA-TTCAAGTT
1 ATTTCAAGTTCAAATT
2029448 A-TTCAAGTT
1 ATTTCAAGTT
2029457 TAAAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 10 0.45
16 7 0.32
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTTCAAGTTCAAATT
Found at i:2038985 original size:14 final size:14
Alignment explanation
Indices: 2038966--2038996 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2038956 CAAATCACCA
2038966 GGCCAGTTTGGTTG
1 GGCCAGTTTGGTTG
2038980 GGCCAGTTTGGTTG
1 GGCCAGTTTGGTTG
2038994 GGC
1 GGC
2038997 TAAATGACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.16, G:0.45, T:0.32
Consensus pattern (14 bp):
GGCCAGTTTGGTTG
Found at i:2044105 original size:14 final size:14
Alignment explanation
Indices: 2044086--2044117 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2044076 TCAAATCACC
2044086 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2044100 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2044114 GGGC
1 GGGC
2044118 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:2045865 original size:28 final size:27
Alignment explanation
Indices: 2045824--2045883 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
2045814 TTTGGATTTT
*
2045824 TTTTTTCTATTTCAACTGTTTTTCTTCAA
1 TTTTTTCTATTTC-ACT-TTTTTCTTAAA
* *
2045853 TTTTTT-TGTTTCACTTTTTTTTTAAA
1 TTTTTTCTATTTCACTTTTTTCTTAAA
2045879 TTTTT
1 TTTTT
2045884 ACCGATGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.50
27 3 0.11
28 5 0.18
29 6 0.21
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (27 bp):
TTTTTTCTATTTCACTTTTTTCTTAAA
Found at i:2048357 original size:28 final size:29
Alignment explanation
Indices: 2048290--2048368 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
2048280 ATTAATAAAT
* *
2048290 AAAAATTTTAAAAATTATATAAAATCATTTA
1 AAAAATATTAAGAATTATA-AAAA-CATTTA
*
2048321 AAAATTATTAAGAATTATAAAAA-ATTTA
1 AAAAATATTAAGAATTATAAAAACATTTA
*
2048349 AAAAATATTACGAATTATAA
1 AAAAATATTAAGAATTATAA
2048369 GAAAGGTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 23 0.53
30 4 0.09
31 16 0.37
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATATTAAGAATTATAAAAACATTTA
Found at i:2054090 original size:29 final size:28
Alignment explanation
Indices: 2054045--2054102 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
2054035 TTATACTTGA
*
2054045 AAAAGTAGAGAGACTAAATTTCTGAAAAT
1 AAAAGTAGAGAGACTAAA-TTCTAAAAAT
*
2054074 AAAAGTATGA-AGGCTAAATTCTAAAAAT
1 AAAAGTA-GAGAGACTAAATTCTAAAAAT
2054102 A
1 A
2054103 TAAATAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 14 0.54
30 2 0.08
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAGTAGAGAGACTAAATTCTAAAAAT
Found at i:2055809 original size:92 final size:91
Alignment explanation
Indices: 2055655--2056021 Score: 314
Period size: 92 Copynumber: 4.0 Consensus size: 91
2055645 AATTGTAACG
* * *
2055655 ATTATTATTTATTATATTTCA-TTTCAGGACACTTGGGCTTGAGTATAGTGGTTCAAAAATATTT
1 ATTATTATTTATTATATTTCATTTTCAGGGCACTTGAGCTTGAGTATAGTGGTACAAAAATATTT
* *
2055719 TTAAGATATTCCGTA-AT-GCTTATAAAA
66 TTAAAAT-TTCC-TAGATAAC-TATAAAA
* * *
2055746 ATTATTATTTATTATATTTCATTTTCGGGGCACTTGAGTTTGAGTATGGTGGTACAAAAATATTT
1 ATTATTATTTATTATATTTCATTTTCAGGGCACTTGAGCTTGAGTATAGTGGTACAAAAATATTT
*
2055811 TTAAAATTTTCTAGGATAACTATAAAA
66 TTAAAATTTCCTA-GATAACTATAAAA
* * * * ***
2055838 GTTATTGTTTATTATATTTCATTTT-TGGGCACTTG-GACTTCAGTATAGTGCCCCAAGAAATAT
1 ATTATTATTTATTATATTTCATTTTCAGGGCACTTGAG-CTTGAGTATAGTGGTACAA-AAATAT
* ** *
2055901 TTTTAAATTTTTTTGAGATAACTGTAAAA
64 TTTTAAAATTTCCT-AGATAACTATAAAA
* * * * * * ** **
2055930 ATTATTATTGATTATATTTTATTTTC-GAAGCATTTGAGCTTAAGTATGGTCATGGAAAAATATT
1 ATTATTATTTATTATATTTCATTTTCAG-GGCACTTGAGCTTGAGTATAGTGGTACAAAAATATT
** *
2055994 TTTAAAATTTTTTGAGGTAACTATAAAA
65 TTTAAAATTTCCT-AGATAACTATAAAA
2056022 GGGCCACAAT
Statistics
Matches: 229, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
90 3 0.01
91 46 0.20
92 159 0.69
93 20 0.09
94 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (91 bp):
ATTATTATTTATTATATTTCATTTTCAGGGCACTTGAGCTTGAGTATAGTGGTACAAAAATATTT
TTAAAATTTCCTAGATAACTATAAAA
Found at i:2064185 original size:46 final size:44
Alignment explanation
Indices: 2064081--2064188 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2064071 TGTCTTTAAC
** * * *
2064081 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2064125 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2064171 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2064189 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2065119 original size:5 final size:5
Alignment explanation
Indices: 2065106--2065178 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
2065096 TTGTTTTATG
2065106 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
2065154 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
2065179 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:2065131 original size:19 final size:19
Alignment explanation
Indices: 2065107--2065149 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2065097 TGTTTTATGT
2065107 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
2065126 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
2065145 ATATA
1 ATATA
2065150 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:2065159 original size:24 final size:25
Alignment explanation
Indices: 2065113--2065177 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2065103 ATGTATATAT
* *
2065113 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
2065137 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
2065162 TTACTATAATATAATA
1 ATAATATAATATAATA
2065178 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:2070320 original size:46 final size:44
Alignment explanation
Indices: 2070216--2070323 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2070206 TGTCTTTAAC
** * * *
2070216 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2070260 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2070306 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2070324 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2071214 original size:9 final size:9
