Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005494.1 Hibiscus syriacus cultivar Beakdansim tig00012638_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 54326
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:5104 original size:83 final size:82
Alignment explanation
Indices: 4603--5473 Score: 741
Period size: 80 Copynumber: 10.7 Consensus size: 82
4593 GCTTAAGTCG
* * *
4603 AGAAGGGCTATCTGC-CAAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTA
1 AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTA
*
4667 CAGCATAACTCAACGCT
66 CAGCATAACTCAAGGCT
* * * *
4684 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATT
1 AGAAGGGTTATCTG-CA-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATT
** * * * * *
4748 TGTAGTATAGCTTAAGTCG
64 TACAGCATAACTCAAGGCT
* * * *
4767 AGAAGGGCTCTCTTC-C-AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
1 AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTA
*
4830 TAGCATAACTCAAGGCT
66 CAGCATAACTCAAGGCT
* * *
4847 AGAA-GGTTATCTGCAACCAAAGACCTTCGAGTTCGACT--ACTCAGC-TCCAAGGCACATCATT
1 AGAAGGGTTATCTGC-A-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATT
* * * * *
4908 TGCAGCATAGCTTAAGTCG
64 TACAGCATAACTCAAGGCT
* * *
4927 AGAA-GGCTATATGC-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
1 AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTA
*
4990 CGGCATAACTCAAGGCT
66 CAGCATAACTCAAGGCT
** * * *
5007 AGAACAGTTATCTGTCAACAAAGACCCTCGAGTTTGATTAC-CTCAGCTTCGAAGGAATATCATT
1 AGAAGGGTTATCTG-C-ACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATT
*
5071 TACAACATAACTCAAGGCT
64 TACAGCATAACTCAAGGCT
* * * * * *
5090 AGAAGGGTTATCTGTGACCAAAAGACCCTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCAT
1 AGAAGGGTTATCTG-CA-C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCAT
* * * * *
5154 TTGCATCATAACTTAAGTCG
63 TTACAGCATAACTCAAGGCT
* * * * *
5174 AGTAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT--G-TTCCAAGG--CATCAT
1 AGAAGGGTTATCTG-C-A-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCAT
* * *
5234 TTGCAGCATAGCTTAA-G-T
63 TTACAGCATAACTCAAGGCT
* * *
5252 CGAAGGGTTATCTGC-TAAAGACCCTCGAGTTCGATTACACTCAGCTTCG-AGGCACATAATTTA
1 AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTA
* *
5315 CGGCATAAATCAAGGCT
66 CAGCATAACTCAAGGCT
* * * * *
5332 AGAAGGGTTATCTGTCA-ACAAGACCTTCGAGTTCGACTCCACTCAGC-TCAAAGGAACCATCAT
1 AGAAGGGTTATCTG-CACA-AAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCA-CATCAT
* * *
5395 TTGCAGTATAGCTCAAGG-T
63 TTACAGCATAACTCAAGGCT
* * * * *
5414 AAGAAGGGTTATCTGC-CAAAGACCTTCGAGTTCGATTCCATTCAGC-TCGAGGGCATATCA
1 -AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCA
5474 ACCACGTTGC
Statistics
Matches: 641, Mismatches: 115, Indels: 69
0.78 0.14 0.08
Matches are distributed among these distances:
74 22 0.03
76 4 0.01
77 23 0.04
78 28 0.04
79 42 0.07
80 137 0.21
81 62 0.10
82 45 0.07
83 134 0.21
84 135 0.21
85 9 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (82 bp):
AGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTA
CAGCATAACTCAAGGCT
Found at i:5445 original size:163 final size:163
Alignment explanation
Indices: 4581--5473 Score: 1026
Period size: 163 Copynumber: 5.5 Consensus size: 163
4571 TAAAGAAACT
4581 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * *
4646 GCTTTGAGGGCACATCATTTACAGCATAACTCAACGCTAGAAGGGTTATCTGCCACCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCT
* * * *
4711 TTGAGTTCGACTACGCTCAGCTTCAAGGCACATC
131 TCGAGTTCGACT-CACTCAGCTCCAAGGAACATC
* * * *
4745 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTCTCTTCC-AAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
*
4809 GCTTCGAGGGCACATCATTTATAGCATAACTCAAGGCTAGAA-GGTTATCTG-CAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACC
*
4872 TTCGAGTTCGACT-ACTCAGCTCCAAGGCACATC
130 TTCGAGTTCGACTCACTCAGCTCCAAGGAACATC
*
4905 ATTTGCAGCATAGCTTAAGTCGAGAA-GGCTATATGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* ** * *
4969 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAACAGTTATCTGTCAACAAAGACCC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCT
* * * *
5034 TCGAGTTTGA-TTACCTCAGCTTCGAAGGAATATC
131 TCGAGTTCGACTCA-CTCAGC-TCCAAGGAACATC
* * * * * * * * * *
5068 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCTCGAGTTTGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTCGAGTTCGATTACA
* * * * * * * * *
5133 CTCAGC-TCCAAGGCATATCATTTGCATCATAACTTAAGTCGAGTAGGGTTATCTGCCAACCAAA
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAA
* * *
5197 GACCTTCGAGTTCGACT-ACGCTGTTCCAAGG--CATC
126 GACCTTCGAGTTCGACTCACTCAGCTCCAAGGAACATC
* *
5232 ATTTGCAGCATAGCTTAAGTC--GAAGGGTTATCTGCTAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * * *
5295 GCTTCGA-GGCACATAATTTACGGCATAAATCAAGGCTAGAAGGGTTATCTGTCAAC-AAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCT
*
5358 TCGAGTTCGACTCCACTCAGCTCAAAGGAACCATC
131 TCGAGTTCGACT-CACTCAGCTCCAAGGAA-CATC
* * * * * * *
5393 ATTTGCAGTATAGCTCAAGGT-AAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTCCATTC
1 ATTTGCAGCATAGCTTAA-GTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
*
5457 AGC-TCGAGGGCATATCA
65 AGCTTCGAGGGCACATCA
5474 ACCACGTTGC
Statistics
Matches: 617, Mismatches: 88, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
156 19 0.03
157 1 0.00
158 73 0.12
159 12 0.02
160 111 0.18
161 48 0.08
162 55 0.09
163 142 0.23
164 58 0.09
166 8 0.01
167 45 0.07
168 44 0.07
169 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCT
TCGAGTTCGACTCACTCAGCTCCAAGGAACATC
Found at i:5813 original size:25 final size:25
Alignment explanation
Indices: 5783--5835 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5773 AATTTTACTA
*
5783 TATTA-TATATTA-TTTATTT-ATT
1 TATTATTATATTATTTTTTTTAATT
5805 TATTATTATATTATTTTTTTTAATT
1 TATTATTATATTATTTTTTTTAATT
5830 TATTAT
1 TATTAT
5836 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 7 0.26
24 6 0.22
25 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TATTATTATATTATTTTTTTTAATT
Found at i:5835 original size:22 final size:22
Alignment explanation
Indices: 5775--5844 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
5765 TCTACAAAAA
*
5775 TTTTACTATATTA-TATATTATT
1 TTTTATTA-ATTATTATATTATT
*
5797 TATTTATTTATTATTATATTATT
1 T-TTTATTAATTATTATATTATT
5820 TTTT-TTAATTTATTATATTATT