Alignment explanation
Indices: 2071200--2071233 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2071190 TTCTATTCTG
2071200 TTTCTTTTC
1 TTTCTTTTC
2071209 TTTCTTTT-
1 TTTCTTTTC
*
2071217 TTTCTATTC
1 TTTCTTTTC
2071226 TTTCTTTT
1 TTTCTTTT
2071234 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:2071226 original size:17 final size:17
Alignment explanation
Indices: 2071200--2071233 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2071190 TTCTATTCTG
*
2071200 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
2071217 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
2071234 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:2071255 original size:5 final size:5
Alignment explanation
Indices: 2071242--2071314 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
2071232 TTGTTTTATG
2071242 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
2071290 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
2071315 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:2071267 original size:19 final size:19
Alignment explanation
Indices: 2071243--2071285 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2071233 TGTTTTATGT
2071243 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
2071262 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
2071281 ATATA
1 ATATA
2071286 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:2071295 original size:24 final size:25
Alignment explanation
Indices: 2071249--2071313 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2071239 ATGTATATAT
* *
2071249 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
2071273 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
2071298 TTACTATAATATAATA
1 ATAATATAATATAATA
2071314 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:2075792 original size:141 final size:141
Alignment explanation
Indices: 2075538--2075817 Score: 438
Period size: 141 Copynumber: 2.0 Consensus size: 141
2075528 TAAATAAGAA
* * *
2075538 TAAGTTTGCATAGGTCCACAACCTCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTTTCGCC
1 TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTGTCGCC
** * *
2075603 AAGTTTATCCTAACTCTGAGCTTGAGGACAAGCTTTTTCTCTAGCAAGGGAGTAATATTATGGGC
66 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
*
2075668 TGAATCTATAC
131 CGAATCTATAC
2075679 TAAGTTTGTC-TAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTAGT-G
1 TAAGTTTG-CATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCT-GTCG
* *
2075742 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTGATCTTATGG
64 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGG
2075807 GCCGAATCTAT
129 GCCGAATCTAT
2075818 GTTAGGAAAG
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
141 125 0.98
142 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (141 bp):
TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTGTCGCC
AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
CGAATCTATAC
Found at i:2076260 original size:142 final size:142
Alignment explanation
Indices: 2076001--2076412 Score: 585
Period size: 142 Copynumber: 2.9 Consensus size: 142
2075991 AATACATGAG
* * *
2076001 AATAAGTTTGTGTAGGTCCACGACCCCTATCGGTTTTGACAATTAGTAATGGAAGGGACCTTTCG
1 AATAAGTTTGTGTAGGTCCACGACCCCTATCGGTTTCGACTATTAGTAACGGAAGGGACCTTTCG
** * *
2076066 -CACAAGTTTATTGTAACTCTGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAAAATTAT
66 CCA-AAGTTTATCATAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
*
2076130 GCGCCAAATCTAT
130 GAGCCAAATCTAT
* * * * * *
2076143 AATAAGTTTGTTTAAGTCTACAACCCCTATCGGTTTCAACTATTAGTAACGGAAGGGACCTTTTG
1 AATAAGTTTGTGTAGGTCCACGACCCCTATCGGTTTCGACTATTAGTAACGGAAGGGACCTTTCG
* * *
2076208 CCAAAGTTCATCATAGCTCCGAGCTTGAGGACAAGCTCTTTCTCTAGTAAGGGAGTAATATTATG
66 CCAAAGTTTATCATAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATG
*
2076273 AGCCGAATCTAT
131 AGCCAAATCTAT
* *
2076285 AATAAGTTTGTGTAGGTCCATGACCCCTATCGGTTTCGACTATTAGTAACGAAAGGGACCTTTCG
1 AATAAGTTTGTGTAGGTCCACGACCCCTATCGGTTTCGACTATTAGTAACGGAAGGGACCTTTCG
* * * *
2076350 CC-AAGTTTATCTTAACTCCAAGCTTGAGGACAAGCTCGTTCTCTAGCAAGGTAGTAATATTAT
66 CCAAAGTTTATCATAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
2076413 CGGCCGAATC
Statistics
Matches: 236, Mismatches: 33, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
141 54 0.23
142 180 0.76
143 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (142 bp):
AATAAGTTTGTGTAGGTCCACGACCCCTATCGGTTTCGACTATTAGTAACGGAAGGGACCTTTCG
CCAAAGTTTATCATAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATG
AGCCAAATCTAT
Found at i:2076863 original size:141 final size:141
Alignment explanation
Indices: 2076609--2077305 Score: 919
Period size: 141 Copynumber: 5.0 Consensus size: 141
2076599 GGTGCTAATA
* ** * * * *
2076609 AATAAATTTGTGTAGGTCCATGACCCCCATTAGTCTCGACTATTAGTAATGAAAGGGACCTTTCA
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
*
2076674 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
**
2076739 GTTGAATCTAT
131 GCCGAATCTAT
* * * *
2076750 AATAAGTTTGTATAGGTCCACAACCCCTATCGGTTTCAACTATTAGCAATGGAAGGGACCTTTCA
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
* **
2076815 CCATGTTTATCCTAACTCTAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
2076880 GCCGAATCTAT
131 GCCGAATCTAT
* * *
2076891 AACAAGTTTGTGTAGGTCCA-AGACCCATATCAGTTTCAAC---T--TAATG-AGGGGACCTTTC
1 AATAAGTTTGTGTAGGTCCACA-ACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTC
* * * * *
2076949 TCCAAGTTTATCCTAGCTCCGAGCTTGAGGATAAGCTTTTTCTCTAGCAAGGGAGTGATATTATG
65 ACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATG
2077014 GGCCGAATCTAT
130 GGCCGAATCTAT
* * *
2077026 AATAAGTTTGGGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGGCCTTTCG
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
* * *
2077091 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTACTCTAGCAAGGGAGTAAGATTATGA