1 TTTTATTAA-TTATTATATTATT
5842 TTT
1 TTT
5845 ACAGGCCTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.07
22 24 0.57
23 15 0.36
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTAATTATTATATTATT
Found at i:5841 original size:25 final size:26
Alignment explanation
Indices: 5776--5841 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 26
5766 CTACAAAAAT
*
5776 TTTACTATATTATATATTATTTATTTA
1 TTTATTATATTAT-TATTATTTATTTA
5803 TTTATTAT-TATATTATT-TTT-TTTAA
1 TTTATTATAT-TATTATTATTTATTT-A
5828 TTTATTATATTATT
1 TTTATTATATTATT
5842 TTTACAGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 6 0.17
27 10 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATTATATTATTATTATTTATTTA
Found at i:5960 original size:33 final size:31
Alignment explanation
Indices: 5890--5960 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
5880 TTCAGAAAAT
* * *
5890 AAACCAACGTATTTGAGTCTTACTGAATCTA
1 AAACCAACGTATTTGAGTCATACTAAAACTA
*
5921 AAACCAACGTATTTGAGTCATATTAAAACACTA
1 AAACCAACGTATTTGAGTCATACT-AAA-ACTA
5954 AAACCAA
1 AAACCAA
5961 AGCATTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 22 0.65
32 2 0.06
33 10 0.29
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (31 bp):
AAACCAACGTATTTGAGTCATACTAAAACTA
Found at i:5989 original size:34 final size:33
Alignment explanation
Indices: 5917--5989 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 33
5907 TCTTACTGAA
* * *
5917 TCTAAAACCAACGTATTTGAGTCATATTAAAAC
1 TCTAAAACCAAAGCATTTGAGTCATAGTAAAAC
* *
5950 ACTAAAACCAAAGCATTTTGAGTCCA-AGTAGAAC
1 TCTAAAACCAAAGCA-TTTGAGT-CATAGTAAAAC
5984 TCTAAA
1 TCTAAA
5990 TCTGAGCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
33 12 0.38
34 18 0.56
35 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
TCTAAAACCAAAGCATTTGAGTCATAGTAAAAC
Found at i:6337 original size:4 final size:4
Alignment explanation
Indices: 6328--6352 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6318 TACATTGTTA
6328 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
6353 CGTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:7660 original size:20 final size:19
Alignment explanation
Indices: 7614--7669 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
7604 ATCTTATTCT
* *
7614 TTAGTAATATTACATTCTC
1 TTAGTAATCTTACATTCCC
*
7633 -TGGTAATCTTACATTCCC
1 TTAGTAATCTTACATTCCC
7651 ATTAGTAATCTTACATTCC
1 -TTAGTAATCTTACATTCC
7670 GTAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 15 0.48
20 16 0.52
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (19 bp):
TTAGTAATCTTACATTCCC
Found at i:8854 original size:21 final size:21
Alignment explanation
Indices: 8818--8883 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
8808 CGATCCATTA
*
8818 ATCCGATCT-GAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
8838 ATCCGATCTAAAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
*
8859 ATCCAATCTAAAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
8880 ATCC
1 ATCC
8884 AATCCGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
20 9 0.21
21 34 0.79
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (21 bp):
ATCCGATCTAAAAAATCGGAT
Found at i:8884 original size:21 final size:21
Alignment explanation
Indices: 8828--8887 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
8818 ATCCGATCTG
*
8828 AAAATCGGATATCCGATCTAA
1 AAAATCGGATATCCAATCTAA
8849 AAAATCGGATATCCAATCTAA
1 AAAATCGGATATCCAATCTAA
8870 AAAATCGGATATCCAATC
1 AAAATCGGATATCCAATC
8888 CGTTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAATCGGATATCCAATCTAA
Found at i:9839 original size:17 final size:16
Alignment explanation
Indices: 9791--9839 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
9781 CGGATATCCG
*
9791 ATCCGAAATTTTGGAT
1 ATCCGAATTTTTGGAT
9807 ATCCGAATTTTTGGAT
1 ATCCGAATTTTTGGAT
* *
9823 ATCTGATTTTTTCGGAT
1 ATCCGAATTTTT-GGAT
9840 TGGATACGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 25 0.86
17 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (16 bp):
ATCCGAATTTTTGGAT
Found at i:14991 original size:20 final size:20
Alignment explanation
Indices: 14952--14992 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
14942 AATATCAAGT
* * *
14952 AGAAGCAAGCAATGTCAAAC
1 AGAAGCAAACAATATAAAAC
14972 AGAAGCAAACAATATAAAAC
1 AGAAGCAAACAATATAAAAC
14992 A
1 A
14993 TAATAAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.17, G:0.15, T:0.10
Consensus pattern (20 bp):
AGAAGCAAACAATATAAAAC
Found at i:16553 original size:63 final size:63
Alignment explanation
Indices: 16429--16585 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 63
16419 TTAAATCAAT
* * * ** * *
16429 TGCTTCGGACAGTAAATCATTTACATCCCCTTGCAAAAAAAAACCATGGTTAGTTTACATTAAA
1 TGCTTCTGACAATATATCATTTACAT-CAATAGCAAAAAAAAACCAGGGTTAGTTTACATTAAA
*
16493 TGCTTCTGACAATATATCATTTACATCAATAGCAATAAAAAACCAGGGTTAGTTTACATTAAA
1 TGCTTCTGACAATATATCATTTACATCAATAGCAAAAAAAAACCAGGGTTAGTTTACATTAAA
*
16556 TGC-T-TGACATTATATCATTTACATCAATAG
1 TGCTTCTGACAATATATCATTTACATCAATAG
16586 ATTTATACCA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
61 25 0.30
62 1 0.01
63 35 0.42
64 23 0.27
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (63 bp):
TGCTTCTGACAATATATCATTTACATCAATAGCAAAAAAAAACCAGGGTTAGTTTACATTAAA
Found at i:16603 original size:2 final size:2
Alignment explanation
Indices: 16596--16626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16586 ATTTATACCA
16596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16627 CAAAGAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16758 original size:6 final size:6
Alignment explanation
Indices: 16727--16751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16717 TAATTTGAAT
16727 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
16752 ATGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:16880 original size:18 final size:18
Alignment explanation
Indices: 16847--16881 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16837 TCAAATAGTT
*
16847 TGGGTTCGGGTATGGGTA
1 TGGGTTCGGATATGGGTA
*
16865 TGGGTTCGGATTTGGGT
1 TGGGTTCGGATATGGGT
16882 TCGAGTTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.49, T:0.37
Consensus pattern (18 bp):
TGGGTTCGGATATGGGTA
Found at i:16918 original size:18 final size:18
Alignment explanation
Indices: 16878--16919 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16868 GTTCGGATTT