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
*
2077156 GCCAAATCTAT
131 GCCGAATCTAT
* * * * * * *
2077167 TATAAGTTTGTGTAGGTCCACAACCCTTATCGGTTTCGACTATTAGTAA-CAAGGGGACCTTTCC
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
* * * *
2077231 CCAAGTTTATCCTAACCCCGAG-TTCGAGGACAAGTTCTTTCTCTAGCAAGGGAGTGA-CTTATG
66 CCAAGTTTATCCTAACTCCGAGCTT-GAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATG
2077294 GGCCGAATCTAT
130 GGCCGAATCTAT
2077306 GTTAGGAAAG
Statistics
Matches: 488, Mismatches: 59, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
135 115 0.24
136 5 0.01
138 2 0.00
139 17 0.03
140 67 0.14
141 282 0.58
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (141 bp):
AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
GCCGAATCTAT
Found at i:2077166 original size:276 final size:279
Alignment explanation
Indices: 2076663--2077305 Score: 904
Period size: 276 Copynumber: 2.3 Consensus size: 279
2076653 AGTAATGAAA
* *
2076663 GGGACCTTTCACCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAG
1 GGGACCTTTCACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTTTTTCTCTAGCAAGGGAG
* ** * *
2076728 TAATATTATGGGTTGAATCTATAATAAGTTTGTATAGGTCCACAACCCCTATCGGTTTCAACTAT
66 TGATATTATGGGCCGAATCTATAATAAGTTTGGATAGGTCCACAACCCCTATCAGTTTCAACTAT
* * * *
2076793 TAGCAATGGAAGGGACCTTTCACCATGTTTATCCTAACTCTAAGCTTGAGGACAAGCTCTTTCTC
131 TAGCAATGAAAGGGACCTTTCACCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTACTC
* * *
2076858 TAGCAAGGGAGTAATATTATGGGCCGAATCTATAACAAGTTTGTGTAGGTCCA-AGACCCATATC
196 TAGCAAGGGAGTAAGATTATGAGCCAAATCTATAACAAGTTTGTGTAGGTCCACA-ACCCATATC
**
2076922 AGTTTC-A-ACT-TAATGAG
260 AGTTTCGACACTATAACAAG
* * *
2076939 GGGACCTTTCTCCAAGTTTATCCTAGCTCCGAGCTTGAGGATAAGCTTTTTCTCTAGCAAGGGAG
1 GGGACCTTTCACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTTTTTCTCTAGCAAGGGAG
*
2077004 TGATATTATGGGCCGAATCTATAATAAGTTTGGGTAGGTCCACAACCCCTATCAGTTTCAACTAT
66 TGATATTATGGGCCGAATCTATAATAAGTTTGGATAGGTCCACAACCCCTATCAGTTTCAACTAT
* * * *
2077069 TAGTAATGAAAGGGGCCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTACTC
131 TAGCAATGAAAGGGACCTTTCACCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTACTC
* * * *
2077134 TAGCAAGGGAGTAAGATTATGAGCCAAATCTATTATAAGTTTGTGTAGGTCCACAACCCTTATCG
196 TAGCAAGGGAGTAAGATTATGAGCCAAATCTATAACAAGTTTGTGTAGGTCCACAACCCATATCA
*
2077199 GTTTCGACTATTAGTAACAAG
261 GTTTCGAC-ACTA-TAACAAG
* *
2077220 GGGACCTTTCCCCAAGTTTATCCTAACCCCGAG-TTCGAGGACAAG-TTCTTTCTCTAGCAAGGG
1 GGGACCTTTCACCAAGTTTATCCTAACTCCGAGCTT-GAGGACAAGCTT-TTTCTCTAGCAAGGG
*
2077283 AGTGA-CTTATGGGCCGAATCTAT
64 AGTGATATTATGGGCCGAATCTAT
2077306 GTTAGGAAAG
Statistics
Matches: 325, Mismatches: 34, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
276 237 0.73
277 2 0.01
279 2 0.01
280 21 0.06
281 63 0.19
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (279 bp):
GGGACCTTTCACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTTTTTCTCTAGCAAGGGAG
TGATATTATGGGCCGAATCTATAATAAGTTTGGATAGGTCCACAACCCCTATCAGTTTCAACTAT
TAGCAATGAAAGGGACCTTTCACCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTACTC
TAGCAAGGGAGTAAGATTATGAGCCAAATCTATAACAAGTTTGTGTAGGTCCACAACCCATATCA
GTTTCGACACTATAACAAG
Found at i:2078770 original size:13 final size:13
Alignment explanation
Indices: 2078740--2078769 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2078730 CACCTTTTCC
2078740 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
2078753 TTTTTCTTTT-TT
1 TTTTTCTTTTCTT
2078765 TTTTT
1 TTTTT
2078770 TAAAAAGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:2084457 original size:21 final size:22
Alignment explanation
Indices: 2084428--2084474 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2084418 CAGAAGGAGT
*
2084428 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2084450 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2084471 GAGT
1 GAGT
2084475 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:2087633 original size:45 final size:46
Alignment explanation
Indices: 2087540--2088463 Score: 450
Period size: 45 Copynumber: 20.9 Consensus size: 46
2087530 GGGAGGTAAA
* * * *
2087540 ATCTGCCATCTTCGATCTTCTTCGCTGCCAAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * *
2087586 ATCTG-TAATCTTCGATCTACTTCAC-GCTAAATACATGAAGATAAG
1 ATCTGCT-ATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * ** * **
2087631 ATCTGCTTTCTTCGATCTACTTCGCCACC-AGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * * **
2087676 ATCTGC-ATCGTCAATCCACTTC-CTACC-AATATAGGAAGACCGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * *
2087719 ATCTGCTACCTTTGATCTACTTCAC-GCC-AATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * ** **
2087763 ATCTGCTTTCTGCAATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * * *
2087808 ATCTGC-ATCTTCGGTCCACTTC-CTACC-AATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * ** **
2087851 ATCTGCTACCTTCGATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * ** **
2087896 ATCTGCTTTCTGCAATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * *
2087941 ATCTGC-ATCTTCGATCCACTTC-CTACC-AATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * ** **
2087984 ATCTGCTACCTTCGATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * * ** **
2088029 ATCTGATTTCTGCAATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * * **
2088074 ATCTGC-ATCGTCAATCCACTTC-CTACC-AATATAGGAAGACCGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * *
2088117 ATCTGCTACCTTTGATCTACTTCAC-GCC-AATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * ** *
2088161 ATCTGCTTTCTGCAATCTACTTCGCCACC-AATA-TGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * *
2088205 ATCTGC-ATCTTCG-TCCACTTC-CTACC-AATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * ** **
2088247 ATCTGCTACCTTCGATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * ** **
2088292 ATCTGCTTTCTGCAATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * *
2088337 ATCTGC-ATCTTCGATCCACTTC-CTACC-AATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * ** **
2088380 ATCTGCTACCTTCGATCTACTTCGCCACC-AATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
* * * * *
2088425 ATTTG-TATCTTTGATCCACTTC-CTACC-AATATAGGAAGA
1 ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGA
2088464 TAGGACCTAT
Statistics
Matches: 709, Mismatches: 150, Indels: 41
0.79 0.17 0.05
Matches are distributed among these distances:
41 8 0.01
42 21 0.03
43 139 0.20
44 224 0.32
45 294 0.41
46 23 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (46 bp):
ATCTGCTATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAG
Found at i:2087736 original size:88 final size:90
Alignment explanation
Indices: 2087540--2088463 Score: 873
Period size: 88 Copynumber: 10.5 Consensus size: 90
2087530 GGGAGGTAAA
* * ** * * *
2087540 ATCTGCCATCTTCGATCTTCTTCGCTGCCAAATACAGGAAGGCAAGATCTG-TAATCTTCGATCT
1 ATCTGCTATCTTCGATCTACTTCGCCACC-AATATAGGAAGACAAGATCTGCT-ATCTTCAATCT
* *** *
2087604 ACTTCACGCTA--AATACATGAAGATAAG
64 ACTT--CGCCACCAATATGGGAAGACAAG
* * * * *
2087631 ATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-ATCGTCAATCCAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
* * **
2087695 TTC-CTACCAATATAGGAAGACCGG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * * * * *
2087719 ATCTGCTACCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTGCAATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
2087783 TTCGCCACCAATATGGGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * * * *
2087808 ATCTGC-ATCTTCGGTCCACTTC-CTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
2087871 TTCGCCACCAATATGGGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * * *
2087896 ATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
* * * *
2087960 TTC-CTACCAATATAGGAAGATAGG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * *
2087984 ATCTGCTACCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGATTTCTGCAATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
2088049 TTCGCCACCAATATGGGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * ** * **
2088074 ATCTGC-ATCGTCAATCCACTTC-CTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
* * ***
2088137 TTC-ACGCCAATACATGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * *
2088161 ATCTGCTTTCTGCAATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGC-ATCTTC-GTCCAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
* * * *
2088223 TTC-CTACCAATATAGGAAGATAGG
66 TTCGCCACCAATATGGGAAGACAAG
* * * *
2088247 ATCTGCTACCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTTTCTGCAATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
2088312 TTCGCCACCAATATGGGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * * * *
2088337 ATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTAC
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
2088400 TTCGCCACCAATATGGGAAGACAAG
66 TTCGCCACCAATATGGGAAGACAAG
* * * *
2088425 ATTTG-TATCTTTGATCCACTTC-CTACCAATATAGGAAGA
1 ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGA
2088464 TAGGACCTAT
Statistics
Matches: 679, Mismatches: 138, Indels: 35
0.80 0.16 0.04
Matches are distributed among these distances:
86 54 0.08
87 64 0.09
88 337 0.50
89 114 0.17
90 86 0.13
91 24 0.04
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (90 bp):
ATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCAATCTAC
TTCGCCACCAATATGGGAAGACAAG
Found at i:2087948 original size:133 final size:133
Alignment explanation
Indices: 2087622--2088426 Score: 1348
Period size: 133 Copynumber: 6.1 Consensus size: 133
2087612 CTAAATACAT
* * * * *
2087622 GAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCGT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
* ** * * *
2087687 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTC-ACGCCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
***
2087751 CAT
131 TGG
2087754 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
2087819 CGGTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
2087884 TGG
131 TGG
2087887 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
2087952 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
2088017 TGG
131 TGG
* *
2088020 GAAGACAAGATCTGATTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
* ** * * *
2088085 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTC-ACGCCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
***
2088149 CAT
131 TGG
2088152 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
2088216 CG-TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
2088280 TGG
131 TGG
2088283 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
2088348 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
66 CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
2088413 TGG
131 TGG
2088416 GAAGACAAGAT
1 GAAGACAAGAT
2088427 TTGTATCTTT
Statistics
Matches: 631, Mismatches: 38, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
130 49 0.08
131 71 0.11
132 182 0.29
133 329 0.52
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (133 bp):
GAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAATA
TGG
Found at i:2088391 original size:396 final size:398
Alignment explanation
Indices: 2087622--2088426 Score: 1551
Period size: 396 Copynumber: 2.0 Consensus size: 398
2087612 CTAAATACAT
* * * * *
2087622 GAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCGT
1 GAAGACAAGATCTGATTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
2087687 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTCACGCCAATAC
66 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTCACGCCAATAC
2087752 ATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
131 ATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
2087817 TTCGGTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAA
196 TTCGGTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAA
2087882 TATGGGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
261 TATGGGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
2087947 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCAC
326 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCAC
2088012 CAATATGG
391 CAATATGG
2088020 GAAGACAAGATCTGATTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
1 GAAGACAAGATCTGATTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
2088085 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTCACGCCAATAC
66 CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTCACGCCAATAC
2088150 ATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATAT-GGAAGACAAGATCTGCATC
131 ATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
2088214 TTC-GTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAA
196 TTCGGTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAA
2088278 TATGGGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
261 TATGGGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
2088343 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCAC
326 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCAC
2088408 CAATATGG
391 CAATATGG
2088416 GAAGACAAGAT
1 GAAGACAAGAT
2088427 TTGTATCTTT
Statistics
Matches: 402, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
396 210 0.52
397 22 0.05
398 170 0.42
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (398 bp):
GAAGACAAGATCTGATTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
CAATCCACTTCCTACCAATATAGGAAGACCGGATCTGCTACCTTTGATCTACTTCACGCCAATAC
ATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATC
TTCGGTCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCACCAA
TATGGGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCGCCAC
CAATATGG
Found at i:2101173 original size:11 final size:12
Alignment explanation
Indices: 2101157--2101191 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
2101147 AAGAAAAAAA
2101157 AAGAGAG-AGGG
1 AAGAGAGAAGGG
2101168 AAGAGAGAAGGG
1 AAGAGAGAAGGG
2101180 -AGAGAGAAGGG
1 AAGAGAGAAGGG
2101191 A
1 A
2101192 GGGAATCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:2106877 original size:118 final size:121
Alignment explanation
Indices: 2106666--2106984 Score: 367
Period size: 118 Copynumber: 2.6 Consensus size: 121
2106656 GTGCAAATTA
* *
2106666 TTCATTTAATAATTTACGTGTTTTAATTATATTTCACGTCACAATCAAAATAACATTTAATACTC
1 TTCATTAAATAATTTACGTGTTTTAATTATATTTCACGTCACATTCAAAATAACATTTAATACTC
* * * *
2106731 AAATCTAACTTTTGCATGCAGTAAGTC-T-TC-C-TCTTTACCAATCATGCCAAAAC
66 GAATTTAACTTTTACATGCAGTAAGTCTTATCTCTTCTTTACCAATCATACC-AAAC
* * * *
2106784 TTCATTAAATAATTTACGTATTTTAATTATATTTTACGTCACTTTCAAAATAACATTTAGTACTC
1 TTCATTAAATAATTTACGTGTTTTAATTATATTTCACGTCACATTCAAAATAACATTTAATACTC
** * * *
2106849 GAATTTAACTTTTACATGTGGTAGGTCTTGAATCTTCTTCTTTACCAATCGTATCAAAC
66 GAATTTAACTTTTACATGCAGTAAGTCTT--ATC-TCTTCTTTACCAATCATACCAAAC
* * *
2106908 TTCATTTAATAATTTATGTTACGTGTTTTAGTTATATTCCACGTCACATTCAAAATAACATTTAA
1 TTCA-TT-A-AA-TAAT-TTACGTGTTTTAATTATATTTCACGTCACATTCAAAATAACATTTAA
2106973 TACTCGAATTTA
61 TACTCGAATTTA
2106985 TGATTAAATT
Statistics
Matches: 167, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
118 80 0.48
119 1 0.01
122 2 0.01
124 9 0.05
125 16 0.10
126 1 0.01
127 2 0.01
128 3 0.02
129 53 0.32
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (121 bp):
TTCATTAAATAATTTACGTGTTTTAATTATATTTCACGTCACATTCAAAATAACATTTAATACTC
GAATTTAACTTTTACATGCAGTAAGTCTTATCTCTTCTTTACCAATCATACCAAAC
Found at i:2117760 original size:14 final size:15
Alignment explanation
Indices: 2117743--2117786 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
2117733 AGAAATTTGG
2117743 AATTTAATTAT-TAT
1 AATTTAATTATATAT
*
2117757 AATTTAATTTTATAT
1 AATTTAATTATATAT
*
2117772 AATTTAGTT-TATAT
1 AATTTAATTATATAT
2117786 A
1 A
2117787 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
AATTTAATTATATAT
Found at i:2117786 original size:16 final size:16
Alignment explanation
Indices: 2117743--2117787 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
2117733 AGAAATTTGG
2117743 AATTTAA-TTAT-TAT
1 AATTTAATTTATATAT
2117757 AATTTAATTT-TATAT
1 AATTTAATTTATATAT
*
2117772 AATTTAGTTTATATAT
1 AATTTAATTTATATAT
2117788 TTTTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 14 0.52
16 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
AATTTAATTTATATAT
Found at i:2121841 original size:25 final size:24
Alignment explanation
Indices: 2121813--2121886 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
2121803 TTTACATCAA
2121813 TAAAATATTAATTTTATTATTAAAT
1 TAAAAT-TTAATTTTATTATTAAAT
*
2121838 TAAAACTTT-ATTTTAATA-TAATATT
1 TAAAA-TTTAATTTTATTATTAA-A-T
* *
2121863 TACATTTTAATTTTATTATGTAAA
1 TAAAATTTAATTTTATTAT-TAAA
2121887 CTTTATTACC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
23 3 0.08
24 12 0.31
25 19 0.49
26 2 0.05
27 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (24 bp):
TAAAATTTAATTTTATTATTAAAT
Found at i:2123938 original size:25 final size:25
Alignment explanation
Indices: 2123910--2123961 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2123900 TTGTATTTAA
*
2123910 CAGTTATCTAATTTAATCCACAGCT
1 CAGTTATCCAATTTAATCCACAGCT
2123935 CAGTTATCCAATTTAATCCACAGCT
1 CAGTTATCCAATTTAATCCACAGCT
2123960 CA
1 CA
2123962 AAGATAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.33
Consensus pattern (25 bp):
CAGTTATCCAATTTAATCCACAGCT
Found at i:2130038 original size:151 final size:151
Alignment explanation
Indices: 2129764--2130044 Score: 375
Period size: 151 Copynumber: 1.9 Consensus size: 151
2129754 GAGGAGTTAT
* * * * *
2129764 AAGTATCAAATTATTACAACATAGATTGTTCGAAGAATCACAAAATAGATCAAACATTAAAGTAT
1 AAGTATCAAATTATTACAACATAGACTATCCGAAGAATCACAAAATAGATCAAACATTAAAGCAC
** * * *
2129829 AATTGAAATAAGAATCGGTACAGTTTAGATTAAGGCCAACAAACTGAACTAACTTGACTAAAACC
66 AACAGAAATAAGAATCGGTACACTTTAGACTAAAGCCAACAAACTGAACTAACTTGACTAAAACC
2129894 TACACATGTTCGTGGAACTAA
131 TACACATGTTCGTGGAACTAA
* * * * * *
2129915 AAGTATCAAATTATTATAGCATGGACTATCCGAAGAATCACAAAGTAGATCAATCGTTAAAGCAC
1 AAGTATCAAATTATTACAACATAGACTATCCGAAGAATCACAAAATAGATCAAACATTAAAGCAC
* * *
2129980 AACCAG-AATAAGAATTGGTACACTTTAGACTAAAGCTAATAAACTGAACTAACTTGACTAAAAC
66 AA-CAGAAATAAGAATCGGTACACTTTAGACTAAAGCCAACAAACTGAACTAACTTGACTAAAAC
2130044 C
130 C
2130045 CACATATGAC
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
151 109 0.99
152 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (151 bp):
AAGTATCAAATTATTACAACATAGACTATCCGAAGAATCACAAAATAGATCAAACATTAAAGCAC
AACAGAAATAAGAATCGGTACACTTTAGACTAAAGCCAACAAACTGAACTAACTTGACTAAAACC
TACACATGTTCGTGGAACTAA
Found at i:2139456 original size:18 final size:18
Alignment explanation
Indices: 2139433--2139525 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
2139423 CCCAACTACT
*
2139433 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
2139451 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
2139469 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
2139487 GTATACGTGAATCGTGCC
1 GTATACGTGAATAGTACC
*
2139505 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
2139523 GTA
1 GTA
2139526 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2139485 original size:36 final size:36
Alignment explanation
Indices: 2139433--2139525 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
2139423 CCCAACTACT
*
2139433 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
* *
2139469 GTATACGTGAATAGTACTGTATACGTGAATCGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
2139505 GTATACATGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
2139526 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:2141045 original size:26 final size:26
Alignment explanation
Indices: 2141016--2141066 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2141006 ATGACTGGGC
*
2141016 CGAGGCTTGATTCCAAATTTCTTTTT
1 CGAGGCTCGATTCCAAATTTCTTTTT
2141042 CGAGGCTCGATTCCAAATTTCTTTT
1 CGAGGCTCGATTCCAAATTTCTTTT
2141067 GCATGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (26 bp):
CGAGGCTCGATTCCAAATTTCTTTTT
Found at i:2143483 original size:13 final size:14
Alignment explanation
Indices: 2143467--2143508 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
2143457 TTTTAATTTT
2143467 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
2143480 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
2143495 ATTTTAAATAATAT
1 ATTTT-AATAATAT
2143509 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:2143493 original size:16 final size:16
Alignment explanation
Indices: 2143471--2143507 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2143461 AATTTTATTT
2143471 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
2143488 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
2143503 TAATA
1 TAATA
2143508 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:2151415 original size:12 final size:12
Alignment explanation
Indices: 2151392--2151426 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2151382 GTAATTCAGT
2151392 TTTAAAAAATTA
1 TTTAAAAAATTA
2151404 -TTAAATAAATTA
1 TTTAAA-AAATTA
2151416 TTTAAAAAATT
1 TTTAAAAAATT
2151427 TAAACAGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTAAAAAATTA
Found at i:2152311 original size:17 final size:18
Alignment explanation
Indices: 2152275--2152313 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2152265 AATAGAAATT
2152275 TATTTTAAAATAAGATAA
1 TATTTTAAAATAAGATAA
*
2152293 TATTTTATAATAA-ATAA
1 TATTTTAAAATAAGATAA
2152310 TATT
1 TATT
2152314 ATATGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTTTAAAATAAGATAA
Found at i:2152356 original size:28 final size:28
Alignment explanation
Indices: 2152299--2152356 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2152289 ATAATATTTT
* *
2152299 ATAATAAATAATATTATATGCAAAATTA
1 ATAATAAACAATATTATATGCAAAACTA
2152327 ATAATAAACAATAGTTA-AT-CAAAACCTA
1 ATAATAAACAATA-TTATATGCAAAA-CTA
2152355 AT
1 AT
2152357 TTAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 18 0.69
29 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (28 bp):
ATAATAAACAATATTATATGCAAAACTA
Found at i:2152564 original size:19 final size:19
Alignment explanation
Indices: 2152495--2152565 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
2152485 ATACAACATT
*
2152495 TATTATTAAATATTTATAAA
1 TATTATTAAA-ATTTAAAAA
** * *
2152515 TGGTA-TAATATATTAAGAA
1 TATTATTAAAAT-TTAAAAA
2152534 TATTATTTAAAATTTAAAAA
1 TATTA-TTAAAATTTAAAAA
2152554 TATTATTAAAAT
1 TATTATTAAAAT
2152566 AAAATTATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 14 0.36
21 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
TATTATTAAAATTTAAAAA
Found at i:2152568 original size:17 final size:19
Alignment explanation
Indices: 2152526--2152569 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2152516 GGTATAATAT
*
2152526 ATTAAGAATATTATTTAAA
1 ATTAAAAATATTATTTAAA
2152545 ATTTAAAAATATTA-TTAAA
1 A-TTAAAAATATTATTTAAA
2152564 A-TAAAA
1 ATTAAAA
2152570 TTATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
19 7 0.30
20 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAAAAATATTATTTAAA
Found at i:2157419 original size:34 final size:33
Alignment explanation
Indices: 2157380--2157443 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2157370 GATTTTCGTT
*
2157380 ATTAAATCAGA-TTATTAAATTTATATTCAAATTA
1 ATTAAATCAGATTTA-CAAATTTATA-TCAAATTA
*
2157414 ATTAAATCGGATTTACAAATTTATATCAAA
1 ATTAAATCAGATTTACAAATTTATATCAAA
2157444 ACCCAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 5 0.19
34 19 0.70
35 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (33 bp):
ATTAAATCAGATTTACAAATTTATATCAAATTA
Found at i:2161108 original size:5 final size:5
Alignment explanation
Indices: 2161091--2161120 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2161081 AAAAATGATA
2161091 GGCCC GAGCCC GGCCC GGCCC GGCCC GGCC
1 GGCCC G-GCCC GGCCC GGCCC GGCCC GGCC