16878 GGGTTCGAGTTTGGGTCC
1 GGGTTCGAGTTTGGGTCC
* * *
16896 AGGTTCTAGTTTGGGTTC
1 GGGTTCGAGTTTGGGTCC
16914 GGGTTC
1 GGGTTC
16920 CGGTTCGGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.14, G:0.40, T:0.38
Consensus pattern (18 bp):
GGGTTCGAGTTTGGGTCC
Found at i:17574 original size:24 final size:23
Alignment explanation
Indices: 17547--17619 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
17537 ATCAAAATTT
17547 AAAACATAATTCAGGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
* * *
17571 AAAACAGAGTCCATGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
*
17595 ATATAA-AAATTCAGGTCAAATATC
1 A-A-AACAAATTCAGGTCAAGTATC
17619 A
1 A
17620 TATCGGAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 35 0.90
25 2 0.05
26 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (23 bp):
AAAACAAATTCAGGTCAAGTATC
Found at i:17620 original size:24 final size:24
Alignment explanation
Indices: 17580--17648 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
17570 CAAAACAGAG
* *
17580 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* ***
17604 TTCAGGTCAAATATCATATCGGAA
1 TCCAGGTCAAATATCATATAAAAA
*
17628 TCCAGGTCAAA-ATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
17649 CTATTTATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:18332 original size:13 final size:13
Alignment explanation
Indices: 18314--18349 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
18304 AGCGGTCAAC
18314 GGTCAACGGGTCG
1 GGTCAACGGGTCG
18327 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
18339 GGTAAACGGGT
1 GGTCAACGGGT
18350 AAACGGTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:18337 original size:7 final size:7
Alignment explanation
Indices: 18293--18322 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
18283 GAATAGCACT
18293 GGTCAAC
1 GGTCAAC
*
18300 GGTCAGC
1 GGTCAAC
18307 GGTCAAC
1 GGTCAAC
18314 GGTCAAC
1 GGTCAAC
18321 GG
1 GG
18323 GTCGGGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.37, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:18339 original size:12 final size:12
Alignment explanation
Indices: 18322--18387 Score: 77
Period size: 12 Copynumber: 5.7 Consensus size: 12
18312 ACGGTCAACG
*
18322 GGTCGGGTCAAC
1 GGTCGGGTAAAC
18334 GGTCGGGTAAA-
1 GGTCGGGTAAAC
18345 ---CGGGTAAAC
1 GGTCGGGTAAAC
18354 GGTCGGGTAAAC
1 GGTCGGGTAAAC
18366 GGTCGGGGTAAAC
1 GGTC-GGGTAAAC
18379 GGGTCGGGT
1 -GGTCGGGT
18388 CGGGTAAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
8 8 0.17
12 23 0.49
13 12 0.26
14 4 0.09
ACGTcount: A:0.21, C:0.17, G:0.45, T:0.17
Consensus pattern (12 bp):
GGTCGGGTAAAC
Found at i:18348 original size:20 final size:20
Alignment explanation
Indices: 18325--18367 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
18315 GTCAACGGGT
*
18325 CGGGTCAACGGTCGGGTAAA
1 CGGGTAAACGGTCGGGTAAA
18345 CGGGTAAACGGTCGGGTAAA
1 CGGGTAAACGGTCGGGTAAA
18365 CGG
1 CGG
18368 TCGGGGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.42, T:0.14
Consensus pattern (20 bp):
CGGGTAAACGGTCGGGTAAA
Found at i:18358 original size:32 final size:34
Alignment explanation
Indices: 18293--18398 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 34
18283 GAATAGCACT
* *
18293 GGTCAACGGTCAGCGGTCAAC-GGTCAACGGGTCG
1 GGTCAACGGTCAG-GGTAAACGGGTAAACGGGTCG
18327 GGTCAACGGTC-GGGTAAACGGGTAAAC-GGTCG
1 GGTCAACGGTCAGGGTAAACGGGTAAACGGGTCG
* *
18359 GGTAAACGGTCGGGGTAAACGGGT---CGGGTCG
1 GGTCAACGGTCAGGGTAAACGGGTAAACGGGTCG
*
18390 GGTAAACGG
1 GGTCAACGG
18399 GTCGTGACCG
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
30 1 0.02
31 14 0.21
32 21 0.32
33 19 0.29
34 11 0.17
ACGTcount: A:0.23, C:0.20, G:0.42, T:0.15
Consensus pattern (34 bp):
GGTCAACGGTCAGGGTAAACGGGTAAACGGGTCG
Found at i:24669 original size:24 final size:23
Alignment explanation
Indices: 24642--24714 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
24632 TCAAAAATTT
24642 AAAACATAATTCAGGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
* * *
24666 AAAACAGAGTCCATGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
*
24690 ATATAA-AAATTCAGGTCAAATATC
1 A-A-AACAAATTCAGGTCAAGTATC
24714 A
1 A
24715 TATCGGAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 35 0.90
25 2 0.05
26 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (23 bp):
AAAACAAATTCAGGTCAAGTATC
Found at i:25453 original size:18 final size:18
Alignment explanation
Indices: 25430--25465 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25420 TTGGGTCAAC
*
25430 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
25448 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
25466 TGACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:26539 original size:102 final size:100
Alignment explanation
Indices: 26353--26688 Score: 374
Period size: 102 Copynumber: 3.2 Consensus size: 100
26343 TTTGTAAGGA
* **
26353 TTTGGGGAAGAACAT-GAATGAACAATGGATGAAT-TTGTGGGTGTTTGATCGGAAAAAACATTT
1 TTTGGGGAAGAAC-TGGGATGAACAA-GGATGAATATT-TGGGTGTTTGATC-GAAAAAA-ATGA
* *
26416 AATGGTTTGGGTTTCGGTGTTTTTGAAGATCAAATGAGGGT
61 AATGGTTTGTGTTT-TGTGTTTTTGAAGATCAAATGAGGGT
**
26457 TTTGGGGAAGATTTGGGATGAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAATATGAAATG
1 TTTGGGGAAGAACTGGGATGAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAA-ATGAAATG
26522 GTTTGTGTTTTAGTGTTTTTGAAGATCAAATGAGGGT
65 GTTTGTGTTTT-GTGTTTTTGAAGATCAAATGAGGGT
*
26559 TTTAGGGAAGAACTGGATGAACAAATGAAGAACAAGGATGAATATTTGGGTGTTTGATCGAAAAA
1 TTTGGGGAAGAACTGG--G-----AT---GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAA
* * * *
26624 AACGAAATTGTTTGT-TTGTGT-TTTTTGAAGATCAAATTAGGGT
56 AATGAAATGGTTTGTGTTTTGTGTTTTTGAAGATCAAATGAGGGT
26667 TTTGGGGAAGAACTGGGATGAA
1 TTTGGGGAAGAACTGGGATGAA
26689 AAAAAAATGA
Statistics
Matches: 203, Mismatches: 16, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
98 3 0.01
101 2 0.01
102 60 0.30
103 22 0.11
104 23 0.11
106 1 0.00
108 36 0.18
109 4 0.02
110 3 0.01
111 12 0.06
112 37 0.18
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (100 bp):
TTTGGGGAAGAACTGGGATGAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAAATGAAATGG
TTTGTGTTTTGTGTTTTTGAAGATCAAATGAGGGT
Found at i:26704 original size:112 final size:112
Alignment explanation
Indices: 26476--26692 Score: 343
Period size: 112 Copynumber: 2.0 Consensus size: 112