2161121 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.03, C:0.57, G:0.40, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:2161175 original size:24 final size:25
Alignment explanation
Indices: 2161148--2161203 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
2161138 TTTTTTTTAT
*
2161148 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
2161172 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
2161197 -AAATAAA
1 TAAATAAA
2161204 TATTAAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:2161189 original size:25 final size:23
Alignment explanation
Indices: 2161160--2161205 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2161150 AATAAAAAAC
*
2161160 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAAT-AAATACA
2161185 TTTAAAACATAAAAATAAATA
1 TTTAAAACATAAAAATAAATA
2161206 TTAAAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (23 bp):
TTTAAAACATAAAAATAAATACA
Found at i:2162452 original size:3 final size:3
Alignment explanation
Indices: 2162444--2162481 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2162434 TTATATATAT
* *
2162444 TTA TTA TTA -TA TTA TTA CTA TTA TTC TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2162482 AGTATATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2162921 original size:30 final size:32
Alignment explanation
Indices: 2162885--2162956 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2162875 ATATGTATAT
*
2162885 TATATGTATTCTT-TTAATA-TGTATTACATA
1 TATATGTATTCTTATTAATATTATATTACATA
* *
2162915 TATATGTATTTTTATTAATATTATATTATATA
1 TATATGTATTCTTATTAATATTATATTACATA
2162947 TATAT-TATTC
1 TATATGTATTC
2162957 ATATATCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.33
31 10 0.28
32 14 0.39
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (32 bp):
TATATGTATTCTTATTAATATTATATTACATA
Found at i:2165616 original size:11 final size:11
Alignment explanation
Indices: 2165600--2165641 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
2165590 TAGTTATTTA
2165600 TAATAAAATAT
1 TAATAAAATAT
2165611 TAATAAAATAT
1 TAATAAAATAT
*
2165622 CTCATTAAAATAT
1 -T-AATAAAATAT
2165635 TAATAAA
1 TAATAAA
2165642 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:2168115 original size:19 final size:18
Alignment explanation
Indices: 2168093--2168136 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2168083 AAATTACAAA
*
2168093 AAAAATTAAAATAATTTTT
1 AAAAATTAAAAT-ATTTAT
*
2168112 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
2168130 AAAAATT
1 AAAAATT
2168137 TCAGAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:2168137 original size:19 final size:19
Alignment explanation
Indices: 2168092--2168156 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2168082 AAAATTACAA
*
2168092 AAAAAATTAAAATAATTTT
1 AAAAATTTAAAATAATTTT
*
2168111 TAAAATTTAAAAT-ATTTAT
1 AAAAATTTAAAATAATTT-T
*
2168130 AAAAATTTCAGAAATAAATTCT
1 AAAAATTT-A-AAAT-AATTTT
2168152 AAAAA
1 AAAAA
2168157 ATATAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 1 0.03
21 4 0.11
22 6 0.16
23 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTTAAAATAATTTT
Found at i:2168693 original size:16 final size:15
Alignment explanation
Indices: 2168652--2168701 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
2168642 AAAAATAAAG
*
2168652 AATTCAAAATAATTA
1 AATTCAAAAAAATTA
*
2168667 AATTATAAAAAAATTA
1 AATT-CAAAAAAATTA
2168683 AATTCACAAAAAATATA
1 AATTCA-AAAAAAT-TA
2168700 AA
1 AA
2168702 CTTGGCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTCAAAAAAATTA
Found at i:2168701 original size:17 final size:16
Alignment explanation
Indices: 2168641--2168701 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2168631 TACATATTTT
*
2168641 AAAAAATAAAGAATTCA
1 AAAAAATATA-AATTCA
* *
2168658 AAATAAT-TAAATTATA
1 AAAAAATATAAATT-CA
2168674 AAAAAAT-TAAATTCA
1 AAAAAATATAAATTCA
2168689 CAAAAAATATAAA
1 -AAAAAATATAAA
2168702 CTTGGCGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 5 0.14
16 21 0.58
17 10 0.28
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAAAATATAAATTCA
Found at i:2172135 original size:29 final size:28
Alignment explanation
Indices: 2172098--2172170 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
2172088 TTAAATTAGT
*
2172098 AATGGTAAAATTATATATTAA-CTCTTTAA
1 AATGATAAAATTATAT-TTAATCT-TTTAA
2172127 AATGATAAAAATT-TGATTTAATCTTTTAA
1 AATGAT-AAAATTAT-ATTTAATCTTTTAA
* *
2172156 AATTATAAAAATATA
1 AATGATAAAATTATA
2172171 GGTTATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 6 0.16
29 21 0.57
30 10 0.27
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (28 bp):
AATGATAAAATTATATTTAATCTTTTAA
Found at i:2182064 original size:24 final size:24
Alignment explanation
Indices: 2182037--2182085 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2182027 GTCTCTAATT
2182037 AAGTTAGTGTTACGAGTTAATCAG
1 AAGTTAGTGTTACGAGTTAATCAG
2182061 AAGTTAGTGTTACGAGTTAATCAG
1 AAGTTAGTGTTACGAGTTAATCAG
2182085 A
1 A
2182086 CATCAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (24 bp):
AAGTTAGTGTTACGAGTTAATCAG
Found at i:2185842 original size:14 final size:15
Alignment explanation
Indices: 2185823--2185855 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2185813 GTTTATTTTT
2185823 TTTGAATA-AATAAA
1 TTTGAATATAATAAA
*
2185837 TTTGAATATAATGAA
1 TTTGAATATAATAAA
2185852 TTTG
1 TTTG
2185856 TTAATTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTGAATATAATAAA
Found at i:2186082 original size:42 final size:42
Alignment explanation
Indices: 2186035--2186119 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
2186025 TACAATAATC
* *
2186035 ATTTTATAGCTTTATGAAGTTAAGTGATCAAAATATGAACTT
1 ATTTTATAGCTTTATAAAGTTAAGTGACCAAAATATGAACTT
*
2186077 ATTTTATAGTTTTATAAAGTTAAGTGACCAAAATATGAACTT
1 ATTTTATAGCTTTATAAAGTTAAGTGACCAAAATATGAACTT
2186119 A
1 A
2186120 CTAAAAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (42 bp):
ATTTTATAGCTTTATAAAGTTAAGTGACCAAAATATGAACTT
Found at i:2188546 original size:19 final size:20
Alignment explanation