26466 GATTTGGGAT
* *
26476 GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAATATGAAATGGTTTGTGTTTTAGTGTTTT
1 GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAATACGAAATGGTTTGTGTTGTAGTGTTTT
*
26541 TGAAGATCAAATGAGGGTTTTAGGGAAGAACTGGATGAACAAATGAA
66 TGAAGATCAAATGAGGGTTTTAGGGAAGAACTGGATGAAAAAATGAA
*
26588 GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAA-ACGAAATTGTTTGT-TTGT-GT-TTTT
1 GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAATACGAAATGGTTTGTGTTGTAGTGTTTT
* *
26649 TGAAGATCAAATTAGGGTTTTGGGGAAGAACTGGGATGAAAAAA
66 TGAAGATCAAATGAGGGTTTTAGGGAAGAACT-GGATGAAAAAA
26693 AAATGAAGAA
Statistics
Matches: 98, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
108 34 0.35
109 12 0.12
110 3 0.03
111 12 0.12
112 37 0.38
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (112 bp):
GAACAAGGATGAATATTTGGGTGTTTGATCGAAAAAATACGAAATGGTTTGTGTTGTAGTGTTTT
TGAAGATCAAATGAGGGTTTTAGGGAAGAACTGGATGAAAAAATGAA
Found at i:27159 original size:16 final size:16
Alignment explanation
Indices: 27138--27168 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27128 ATCTTTTCAA
27138 TATATAGTTTATATAC
1 TATATAGTTTATATAC
27154 TATATAGTTTATATA
1 TATATAGTTTATATA
27169 TACTAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATAGTTTATATAC
Found at i:27184 original size:33 final size:31
Alignment explanation
Indices: 27147--27335 Score: 123
Period size: 33 Copynumber: 5.8 Consensus size: 31
27137 ATATATAGTT
*
27147 TATATACTATATAGTTTATATATACTAATGAA
1 TATATAATATATAGTTTATATATA-TAATGAA
*
27179 CTATATAATATATAGTTTATATA-ATGA--AA
1 -TATATAATATATAGTTTATATATATAATGAA
* *
27208 TATATAATGTATAGTTTATATATATTATATAGTTTA
1 TATATAATATATAGTTTATATATA-TA-AT-G--AA
* * * * * * **
27244 TATATACTAATAAACTATATAATGTATAGTTTTA
1 TATATAAT-ATATAGTTTAT-ATATATA-ATGAA
**
27278 TATATACCATATAGTTTATATATACTAATGAA
1 TATATAATATATAGTTTATATATA-TAATGAA
27310 CTATATAATATATAGTTTATATATAT
1 -TATATAATATATAGTTTATATATAT
27336 TATATAGTTT
Statistics
Matches: 120, Mismatches: 24, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
28 21 0.17
29 3 0.03
30 1 0.01
31 3 0.03
32 8 0.07
33 53 0.44
34 9 0.08
36 8 0.07
37 10 0.08
38 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TATATAATATATAGTTTATATATATAATGAA
Found at i:27189 original size:49 final size:49
Alignment explanation
Indices: 27105--27201 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
27095 AATAAATTAA
* *
27105 TATATAGGTTATATATACTAATGATCTTTTCAATATATAGTTTATATAC
1 TATATAGGTTATATATACTAATGAACTTATCAATATATAGTTTATATAC
*
27154 TATATAGTTTATATATACTAATGAACTATAT-AATATATAGTTTATATA
1 TATATAGGTTATATATACTAATGAACT-TATCAATATATAGTTTATATA
27202 ATGAAATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 42 0.95
50 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (49 bp):
TATATAGGTTATATATACTAATGAACTTATCAATATATAGTTTATATAC
Found at i:27486 original size:7 final size:6
Alignment explanation
Indices: 27180--27998 Score: 85
Period size: 7 Copynumber: 130.2 Consensus size: 6
27170 ACTAATGAAC
* * * *
27180 TATATA -ATATA TAGTTTA TATA-A TGAAATA TATA-A TGTATA GTTTATA
1 TATATA TATATA TA-TATA TATATA T-ATATA TATATA TATATA -TATATA
* * * *
27228 TATAT- TATATA GTTTATA TATACTA -ATAAA CTATATA -ATGTA TAGT-TT
1 TATATA TATATA -TATATA TATA-TA TATATA -TATATA TATATA TA-TATA
* * *
27276 TATATA TACCATA TAGTTTA TATATA CTA-ATGA -ACTATA TA-ATA TATAGTT
1 TATATA TA-TATA TA-TATA TATATA -TATAT-A TA-TATA TATATA TATA-TA
* *
27327 TATATA TAT-TA TATAGTT TATATA TA-ATA TA-ATA TAAAT- TATAGTA
1 TATATA TATATA TATA-TA TATATA TATATA TATATA TATATA TATA-TA
* * * *
27373 TATAGTA TATAAA TATCA-A CTATAGTA TATAGTT TATATA GTTTTTA
1 TATA-TA TATATA TAT-ATA -TATA-TA TATA-TA TATATA -TATATA
* * *
27420 TATATA GT-TCATA TGTAAA T-TATA CTATATA T-TATA TATAGTT TATATA
1 TATATA -TAT-ATA TATATA TATATA -TATATA TATATA TATA-TA TATATA
* * * * *
27469 TATA-A TATATA TAGTATA TAAATA TAAACTA TAGTATG TAGTACA TAAATA
1 TATATA TATATA TA-TATA TATATA TATA-TA TA-TATA TA-TATA TATATA
* * * * *
27520 TA-AAA TATAGTT TATATA TATAT- TATATA CTATATA AAT-TG TTTATA
1 TATATA TATA-TA TATATA TATATA TATATA -TATATA TATATA TATATA
* ** * *
27567 TAGT-TCA CTA-ATA AACTATA TATATA GGTCATA TGTAAA CTATATA
1 TA-TAT-A -TATATA TA-TATA TATATA TAT-ATA TATATA -TATATA
* * * * * * *
27613 GTTTATA TATATA GT-TCATA TGTAAA TATCAAA TATAGTT TATATG TAAACTA
1 -TATATA TATATA -TAT-ATA TATATA TAT-ATA TATA-TA TATATA TATA-TA
* * *
27666 TAGT-TA GTATATA AACTATA TAGTTTA TATATA AACTATA GT-TCATA
1 TA-TATA -TATATA TA-TATA TA-TATA TATATA TA-TATA -TAT-ATA
* * * *
27713 TATAAA TATCAAA TATAGTA TATATA TAGT-TCA TATGTA AACTATA GT-TCATA
1 TATATA TAT-ATA TATA-TA TATATA TA-TAT-A TATATA TA-TATA -TAT-ATA
* * * * *
27766 TATATA GTATATA AATATA AACTATA GTTTATA TAAATA GTATA-A AATATA
1 TATATA -TATATA TATATA TA-TATA -TATATA TATATA -TATATA TATATA
* * * * * *
27817 GTATATA -AAAT- TATAAA TATAAA CTATAGTA TGTAGTA TATAAA TATAAA
1 -TATATA TATATA TATATA TATATA -TATA-TA TATA-TA TATATA TATATA
* * *
27867 CTATA-A TTTATA TAT-TA TATATA GTATATA CTATATA AATAGTT TATATA
1 -TATATA TATATA TATATA TATATA -TATATA -TATATA TATA-TA TATATA
* * *
27917 T-TATA TATAGTC TATACTA TATAAA TAGTTTA TATAGT- TCACTA-A
1 TATATA TATA-TA TATA-TA TATATA TA-TATA TATA-TA T-A-TATA
*
27962 TAAACTA TATATA TATATA TATATA TATATA TA-ATA T
1 TATA-TA TATATA TATATA TATATA TATATA TATATA T
27999 GTAAACTATA
Statistics
Matches: 596, Mismatches: 114, Indels: 207
0.65 0.12 0.23
Matches are distributed among these distances:
5 97 0.16
6 212 0.36
7 280 0.47
8 7 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:27555 original size:9 final size:8
Alignment explanation
Indices: 27180--27998 Score: 85
Period size: 9 Copynumber: 97.6 Consensus size: 8
27170 ACTAATGAAC
27180 TATATA-A
1 TATATATA
*
27187 TATATAGTT
1 TATATA-TA
27196 TATATA-A
1 TATATATA
*
27203 TGAAATATA
1 T-ATATATA
*
27212 TA-ATGTA
1 TATATATA
*
27219 TAGTTTATA
1 TA-TATATA
27228 TATAT-TA
1 TATATATA
*
27235 TATAGTTTA
1 TATA-TATA
27244 TATATACTA
1 TATATA-TA
*
27253 -ATAAACTA
1 TATATA-TA
*
27261 TATA-ATG
1 TATATATA
*
27268 TATAGT-TT
1 TATA-TATA
27276 TATATATA
1 TATATATA
* *
27284 CCATATAGTT
1 -TATATA-TA
27294 TATATATA
1 TATATATA
27302 CTA-ATGA-A
1 -TATAT-ATA
27310 CTATATA-A
1 -TATATATA
*
27318 TATATAGTT
1 TATATA-TA
27327 TATATATA
1 TATATATA
27335 T-TATATA
1 TATATATA