Indices: 2188522--2188559 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2188512 TCTATACAGC
2188522 ATTGTTGTATAG-GTTTTTA
1 ATTGTTGTATAGAGTTTTTA
2188541 ATTGTTGTATAGAGTTTTT
1 ATTGTTGTATAGAGTTTTT
2188560 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTGTTGTATAGAGTTTTTA
Found at i:2196696 original size:25 final size:26
Alignment explanation
Indices: 2196668--2196732 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
2196658 AAAGAATGTA
2196668 TAAAAAAACTTAAAATAAAT-AATAC
1 TAAAAAAACTTAAAATAAATAAATAC
* * *
2196693 TAAAGAAGCCTAAAATAAATAAATAC
1 TAAAAAAACTTAAAATAAATAAATAC
*
2196719 -AAAAGAAATTTAAA
1 TAAAA-AAACTTAAA
2196733 GGTGAATAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.22
Consensus pattern (26 bp):
TAAAAAAACTTAAAATAAATAAATAC
Found at i:2196732 original size:26 final size:25
Alignment explanation
Indices: 2196669--2196732 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 25
2196659 AAGAATGTAT
2196669 AAAA-AAACTTAAAATAAATAATAC
1 AAAAGAAACTTAAAATAAATAATAC
* * *
2196693 TAAAGAAGCCTAAAATAAATAAATAC
1 AAAAGAAACTTAAAATAAAT-AATAC
*
2196719 AAAAGAAATTTAAA
1 AAAAGAAACTTAAA
2196733 GGTGAATAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
24 3 0.10
25 13 0.42
26 15 0.48
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.20
Consensus pattern (25 bp):
AAAAGAAACTTAAAATAAATAATAC
Found at i:2196989 original size:19 final size:17
Alignment explanation
Indices: 2196965--2197000 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2196955 AATAAAAAGG
2196965 TATTTAATAGTTTTCAAAA
1 TATTTAATA-TTTT-AAAA
2196984 TATTTAATATTTTAAAA
1 TATTTAATATTTTAAAA
2197001 CAAATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTTAATATTTTAAAA
Found at i:2204874 original size:53 final size:52
Alignment explanation
Indices: 2204793--2204933 Score: 178
Period size: 53 Copynumber: 2.7 Consensus size: 52
2204783 CTGATTACAT
* * *
2204793 ATCATACCGATGCCATATCCCAGATATGGTCTTATAC-GGAATCACATTATCAC
1 ATCATACCAATGCCATAACCCAGCTATGGTCTTATACGGGAA-CACA-TATCAC
*
2204846 ATCATACCAATGCCATAACCTAGCTATGGTCTTATACGGGAACACATATCAC
1 ATCATACCAATGCCATAACCCAGCTATGGTCTTATACGGGAACACATATCAC
*** *
2204898 ATTGCACCAATGCCATAGCCCAGCTAT-GTCTTATAC
1 ATCATACCAATGCCATAACCCAGCTATGGTCTTATAC
2204934 AGAAGCATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 9 0.12
52 28 0.36
53 37 0.47
54 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (52 bp):
ATCATACCAATGCCATAACCCAGCTATGGTCTTATACGGGAACACATATCAC
Found at i:2207910 original size:27 final size:28
Alignment explanation
Indices: 2207876--2207943 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
2207866 ATGCCTTATT
* *
2207876 GGTGTGTTTGGGAGGA-TATATTATACC
1 GGTGTGTTTGGGAGGATTACAATATACC
*
2207903 GGTGTGTTAT-GGAGGATTTACAATATTCC
1 GGTGTGTT-TGGGAGGA-TTACAATATACC
2207932 GGTGTGTTTGGG
1 GGTGTGTTTGGG
2207944 TTGGATATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 14 0.41
28 2 0.06
29 18 0.53
ACGTcount: A:0.19, C:0.07, G:0.35, T:0.38
Consensus pattern (28 bp):
GGTGTGTTTGGGAGGATTACAATATACC
Found at i:2223886 original size:5 final size:5
Alignment explanation
Indices: 2223876--2223903 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2223866 CAATTTGGGA
2223876 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
2223904 CAAAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:2225669 original size:11 final size:11
Alignment explanation
Indices: 2225639--2225677 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2225629 AAATAACAAA
*
2225639 AAAATAGTAGC
1 AAAATAATAGC
* *
2225650 AATATAATAGT
1 AAAATAATAGC
2225661 AAAATAATAGC
1 AAAATAATAGC
2225672 AAAATA
1 AAAATA
2225678 GTAAAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:2225686 original size:22 final size:22
Alignment explanation
Indices: 2225636--2225706 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
2225626 ATAAAATAAC
* * *
2225636 AAAAAAATAGTAGCAATATAAT
1 AAAAAAATAATAGCAAAATAGT
**
2225658 AGTAAAATAATAGCAAAATAGT
1 AAAAAAATAATAGCAAAATAGT
2225680 AAAAAAA-ACA-AG-AAAATAGT
1 AAAAAAATA-ATAGCAAAATAGT
*
2225700 AATAAAA
1 AAAAAAA
2225707 CAGTAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 14 0.35
21 3 0.08
22 23 0.57
ACGTcount: A:0.68, C:0.04, G:0.10, T:0.18
Consensus pattern (22 bp):
AAAAAAATAATAGCAAAATAGT
Found at i:2226799 original size:42 final size:42
Alignment explanation
Indices: 2226740--2226824 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2226730 CAATTTGATG
2226740 ATAGTTCCCATTACTAAGGGAGATAATCATAATCTGTGGTTC
1 ATAGTTCCCATTACTAAGGGAGATAATCATAATCTGTGGTTC
2226782 ATAGTTCCCATTACTAAGGGAGATAATCATAATCTGTGGTTC
1 ATAGTTCCCATTACTAAGGGAGATAATCATAATCTGTGGTTC
2226824 A
1 A
2226825 ATGGCTTCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (42 bp):
ATAGTTCCCATTACTAAGGGAGATAATCATAATCTGTGGTTC
Found at i:2232299 original size:57 final size:57
Alignment explanation
Indices: 2232225--2232492 Score: 333
Period size: 57 Copynumber: 4.7 Consensus size: 57
2232215 TTCGTGACGA
* * * *
2232225 CATCACTAAACGAATGACCTTTACCTCCTTCACTTGGACCTGAATTGG-GGTTGACAG
1 CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACCTGAATTGGTGG-TGACAG
* * *
2232282 CATCAGTAAATGCATGACCTTTGCCGCCTTCACTTGGACCTGAATTGG-GGTTGACAG
1 CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACCTGAATTGGTGG-TGACAG
* * * *
2232339 CATCAGTAAATGCATGACCTTTACCTCCTGGACTTGGACCTGAGTTGGTGGTGACAG
1 CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACCTGAATTGGTGGTGACAG
* * * * *
2232396 CATCACTATATGCATGACCTTTGCCACCAGAACTTGGCCCTGAATTGGTGGTGACAG
1 CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACCTGAATTGGTGGTGACAG
* * *
2232453 AATCACTAAATGCATGACCTTTGCCTCCTGGACTAGGACC
1 CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACC
2232493 ACTGGTTTTG
Statistics
Matches: 185, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
57 183 0.99
58 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (57 bp):
CATCACTAAATGCATGACCTTTGCCTCCTGCACTTGGACCTGAATTGGTGGTGACAG
Done.