*
27342 GTTTATATA
1 -TATATATA
27351 TA-ATATA
1 TATATATA
*
27358 -ATATAAA
1 TATATATA
27365 T-TATAGTA
1 TATATA-TA
27373 TATAGTATA
1 TATA-TATA
*
27382 TAAATATCA
1 TATATAT-A
27391 -ACTATAGTA
1 TA-TATA-TA
*
27400 TATAGTTTA
1 TATA-TATA
* *
27409 TATAGTTTT
1 TATA-TATA
27418 TATATATA
1 TATATATA
*
27426 GT-TCATATG
1 -TAT-ATATA
*
27435 TAAAT-TA
1 TATATATA
27442 TACTATATA
1 TA-TATATA
27451 T-TATATA
1 TATATATA
*
27458 TAGTTTATA
1 TA-TATATA
27467 TATATA-A
1 TATATATA
27474 TATATATA
1 TATATATA
*
27482 GTATATAAA
1 -TATATATA
*
27491 TATAAACTA
1 TATATA-TA
*
27500 TAGTATGTA
1 TA-TATATA
* *
27509 GTACATAAA
1 -TATATATA
*
27518 TATA-AAA
1 TATATATA
*
27525 TATAGTTTA
1 TATA-TATA
27534 TATATATA
1 TATATATA
27542 T-TATATA
1 TATATATA
*
27549 CTATATAAA
1 -TATATATA
* *
27558 T-TGTTTA
1 TATATATA
27565 TATAGT-TCA
1 TATA-TAT-A
*
27574 CTA-ATAAA
1 -TATATATA
27582 CTATATATA
1 -TATATATA
**
27591 TAGGTCATA
1 TATAT-ATA
* *
27600 TGTAAACTA
1 TATATA-TA
*
27609 TATAGTTTA
1 TATA-TATA
27618 TATATATA
1 TATATATA
*
27626 GT-TCATATG
1 -TAT-ATATA
*
27635 TAAATATCA
1 TATATAT-A
* *
27644 AATATAGTT
1 TATATA-TA
*
27653 TATATGTA
1 TATATATA
*
27661 AACTATAGT-
1 TA-TATA-TA
27670 TAGTATATA
1 TA-TATATA
*
27679 AACTATATA
1 TA-TATATA
*
27688 GTTTATATA
1 -TATATATA
*
27697 TAAACTATA
1 TATA-TATA
27706 GT-TCATATA
1 -TAT-ATATA
*
27715 TAAATATCA
1 TATATAT-A
*
27724 AATATAGTA
1 TATATA-TA
27733 TATATATA
1 TATATATA
*
27741 GT-TCATATG
1 -TAT-ATATA
*
27750 TAAACTATA
1 TATA-TATA
27759 GT-TCATATA
1 -TAT-ATATA
27768 TATAGTATA
1 TATA-TATA
*
27777 TAAATATA
1 TATATATA
* *
27785 AACTATAGTT
1 TA-TATA-TA
*
27795 TATATAAA
1 TATATATA
27803 TAGTATA-A
1 TA-TATATA
*
27811 AATATAGTA
1 TATATA-TA
*
27820 TATA-AAA
1 TATATATA
*
27827 T-TATAAA
1 TATATATA
*
27834 TATAAACTA
1 TATATA-TA
*
27843 TAGTATGTA
1 TA-TATATA
*
27852 GTATATAAA
1 -TATATATA
*
27861 TATAAACTA
1 TATATA-TA
*
27870 TA-ATTTA
1 TATATATA
27877 TATAT-TA
1 TATATATA
27884 TATATAGTA
1 TATATA-TA
27893 TATACTATA
1 TATA-TATA
* *
27902 TAAATAGTT
1 TATATA-TA
27911 TATATAT-
1 TATATATA
27918 TATATATA
1 TATATATA
*
27926 GTCTATACTA
1 -TATATA-TA
*
27936 TATAAATA
1 TATATATA
*
27944 GTTTATATA
1 -TATATATA
27953 GT-TCACTA-A
1 -TAT-A-TATA
*
27962 TAAACTATA
1 TATA-TATA
27971 TATATATA
1 TATATATA
27979 TATATATA
1 TATATATA
27987 TATATATA
1 TATATATA
27995 -ATAT
1 TATAT
27999 GTAAACTATA
Statistics
Matches: 588, Mismatches: 120, Indels: 208
0.64 0.13 0.23
Matches are distributed among these distances:
6 3 0.01
7 116 0.20
8 157 0.27
9 281 0.48
10 31 0.05
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (8 bp):
TATATATA
Found at i:27612 original size:57 final size:57
Alignment explanation
Indices: 27548--27667 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
27538 TATATTATAT
* * *
27548 ACTATATAAATTGTTTATATAGTTCACTA-ATAAACTAT-ATATATAGGTCATATGTAA
1 ACTATATAAATTATATATATAGTTCA-TATATAAA-TATCAAATATAGGTCATATGTAA
** * * *
27605 ACTATATAGTTTATATATATAGTTCATATGTAAATATCAAATATAGTTTATATGTAA
1 ACTATATAAATTATATATATAGTTCATATATAAATATCAAATATAGGTCATATGTAA
27662 ACTATA
1 ACTATA
27668 GTTAGTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 5 0.09
57 48 0.91
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (57 bp):
ACTATATAAATTATATATATAGTTCATATATAAATATCAAATATAGGTCATATGTAA
Found at i:27669 original size:18 final size:18
Alignment explanation
Indices: 27646--27800 Score: 117
Period size: 18 Copynumber: 8.7 Consensus size: 18
27636 AAATATCAAA
*
27646 TATAGTTTATATGTAAAC
1 TATAGTTTATATATAAAC
27664 TATAG-TTAGTATATAAAC
1 TATAGTTTA-TATATAAAC
27682 TATATAGTTTATATATAAAC
1 --TATAGTTTATATATAAAC
*
27702 TATAGTTCATATATAAA-
1 TATAGTTTATATATAAAC
** *
27719 TATCA-AATATAGTATATA-
1 TAT-AGTTTATA-TATAAAC
* *
27737 TATAGTTCATATGTAAAC
1 TATAGTTTATATATAAAC
* * *
27755 TATAGTTCATATATATAG
1 TATAGTTTATATATAAAC
*
27773 TATA---TAAATATAAAC
1 TATAGTTTATATATAAAC
27788 TATAGTTTATATA
1 TATAGTTTATATA
27801 AATAGTATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
15 11 0.10
17 14 0.13
18 65 0.61
20 14 0.13
21 3 0.03
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAGTTTATATATAAAC
Found at i:27694 original size:38 final size:38
Alignment explanation
Indices: 27589--27758 Score: 128
Period size: 38 Copynumber: 4.6 Consensus size: 38
27579 AAACTATATA
* *
27589 TATAGGTCATATGTAAACTATATAG-TT-TATAT--A-
1 TATAGTTCATATATAAACTATATAGTTTATATATAAAC
* * *
27622 TATAGTTCATATGTAAATATCAAATATAGTTTATATGTAAAC
1 TATAGTTCATATAT-AA-A-C-TATATAGTTTATATATAAAC
27664 TATAGTT-AGTATATAAACTATATAGTTTATATATAAAC
1 TATAGTTCA-TATATAAACTATATAGTTTATATATAAAC
* *
27702 TATAGTTCATATATAAA-TATCA-A--ATATAGTATATA-
1 TATAGTTCATATATAAACTAT-ATAGTTTATA-TATAAAC
*
27737 TATAGTTCATATGTAAACTATA
1 TATAGTTCATATATAAACTATA
27759 GTTCATATAT
Statistics
Matches: 114, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
33 13 0.11
34 2 0.02
35 22 0.19
36 9 0.08
37 10 0.09
38 36 0.32
39 6 0.05
40 1 0.01
41 4 0.04
42 11 0.10
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (38 bp):
TATAGTTCATATATAAACTATATAGTTTATATATAAAC
Found at i:27787 original size:33 final size:32
Alignment explanation
Indices: 27711--27816 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 32
27701 CTATAGTTCA
27711 TATATAAATATCAAA-TATAG-TATATATATAG
1 TATATAAATAT-AAACTATAGTTATATATATAG
*
27742 T-TCAT--ATGTAAACTATAGTTCATATATATAG
1 TAT-ATAAATATAAACTATAGTT-ATATATATAG
*
27773 TATATAAATATAAACTATAGTTTATATAAATAG
1 TATATAAATATAAACTATAG-TTATATATATAG
27806 TATA-AAATATA
1 TATATAAATATA
27817 GTATATAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
28 3 0.05
29 8 0.12
30 2 0.03
31 16 0.25
32 8 0.12
33 25 0.39
34 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (32 bp):
TATATAAATATAAACTATAGTTATATATATAG
Found at i:27816 original size:25 final size:24
Alignment explanation
Indices: 27767--27827 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 24
27757 TAGTTCATAT
27767 ATATAGTATAT--AA-A-TATAAA
1 ATATAGTATATAAAATAGTATAAA
* *
27787 CTATAGTTTATATAAATAGTATAAA
1 ATATAGTATATA-AAATAGTATAAA
27812 ATATAGTATATAAAAT
1 ATATAGTATATAAAAT
27828 TATAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 9 0.28
23 2 0.06
24 5 0.16
25 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (24 bp):
ATATAGTATATAAAATAGTATAAA
Found at i:27885 original size:27 final size:27
Alignment explanation
Indices: 27694--27885 Score: 121
Period size: 27 Copynumber: 7.0 Consensus size: 27
27684 TATAGTTTAT
*
27694 ATATAAACTATAGT-T-CATA-TATAA
1 ATATAAACTATAGTATATATATTATAA
*
27718 ATATCAAA-TATAGTATATATA-TAGTTCAT
1 ATAT-AAACTATAGTATATATATTA--T-AA
*
27747 ATGTAAACTATAGTTCATATATATAGTATATAA
1 ATATAAACTATAG----TATATATA-T-TATAA
* *
27780 ATATAAACTATAGTTTATATA-AAT-A
1 ATATAAACTATAGTATATATATTATAA
* * *
27805 GTATAAAATATAGTATATAAAATTATAA
1 ATATAAACTATAGTATAT-ATATTATAA
*
27833 ATATAAACTATAGTATGTAGTA-TATAA
1 ATATAAACTATAGTATATA-TATTATAA
* *
27860 ATATAAACTATAATTTATATATTATA
1 ATATAAACTATAGTATATATATTATA
27886 TATAGTATAT
Statistics
Matches: 130, Mismatches: 19, Indels: 35
0.71 0.10 0.19
Matches are distributed among these distances:
24 10 0.08
25 20 0.15
26 11 0.08
27 28 0.22
28 21 0.16
29 16 0.12
33 21 0.16
34 1 0.01
36 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATAAACTATAGTATATATATTATAA
Found at i:27920 original size:36 final size:36
Alignment explanation
Indices: 27873--27952 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
27863 TAAACTATAA
27873 TTTATATATTATATATAGTATATACTATATAAATAG
1 TTTATATATTATATATAGTATATACTATATAAATAG
*
27909 TTTATATATTATATATAGTCTATACTATATAAATAG
1 TTTATATATTATATATAGTATATACTATATAAATAG
27945 TTTATATA
1 TTTATATA
27953 GTTCACTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (36 bp):
TTTATATATTATATATAGTATATACTATATAAATAG
Found at i:28010 original size:2 final size:2
Alignment explanation
Indices: 27180--27998 Score: 85
Period size: 2 Copynumber: 390.5 Consensus size: 2
27170 ACTAATGAAC
* * *
27180 TA TA TA -A TA TA TA GTT TA TA TA -A TGA AA TA TA TA -A TG TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* * *
27221 GTT TA TA TA TA T- TA TA TA GTT TA TA TA TA CTA -A TA AA CTA TA
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
27263 TA -A TG TA TA GT- TT TA TA TA TA CCA TA TA GTT TA TA TA TA CTA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA
* *
27305 -A TGA -A CTA TA TA -A TA TA TA GTT TA TA TA TA T- TA TA TA GTT
1 TA T-A TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* *
27345 TA TA TA TA -A TA TA -A TA TA AA T- TA TA GTA TA TA GTA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
27386 TA TCA -A CTA TA GTA TA TA GTT TA TA TA GTT TT TA TA TA TA GT-
1 TA T-A TA -TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA
* * *
27428 TCA TA TG TA AA T- TA TA CTA TA TA T- TA TA TA TA GTT TA TA TA
1 T-A TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
27469 TA TA -A TA TA TA TA GTA TA TA AA TA TA AA CTA TA GTA TG TA GTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA -TA
* * * *
27512 CA TA AA TA TA -A AA TA TA GTT TA TA TA TA TA T- TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * **
27554 TA AA T- TG TT TA TA TA GT- TCA CTA -A TA AA CTA TA TA TA TA GG
1 TA TA TA TA TA TA TA TA -TA T-A -TA TA TA TA -TA TA TA TA TA TA
* * * * *
27595 TCA TA TG TA AA CTA TA TA GTT TA TA TA TA TA GT- TCA TA TG TA AA
1 T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA
* * * * *
27639 TA TCA AA TA TA GTT TA TA TG TA AA CTA TA GT- TA GTA TA TA AA CTA
1 TA T-A TA TA TA -TA TA TA TA TA TA -TA TA -TA TA -TA TA TA TA -TA
* * * *
27684 TA TA GTT TA TA TA TA AA CTA TA GT- TCA TA TA TA AA TA TCA AA TA
1 TA TA -TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA T-A TA TA
* *
27728 TA GTA TA TA TA TA GT- TCA TA TG TA AA CTA TA GT- TCA TA TA TA
1 TA -TA TA TA TA TA -TA T-A TA TA TA TA -TA TA -TA T-A TA TA TA
* * * * *
27770 TA GTA TA TA AA TA TA AA CTA TA GTT TA TA TA AA TA GTA TA -A AA
1 TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA TA TA TA
* * * *
27813 TA TA GTA TA TA -A AA T- TA TA AA TA TA AA CTA TA GTA TG TA GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA -TA
* * *
27855 TA TA AA TA TA AA CTA TA -A TT TA TA TA T- TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
27897 CTA TA TA AA TA GTT TA TA TA T- TA TA TA TA GTC TA TA CTA TA TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * *
27940 AA TA GTT TA TA TA GT- TCA CTA -A TA AA CTA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA -TA T-A -TA TA TA TA -TA TA TA TA TA TA TA TA
27983 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
27999 GTAAACTATA
Statistics
Matches: 577, Mismatches: 126, Indels: 228
0.62 0.14 0.24
Matches are distributed among these distances:
1 38 0.07
2 443 0.77
3 94 0.16
4 2 0.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:28102 original size:29 final size:29
Alignment explanation
Indices: 27968--28104 Score: 93
Period size: 29 Copynumber: 4.8 Consensus size: 29
27958 CTAATAAACT
* * * *
27968 ATATATATA-TATATA-TATATATATATA
1 ATATATAAACTATATAGTATATATTTTTC
* * * *
27995 ATATGTAAACTATATAGTTTACATAGTTT-
1 ATATATAAACTATATAGTATATAT-TTTTC
* * *
28024 ATATATAAACTATGTAGTTTCTATTTTTC
1 ATATATAAACTATATAGTATATATTTTTC
* * * *
28053 ATATTTGATA-TATAAATTATATATTTTTC
1 ATATAT-AAACTATATAGTATATATTTTTC
28082 ATATATAAACTATATAGTATATA
1 ATATATAAACTATATAGTATATA
28105 CTATATAAAT
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
27 7 0.09
28 11 0.13
29 60 0.73
30 4 0.05
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (29 bp):
ATATATAAACTATATAGTATATATTTTTC
Found at i:28240 original size:18 final size:18
Alignment explanation
Indices: 28219--28259 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
28209 TACATGGTAT
28219 ATATAGTTTATACATAAC
1 ATATAGTTTATACATAAC
*
28237 ATATAGTTTATACATAAT
1 ATATAGTTTATACATAAC
28255 ATATA
1 ATATA
28260 TATATAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATAGTTTATACATAAC
Found at i:28905 original size:216 final size:216
Alignment explanation
Indices: 28349--29260 Score: 1578
Period size: 215 Copynumber: 4.2 Consensus size: 216
28339 TCCCTTTGTT
* * * *
28349 TTGTTTAATTTACTTAAATTTTTATTTGTAATTTTAAATTTTTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
* *
28414 ATTTGCATCTAAAAGTGACCCATACTTGTTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
*
28479 TAAATGGGTATAATTTGGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
* *
28544 TTAATACCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
28565 TT-TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
28629 ATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
28694 TAAATTGGTATAATTTGGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
28759 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
*
28780 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
28845 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTATAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
*
28910 TAAATGGGTATAATTTAGTA-TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCTAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
28974 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
** * *
28995 TTGTTTAATTTATTTAAATTTTTATTTGTAGGTCCATATTTGTTCAATTTAGGCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
29060 ATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
29125 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAATCTCACAATCTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
* *
29190 TTGATCCCTCAACAATGTGTA
196 TTGATCCCTCATCAATGTGTG
*
29211 TTGTTTAATTTATTTAAA-TTTTATTTGTAATTTCATATTTCTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
29261 ATTCTTAAAT
Statistics
Matches: 662, Mismatches: 32, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
215 440 0.66
216 222 0.34
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (216 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
TTGATCCCTCATCAATGTGTG
Found at i:29152 original size:431 final size:431
Alignment explanation
Indices: 28349--29260 Score: 1585
Period size: 431 Copynumber: 2.1 Consensus size: 431
28339 TCCCTTTGTT
* * *
28349 TTGTTTAATTTACTTAAATTTTTATTTGTAATTTTAAATTTTTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTCTTCAATTTAGTCCTCCAAATTTT
* *
28414 ATTTGCATCTAAAAGTGACCCATACTTGTTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAAGTGACCCATACTTATTACTTATTTCTATTTTATAATTGGCCCATAACTTTT
*
28479 TAAATGGGTATAATTTGGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
* *
28544 TTAATACCTCATCAATGTGTGTTTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTC
196 TTAATACCTCATCAATGTGTGTTTTTAATTTATTTAAATTTTTATTTGTAAGTCCATATTTGTTC
* * *
28609 AATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTT
261 AATTTAGGCCTCCAAATTTTATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTTT
* *
28674 TTAATTGGCCCATAACTTTTTAAATTGGTATAATTTGGTACTTTTTTGTATTAATTTCAACCTCA
326 TTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCA
* * *
28739 CAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTG
391 CAATCTAAAATTATTTCGATTTGATCCCTCAACAATGTGTA
*
28780 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTCTTCAATTTAGTCCTCCAAATTTT
*
28845 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTATAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAAGTGACCCATACTTATTACTTATTTCTATTTTATAATTGGCCCATAACTTTT
*
28910 TAAATGGGTATAATTTAGTA-TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCTAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
* * *
28974 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAGGTCCATATTTGTT
196 TTAATACCTCATCAATGTGTGTT-TTTAATTTATTTAAATTTTTATTTGTAAGTCCATATTTGTT
29039 CAATTTAGGCCTCCAAATTTTATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTT
260 CAATTTAGGCCTCCAAATTTTATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTT
*
29104 TTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAATCTC
325 TTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTC
29169 ACAATCTAAAATTATTTCGATTTGATCCCTCAACAATGTGTA
390 ACAATCTAAAATTATTTCGATTTGATCCCTCAACAATGTGTA
*
29211 TTGTTTAATTTATTTAAA-TTTTATTTGTAATTTCATATTTCTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTCTTCAATTTA
29261 ATTCTTAAAT
Statistics
Matches: 456, Mismatches: 24, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
430 94 0.21
431 362 0.79
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (431 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTCTTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAAGTGACCCATACTTATTACTTATTTCTATTTTATAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
TTAATACCTCATCAATGTGTGTTTTTAATTTATTTAAATTTTTATTTGTAAGTCCATATTTGTTC
AATTTAGGCCTCCAAATTTTATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTTT
TTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCA
CAATCTAAAATTATTTCGATTTGATCCCTCAACAATGTGTA
Found at i:33520 original size:49 final size:49
Alignment explanation
Indices: 33448--33547 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
33438 AATGGTTTTG
*
33448 CATTATTTAACAAAATGAAGTTTATTCGTGATACATGCACTACAAGCCA
1 CATTATTTAACAAAATGAAGTTTATTCGTGATACATGCACCACAAGCCA
33497 CATTATTTAACAAAATGAAGTTTATTCGTGATACATGCACCACAAGCCA
1 CATTATTTAACAAAATGAAGTTTATTCGTGATACATGCACCACAAGCCA
33546 CA
1 CA
33548 GGACAAAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (49 bp):
CATTATTTAACAAAATGAAGTTTATTCGTGATACATGCACCACAAGCCA
Found at i:39989 original size:26 final size:26
Alignment explanation
Indices: 39960--40041 Score: 116
Period size: 26 Copynumber: 3.3 Consensus size: 26
39950 AGTTTAAGAT
* *
39960 ATAAACGAAAGATAAACTAATACTAA
1 ATAAACGAAATATAAACGAATACTAA
*
39986 ATAAACAAAATATAAACGAATACTAA
1 ATAAACGAAATATAAACGAATACTAA
40012 ATAAAC---ATATAAACGAATACTAA
1 ATAAACGAAATATAAACGAATACTAA
40035 ATAAACG
1 ATAAACG
40042 TTAAATAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
23 23 0.44
26 29 0.56
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.20
Consensus pattern (26 bp):
ATAAACGAAATATAAACGAATACTAA
Found at i:40025 original size:23 final size:24
Alignment explanation
Indices: 39971--40040 Score: 106
Period size: 23 Copynumber: 2.9 Consensus size: 24
39961 TAAACGAAAG
*
39971 ATAAACTAATACTAAATAAACAAAAT
1 ATAAACGAATACTAAATAAAC--AAT
39997 ATAAACGAATACTAAATAAAC-AT
1 ATAAACGAATACTAAATAAACAAT
40020 ATAAACGAATACTAAATAAAC
1 ATAAACGAATACTAAATAAAC
40041 GTTAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
23 23 0.53
26 20 0.47
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.21
Consensus pattern (24 bp):
ATAAACGAATACTAAATAAACAAT
Found at i:40113 original size:23 final size:23
Alignment explanation
Indices: 40087--40143 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
40077 CTCGTGAACT
* *
40087 TTAAACGAATACGTTGACAAATA
1 TTAAACGAATACGTTCACAAACA
* *
40110 TTAAACGAACATGTTCACAAACA
1 TTAAACGAATACGTTCACAAACA
*
40133 TTAAATGAATA
1 TTAAACGAATA
40144 TATTCGCGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (23 bp):
TTAAACGAATACGTTCACAAACA
Found at i:40271 original size:30 final size:30
Alignment explanation
Indices: 40155--40271 Score: 81
Period size: 30 Copynumber: 3.7 Consensus size: 30
40145 ATTCGCGAAC
* *
40155 AATAAATAAACGAAAACGAACACCTTTAAA
1 AATAAACAAACGAACACGAACACCTTTAAA
* * * * **
40185 AATAAATAAATGAACACAAATATGATATTAAA
1 AATAAACAAACGAACACGAACA-CCT-TTAAA
* * *
40217 AAAAAACATGAATCAAACATGAACACCTTTAAA
1 AATAAACA--AA-CGAACACGAACACCTTTAAA
*
40250 AATAAACAAACGAATACGAACA
1 AATAAACAAACGAACACGAACA
40272 TTACTTTATT
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
30 27 0.43
31 3 0.05
32 11 0.17
33 12 0.19
34 3 0.05
35 7 0.11
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.18
Consensus pattern (30 bp):
AATAAACAAACGAACACGAACACCTTTAAA
Found at i:46237 original size:82 final size:82
Alignment explanation
Indices: 46034--46564 Score: 539
Period size: 82 Copynumber: 6.5 Consensus size: 82
46024 GGGTATCCAT
* * * * * * * *
46034 ATCAATTTTGGAAGACGAGT-TCGCTTCGCTTTTCTTTCAGGGTAAATCAAACTTGATATGTTCC
1 ATCAATTTTGGAAGACGTGTCT-GCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCC
* * *
46098 TCTTTTTCGGGTAGTCGG
65 TCTTTTTCAGGTAGACAG
* * * * * * ** * * *
46116 ATCAAATTTAGAAGATGAGTCTGTTCCACTCTTTTTTCAGGGGAGATCAGACTTGATATGTTCTT
1 ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCCT
* *
46181 CTTTTTTAGGTAGTCAG
66 CTTTTTCAGGTAGACAG
* * * * *
46198 ATCAATTTTAGAAGACGTGTATACTCTACTATTCATTCAGGGGAAATCAGACTTGATTTGTGCCT
1 ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCCT
46263 CTTTTTTCAGGTAGACAG
66 C-TTTTTCAGGTAGACAG
* * * *
46281 ATCTATTTTGAAAGACGTGTCTACTCCACTATTCATTCAGGGGAAATAAGACTTGATATGTGCCT
1 ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCCT
** *
46346 CTTTTTTGGGTAGACAT
66 CTTTTTCAGGTAGACAG
* * * * *
46363 AT-ATATTTTGGAAGAAGTGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACC
1 ATCA-ATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCC
46427 TCTTTTTCAGGTAGACAG
65 TCTTTTTCAGGTAGACAG
* * * * *
46445 ATCTATTTTGGAAGA--TGTATGCTCCACTATTCATTCAGGGAAAATTAGACTTGATCTGTGCCT
1 ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCCT
* * *
46508 CTCTTTCGGGTAGACAT
66 CTTTTTCAGGTAGACAG
* * *
46525 ATCTATTTTGGAAGACATGTCTGCTCTACTATTCATTCAG
1 ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAG
46565 TGAGATAAGA
Statistics
Matches: 380, Mismatches: 63, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
80 73 0.19
82 233 0.61
83 74 0.19
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (82 bp):
ATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAAATCAGACTTGATATGTGCCT
CTTTTTCAGGTAGACAG
Found at i:46392 original size:165 final size:162
Alignment explanation
Indices: 46151--46564 Score: 562
Period size: 165 Copynumber: 2.5 Consensus size: 162
46141 CCACTCTTTT
* * * * * * * * *
46151 TTCAGGGGAGATCAGACTTGATATGTTCTTCTTTTTTAGGTAGTCAGATCA-ATTTTAGAAGACG
1 TTCAGGGGAAATAAGACTTGATATGTGCCTCTTTTTTGGGTAGACATAT-ATATTTTGGAAGAAG
* * * * *
46215 TGTATACTCTACTATTCATTCAGGGGAAATCAGACTTGATTTGTGCCTCTTTTTTCAGGTAGACA
65 TGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTC-TTTTTCAGGTAGACA
*
46280 GATCTATTTTGAAAGACGTGTCTACTCCACTATTCA
129 GATCTATTTTGAAAGA--TGTATACTCCACTATTCA
46316 TTCAGGGGAAATAAGACTTGATATGTGCCTCTTTTTTGGGTAGACATATATATTTTGGAAGAAGT
1 TTCAGGGGAAATAAGACTTGATATGTGCCTCTTTTTTGGGTAGACATATATATTTTGGAAGAAGT
46381 GTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTTTTCAGGTAGACAGA
66 GTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTTTTCAGGTAGACAGA
* *
46446 TCTATTTTGGAAGATGTATGCTCCACTATTCA
131 TCTATTTTGAAAGATGTATACTCCACTATTCA
* * * * * *
46478 TTCAGGGAAAATTAGACTTGATCTGTGCCTCTCTTTCGGGTAGACATATCTATTTTGGAAGACA-
1 TTCAGGGGAAATAAGACTTGATATGTGCCTCTTTTTTGGGTAGACATATATATTTTGGAAGA-AG
46542 TGTCTGCTCTACTATTCATTCAG
65 TGTCTGCTCTACTATTCATTCAG
46565 TGAGATAAGA
Statistics
Matches: 224, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
162 95 0.42
163 1 0.00
164 31 0.14
165 97 0.43
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (162 bp):
TTCAGGGGAAATAAGACTTGATATGTGCCTCTTTTTTGGGTAGACATATATATTTTGGAAGAAGT
GTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTTTTCAGGTAGACAGA
TCTATTTTGAAAGATGTATACTCCACTATTCA
Found at i:46521 original size:162 final size:164
Alignment explanation
Indices: 46202--46564 Score: 543
Period size: 162 Copynumber: 2.2 Consensus size: 164
46192 AGTCAGATCA
* * * * * * *
46202 ATTTTAGAAGACGTGTATACTCTACTATTCATTCAGGGGAAATCAGACTTGATTTGTGCCTCTTT
1 ATTTTGGAAGAAGTGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTT
* *
46267 TTTCAGGTAGACAGATCTATTTTGAAAGACGTGTCTACTCCACTATTCATTCAGGGGAAATAAGA
66 TTTCAGGTAGACAGATCTATTTTGAAAGAC-TGTATACTCCACTATTCATTCAGGGAAAATAAGA
* *
46332 CTTGATATGTGCCTCTTTTTTGGGTAGACATATAT
130 CTTGATATGTGCCTCTCTTTCGGGTAGACATATAT
46367 ATTTTGGAAGAAGTGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTC-TT
1 ATTTTGGAAGAAGTGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTT
* * *
46431 TTTCAGGTAGACAGATCTATTTTGGAAGA-TGTATGCTCCACTATTCATTCAGGGAAAATTAGAC
66 TTTCAGGTAGACAGATCTATTTTGAAAGACTGTATACTCCACTATTCATTCAGGGAAAATAAGAC
* *
46495 TTGATCTGTGCCTCTCTTTCGGGTAGACATATCT
131 TTGATATGTGCCTCTCTTTCGGGTAGACATATAT
46529 ATTTTGGAAGACA-TGTCTGCTCTACTATTCATTCAG
1 ATTTTGGAAGA-AGTGTCTGCTCTACTATTCATTCAG
46565 TGAGATAAGA
Statistics
Matches: 181, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
162 95 0.52
163 1 0.01
164 30 0.17
165 55 0.30
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (164 bp):
ATTTTGGAAGAAGTGTCTGCTCTACTATTCATTCAGGGAAAATCAGACTTGATCTGTACCTCTTT
TTTCAGGTAGACAGATCTATTTTGAAAGACTGTATACTCCACTATTCATTCAGGGAAAATAAGAC
TTGATATGTGCCTCTCTTTCGGGTAGACATATAT
Found at i:47356 original size:45 final size:45
Alignment explanation
Indices: 47249--47377 Score: 147
Period size: 45 Copynumber: 2.8 Consensus size: 45
47239 ACTAGTTGAC
* * *
47249 TCTTCTACACGAGAAAGTCAAGAATCACAACACTGAAAGATTGACT
1 TCTTCTACA-GAGAAAGTCAAGAATGACAACACTAAAAGATCGACT
*
47295 TCTCTTTAC-GAGAAAGTCAAGAATGACAACACTAAAAGATCGA-T
1 TCT-TCTACAGAGAAAGTCAAGAATGACAACACTAAAAGATCGACT
* *
47339 TCTTCTACAAGATAAAGTCAAGGAA-GACAATACTAAAAG
1 TCTTCTAC-AGAGAAAGTCAA-GAATGACAACACTAAAAG
47378 GTTGACTCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.06
44 4 0.06
45 54 0.75
46 6 0.08
47 4 0.06
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (45 bp):
TCTTCTACAGAGAAAGTCAAGAATGACAACACTAAAAGATCGACT
Done.